{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T11:57:21Z","timestamp":1774526241521,"version":"3.50.1"},"reference-count":439,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2022,2,25]],"date-time":"2022-02-25T00:00:00Z","timestamp":1645747200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.<\/jats:p>","DOI":"10.3390\/cells11050806","type":"journal-article","created":{"date-parts":[[2022,2,25]],"date-time":"2022-02-25T10:00:40Z","timestamp":1645783240000},"page":"806","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4922-1245","authenticated-orcid":false,"given":"Cristina","family":"Zibetti","sequence":"first","affiliation":[{"name":"Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/B978-0-12-385044-7.00003-5","article-title":"Eye morphogenesis and patterning of the optic vesicle","volume":"93","author":"Fuhrmann","year":"2010","journal-title":"Curr. Top. Dev. Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"87","DOI":"10.3389\/fnins.2018.00087","article-title":"The Birth of the Eye Vesicle: When Fate Decision Equals Morphogenesis","volume":"12","author":"Giger","year":"2018","journal-title":"Front. Neurosci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/bs.ctdb.2018.12.008","article-title":"Eye organogenesis: A hierarchical view of ocular development","volume":"132","author":"Miesfeld","year":"2019","journal-title":"Curr. Top. Dev. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"200","DOI":"10.3389\/fnins.2010.00200","article-title":"Modular and Hierarchically Modular Organization of Brain Networks","volume":"4","author":"Meunier","year":"2010","journal-title":"Front. Neurosci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"54","DOI":"10.3389\/fnana.2017.00054","article-title":"The Functioning of a Cortex without Layers","volume":"11","author":"Guy","year":"2017","journal-title":"Front. Neuroanat."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.preteyeres.2014.06.003","article-title":"Functional architecture of the retina: Development and disease","volume":"42","author":"Hoon","year":"2014","journal-title":"Prog. Retin. Eye Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"742","DOI":"10.3389\/fnins.2017.00742","article-title":"Neuronal Migration and Lamination in the Vertebrate Retina","volume":"11","author":"Amini","year":"2017","journal-title":"Front. Neurosci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.semcdb.2005.02.012","article-title":"Regulation of proliferation during central nervous system development","volume":"16","author":"Donovan","year":"2005","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/nrn3618","article-title":"Temporal fate specification and neural progenitor competence during development","volume":"14","author":"Kohwi","year":"2013","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"3740","DOI":"10.1523\/JNEUROSCI.21-11-03740.2001","article-title":"Protective autoimmunity is a physiological response to CNS trauma","volume":"21","author":"Yoles","year":"2001","journal-title":"J. Neurosci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.expneurol.2007.05.025","article-title":"Rewiring the injured CNS: Lessons from the optic nerve","volume":"209","author":"Benowitz","year":"2008","journal-title":"Exp. Neurol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.neuron.2015.05.019","article-title":"Dealing with Danger in the CNS: The Response of the Immune System to Injury","volume":"87","author":"Gadani","year":"2015","journal-title":"Neuron"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nrneurol.2017.13","article-title":"The far-reaching scope of neuroinflammation after traumatic brain injury","volume":"13","author":"Simon","year":"2017","journal-title":"Nat. Rev. Neurol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.preteyeres.2018.10.003","article-title":"Immune regulation in the aging retina","volume":"69","author":"Chen","year":"2019","journal-title":"Prog. Retin. Eye Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.trsl.2021.05.005","article-title":"Immune responses to injury and their links to eye disease","volume":"236","author":"Stepp","year":"2021","journal-title":"Transl. Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nrneurol.2012.227","article-title":"The retina as a window to the brain\u2014From eye research to CNS disorders","volume":"9","author":"London","year":"2013","journal-title":"Nat. Rev. Neurol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2243","DOI":"10.12659\/MSM.890861","article-title":"Ophthalmological features of Parkinson disease","volume":"20","author":"Nowacka","year":"2014","journal-title":"Med. Sci. Monit."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1007\/s10633-020-09782-z","article-title":"Progress of macular atrophy during 30 months\u2019 follow-up in a patient with spinocerebellar ataxia type1 (SCA1)","volume":"142","author":"Hirose","year":"2021","journal-title":"Doc. Ophthalmol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Liao, C., Xu, J., Chen, Y., and Ip, N.Y. (2021). Retinal Dysfunction in Alzheimer\u2019s Disease and Implications for Biomarkers. Biomolecules, 11.","DOI":"10.3390\/biom11081215"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1212\/CPJ.0000000000000381","article-title":"King-Devick Test identifies real-time concussion and asymptomatic concussion in youth athletes","volume":"7","author":"Dhawan","year":"2017","journal-title":"Neurol. Clin. Pract."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.ophtha.2005.10.040","article-title":"Relation of visual function to retinal nerve fiber layer thickness in multiple sclerosis","volume":"113","author":"Fisher","year":"2006","journal-title":"Ophthalmology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1002\/ana.22005","article-title":"Longitudinal study of vision and retinal nerve fiber layer thickness in multiple sclerosis","volume":"67","author":"Talman","year":"2010","journal-title":"Ann. Neurol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1016\/S1474-4422(10)70168-X","article-title":"Optical coherence tomography in multiple sclerosis: A systematic review and meta-analysis","volume":"9","author":"Petzold","year":"2010","journal-title":"Lancet Neurol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1016\/j.parkreldis.2015.08.002","article-title":"Optical coherence tomography as a tool to evaluate retinal changes in Parkinson\u2019s disease","volume":"21","author":"Mailankody","year":"2015","journal-title":"Parkinsonism Relat. Disord."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e1003","DOI":"10.1212\/WNL.0000000000006157","article-title":"Retinal thinning associates with nigral dopaminergic loss in de novo Parkinson disease","volume":"91","author":"Ahn","year":"2018","journal-title":"Neurology"},{"key":"ref_26","first-page":"e16224","article-title":"Retinal Nerve Fiber Layer and Macular Thickness in Parkinson\u2019s Disease Patients","volume":"13","year":"2021","journal-title":"Cureus"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1177\/1352458517690822","article-title":"Validity of low-contrast letter acuity as a visual performance outcome measure for multiple sclerosis","volume":"23","author":"Balcer","year":"2017","journal-title":"Mult. Scler. J."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jns.2018.08.019","article-title":"Mobile Universal Lexicon Evaluation System (MULES) in MS: Evaluation of a new visual test of rapid picture naming","volume":"394","author":"Seay","year":"2018","journal-title":"J. Neurol. Sci."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"116680","DOI":"10.1016\/j.jns.2020.116680","article-title":"Rapid picture naming in Parkinson\u2019s disease using the Mobile Universal Lexicon Evaluation System (MULES)","volume":"410","author":"Conway","year":"2020","journal-title":"J. Neurol. Sci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1001\/jamaophthalmol.2018.3556","article-title":"Association of Preclinical Alzheimer Disease with Optical Coherence Tomographic Angiography Findings","volume":"136","author":"Apte","year":"2018","journal-title":"JAMA Ophthalmol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"604049","DOI":"10.3389\/fneur.2020.604049","article-title":"Optical Coherence Tomography Angiography (OCTA) in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorder","volume":"11","author":"Kleerekooper","year":"2020","journal-title":"Front. Neurol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2040622320905215","DOI":"10.1177\/2040622320905215","article-title":"Retinal correlates of psychiatric disorders","volume":"11","author":"Almonte","year":"2020","journal-title":"Ther. Adv. Chronic Dis."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.schres.2019.09.016","article-title":"Schizophrenia and the retina: Towards a 2020 perspective","volume":"219","author":"Silverstein","year":"2020","journal-title":"Schizophr. Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"714810","DOI":"10.3389\/fnbeh.2021.714810","article-title":"Sex-Specific Retinal Anomalies Induced by Chronic Social Defeat Stress in Mice","volume":"15","author":"Arsenault","year":"2021","journal-title":"Front. Behav. Neurosci."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/328131a0","article-title":"A common progenitor for neurons and glia persists in rat retina late in development","volume":"328","author":"Turner","year":"1987","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.brainres.2007.04.014","article-title":"Regulation of retinal cell fate specification by multiple TFs","volume":"1192","author":"Ohsawa","year":"2008","journal-title":"Brain Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.tins.2012.05.004","article-title":"Cell fate determination in the vertebrate retina","volume":"35","author":"Bassett","year":"2012","journal-title":"Trends Neurosci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1016\/j.neuron.2015.05.018","article-title":"Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain","volume":"86","author":"Mo","year":"2015","journal-title":"Neuron"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1002\/ar.1092120215","article-title":"Cell differentiation in the retina of the mouse","volume":"212","author":"Young","year":"1985","journal-title":"Anat. Rec."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/35053522","article-title":"Vertebrate neural cell-fate determination: Lessons from the retina","volume":"2","author":"Livesey","year":"2001","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1002\/cne.20134","article-title":"Timing and topography of cell genesis in the rat retina","volume":"474","author":"Rapaport","year":"2004","journal-title":"J. Comp. Neurol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"8963","DOI":"10.1073\/pnas.0901484106","article-title":"Developmental sources of conservation and variation in the evolution of the primate eye","volume":"106","author":"Dyer","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1016\/j.neuron.2012.06.033","article-title":"How variable clones build an invariant retina","volume":"75","author":"He","year":"2012","journal-title":"Neuron"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/nrn3767","article-title":"Intrinsically different retinal progenitor cells produce specific types of progeny","volume":"15","author":"Cepko","year":"2014","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.conb.2016.11.010","article-title":"Timing temporal transitions during brain development","volume":"42","author":"Rossi","year":"2017","journal-title":"Curr. Opin. Neurobiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1101\/SQB.1993.058.01.085","article-title":"Role of chromosome territories in the functional compartmentalization of the cell nucleus. Role of chromosome territories in the functional compartmentalization of the cell nucleus","volume":"58","author":"Cremer","year":"1993","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1083\/jcb.145.6.1119","article-title":"Differences in the localization and morphology of chromosomes in the human nucleus","volume":"145","author":"Croft","year":"1999","journal-title":"J. Cell Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4424","DOI":"10.1073\/pnas.072618599","article-title":"Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates","volume":"99","author":"Tanabe","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/j.cell.2007.01.028","article-title":"Beyond the sequence: Cellular organization of genome function","volume":"128","author":"Misteli","year":"2007","journal-title":"Cell"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Williams","year":"2009","journal-title":"Science"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.ceb.2013.02.005","article-title":"Genome organization and long-range regulation of gene expression by enhancers","volume":"25","author":"Smallwood","year":"2013","journal-title":"Curr. Opin. Cell Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/s41588-018-0098-8","article-title":"Polymer physics predicts the effects of structural variants on chromatin architecture","volume":"50","author":"Bianco","year":"2018","journal-title":"Nat. Genet."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/s41580-021-00362-w","article-title":"Understanding 3D genome organization by multidisciplinary methods","volume":"22","author":"Cavalli","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1016\/j.cell.2015.04.004","article-title":"Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions","volume":"161","author":"Lupianez","year":"2015","journal-title":"Cell"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1016\/j.cell.2013.09.053","article-title":"Super-enhancers in the control of cell identity and disease","volume":"155","author":"Hnisz","year":"2013","journal-title":"Cell"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1748-7188-9-14","article-title":"Identification of alternative topological domains in chromatin","volume":"9","author":"Filippova","year":"2014","journal-title":"Algorithms Mol. Biol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nature19847","article-title":"Chromosome conformation elucidates regulatory relationships in developing human brain","volume":"538","author":"Won","year":"2016","journal-title":"Nature"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Freire-Pritchett, P., Schoenfelder, S., Varnai, C., Wingett, S.W., Cairns, J., Collier, A.J., Garcia-Vilchez, R., Furlan-Magaril, M., Osborne, C.S., and Fraser, P. (2017). Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. eLife, 6.","DOI":"10.7554\/eLife.21926"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/nature23884","article-title":"The 4D nucleome project","volume":"549","author":"Dekker","year":"2017","journal-title":"Nature"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1016\/j.devcel.2017.10.029","article-title":"Molecular Anatomy of the Developing Human Retina","volume":"43","author":"Hoshino","year":"2017","journal-title":"Dev. Cell"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1038\/s41467-018-05134-3","article-title":"Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes","volume":"9","author":"Rheaume","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1016\/j.cell.2019.01.004","article-title":"Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina","volume":"176","author":"Peng","year":"2019","journal-title":"Cell"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"15778","DOI":"10.1038\/s41598-019-52215-4","article-title":"Molecular signatures of retinal ganglion cells revealed through single cell profiling","volume":"9","author":"Laboissonniere","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1016\/j.neuron.2019.11.006","article-title":"Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes","volume":"104","author":"Tran","year":"2019","journal-title":"Neuron"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1016\/j.neuron.2020.12.003","article-title":"Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior","volume":"109","author":"Kolsch","year":"2021","journal-title":"Neuron"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Xie, H., Zhang, W., Zhang, M., Akhtar, T., Li, Y., Yi, W., Sun, X., Zuo, Z., Wei, M., and Fang, X. (2020). Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids. Sci. Adv., 6.","DOI":"10.1126\/sciadv.aay5247"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"9001","DOI":"10.1073\/pnas.1922501117","article-title":"Mapping the cis-regulatory architecture of the human retina reveals noncoding genetic variation in disease","volume":"117","author":"Cherry","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1016\/j.celrep.2020.01.007","article-title":"Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures","volume":"30","author":"Sridhar","year":"2020","journal-title":"Cell Rep."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1016\/j.cell.2020.08.013","article-title":"Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution","volume":"182","author":"Cowan","year":"2020","journal-title":"Cell"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.neuron.2020.12.010","article-title":"Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes","volume":"109","author":"Armand","year":"2021","journal-title":"Neuron"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/s41586-020-2879-3","article-title":"Neuronal diversity and convergence in a visual system developmental atlas","volume":"589","author":"Ozel","year":"2021","journal-title":"Nature"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1038\/s42003-019-0375-9","article-title":"Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin","volume":"2","author":"Zibetti","year":"2019","journal-title":"Commun. Biol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"4001","DOI":"10.1093\/hmg\/ddu114","article-title":"Comprehensive analysis of gene expression in human retina and supporting tissues","volume":"23","author":"Li","year":"2014","journal-title":"Hum. Mol. Genet."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1101\/gr.4074106","article-title":"Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)","volume":"16","author":"Crawford","year":"2006","journal-title":"Genome Res."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nature13990","article-title":"Dissecting neural differentiation regulatory networks through epigenetic footprinting","volume":"518","author":"Ziller","year":"2015","journal-title":"Nature"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1101\/gr.5571506","article-title":"Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements","volume":"16","author":"Dostie","year":"2006","journal-title":"Genome Res."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s13059-017-1161-y","article-title":"Software tools for visualizing Hi-C data","volume":"18","author":"Yardimci","year":"2017","journal-title":"Genome Biol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.neuron.2017.04.022","article-title":"The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis","volume":"94","author":"Aldiri","year":"2017","journal-title":"Neuron"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: Automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"21931","DOI":"10.1073\/pnas.1016071107","article-title":"Histone H3K27ac separates active from poised enhancers and predicts developmental state","volume":"107","author":"Creyghton","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1038\/nature07730","article-title":"ChIP-seq accurately predicts tissue-specific activity of enhancers","volume":"457","author":"Visel","year":"2009","journal-title":"Nature"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"3519","DOI":"10.1242\/dev.064006","article-title":"Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina","volume":"138","author":"Brzezinski","year":"2011","journal-title":"Development"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s41583-019-0242-1","article-title":"Understanding the retinal basis of vision across species","volume":"21","author":"Baden","year":"2020","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Todd, L., and Reh, T.A. (2021). Comparative Biology of Vertebrate Retinal Regeneration: Restoration of Vision through Cellular Reprogramming. Cold Spring Harb. Perspect. Biol., 14.","DOI":"10.1101\/cshperspect.a040816"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/0079-6107(72)90004-1","article-title":"The physics and biology of animal reflectors","volume":"24","author":"Land","year":"1972","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1700","DOI":"10.1126\/science.1218072","article-title":"Photonic crystal light collectors in fish retina improve vision in turbid water","volume":"336","author":"Kreysing","year":"2012","journal-title":"Science"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"11043","DOI":"10.1364\/OE.22.011043","article-title":"Direct observation of light focusing by single photoreceptor cell nuclei","volume":"22","author":"Blaszczak","year":"2014","journal-title":"Opt. Express"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Subramanian, K., Weigert, M., Borsch, O., Petzold, H., Garcia-Ulloa, A., Myers, E.W., Ader, M., Solovei, I., and Kreysing, M. (2019). Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice. eLife, 8.","DOI":"10.7554\/eLife.49542"},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Subramanian, K., Petzold, H., Seelbinder, B., Hersemann, L., Nusslein, I., and Kreysing, M. (2021). Optical plasticity of mammalian cells. J. Biophotonics, 14.","DOI":"10.1002\/jbio.202000457"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1016\/j.cell.2009.01.052","article-title":"Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution","volume":"137","author":"Solovei","year":"2009","journal-title":"Cell"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1364\/OL.35.002639","article-title":"Physical insight into light scattering by photoreceptor cell nuclei","volume":"35","author":"Kreysing","year":"2010","journal-title":"Opt. Lett."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1016\/j.celrep.2018.01.075","article-title":"Retinal Cell Type DNA Methylation and Histone Modifications Predict Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures","volume":"22","author":"Wang","year":"2018","journal-title":"Cell Rep."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/j.neuron.2019.08.002","article-title":"Nucleome Dynamics during Retinal Development","volume":"104","author":"Norrie","year":"2019","journal-title":"Neuron"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"5207","DOI":"10.1038\/onc.2014.474","article-title":"Pediatric solid tumor genomics and developmental pliancy","volume":"34","author":"Chen","year":"2015","journal-title":"Oncogene"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.cell.2016.05.052","article-title":"Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility","volume":"166","author":"Denny","year":"2016","journal-title":"Cell"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1210\/en.2015-1312","article-title":"Nfib Regulates Transcriptional Networks That Control the Development of Prostatic Hyperplasia","volume":"157","author":"Grabowska","year":"2016","journal-title":"Endocrinology"},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Aldiri, I., Valentine, M., Xu, B., Putnam, D., Griffiths, L., Lupo, M., Norrie, J., Zhang, J., Johnson, D., and Easton, J. (2018). The Nucleome of Developing Murine Rod Photoreceptors. bioRxiv.","DOI":"10.1101\/369702"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1101\/gad.259003","article-title":"The Sox9 TF determines glial fate choice in the developing spinal cord","volume":"17","author":"Stolt","year":"2003","journal-title":"Genes Dev."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.neuron.2008.08.008","article-title":"Ikaros confers early temporal competence to mouse retinal progenitor cells","volume":"60","author":"Elliott","year":"2008","journal-title":"Neuron"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"E716","DOI":"10.1073\/pnas.1215707110","article-title":"Ikaros promotes early-born neuronal fates in the cerebral cortex","volume":"110","author":"Alsio","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_106","first-page":"E2362","article-title":"Conserved microRNA pathway regulates developmental timing of retinal neurogenesis","volume":"110","author":"Georgi","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1749-8104-8-14","article-title":"Dicer is required for neural stem cell multipotency and lineage progression during cerebral cortex development","volume":"8","author":"Saurat","year":"2013","journal-title":"Neural Dev."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1016\/j.devcel.2014.07.018","article-title":"A gene regulatory network controls the binary fate decision of rod and bipolar cells in the vertebrate retina","volume":"30","author":"Wang","year":"2014","journal-title":"Dev. Cell"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"ORSFe1","DOI":"10.1167\/iovs.15-17672","article-title":"Photoreceptor Fate Determination in the Vertebrate Retina","volume":"57","author":"Wang","year":"2016","journal-title":"Investig. Opthalmol. Vis. Sci."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/bs.pmbts.2015.06.006","article-title":"Development of the Vertebrate Eye and Retina","volume":"134","author":"Stenkamp","year":"2015","journal-title":"Prog. Mol. Biol. Transl. Sci."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1242\/dev.128.6.943","article-title":"Regulation of retinal ganglion cell production by Sonic hedgehog","volume":"128","author":"Zhang","year":"2001","journal-title":"Development"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"3870","DOI":"10.1242\/dev.081083","article-title":"Gde2 regulates cortical neuronal identity by controlling the timing of cortical progenitor differentiation","volume":"139","author":"Rodriguez","year":"2012","journal-title":"Development"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1006\/scdb.2001.0273","article-title":"The role of basic helix-loop-helix genes in vertebrate retinogenesis","volume":"12","author":"Vetter","year":"2001","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.yexcr.2005.03.015","article-title":"Roles of bHLH genes in neural stem cell differentiation","volume":"306","author":"Kageyama","year":"2005","journal-title":"Exp. Cell Res."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.neuron.2012.10.002","article-title":"The neuronal organization of the retina","volume":"76","author":"Masland","year":"2012","journal-title":"Neuron"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.conb.2014.02.014","article-title":"Reconciling competence and transcriptional hierarchies with stochasticity in retinal lineages","volume":"27","author":"Boije","year":"2014","journal-title":"Curr. Opin. Neurobiol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.ydbio.2015.05.010","article-title":"Ezh2 maintains retinal progenitor proliferation, transcriptional integrity, and the timing of late differentiation","volume":"403","author":"Zhang","year":"2015","journal-title":"Dev. Biol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"dev169474","DOI":"10.1242\/dev.169474","article-title":"An integrated transcriptional analysis of the developing human retina","volume":"146","author":"Mellough","year":"2019","journal-title":"Development"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"13615","DOI":"10.1038\/s41598-020-70334-1","article-title":"Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Muller Glial regenerative potential","volume":"10","author":"VandenBosch","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1101\/gr.109405.110","article-title":"CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors","volume":"20","author":"Corbo","year":"2010","journal-title":"Genome Res."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13072-018-0212-2","article-title":"CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites","volume":"11","author":"Ruzycki","year":"2018","journal-title":"Epigenet. Chromatin"},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Samuel, A., Housset, M., Fant, B., and Lamonerie, T. (2014). Otx2 ChIP-seq reveals unique and redundant functions in the mature mouse retina. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0089110"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nrn2880","article-title":"Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina","volume":"11","author":"Swaroop","year":"2010","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"109994","DOI":"10.1016\/j.celrep.2021.109994","article-title":"Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina","volume":"37","author":"Lyu","year":"2021","journal-title":"Cell Rep."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.neuron.2015.02.038","article-title":"MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers","volume":"86","author":"Andzelm","year":"2015","journal-title":"Neuron"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1016\/j.cell.2018.05.021","article-title":"Phenotypic Convergence: Distinct TFs Regulate Common Terminal Features","volume":"174","author":"Konstantinides","year":"2018","journal-title":"Cell"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/j.neuron.2019.04.010","article-title":"Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification","volume":"102","author":"Clark","year":"2019","journal-title":"Neuron"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/j.devcel.2020.04.009","article-title":"Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development","volume":"53","author":"Lu","year":"2020","journal-title":"Dev. Cell"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.ydbio.2013.10.006","article-title":"Blimp1 (Prdm1) prevents re-specification of photoreceptors into retinal bipolar cells by restricting competence","volume":"384","author":"Brzezinski","year":"2013","journal-title":"Dev. Biol."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"7753","DOI":"10.1093\/nar\/gkt567","article-title":"LHX2 regulates the neural differentiation of human embryonic stem cells via transcriptional modulation of PAX6 and CER1","volume":"41","author":"Hou","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"12197","DOI":"10.1523\/JNEUROSCI.1494-13.2013","article-title":"Lhx2 balances progenitor maintenance with neurogenic output and promotes competence state progression in the developing retina","volume":"33","author":"Gordon","year":"2013","journal-title":"J. Neurosci."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.1523\/JNEUROSCI.3145-15.2016","article-title":"Lhx2 Is an Essential Factor for Retinal Gliogenesis and Notch Signaling","volume":"36","author":"Zibetti","year":"2016","journal-title":"J. Neurosci."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"32757","DOI":"10.1038\/srep32757","article-title":"Multiple intrinsic factors act in concert with Lhx2 to direct retinal gliogenesis","volume":"6","author":"Clark","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"6877","DOI":"10.1523\/JNEUROSCI.4216-12.2013","article-title":"LHX2 is necessary for the maintenance of optic identity and for the progression of optic morphogenesis","volume":"33","author":"Roy","year":"2013","journal-title":"J. Neurosci."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1126\/science.1151695","article-title":"Lhx2 selector activity specifies cortical identity and suppresses hippocampal organizer fate","volume":"319","author":"Mangale","year":"2008","journal-title":"Science"},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1038\/nn.2427","article-title":"Lhx2 specifies regional fate in Emx1 lineage of telencephalic progenitors generating cerebral cortex","volume":"12","author":"Chou","year":"2009","journal-title":"Nat. Neurosci."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"E265","DOI":"10.1073\/pnas.1101109108","article-title":"TF Lhx2 is necessary and sufficient to suppress astro-gliogenesis and promote neurogenesis in the developing hippocampus","volume":"108","author":"Subramanian","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.mcn.2013.02.006","article-title":"Role for Lhx2 in corticogenesis through regulation of progenitor differentiation","volume":"56","author":"Chou","year":"2013","journal-title":"Mol. Cell. Neurosci."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1093\/cercor\/bhu067","article-title":"Agenesis of the Corpus Callosum Due to Defective Glial Wedge Formation in Lhx2 Mutant Mice","volume":"25","author":"Chinn","year":"2015","journal-title":"Cereb. Cortex"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"2935","DOI":"10.1242\/dev.124.15.2935","article-title":"Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development","volume":"124","author":"Porter","year":"1997","journal-title":"Development"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.ydbio.2008.12.022","article-title":"The LIM homeobox TF Lhx2 is required to specify the retina field and synergistically cooperates with Pax6 for Six6 transactivation","volume":"327","author":"Tetreault","year":"2009","journal-title":"Dev. Biol."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/S0896-6273(01)00504-9","article-title":"Patterning of the dorsal telencephalon and cerebral cortex by a roof plate-Lhx2 pathway","volume":"32","author":"Monuki","year":"2001","journal-title":"Neuron"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"4047","DOI":"10.1038\/ncomms5047","article-title":"Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs","volume":"5","author":"Zhong","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1002\/stem.1667","article-title":"Modeling human retinal development with patient-specific induced pluripotent stem cells reveals multiple roles for visual system homeobox 2","volume":"32","author":"Phillips","year":"2014","journal-title":"Stem Cells"},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"6332","DOI":"10.1093\/hmg\/ddu351","article-title":"Loss of MITF expression during human embryonic stem cell differentiation disrupts retinal pigment epithelium development and optic vesicle cell proliferation","volume":"23","author":"Capowski","year":"2014","journal-title":"Hum. Mol. Genet."},{"key":"ref_146","doi-asserted-by":"crossref","unstructured":"Raviv, S., Bharti, K., Rencus-Lazar, S., Cohen-Tayar, Y., Schyr, R., Evantal, N., Meshorer, E., Zilberberg, A., Idelson, M., and Reubinoff, B. (2014). PAX6 regulates melanogenesis in the retinal pigmented epithelium through feed-forward regulatory interactions with MITF. PLoS Genet., 10.","DOI":"10.1371\/journal.pgen.1004360"},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1089\/scd.2015.0144","article-title":"Characterization of Three-Dimensional Retinal Tissue Derived from Human Embryonic Stem Cells in Adherent Monolayer Cultures","volume":"24","author":"Singh","year":"2015","journal-title":"Stem Cells Dev."},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"O\u2019Hara-Wright, M., and Gonzalez-Cordero, A. (2020). Retinal organoids: A window into human retinal development. Development, 147.","DOI":"10.1242\/dev.189746"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature09941","article-title":"Self-organizing optic-cup morphogenesis in three-dimensional culture","volume":"472","author":"Eiraku","year":"2011","journal-title":"Nature"},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Bharti, K., Gasper, M., Ou, J., Brucato, M., Clore-Gronenborn, K., Pickel, J., and Arnheiter, H. (2012). A regulatory loop involving PAX6, MITF, and WNT signaling controls retinal pigment epithelium development. PLoS Genet., 8.","DOI":"10.1371\/journal.pgen.1002757"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"2903","DOI":"10.1242\/dev.00450","article-title":"Retinal pigmented epithelium determination requires the redundant activities of Pax2 and Pax6","volume":"130","author":"Baumer","year":"2003","journal-title":"Development"},{"key":"ref_152","doi-asserted-by":"crossref","unstructured":"Capowski, E.E., Samimi, K., Mayerl, S.J., Phillips, M.J., Pinilla, I., Howden, S.E., Saha, J., Jansen, A.D., Edwards, K.L., and Jager, L.D. (2019). Reproducibility and staging of 3D human retinal organoids across multiple pluripotent stem cell lines. Development, 146.","DOI":"10.1242\/dev.171686"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"4657","DOI":"10.1073\/pnas.1107488109","article-title":"Injury-independent induction of reactive gliosis in retina by loss of function of the LIM homeodomain TF Lhx2","volume":"109","author":"Miki","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1242\/dev.071878","article-title":"SOX2 maintains the quiescent progenitor cell state of postnatal retinal Muller glia","volume":"140","author":"Surzenko","year":"2013","journal-title":"Development"},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/j.exer.2009.05.006","article-title":"The group E Sox genes Sox8 and Sox9 are regulated by Notch signaling and are required for Muller glial cell development in mouse retina","volume":"89","author":"Muto","year":"2009","journal-title":"Exp. Eye Res."},{"key":"ref_156","doi-asserted-by":"crossref","unstructured":"de Melo, J., Clark, B.S., Venkataraman, A., Shiau, F., Zibetti, C., and Blackshaw, S. (2018). Ldb1- and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in the retina. Development, 145.","DOI":"10.1242\/dev.159970"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"11902","DOI":"10.1038\/s41598-018-30355-3","article-title":"MLL1 is essential for retinal neurogenesis and horizontal inner neuron integrity","volume":"8","author":"Brightman","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"2867","DOI":"10.1242\/dev.088096","article-title":"Polycomb repressive complex PRC2 regulates Xenopus retina development downstream of Wnt\/beta-catenin signaling","volume":"140","author":"Aldiri","year":"2013","journal-title":"Development"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.ydbio.2017.11.004","article-title":"Polycomb repression complex 2 is required for the maintenance of retinal progenitor cells and balanced retinal differentiation","volume":"433","author":"Fujimura","year":"2018","journal-title":"Dev. Biol."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1002\/dneu.22261","article-title":"Roles of histone H3K27 trimethylase Ezh2 in retinal proliferation and differentiation","volume":"75","author":"Iida","year":"2015","journal-title":"Dev. Neurobiol."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"3751","DOI":"10.1073\/pnas.1311480111","article-title":"Histone demethylase Jmjd3 is required for the development of subsets of retinal bipolar cells","volume":"111","author":"Iida","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_162","doi-asserted-by":"crossref","unstructured":"Cheng, L., Wong, L.J., Yan, N., Han, R.C., Yu, H., Guo, C., Batsuuri, K., Zinzuwadia, A., Guan, R., and Cho, K.S. (2018). Ezh2 does not mediate retinal ganglion cell homeostasis or their susceptibility to injury. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0191853"},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"33887","DOI":"10.1038\/srep33887","article-title":"Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1","volume":"6","author":"Yan","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"E7987","DOI":"10.1073\/pnas.1803069115","article-title":"Casz1 controls higher-order nuclear organization in rod photoreceptors","volume":"115","author":"Mattar","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1016\/j.stem.2017.02.004","article-title":"PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation","volume":"20","author":"Respuela","year":"2017","journal-title":"Cell Stem Cell"},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.201624.115","article-title":"SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells","volume":"26","author":"Barutcu","year":"2016","journal-title":"Genome Res."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"35187","DOI":"10.1074\/jbc.M706742200","article-title":"SWI\/SNF chromatin remodeling ATPase Brm regulates the differentiation of early retinal stem cells\/progenitors by influencing Brn3b expression and Notch signaling","volume":"282","author":"Das","year":"2007","journal-title":"J. Biol. Chem."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"4092","DOI":"10.1242\/dev.124800","article-title":"Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma","volume":"142","author":"Aldiri","year":"2015","journal-title":"Development"},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"14648","DOI":"10.1038\/ncomms14648","article-title":"The SWI\/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers","volume":"8","author":"Alver","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Perez-Cervantes, C., Smith, L.A., Nadadur, R.D., Hughes, A.E.O., Wang, S., Corbo, J.C., Cepko, C., Lonfat, N., and Moskowitz, I.P. (2020). Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types. Development, 147.","DOI":"10.1242\/dev.184432"},{"key":"ref_171","doi-asserted-by":"crossref","unstructured":"Goodson, N.B., Kaufman, M.A., Park, K.U., and Brzezinski, J.A. (2020). Simultaneous deletion of Prdm1 and Vsx2 enhancers in the retina alters photoreceptor and bipolar cell fate specification, yet differs from deleting both genes. Development, 147.","DOI":"10.1242\/dev.190272"},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.ydbio.2011.09.012","article-title":"Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors","volume":"360","author":"Emerson","year":"2011","journal-title":"Dev. Biol."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"dev199399","DOI":"10.1242\/dev.199399","article-title":"Initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity","volume":"148","author":"Kaufman","year":"2021","journal-title":"Development"},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/j.cell.2015.03.017","article-title":"Pioneer TFs target partial DNA motifs on nucleosomes to initiate reprogramming","volume":"161","author":"Soufi","year":"2015","journal-title":"Cell"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1101\/gr.192294.115","article-title":"Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions","volume":"25","author":"Schep","year":"2015","journal-title":"Genome Res."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1101\/gr.142067.112","article-title":"DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing","volume":"23","author":"Chen","year":"2013","journal-title":"Genome Res."},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.cell.2006.07.024","article-title":"Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors","volume":"126","author":"Takahashi","year":"2006","journal-title":"Cell"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/cr.2008.309","article-title":"Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells","volume":"18","author":"Liu","year":"2008","journal-title":"Cell Res."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nbt.2798","article-title":"Discovery of directional and nondirectional pioneer TFs by modeling DNase profile magnitude and shape","volume":"32","author":"Sherwood","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: Scanning for occurrences of a given motif","volume":"27","author":"Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1101\/gr.112623.110","article-title":"Accurate inference of TF binding from DNA sequence and chromatin accessibility data","volume":"21","author":"Degner","year":"2011","journal-title":"Genome Res."},{"key":"ref_182","doi-asserted-by":"crossref","unstructured":"Liu, S., Zibetti, C., Wan, J., Wang, G., Blackshaw, S., and Qian, J. (2017). Assessing the model transferability for prediction of TF binding sites based on chromatin accessibility. BMC Bioinform., 18.","DOI":"10.1186\/s12859-017-1769-7"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl Variant Effect Predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"2784","DOI":"10.1074\/jbc.M114.593384","article-title":"HTRA1 (high temperature requirement A serine peptidase 1) gene is transcriptionally regulated by insertion\/deletion nucleotides located at the 3\u2032 end of the ARMS2 (age-related maculopathy susceptibility 2) gene in patients with age-related macular degeneration","volume":"290","author":"Iejima","year":"2015","journal-title":"J. Biol. Chem."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.cels.2019.04.004","article-title":"Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species","volume":"8","author":"Clark","year":"2019","journal-title":"Cell Syst."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/S0959-437X(97)80147-5","article-title":"Sox genes find their feet","volume":"7","author":"Pevny","year":"1997","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1038\/nn.2397","article-title":"Hippocampal development and neural stem cell maintenance require Sox2-dependent regulation of Shh","volume":"12","author":"Favaro","year":"2009","journal-title":"Nat. Neurosci."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"3805","DOI":"10.1242\/dev.01204","article-title":"Sox2 deficiency causes neurodegeneration and impaired neurogenesis in the adult mouse brain","volume":"131","author":"Ferri","year":"2004","journal-title":"Development"},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/j.tins.2005.08.008","article-title":"From stem cells to neurons and glia: A Soxist\u2019s view of neural development","volume":"28","author":"Wegner","year":"2005","journal-title":"Trends Neurosci."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"2423","DOI":"10.1101\/gad.181487.111","article-title":"SOX after SOX: SOXession regulates neurogenesis","volume":"25","author":"Wegner","year":"2011","journal-title":"Genes Dev."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1101\/gad.1407906","article-title":"SOX2 is a dose-dependent regulator of retinal neural progenitor competence","volume":"20","author":"Taranova","year":"2006","journal-title":"Genes Dev."},{"key":"ref_192","doi-asserted-by":"crossref","unstructured":"Lodato, M.A., Ng, C.W., Wamstad, J.A., Cheng, A.W., Thai, K.K., Fraenkel, E., Jaenisch, R., and Boyer, L.A. (2013). SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state. PLoS Genet., 9.","DOI":"10.1371\/journal.pgen.1003288"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1167\/iovs.07-1619","article-title":"Sox2 plays a role in the induction of amacrine and Muller glial cells in mouse retinal progenitor cells","volume":"50","author":"Lin","year":"2009","journal-title":"Investig. Opthalmol. Vis. Sci."},{"key":"ref_194","doi-asserted-by":"crossref","unstructured":"Wohl, S.G., Hooper, M.J., and Reh, T.A. (2019). MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Muller glia in mice. Development, 146.","DOI":"10.1242\/dev.179556"},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1002\/cne.21746","article-title":"Sox9 is expressed in mouse multipotent retinal progenitor cells and functions in Muller glial cell development","volume":"510","author":"Poche","year":"2008","journal-title":"J. Comp. Neurol."},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"12908","DOI":"10.1074\/jbc.M114.556738","article-title":"TF SOX9 plays a key role in the regulation of visual cycle gene expression in the retinal pigment epithelium","volume":"289","author":"Masuda","year":"2014","journal-title":"J. Biol. Chem."},{"key":"ref_197","doi-asserted-by":"crossref","unstructured":"Cohen-Tayar, Y., Cohen, H., Mitiagin, Y., Abravanel, Z., Levy, C., Idelson, M., Reubinoff, B., Itzkovitz, S., Raviv, S., and Kaestner, K.H. (2018). Pax6 regulation of Sox9 in the mouse retinal pigmented epithelium controls its timely differentiation and choroid vasculature development. Development, 145.","DOI":"10.1242\/dev.163691"},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"10268","DOI":"10.1038\/s41598-018-28596-3","article-title":"TF profiling identifies Sox9 as regulator of proliferation and differentiation in corneal epithelial stem\/progenitor cells","volume":"8","author":"Zenkel","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13041-015-0115-0","article-title":"Sox9 is critical for suppression of neurogenesis but not initiation of gliogenesis in the cerebellum","volume":"8","author":"Vong","year":"2015","journal-title":"Mol. Brain"},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.neuron.2012.01.024","article-title":"Sox9 and NFIA coordinate a transcriptional regulatory cascade during the initiation of gliogenesis","volume":"74","author":"Kang","year":"2012","journal-title":"Neuron"},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1111\/j.1365-2443.1996.tb00016.x","article-title":"Mash1 promotes neuronal differentiation in the retina","volume":"1","author":"Tomita","year":"1996","journal-title":"Genes Cells"},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1038\/ncb2115","article-title":"Ascl1a regulates Muller glia dedifferentiation and retinal regeneration through a Lin-28-dependent, let-7 microRNA signalling pathway","volume":"12","author":"Ramachandran","year":"2010","journal-title":"Nat. Cell Biol."},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1038\/nature23283","article-title":"Stimulation of functional neuronal regeneration from Muller glia in adult mice","volume":"548","author":"Jorstad","year":"2017","journal-title":"Nature"},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.neulet.2011.07.048","article-title":"Induction of pluripotent stem cells from autopsy donor-derived somatic cells","volume":"502","author":"Hjelm","year":"2011","journal-title":"Neurosci. Lett."},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1038\/nbt1483","article-title":"A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types","volume":"26","author":"Wernig","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"22490","DOI":"10.1038\/srep22490","article-title":"In vivo reprogramming reactive glia into iPSCs to produce new neurons in the cortex following traumatic brain injury","volume":"6","author":"Gao","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_207","first-page":"2610","article-title":"Hedgehog signaling stimulates the formation of proliferating Muller glia-derived progenitor cells in the chick retina","volume":"142","author":"Todd","year":"2015","journal-title":"Development"},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1002\/stem.2742","article-title":"Retinoic Acid-Signaling Regulates the Proliferative and Neurogenic Capacity of Muller Glia-Derived Progenitor Cells in the Avian Retina","volume":"36","author":"Todd","year":"2018","journal-title":"Stem Cells"},{"key":"ref_209","first-page":"1859","article-title":"mTor signaling is required for the formation of proliferating Muller glia-derived progenitor cells in the chick retina","volume":"143","author":"Zelinka","year":"2016","journal-title":"Development"},{"key":"ref_210","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1126\/science.1175737","article-title":"KLF family members regulate intrinsic axon regeneration ability","volume":"326","author":"Moore","year":"2009","journal-title":"Science"},{"key":"ref_211","doi-asserted-by":"crossref","unstructured":"Fang, J., Shaw, P.X., Wang, Y., and Goldberg, J.L. (2016). Kruppel-Like Factor 4 (KLF4) Is Not Required for Retinal Cell Differentiation. eNeuro, 3.","DOI":"10.1523\/ENEURO.0117-15.2016"},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"4372","DOI":"10.1523\/JNEUROSCI.5851-11.2012","article-title":"The Lhx2 TF controls thalamocortical axonal guidance by specific regulation of robo1 and robo2 receptors","volume":"32","author":"Peregrin","year":"2012","journal-title":"J. Neurosci."},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1002\/glia.23189","article-title":"Astrocytes follow ganglion cell axons to establish an angiogenic template during retinal development","volume":"65","author":"Punal","year":"2017","journal-title":"Glia"},{"key":"ref_214","doi-asserted-by":"crossref","unstructured":"Rocha-Martins, M., de Toledo, B.C., Santos-Franca, P.L., Oliveira-Valenca, V.M., Vieira-Vieira, C.H., Matos-Rodrigues, G.E., Linden, R., Norden, C., Martins, R.A.P., and Silveira, M.S. (2019). De novo genesis of retinal ganglion cells by targeted expression of Klf4 in vivo. Development, 146.","DOI":"10.1242\/dev.176586"},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"2497","DOI":"10.1242\/dev.128.13.2497","article-title":"Math5 is required for retinal ganglion cell and optic nerve formation","volume":"128","author":"Brown","year":"2001","journal-title":"Development"},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.1242\/dev.010751","article-title":"ISL1 and BRN3B co-regulate the differentiation of murine retinal ganglion cells","volume":"135","author":"Pan","year":"2008","journal-title":"Development"},{"key":"ref_217","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.ydbio.2012.03.006","article-title":"Math5 defines the ganglion cell competence state in a subpopulation of retinal progenitor cells exiting the cell cycle","volume":"365","author":"Brzezinski","year":"2012","journal-title":"Dev. Biol."},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"E1559","DOI":"10.1073\/pnas.1421535112","article-title":"Two TFs, Pou4f2 and Isl1, are sufficient to specify the retinal ganglion cell fate","volume":"112","author":"Wu","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"21690","DOI":"10.1073\/pnas.2006888117","article-title":"The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development","volume":"117","author":"Miesfeld","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_220","doi-asserted-by":"crossref","unstructured":"Dupacova, N., Antosova, B., Paces, J., and Kozmik, Z. (2021). Meis homeobox genes control progenitor competence in the retina. Proc. Natl. Acad. Sci. USA, 118.","DOI":"10.1073\/pnas.2013136118"},{"key":"ref_221","doi-asserted-by":"crossref","unstructured":"Hoang, T., Wang, J., Boyd, P., Wang, F., Santiago, C., Jiang, L., Yoo, S., Lahne, M., Todd, L.J., and Jia, M. (2020). Gene regulatory networks controlling vertebrate retinal regeneration. Science, 370.","DOI":"10.1126\/science.abb8598"},{"key":"ref_222","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1016\/j.neuron.2006.11.019","article-title":"The TF NFIA controls the onset of gliogenesis in the developing spinal cord","volume":"52","author":"Deneen","year":"2006","journal-title":"Neuron"},{"key":"ref_223","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.ydbio.2017.10.019","article-title":"Transcriptional regulation of Nfix by NFIB drives astrocytic maturation within the developing spinal cord","volume":"432","author":"Matuzelski","year":"2017","journal-title":"Dev. Biol."},{"key":"ref_224","doi-asserted-by":"crossref","first-page":"11102","DOI":"10.1038\/ncomms11102","article-title":"Zbtb20 promotes astrocytogenesis during neocortical development","volume":"7","author":"Nagao","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_225","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1016\/j.celrep.2020.01.075","article-title":"STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina","volume":"30","author":"Jorstad","year":"2020","journal-title":"Cell Rep."},{"key":"ref_226","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1038\/s41467-018-03856-y","article-title":"ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration","volume":"9","author":"Wang","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_227","doi-asserted-by":"crossref","first-page":"e888","DOI":"10.1016\/S2214-109X(17)30293-0","article-title":"Magnitude, temporal trends, and projections of the global prevalence of blindness and distance and near vision impairment: A systematic review and meta-analysis","volume":"5","author":"Bourne","year":"2017","journal-title":"Lancet Glob. Health"},{"key":"ref_228","first-page":"493","article-title":"Updates on the Epidemiology of Age-Related Macular Degeneration","volume":"6","author":"Jonas","year":"2017","journal-title":"Asia Pac. J. Ophthalmol."},{"key":"ref_229","doi-asserted-by":"crossref","unstructured":"Cachafeiro, M., Bemelmans, A.P., Samardzija, M., Afanasieva, T., Pournaras, J.A., Grimm, C., Kostic, C., Philippe, S., Wenzel, A., and Arsenijevic, Y. (2013). Hyperactivation of retina by light in mice leads to photoreceptor cell death mediated by VEGF and retinal pigment epithelium permeability. Cell Death Dis., 4.","DOI":"10.1038\/cddis.2013.303"},{"key":"ref_230","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.jneuroim.2008.04.014","article-title":"Role of the chemokine receptor CX3CR1 in the mobilization of phagocytic retinal microglial cells","volume":"198","author":"Raoul","year":"2008","journal-title":"J. Neuroimmunol."},{"key":"ref_231","doi-asserted-by":"crossref","first-page":"8433","DOI":"10.1038\/s41598-017-08702-7","article-title":"Monocyte infiltration and proliferation reestablish myeloid cell homeostasis in the mouse retina following retinal pigment epithelial cell injury","volume":"7","author":"Ma","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_232","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1093\/aje\/kws031","article-title":"The association between complement component 2\/complement factor B polymorphisms and age-related macular degeneration: A HuGE review and meta-analysis","volume":"176","author":"Thakkinstian","year":"2012","journal-title":"Am. J. Epidemiol."},{"key":"ref_233","doi-asserted-by":"crossref","first-page":"e2367","DOI":"10.1038\/cddis.2016.133","article-title":"Clearance of autophagy-associated dying retinal pigment epithelial cells\u2014A possible source for inflammation in age-related macular degeneration","volume":"7","author":"Kristof","year":"2016","journal-title":"Cell Death Dis."},{"key":"ref_234","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s13148-019-0608-2","article-title":"Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes","volume":"11","author":"Porter","year":"2019","journal-title":"Clin. Epigenet."},{"key":"ref_235","doi-asserted-by":"crossref","first-page":"4902","DOI":"10.1038\/s41467-019-12780-8","article-title":"Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration","volume":"10","author":"Menon","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_236","doi-asserted-by":"crossref","unstructured":"Sahaboglu, A., Paquet-Durand, O., Dietter, J., Dengler, K., Bernhard-Kurz, S., Ekstrom, P.A., Hitzmann, B., Ueffing, M., and Paquet-Durand, F. (2013). Retinitis pigmentosa: Rapid neurodegeneration is governed by slow cell death mechanisms. Cell Death Dis., 4.","DOI":"10.1038\/cddis.2013.12"},{"key":"ref_237","doi-asserted-by":"crossref","first-page":"571293","DOI":"10.3389\/fnins.2020.571293","article-title":"An In Vitro Model of Human Retinal Detachment Reveals Successive Death Pathway Activations","volume":"14","author":"Potic","year":"2020","journal-title":"Front. Neurosci."},{"key":"ref_238","doi-asserted-by":"crossref","first-page":"3602","DOI":"10.1093\/nar\/gkf474","article-title":"Imprinting regulator DNMT3L is a transcriptional repressor associated with histone deacetylase activity","volume":"30","author":"Aapola","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_239","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/77023","article-title":"DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci","volume":"25","author":"Rountree","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_240","doi-asserted-by":"crossref","unstructured":"Wahlin, K.J., Enke, R.A., Fuller, J.A., Kalesnykas, G., Zack, D.J., and Merbs, S.L. (2013). Epigenetics and cell death: DNA hypermethylation in programmed retinal cell death. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0079140"},{"key":"ref_241","doi-asserted-by":"crossref","unstructured":"Farinelli, P., Perera, A., Arango-Gonzalez, B., Trifunovic, D., Wagner, M., Carell, T., Biel, M., Zrenner, E., Michalakis, S., and Paquet-Durand, F. (2014). DNA methylation and differential gene regulation in photoreceptor cell death. Cell Death Dis., 5.","DOI":"10.1038\/cddis.2014.512"},{"key":"ref_242","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.preteyeres.2018.03.002","article-title":"Epigenetic control of gene regulation during development and disease: A view from the retina","volume":"65","author":"Jaeger","year":"2018","journal-title":"Prog. Retin. Eye Res."},{"key":"ref_243","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1038\/eye.2014.225","article-title":"The role of epigenetics in age-related macular degeneration","volume":"28","author":"Gemenetzi","year":"2014","journal-title":"Eye"},{"key":"ref_244","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s40662-016-0063-5","article-title":"Epidemiology of age-related macular degeneration (AMD): Associations with cardiovascular disease phenotypes and lipid factors","volume":"3","author":"Pennington","year":"2016","journal-title":"Eye Vis."},{"key":"ref_245","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/j.celrep.2012.10.013","article-title":"Hypomethylation of the IL17RC promoter associates with age-related macular degeneration","volume":"2","author":"Wei","year":"2012","journal-title":"Cell Rep."},{"key":"ref_246","doi-asserted-by":"crossref","first-page":"6526","DOI":"10.1038\/s41598-018-24907-w","article-title":"MALAT1: An Epigenetic Regulator of Inflammation in Diabetic Retinopathy","volume":"8","author":"Biswas","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_247","doi-asserted-by":"crossref","unstructured":"Sancho-Pelluz, J., Alavi, M.V., Sahaboglu, A., Kustermann, S., Farinelli, P., Azadi, S., van Veen, T., Romero, F.J., Paquet-Durand, F., and Ekstrom, P. (2010). Excessive HDAC activation is critical for neurodegeneration in the rd1 mouse. Cell Death Dis., 1.","DOI":"10.1038\/cddis.2010.4"},{"key":"ref_248","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/s41419-018-0349-8","article-title":"DZNep inhibits H3K27me3 deposition and delays retinal degeneration in the rd1 mice","volume":"9","author":"Zheng","year":"2018","journal-title":"Cell Death Dis."},{"key":"ref_249","doi-asserted-by":"crossref","first-page":"598","DOI":"10.2174\/156652412800620048","article-title":"Neuroprotective strategies for the treatment of inherited photoreceptor degeneration","volume":"12","author":"Trifunovic","year":"2012","journal-title":"Curr. Mol. Med."},{"key":"ref_250","first-page":"1527","article-title":"Different effects of valproic acid on photoreceptor loss in Rd1 and Rd10 retinal degeneration mice","volume":"20","author":"Mitton","year":"2014","journal-title":"Mol. Vis."},{"key":"ref_251","first-page":"4462","article-title":"HDAC inhibition in the cpfl1 mouse protects de-generating cone photoreceptors in vivo","volume":"25","author":"Trifunovic","year":"2016","journal-title":"Hum. Mol. Genet."},{"key":"ref_252","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.preteyeres.2017.04.004","article-title":"Roles of exosomes in the normal and diseased eye","volume":"59","author":"Klingeborn","year":"2017","journal-title":"Prog. Retin. Eye Res."},{"key":"ref_253","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pharmthera.2017.01.003","article-title":"Gene therapy for diabetic retinopathy: Are we ready to make the leap from bench to bedside?","volume":"173","author":"Wang","year":"2017","journal-title":"Pharmacol. Ther."},{"key":"ref_254","doi-asserted-by":"crossref","unstructured":"Gonzalez-Fernandez, F.M., Bianchera, A., Gasco, P., Nicoli, S., and Pescina, S. (2021). Lipid-Based Nanocarriers for Ophthalmic Administration: Towards Experimental Design Implementation. Pharmaceutics, 13.","DOI":"10.3390\/pharmaceutics13040447"},{"key":"ref_255","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1016\/j.phrs.2016.07.042","article-title":"Nanosystems based on siRNA silencing HuR expression counteract diabetic retinopathy in rat","volume":"111","author":"Amadio","year":"2016","journal-title":"Pharmacol. Res."},{"key":"ref_256","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/sj.gt.3302653","article-title":"Potential applications for RNAi to probe pathogenesis and develop new treatments for ocular disorders","volume":"13","author":"Campochiaro","year":"2006","journal-title":"Gene Ther."},{"key":"ref_257","doi-asserted-by":"crossref","unstructured":"Haurigot, V., Villacampa, P., Ribera, A., Bosch, A., Ramos, D., Ruberte, J., and Bosch, F. (2012). Long-term retinal PEDF overexpression prevents neovascularization in a murine adult model of retinopathy. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0041511"},{"key":"ref_258","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1016\/j.stemcr.2021.08.008","article-title":"Human stem cell-based retina on chip as new translational model for validation of AAV retinal gene therapy vectors","volume":"16","author":"Achberger","year":"2021","journal-title":"Stem Cell Rep."},{"key":"ref_259","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1089\/hum.2017.179","article-title":"Assessment of Adeno-Associated Virus Serotype Tropism in Human Retinal Explants","volume":"29","author":"Wiley","year":"2018","journal-title":"Hum. Gene Ther."},{"key":"ref_260","doi-asserted-by":"crossref","first-page":"594984","DOI":"10.3389\/fgeed.2020.594984","article-title":"CRISPR Technology for Ocular Angiogenesis","volume":"2","author":"Chung","year":"2020","journal-title":"Front. Genome Ed."},{"key":"ref_261","doi-asserted-by":"crossref","first-page":"794805","DOI":"10.3389\/fgene.2021.794805","article-title":"Gene-Based Therapeutics for Inherited Retinal Diseases","volume":"12","author":"Fenner","year":"2021","journal-title":"Front. Genet."},{"key":"ref_262","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1016\/S0140-6736(17)31868-8","article-title":"Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65-mediated inherited retinal dystrophy: A randomised, controlled, open-label, phase 3 trial","volume":"390","author":"Russell","year":"2017","journal-title":"Lancet"},{"key":"ref_263","doi-asserted-by":"crossref","unstructured":"Latella, M.C., Di Salvo, M.T., Cocchiarella, F., Benati, D., Grisendi, G., Comitato, A., Marigo, V., and Recchia, A. (2016). In Vivo Editing of the Human Mutant Rhodopsin Gene by Electroporation of Plasmid-based CRISPR\/Cas9 in the Mouse Retina. Mol. Ther. Nucleic Acids, 5.","DOI":"10.1038\/mtna.2016.92"},{"key":"ref_264","doi-asserted-by":"crossref","first-page":"11199","DOI":"10.1073\/pnas.1706193114","article-title":"CRISPR-Cas9-based treatment of myocilin-associated glaucoma","volume":"114","author":"Jain","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_265","doi-asserted-by":"crossref","first-page":"E8547","DOI":"10.1073\/pnas.1805055115","article-title":"Mutation-independent rhodopsin gene therapy by knock-down and replacement with a single AAV vector","volume":"115","author":"Cideciyan","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_266","doi-asserted-by":"crossref","unstructured":"Woo, M. (2019). Eyes hint at hidden mental-health conditions. Nature.","DOI":"10.1038\/d41586-019-01114-9"},{"key":"ref_267","doi-asserted-by":"crossref","unstructured":"Wu, W.H., Tsai, Y.T., Huang, I.W., Cheng, C.H., Hsu, C.W., Cui, X., Ryu, J., Quinn, P.M.J., Caruso, S.M., and Lin, C.S. (2022). CRISPR genome surgery in a novel humanized model for autosomal dominant retinitis pigmentosa. Mol. Ther.","DOI":"10.1016\/j.ymthe.2022.02.010"},{"key":"ref_268","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.1016\/j.ymthe.2018.04.017","article-title":"In Situ Gene Therapy via AAV-CRISPR-Cas9-Mediated Targeted Gene Regulation","volume":"26","author":"Moreno","year":"2018","journal-title":"Mol. Ther."},{"key":"ref_269","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1038\/nbt.3149","article-title":"A split-Cas9 architecture for inducible genome editing and transcription modulation","volume":"33","author":"Zetsche","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_270","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1167\/iovs.16-20281","article-title":"The Genetic Causes of Nonsyndromic Congenital Retinal Detachment: A Genetic and Phenotypic Study of Pakistani Families","volume":"58","author":"Keser","year":"2017","journal-title":"Investig. Opthalmol. Vis. Sci."},{"key":"ref_271","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/nn.2798","article-title":"Deletion of a remote enhancer near ATOH7 disrupts retinal neurogenesis, causing NCRNA disease","volume":"14","author":"Ghiasvand","year":"2011","journal-title":"Nat. Neurosci."},{"key":"ref_272","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1016\/j.ajhg.2013.10.028","article-title":"Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia","volume":"93","author":"Bhatia","year":"2013","journal-title":"Am. J. Hum. Genet."},{"key":"ref_273","first-page":"1705","article-title":"Identification of dominant FOXE3 and PAX6 mutations in patients with congenital cataract and aniridia","volume":"16","author":"Bitoun","year":"2010","journal-title":"Mol. Vis."},{"key":"ref_274","doi-asserted-by":"crossref","first-page":"21307","DOI":"10.1038\/srep21307","article-title":"Autosomal recessive retinitis pigmentosa with homozygous rhodopsin mutation E150K and non-coding cis-regulatory variants in CRX-binding regions of SAMD7","volume":"6","author":"Karlstetter","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_275","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1016\/j.ajhg.2020.09.002","article-title":"Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa","volume":"107","author":"Fiorentino","year":"2020","journal-title":"Am. J. Hum. Genet."},{"key":"ref_276","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.cell.2014.11.052","article-title":"Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds","volume":"160","author":"Zalatan","year":"2015","journal-title":"Cell"},{"key":"ref_277","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1016\/j.cell.2021.03.025","article-title":"Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing","volume":"184","author":"Nunez","year":"2021","journal-title":"Cell"},{"key":"ref_278","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/s41392-021-00645-w","article-title":"Spatiotemporal control of CRISPR\/Cas9 gene editing","volume":"6","author":"Zhuo","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_279","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.stem.2016.01.022","article-title":"CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs","volume":"18","author":"Mandegar","year":"2016","journal-title":"Cell Stem Cell"},{"key":"ref_280","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/nature14136","article-title":"Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex","volume":"517","author":"Konermann","year":"2015","journal-title":"Nature"},{"key":"ref_281","doi-asserted-by":"crossref","first-page":"3651","DOI":"10.1038\/s41467-018-06129-w","article-title":"Highly efficient genome editing by CRISPR-Cpf1 using CRISPR RNA with a uridinylate-rich 3\u2032-overhang","volume":"9","author":"Lee","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_282","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1038\/s41591-021-01351-4","article-title":"Partial recovery of visual function in a blind patient after optogenetic therapy","volume":"27","author":"Sahel","year":"2021","journal-title":"Nat. Med."},{"key":"ref_283","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s42234-018-0013-8","article-title":"Development of visual Neuroprostheses: Trends and challenges","volume":"4","author":"Fernandez","year":"2018","journal-title":"Bioelectron. Med."},{"key":"ref_284","doi-asserted-by":"crossref","unstructured":"Kashani, A.H., Lebkowski, J.S., Rahhal, F.M., Avery, R.L., Salehi-Had, H., Dang, W., Lin, C.M., Mitra, D., Zhu, D., and Thomas, B.B. (2018). A bioengineered retinal pigment epithelial monolayer for advanced, dry age-related macular degeneration. Sci. Transl. Med., 10.","DOI":"10.1126\/scitranslmed.aao4097"},{"key":"ref_285","doi-asserted-by":"crossref","first-page":"743","DOI":"10.3389\/fcell.2020.00743","article-title":"Pluripotent Stem Cells for the Treatment of Retinal Degeneration: Current Strategies and Future Directions","volume":"8","author":"Ikelle","year":"2020","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_286","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1002\/dneu.22169","article-title":"Retinal stem\/progenitor cells in the ciliary marginal zone complete retinal regeneration: A study of retinal regeneration in a novel animal model","volume":"74","author":"Miyake","year":"2014","journal-title":"Dev. Neurobiol."},{"key":"ref_287","doi-asserted-by":"crossref","first-page":"3153","DOI":"10.1016\/j.celrep.2016.11.016","article-title":"The Ciliary Margin Zone of the Mammalian Retina Generates Retinal Ganglion Cells","volume":"17","author":"Marcucci","year":"2016","journal-title":"Cell Rep."},{"key":"ref_288","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/0012-1606(87)90311-3","article-title":"A possible role for the vascular membrane in retinal regeneration in Rana catesbienna tadpoles","volume":"122","author":"Reh","year":"1987","journal-title":"Dev. Biol."},{"key":"ref_289","first-page":"833","article-title":"Mechanisms of retina regeneration in urodeles","volume":"40","author":"Mitashov","year":"1996","journal-title":"Int. J. Dev. Biol."},{"key":"ref_290","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/dvdy.10224","article-title":"Eye regeneration at the molecular age","volume":"226","author":"Tsonis","year":"2003","journal-title":"Dev. Dyn."},{"key":"ref_291","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1002\/cne.902930302","article-title":"Immunolabelling by a newt retinal pigment epithelium antibody during retinal development and regeneration","volume":"293","author":"Klein","year":"1990","journal-title":"J. Comp. Neurol."},{"key":"ref_292","doi-asserted-by":"crossref","first-page":"33761","DOI":"10.1038\/srep33761","article-title":"Turning the fate of reprogramming cells from retinal disorder to regeneration by Pax6 in newts","volume":"6","author":"Nakamura","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_293","doi-asserted-by":"crossref","first-page":"6043","DOI":"10.1038\/srep06043","article-title":"The newt reprograms mature RPE cells into a unique multipotent state for retinal regeneration","volume":"4","author":"Islam","year":"2014","journal-title":"Sci. Rep."},{"key":"ref_294","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1007\/BF00239223","article-title":"Regeneration of the goldfish retina after exposure to different doses of ouabain","volume":"202","author":"Maier","year":"1979","journal-title":"Cell Tissue Res."},{"key":"ref_295","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1002\/neu.480270402","article-title":"Retinal pigmented epithelium does not transdifferentiate in adult goldfish","volume":"27","author":"Knight","year":"1995","journal-title":"J. Neurobiol."},{"key":"ref_296","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/0012-1606(65)90022-9","article-title":"Regeneration of neural retina from the pigmented epithelium in the chick embryo","volume":"12","author":"Coulombre","year":"1965","journal-title":"Dev. Biol."},{"key":"ref_297","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/0006-8993(95)00163-K","article-title":"In vitro transdifferentiation of embryonic rat retinal pigment epithelium to neural retina","volume":"677","author":"Zhao","year":"1995","journal-title":"Brain Res."},{"key":"ref_298","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1523\/JNEUROSCI.2980-03.2004","article-title":"Persistent progenitors at the retinal margin of ptc+\/\u2212 mice","volume":"24","author":"Moshiri","year":"2004","journal-title":"J. Neurosci."},{"key":"ref_299","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1038\/85090","article-title":"Muller glia are a potential source of neural regeneration in the postnatal chicken retina","volume":"4","author":"Fischer","year":"2001","journal-title":"Nat. Neurosci."},{"key":"ref_300","doi-asserted-by":"crossref","first-page":"6303","DOI":"10.1523\/JNEUROSCI.0332-06.2006","article-title":"A role for alpha1 tubulin-expressing Muller glia in regeneration of the injured zebrafish retina","volume":"26","author":"Fausett","year":"2006","journal-title":"J. Neurosci."},{"key":"ref_301","doi-asserted-by":"crossref","first-page":"617923","DOI":"10.3389\/fcell.2020.617923","article-title":"The Regenerating Adult Zebrafish Retina Recapitulates Developmental Fate Specification Programs","volume":"8","author":"Lahne","year":"2020","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_302","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.exer.2013.09.003","article-title":"Retinal pigment epithelium development, plasticity, and tissue homeostasis","volume":"123","author":"Fuhrmann","year":"2014","journal-title":"Exp. Eye Res."},{"key":"ref_303","doi-asserted-by":"crossref","first-page":"3860","DOI":"10.1038\/s41598-019-40262-w","article-title":"The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue","volume":"9","author":"Dvoriantchikova","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_304","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1006\/dbio.2000.9622","article-title":"p27(Kip1) regulates cell cycle withdrawal of late multipotent progenitor cells in the mammalian retina","volume":"219","author":"Levine","year":"2000","journal-title":"Dev. Biol."},{"key":"ref_305","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1002\/glia.21174","article-title":"Pax6-positive Muller glia cells express cell cycle markers but do not proliferate after photoreceptor injury in the mouse retina","volume":"59","author":"Joly","year":"2011","journal-title":"Glia"},{"key":"ref_306","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1016\/j.cellsig.2009.07.019","article-title":"Down-regulation of miR-17 family expression in response to retinoic acid induced neuronal differentiation","volume":"21","author":"Beveridge","year":"2009","journal-title":"Cell. Signal."},{"key":"ref_307","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.ydbio.2008.11.016","article-title":"miR-17 family miRNAs are expressed during early mammalian development and regulate stem cell differentiation","volume":"326","author":"Foshay","year":"2009","journal-title":"Dev. Biol."},{"key":"ref_308","doi-asserted-by":"crossref","first-page":"1604","DOI":"10.1073\/pnas.1315567111","article-title":"The miR-17\/106-p38 axis is a key regulator of the neurogenic-to-gliogenic transition in developing neural stem\/progenitor cells","volume":"111","author":"Nakamura","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_309","doi-asserted-by":"crossref","unstructured":"Trompeter, H.I., Abbad, H., Iwaniuk, K.M., Hafner, M., Renwick, N., Tuschl, T., Schira, J., Muller, H.W., and Wernet, P. (2011). MicroRNAs MiR-17, MiR-20a, and MiR-106b act in concert to modulate E2F activity on cell cycle arrest during neuronal lineage differentiation of USSC. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0016138"},{"key":"ref_310","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.brainres.2017.05.001","article-title":"Up-regulation of miR-325-3p suppresses pineal aralkylamine N-acetyltransferase (Aanat) after neonatal hypoxia-ischemia brain injury in rats","volume":"1668","author":"Yang","year":"2017","journal-title":"Brain Res."},{"key":"ref_311","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1002\/cne.21730","article-title":"The transcriptome of retinal Muller glial cells","volume":"509","author":"Roesch","year":"2008","journal-title":"J. Comp. Neurol."},{"key":"ref_312","doi-asserted-by":"crossref","first-page":"19508","DOI":"10.1073\/pnas.0807453105","article-title":"Stimulation of neural regeneration in the mouse retina","volume":"105","author":"Karl","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_313","doi-asserted-by":"crossref","first-page":"13717","DOI":"10.1073\/pnas.1510595112","article-title":"Transgenic expression of the proneural TF Ascl1 in Muller glia stimulates retinal regeneration in young mice","volume":"112","author":"Ueki","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_314","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.gde.2016.05.028","article-title":"Retinal regeneration in birds and mice","volume":"40","author":"Wilken","year":"2016","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_315","doi-asserted-by":"crossref","first-page":"108630","DOI":"10.1016\/j.exer.2021.108630","article-title":"Development and characterization of a chronic photoreceptor degeneration model in adult zebrafish that does not trigger a regenerative response","volume":"209","author":"Turkalj","year":"2021","journal-title":"Exp. Eye Res."},{"key":"ref_316","doi-asserted-by":"crossref","first-page":"E9391","DOI":"10.1073\/pnas.1808903115","article-title":"Developmental stage-specific proliferation and retinoblastoma genesis in RB-deficient human but not mouse cone precursors","volume":"115","author":"Singh","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_317","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1038\/s41593-019-0399-y","article-title":"Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes","volume":"22","author":"Aydin","year":"2019","journal-title":"Nat. Neurosci."},{"key":"ref_318","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.celrep.2016.08.078","article-title":"Wnt Regulates Proliferation and Neurogenic Potential of Muller Glial Cells via a Lin28\/let-7 miRNA-Dependent Pathway in Adult Mammalian Retinas","volume":"17","author":"Yao","year":"2016","journal-title":"Cell Rep."},{"key":"ref_319","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1016\/j.celrep.2019.04.047","article-title":"The Hippo Pathway Blocks Mammalian Retinal Muller Glial Cell Reprogramming","volume":"27","author":"Rueda","year":"2019","journal-title":"Cell Rep."},{"key":"ref_320","doi-asserted-by":"crossref","first-page":"109857","DOI":"10.1016\/j.celrep.2021.109857","article-title":"Efficient stimulation of retinal regeneration from Muller glia in adult mice using combinations of proneural bHLH TFs","volume":"37","author":"Todd","year":"2021","journal-title":"Cell Rep."},{"key":"ref_321","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41586-020-2975-4","article-title":"Reprogramming to recover youthful epigenetic information and restore vision","volume":"588","author":"Lu","year":"2020","journal-title":"Nature"},{"key":"ref_322","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining TFs prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"ref_323","first-page":"245","article-title":"Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins","volume":"338","author":"Berger","year":"2006","journal-title":"Methods Mol. Biol."},{"key":"ref_324","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1126\/science.2200121","article-title":"Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase","volume":"249","author":"Tuerk","year":"1990","journal-title":"Science"},{"key":"ref_325","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1016\/j.cell.2016.08.063","article-title":"Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape","volume":"166","author":"Huang","year":"2016","journal-title":"Cell"},{"key":"ref_326","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1038\/nprot.2017.055","article-title":"Mapping genome-wide transcription-factor binding sites using DAP-seq","volume":"12","author":"Bartlett","year":"2017","journal-title":"Nat. Protoc."},{"key":"ref_327","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1038\/s41592-021-01312-2","article-title":"Persistence and plasticity in bacterial gene regulation","volume":"18","author":"Baumgart","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_328","doi-asserted-by":"crossref","first-page":"e63","DOI":"10.1093\/nar\/gku117","article-title":"A comparative analysis of TF binding models learned from PBM, HT-SELEX and ChIP data","volume":"42","author":"Orenstein","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_329","doi-asserted-by":"crossref","first-page":"3593","DOI":"10.1093\/nar\/gkg567","article-title":"Regulatory sequence analysis tools","volume":"31","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_330","doi-asserted-by":"crossref","first-page":"D108","DOI":"10.1093\/nar\/gkj143","article-title":"TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes","volume":"34","author":"Matys","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_331","doi-asserted-by":"crossref","first-page":"D110","DOI":"10.1093\/nar\/gkv1176","article-title":"JASPAR 2016: A major expansion and update of the open-access database of TF binding profiles","volume":"44","author":"Mathelier","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_332","doi-asserted-by":"crossref","first-page":"D252","DOI":"10.1093\/nar\/gkx1106","article-title":"HOCOMOCO: Towards a complete collection of TF binding models for human and mouse via large-scale ChIP-Seq analysis","volume":"46","author":"Kulakovskiy","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_333","doi-asserted-by":"crossref","first-page":"D260","DOI":"10.1093\/nar\/gkx1126","article-title":"JASPAR 2018: Update of the open-access data-base of transcription factor binding profiles and its web framework","volume":"46","author":"Khan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_334","doi-asserted-by":"crossref","first-page":"D165","DOI":"10.1093\/nar\/gkab1113","article-title":"JASPAR 2022: The 9th release of the open-access database of TF binding profiles","volume":"50","author":"Rauluseviciute","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_335","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/318630a0","article-title":"The Drosophila developmental gene, engrailed, encodes a sequence-specific DNA binding activity","volume":"318","author":"Desplan","year":"1985","journal-title":"Nature"},{"key":"ref_336","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/0092-8674(89)90038-X","article-title":"A single amino acid can determine the DNA binding specificity of homeodomain proteins","volume":"59","author":"Treisman","year":"1989","journal-title":"Cell"},{"key":"ref_337","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/nn.4229","article-title":"Epigenomic annotation of gene regulatory alterations during evolution of the primate brain","volume":"19","author":"Vermunt","year":"2016","journal-title":"Nat. Neurosci."},{"key":"ref_338","doi-asserted-by":"crossref","first-page":"2615","DOI":"10.1093\/gbe\/evx194","article-title":"Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity","volume":"9","author":"Fish","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"ref_339","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1222794","article-title":"Systematic localization of common disease-associated variation in regulatory DNA","volume":"337","author":"Maurano","year":"2012","journal-title":"Science"},{"key":"ref_340","doi-asserted-by":"crossref","first-page":"i185","DOI":"10.1093\/bioinformatics\/btu273","article-title":"GRASP: Analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database","volume":"30","author":"Leslie","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_341","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nature17939","article-title":"Parkinson-associated risk variant in distal enhancer of alpha-synuclein modulates target gene expression","volume":"533","author":"Soldner","year":"2016","journal-title":"Nature"},{"key":"ref_342","doi-asserted-by":"crossref","first-page":"107799","DOI":"10.1016\/j.celrep.2020.107799","article-title":"Recently Evolved Enhancers Emerge with High Interindividual Variability and Less Frequently Associate with Disease","volume":"31","author":"Castelijns","year":"2020","journal-title":"Cell Rep."},{"key":"ref_343","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/nrg3481","article-title":"Evolution of TF binding in metazoans\u2014Mechanisms and functional implications","volume":"15","author":"Villar","year":"2014","journal-title":"Nat. Rev. Genet."},{"key":"ref_344","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.cell.2015.01.006","article-title":"Enhancer evolution across 20 mammalian species","volume":"160","author":"Villar","year":"2015","journal-title":"Cell"},{"key":"ref_345","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1038\/nrg3458","article-title":"Enhancers: Five essential questions","volume":"14","author":"Pennacchio","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"ref_346","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/nature25461","article-title":"Enhancer redundancy provides phenotypic robustness in mammalian development","volume":"554","author":"Osterwalder","year":"2018","journal-title":"Nature"},{"key":"ref_347","doi-asserted-by":"crossref","first-page":"4066","DOI":"10.1038\/s41467-018-06544-z","article-title":"Repurposing of promoters and enhancers during mammalian evolution","volume":"9","author":"Carelli","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_348","doi-asserted-by":"crossref","first-page":"R24","DOI":"10.1186\/gb-2007-8-2-r24","article-title":"Quantifying similarity between motifs","volume":"8","author":"Gupta","year":"2007","journal-title":"Genome Biol."},{"key":"ref_349","doi-asserted-by":"crossref","first-page":"e119","DOI":"10.1093\/nar\/gkx314","article-title":"RSAT matrix-clustering: Dynamic exploration and redundancy reduction of TF binding motif collections","volume":"45","author":"Jaeger","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_350","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"Soldatov","year":"2018","journal-title":"Nature"},{"key":"ref_351","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41587-020-0591-3","article-title":"Generalizing RNA velocity to transient cell states through dynamical modeling","volume":"38","author":"Bergen","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_352","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1038\/s41587-021-01031-1","article-title":"Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin","volume":"40","author":"Tedesco","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_353","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.chemolab.2015.10.018","article-title":"A Sequential Algorithm for Multiblock Orthogonal Projections to Latent Structures","volume":"149","author":"Worley","year":"2015","journal-title":"Chemom. Intell. Lab. Syst."},{"key":"ref_354","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1038\/s41467-021-21038-1","article-title":"A practical solution to pseudoreplication bias in single-cell studies","volume":"12","author":"Zimmerman","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_355","doi-asserted-by":"crossref","first-page":"5306","DOI":"10.1093\/bioinformatics\/btz601","article-title":"scRNABatchQC: Multi-samples quality control for single cell RNA-seq data","volume":"35","author":"Liu","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_356","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/s13059-016-0938-8","article-title":"CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq","volume":"17","author":"Hashimshony","year":"2016","journal-title":"Genome Biol."},{"key":"ref_357","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-015-0844-5","article-title":"MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data","volume":"16","author":"Finak","year":"2015","journal-title":"Genome Biol."},{"key":"ref_358","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1016\/j.cell.2008.09.050","article-title":"Nature, nurture, or chance: Stochastic gene expression and its consequences","volume":"135","author":"Raj","year":"2008","journal-title":"Cell"},{"key":"ref_359","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13059-018-1406-4","article-title":"Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications","volume":"19","author":"Perraudeau","year":"2018","journal-title":"Genome Biol."},{"key":"ref_360","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1186\/s13059-015-0805-z","article-title":"ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis","volume":"16","author":"Pierson","year":"2015","journal-title":"Genome Biol."},{"key":"ref_361","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13059-017-1188-0","article-title":"CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data","volume":"18","author":"Lin","year":"2017","journal-title":"Genome Biol."},{"key":"ref_362","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/s41587-019-0379-5","article-title":"Droplet scRNA-seq is not zero-inflated","volume":"38","author":"Svensson","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_363","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13059-016-0947-7","article-title":"Pooling across cells to normalize single-cell RNA sequencing data with many zero counts","volume":"17","author":"Lun","year":"2016","journal-title":"Genome Biol."},{"key":"ref_364","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1093\/biostatistics\/kxw055","article-title":"Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data","volume":"18","author":"Lun","year":"2017","journal-title":"Biostatistics"},{"key":"ref_365","doi-asserted-by":"crossref","first-page":"6077","DOI":"10.1038\/s41467-020-19894-4","article-title":"muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data","volume":"11","author":"Crowell","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_366","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1016\/j.cell.2018.06.052","article-title":"A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility","volume":"174","author":"Cusanovich","year":"2018","journal-title":"Cell"},{"key":"ref_367","doi-asserted-by":"crossref","unstructured":"Swanson, E., Lord, C., Reading, J., Heubeck, A.T., Genge, P.C., Thomson, Z., Weiss, M.D., Li, X.J., Savage, A.K., and Green, R.R. (2021). Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq. eLife, 10.","DOI":"10.7554\/eLife.63632"},{"key":"ref_368","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1038\/s41467-021-21583-9","article-title":"Comprehensive analysis of single cell ATAC-seq data with SnapATAC","volume":"12","author":"Fang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_369","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1038\/s41576-018-0088-9","article-title":"Challenges in unsupervised clustering of single-cell RNA-seq data","volume":"20","author":"Kiselev","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_370","unstructured":"McInnes, L., Healy, J., and Melville, J. (2018). Umap: Uniform manifold approximation and projection for dimension reduction. arXiv, Available online: https:\/\/arxiv.org\/abs\/1802.03426."},{"key":"ref_371","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_372","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1186\/s13059-019-1854-5","article-title":"Assessment of computational methods for the analysis of single-cell ATAC-seq data","volume":"20","author":"Chen","year":"2019","journal-title":"Genome Biol."},{"key":"ref_373","doi-asserted-by":"crossref","first-page":"646936","DOI":"10.3389\/fgene.2021.646936","article-title":"A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data","volume":"12","author":"Xiang","year":"2021","journal-title":"Front. Genet."},{"key":"ref_374","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/978-1-0716-1307-8_18","article-title":"Dimensionality Reduction of Single-Cell RNA-Seq Data","volume":"2284","author":"Linderman","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"ref_375","doi-asserted-by":"crossref","unstructured":"Ma, K.Y., Schonnesen, A.A., Brock, A., Van Den Berg, C., Eckhardt, S.G., Liu, Z., and Jiang, N. (2019). Single-cell RNA sequencing of lung adenocarcinoma reveals heterogeneity of immune response-related genes. JCI Insight, 4.","DOI":"10.1172\/jci.insight.121387"},{"key":"ref_376","doi-asserted-by":"crossref","unstructured":"Mendoza-Parra, M.A., Van Gool, W., Mohamed Saleem, M.A., Ceschin, D.G., and Gronemeyer, H. (2013). A quality control system for profiles obtained by ChIP sequencing. Nucleic Acids Res., 41.","DOI":"10.1093\/nar\/gkt829"},{"key":"ref_377","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1214\/11-AOAS466","article-title":"Measuring reproducibility of high-throughput experiments","volume":"5","author":"Li","year":"2011","journal-title":"Ann. Appl. Stat."},{"key":"ref_378","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.devcel.2013.02.016","article-title":"Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina","volume":"25","author":"Thanawala","year":"2013","journal-title":"Dev. Cell"},{"key":"ref_379","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13059-017-1385-x","article-title":"A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers","volume":"19","author":"Cole","year":"2018","journal-title":"Genome Biol."},{"key":"ref_380","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13059-019-1654-y","article-title":"Reproducible inference of TF footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling","volume":"20","author":"Hirsekorn","year":"2019","journal-title":"Genome Biol."},{"key":"ref_381","doi-asserted-by":"crossref","first-page":"5356","DOI":"10.1038\/s41467-018-07766-x","article-title":"Local and global chromatin interactions are altered by large genomic deletions associated with human brain development","volume":"9","author":"Zhang","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_382","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/s41576-018-0007-0","article-title":"Structural variation in the 3D genome","volume":"19","author":"Spielmann","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_383","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/s41580-019-0132-4","article-title":"The role of 3D genome organization in development and cell differentiation","volume":"20","author":"Zheng","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_384","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/s41586-019-1035-4","article-title":"Visualizing DNA folding and RNA in embryos at single-cell resolution","volume":"568","author":"Mateo","year":"2019","journal-title":"Nature"},{"key":"ref_385","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1016\/j.bpj.2017.03.024","article-title":"Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH","volume":"112","author":"Takei","year":"2017","journal-title":"Biophys. J."},{"key":"ref_386","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.tig.2019.12.010","article-title":"Advances in Chromatin Imaging at Kilobase-Scale Resolution","volume":"36","author":"Boettiger","year":"2020","journal-title":"Trends Genet."},{"key":"ref_387","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1126\/science.abj1966","article-title":"Single-cell nuclear architecture across cell types in the mouse brain","volume":"374","author":"Takei","year":"2021","journal-title":"Science"},{"key":"ref_388","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.1126\/science.1127344","article-title":"Imaging intracellular fluorescent proteins at nanometer resolution","volume":"313","author":"Betzig","year":"2006","journal-title":"Science"},{"key":"ref_389","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/978-1-4939-7265-4_19","article-title":"In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT","volume":"1663","author":"Beliveau","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"ref_390","doi-asserted-by":"crossref","first-page":"21301","DOI":"10.1073\/pnas.1213818110","article-title":"Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes","volume":"109","author":"Beliveau","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_391","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nmeth.2835","article-title":"Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT","volume":"11","author":"Jungmann","year":"2014","journal-title":"Nat. Methods"},{"key":"ref_392","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/nmeth929","article-title":"Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)","volume":"3","author":"Rust","year":"2006","journal-title":"Nat. Methods"},{"key":"ref_393","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1126\/science.1153529","article-title":"Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy","volume":"319","author":"Huang","year":"2008","journal-title":"Science"},{"key":"ref_394","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1146\/annurev-cellbio-100616-060531","article-title":"The Three-Dimensional Organization of Mammalian Genomes","volume":"33","author":"Yu","year":"2017","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_395","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/s41586-019-1411-0","article-title":"Advances in epigenetics link genetics to the environment and disease","volume":"571","author":"Cavalli","year":"2019","journal-title":"Nature"},{"key":"ref_396","doi-asserted-by":"crossref","unstructured":"Bintu, B., Mateo, L.J., Su, J.H., Sinnott-Armstrong, N.A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A.N., and Zhuang, X. (2018). Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science, 362.","DOI":"10.1126\/science.aau1783"},{"key":"ref_397","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1080\/19491034.2020.1763093","article-title":"Dynamics as a cause for the nanoscale organization of the genome","volume":"11","author":"Barth","year":"2020","journal-title":"Nucleus"},{"key":"ref_398","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1016\/j.cell.2020.07.032","article-title":"Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin","volume":"182","author":"Su","year":"2020","journal-title":"Cell"},{"key":"ref_399","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2020.10.026","article-title":"High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue","volume":"183","author":"Liu","year":"2020","journal-title":"Cell"},{"key":"ref_400","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature21429","article-title":"3D structures of individual mammalian genomes studied by single-cell Hi-C","volume":"544","author":"Stevens","year":"2017","journal-title":"Nature"},{"key":"ref_401","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature23001","article-title":"Cell-cycle dynamics of chromosomal organization at single-cell resolution","volume":"547","author":"Nagano","year":"2017","journal-title":"Nature"},{"key":"ref_402","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/nature21711","article-title":"Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition","volume":"544","author":"Flyamer","year":"2017","journal-title":"Nature"},{"key":"ref_403","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1126\/science.aat5641","article-title":"Three-dimensional genome structures of single diploid human cells","volume":"361","author":"Tan","year":"2018","journal-title":"Science"},{"key":"ref_404","doi-asserted-by":"crossref","unstructured":"Ou, H.D., Phan, S., Deerinck, T.J., Thor, A., Ellisman, M.H., and O\u2019Shea, C.C. (2017). ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science, 357.","DOI":"10.1126\/science.aag0025"},{"key":"ref_405","doi-asserted-by":"crossref","first-page":"3477","DOI":"10.1021\/acs.biochem.9b00611","article-title":"Seeing Is Believing: ORCA Allows Visualization of Three-Dimensional Genome Organization at Single-Cell Resolution","volume":"58","author":"Wang","year":"2019","journal-title":"Biochemistry"},{"key":"ref_406","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1126\/science.aaf8084","article-title":"Spatial organization of chromatin domains and compartments in single chromosomes","volume":"353","author":"Wang","year":"2016","journal-title":"Science"},{"key":"ref_407","doi-asserted-by":"crossref","unstructured":"Nir, G., Farabella, I., Perez Estrada, C., Ebeling, C.G., Beliveau, B.J., Sasaki, H.M., Lee, S.D., Nguyen, S.C., McCole, R.B., and Chattoraj, S. (2018). Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet., 14.","DOI":"10.1371\/journal.pgen.1007872"},{"key":"ref_408","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1038\/nature16496","article-title":"Super-resolution imaging reveals distinct chromatin folding for different epigenetic states","volume":"529","author":"Boettiger","year":"2016","journal-title":"Nature"},{"key":"ref_409","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.molcel.2017.01.009","article-title":"Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation","volume":"65","author":"Kundu","year":"2017","journal-title":"Mol. Cell"},{"key":"ref_410","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nn.4216","article-title":"Adult mouse cortical cell taxonomy revealed by single cell transcriptomics","volume":"19","author":"Tasic","year":"2016","journal-title":"Nat. Neurosci."},{"key":"ref_411","doi-asserted-by":"crossref","unstructured":"Payne, A.C., Chiang, Z.D., Reginato, P.L., Mangiameli, S.M., Murray, E.M., Yao, C.C., Markoulaki, S., Earl, A.S., Labade, A.S., and Jaenisch, R. (2021). In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science, 371.","DOI":"10.1126\/science.aay3446"},{"key":"ref_412","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1038\/s41587-021-01042-y","article-title":"Volumetric interferometric lattice light-sheet imaging","volume":"39","author":"Cao","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_413","doi-asserted-by":"crossref","unstructured":"Li, Y., Eshein, A., Virk, R.K.A., Eid, A., Wu, W., Frederick, J., VanDerway, D., Gladstein, S., Huang, K., and Shim, A.R. (2021). Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function. Sci. Adv., 7.","DOI":"10.1126\/sciadv.abe4310"},{"key":"ref_414","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1126\/science.1254257","article-title":"Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma","volume":"344","author":"Patel","year":"2014","journal-title":"Science"},{"key":"ref_415","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/nn.3881","article-title":"Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing","volume":"18","author":"Usoskin","year":"2015","journal-title":"Nat. Neurosci."},{"key":"ref_416","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nbt.3102","article-title":"Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells","volume":"33","author":"Buettner","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_417","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.stem.2015.09.011","article-title":"Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation","volume":"17","author":"Kolodziejczyk","year":"2015","journal-title":"Cell Stem Cell"},{"key":"ref_418","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.aap8809","article-title":"Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex","volume":"358","author":"Nowakowski","year":"2017","journal-title":"Science"},{"key":"ref_419","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1016\/j.stem.2017.05.009","article-title":"Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions","volume":"20","author":"Li","year":"2017","journal-title":"Cell Stem Cell"},{"key":"ref_420","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nature25999","article-title":"Developmental diversification of cortical inhibitory interneurons","volume":"555","author":"Mayer","year":"2018","journal-title":"Nature"},{"key":"ref_421","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/nature25980","article-title":"A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex","volume":"555","author":"Zhong","year":"2018","journal-title":"Nature"},{"key":"ref_422","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1016\/j.neuron.2019.06.011","article-title":"A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation","volume":"103","author":"Polioudakis","year":"2019","journal-title":"Neuron"},{"key":"ref_423","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/s41587-019-0068-4","article-title":"Characterization of cell fate probabilities in single-cell data with Palantir","volume":"37","author":"Setty","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_424","doi-asserted-by":"crossref","first-page":"5985","DOI":"10.1016\/j.cell.2021.10.024","article-title":"A single-cell atlas of chromatin accessibility in the human genome","volume":"184","author":"Zhang","year":"2021","journal-title":"Cell"},{"key":"ref_425","doi-asserted-by":"crossref","unstructured":"Zibetti, C., Liu, S., Wan, J., Qian, J., and Blackshaw, S. (2017). Lhx2 regulates temporal changes in chromatin accessibility and transcription factor binding in retinal progenitor cells. bioRxiv.","DOI":"10.1101\/238279"},{"key":"ref_426","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1101\/gr.131748.111","article-title":"Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling","volume":"22","author":"Steiner","year":"2012","journal-title":"Genome Res."},{"key":"ref_427","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/bioinformatics\/btaa830","article-title":"Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data","volume":"37","author":"Schreiber","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_428","doi-asserted-by":"crossref","first-page":"e34965","DOI":"10.7554\/eLife.34965","article-title":"The NIH must reduce disparities in funding to maximize its return on investments from taxpayers","volume":"7","author":"Wahls","year":"2018","journal-title":"eLife"},{"key":"ref_429","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s41073-017-0040-0","article-title":"Using democracy to award research funding: An observational study","volume":"2","author":"Barnett","year":"2017","journal-title":"Res. Integr. Peer Rev."},{"key":"ref_430","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.3346\/jkms.2015.30.11.1545","article-title":"Preserving the Integrity of Citations and References by All Stakeholders of Science Communication","volume":"30","author":"Gasparyan","year":"2015","journal-title":"J. Korean Med. Sci."},{"key":"ref_431","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/s41593-020-0658-y","article-title":"The extent and drivers of gender imbalance in neuroscience reference lists","volume":"23","author":"Dworkin","year":"2020","journal-title":"Nat. Neurosci."},{"key":"ref_432","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/j.tics.2020.06.009","article-title":"The Citation Diversity Statement: A Practice of Transparency, A Way of Life","volume":"24","author":"Zurn","year":"2020","journal-title":"Trends Cogn. Sci."},{"key":"ref_433","doi-asserted-by":"crossref","unstructured":"Scanff, A., Naudet, F., Cristea, I.A., Moher, D., Bishop, D.V.M., and Locher, C. (2021). A survey of biomedical journals to detect editorial bias and nepotistic behavior. PLoS Biol., 19.","DOI":"10.1371\/journal.pbio.3001133"},{"key":"ref_434","doi-asserted-by":"crossref","unstructured":"Tiokhin, L., Panchanathan, K., Lakens, D., Vazire, S., Morgan, T., and Zollman, K. (2021). Honest signaling in academic publishing. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0246675"},{"key":"ref_435","doi-asserted-by":"crossref","unstructured":"McConnell, S.C., Westerman, E.L., Pierre, J.F., Heckler, E.J., and Schwartz, N.B. (2018). United States National Postdoc Survey results and the interaction of gender, career choice and mentor impact. eLife, 7.","DOI":"10.7554\/eLife.40189"},{"key":"ref_436","doi-asserted-by":"crossref","unstructured":"Davis, S.M., Singh, H., Weismann, C.M., Bankston, A., and Ruiz Villalobos, J.P. (2020). Actionable recommendations from trainees to improve science training. eLife, 9.","DOI":"10.7554\/eLife.59806"},{"key":"ref_437","doi-asserted-by":"crossref","unstructured":"Byars-Winston, A., and Dahlberg, M.L. (2019). The Science of Effective Mentorship in STEMM., The National Academies Press.","DOI":"10.17226\/25568"},{"key":"ref_438","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1038\/548517a","article-title":"Stop blocking postdocs\u2019 paths to success","volume":"548","author":"Barres","year":"2017","journal-title":"Nature"},{"key":"ref_439","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1002\/job.520","article-title":"Developing and testing a measure for the ethical culture of organizations: The corporate ethical virtues model","volume":"29","author":"Kaptein","year":"2008","journal-title":"J. Organ. Behav."}],"container-title":["Cells"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4409\/11\/5\/806\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:27:33Z","timestamp":1760135253000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4409\/11\/5\/806"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,25]]},"references-count":439,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2022,3]]}},"alternative-id":["cells11050806"],"URL":"https:\/\/doi.org\/10.3390\/cells11050806","relation":{},"ISSN":["2073-4409"],"issn-type":[{"value":"2073-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,25]]}}}