{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T03:22:07Z","timestamp":1791861727866,"version":"4.3.4"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,10,14]],"date-time":"2021-10-14T00:00:00Z","timestamp":1634169600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,10,14]],"date-time":"2021-10-14T00:00:00Z","timestamp":1634169600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Emerging evidence indicates that long noncoding RNAs (lncRNAs) are important regulators of various biological processes, and their expression can be altered following certain pathological conditions, including central nervous system injury. Retinal ganglion cells (RGCs), whose axons form the optic nerve, are a heterogeneous population of neurons with more than 40 molecularly distinct subtypes in mouse. While most RGCs, including the ON-OFF direction-selective RGCs (ooDSGCs), are vulnerable to axonal injury, a small population of RGCs, including the intrinsically photosensitive RGCs (ipRGCs), are more resilient.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>By performing systematic analyses on RNA-sequencing data, here we identify lncRNAs that are expressed in ooDSGCs and ipRGCs with and without axonal injury. Our results reveal a repertoire of different classes of lncRNAs, including long intergenic noncoding RNAs and antisense ncRNAs that are differentially expressed between these RGC types. Strikingly, we also found dozens of lncRNAs whose expressions are altered markedly in response to axonal injury, some of which are expressed exclusively in either one of the types. Moreover, analyses into these lncRNAs unraveled their neighboring coding genes, many of which encode transcription factors and signaling molecules, suggesting that these lncRNAs may act <jats:italic>in cis<\/jats:italic> to regulate important biological processes in these neurons. Lastly, guilt-by-association analysis showed that lncRNAs are correlated with apoptosis associated genes, suggesting potential roles for these lncRNAs in RGC survival.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Overall, the results of this study reveal RGC type-specific expression of lncRNAs and provide a foundation for future investigation of the function of lncRNAs in regulating neuronal type specification and survival.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-08050-x","type":"journal-article","created":{"date-parts":[[2021,10,14]],"date-time":"2021-10-14T16:21:22Z","timestamp":1634228482000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Identification of long noncoding RNAs in injury-resilient and injury-susceptible mouse retinal ganglion cells"],"prefix":"10.1186","volume":"22","author":[{"given":"Ana C.","family":"Ayupe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felipe","family":"Beckedorff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantin","family":"Levay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benito","family":"Yon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yadira","family":"Salgueiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramin","family":"Shiekhattar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin K.","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,14]]},"reference":[{"issue":"18","key":"8050_CR1","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1101\/gad.17446611","volume":"25","author":"MN Cabili","year":"2011","unstructured":"Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25(18):1915\u201327. https:\/\/doi.org\/10.1101\/gad.17446611.","journal-title":"Genes Dev"},{"issue":"9","key":"8050_CR2","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1038\/nsmb.2660","volume":"20","author":"L Yan","year":"2013","unstructured":"Yan L, Yang M, Guo H, Yang L, Wu J, Li R, et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013;20(9):1131\u20139. https:\/\/doi.org\/10.1038\/nsmb.2660.","journal-title":"Nat Struct Mol Biol"},{"issue":"1","key":"8050_CR3","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1002\/cne.24172","volume":"527","author":"NT Sweeney","year":"2019","unstructured":"Sweeney NT, James KN, Nistorica A, Lorig-Roach RM, Feldheim DA. Expression of transcription factors divides retinal ganglion cells into distinct classes. J Comp Neurol. 2019;527(1):225\u201335. https:\/\/doi.org\/10.1002\/cne.24172.","journal-title":"J Comp Neurol"},{"issue":"39","key":"8050_CR4","doi-asserted-by":"publisher","first-page":"13083","DOI":"10.1523\/JNEUROSCI.1027-14.2014","volume":"34","author":"CA Mao","year":"2014","unstructured":"Mao CA, Li H, Zhang Z, Kiyama T, Panda S, Hattar S, et al. T-box transcription regulator Tbr2 is essential for the formation and maintenance of Opn4\/melanopsin-expressing intrinsically photosensitive retinal ganglion cells. J Neurosci. 2014;34(39):13083\u201395. https:\/\/doi.org\/10.1523\/JNEUROSCI.1027-14.2014.","journal-title":"J Neurosci"},{"issue":"20","key":"8050_CR5","doi-asserted-by":"publisher","first-page":"E3974","DOI":"10.1073\/pnas.1618551114","volume":"114","author":"S Sajgo","year":"2017","unstructured":"Sajgo S, Ghinia MG, Brooks M, Kretschmer F, Chuang K, Hiriyanna S, et al. Molecular codes for cell type specification in Brn3 retinal ganglion cells. Proc Natl Acad Sci U S A. 2017;114(20):E3974\u2013E83. https:\/\/doi.org\/10.1073\/pnas.1618551114.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"8050_CR6","doi-asserted-by":"publisher","first-page":"451","DOI":"10.3390\/ijms21020451","volume":"21","author":"KT Nguyen-Ba-Charvet","year":"2020","unstructured":"Nguyen-Ba-Charvet KT, Rebsam A. Neurogenesis and Specification of Retinal Ganglion Cells. Int J Mol Sci. 2020;21(2):451.","journal-title":"Int J Mol Sci"},{"issue":"5","key":"8050_CR7","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1016\/j.cell.2018.04.040","volume":"173","author":"JA Bae","year":"2018","unstructured":"Bae JA, Mu S, Kim JS, Turner NL, Tartavull I, Kemnitz N, et al. Digital Museum of Retinal Ganglion Cells with dense anatomy and physiology. Cell. 2018;173(5):1293\u2013306 e19. https:\/\/doi.org\/10.1016\/j.cell.2018.04.040.","journal-title":"Cell"},{"issue":"7586","key":"8050_CR8","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nature16468","volume":"529","author":"T Baden","year":"2016","unstructured":"Baden T, Berens P, Franke K, Roman Roson M, Bethge M, Euler T. The functional diversity of retinal ganglion cells in the mouse. Nature. 2016;529(7586):345\u201350. https:\/\/doi.org\/10.1038\/nature16468.","journal-title":"Nature"},{"issue":"6","key":"8050_CR9","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1016\/j.neuron.2019.11.006","volume":"104","author":"NM Tran","year":"2019","unstructured":"Tran NM, Shekhar K, Whitney IE, Jacobi A, Benhar I, Hong G, et al. Single-cell profiles of retinal ganglion cells differing in resilience to injury reveal neuroprotective genes. Neuron. 2019;104(6):1039\u201355 e12. https:\/\/doi.org\/10.1016\/j.neuron.2019.11.006.","journal-title":"Neuron"},{"issue":"1","key":"8050_CR10","doi-asserted-by":"publisher","first-page":"2759","DOI":"10.1038\/s41467-018-05134-3","volume":"9","author":"BA Rheaume","year":"2018","unstructured":"Rheaume BA, Jereen A, Bolisetty M, Sajid MS, Yang Y, Renna K, et al. Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes. Nat Commun. 2018;9(1):2759. https:\/\/doi.org\/10.1038\/s41467-018-05134-3.","journal-title":"Nat Commun"},{"issue":"4","key":"8050_CR11","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1016\/j.neuron.2019.05.044","volume":"103","author":"ER Bray","year":"2019","unstructured":"Bray ER, Yungher BJ, Levay K, Ribeiro M, Dvoryanchikov G, Ayupe AC, et al. Thrombospondin-1 mediates axon regeneration in retinal ganglion cells. Neuron. 2019;103(4):642\u201357 e7. https:\/\/doi.org\/10.1016\/j.neuron.2019.05.044.","journal-title":"Neuron"},{"key":"8050_CR12","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1016\/j.neuroscience.2014.11.002","volume":"284","author":"Q Cui","year":"2015","unstructured":"Cui Q, Ren C, Sollars PJ, Pickard GE, So KF. The injury resistant ability of melanopsin-expressing intrinsically photosensitive retinal ganglion cells. Neuroscience. 2015;284:845\u201353. https:\/\/doi.org\/10.1016\/j.neuroscience.2014.11.002.","journal-title":"Neuroscience"},{"issue":"6","key":"8050_CR13","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.1016\/j.neuron.2015.02.017","volume":"85","author":"X Duan","year":"2015","unstructured":"Duan X, Qiao M, Bei F, Kim IJ, He Z, Sanes JR. Subtype-specific regeneration of retinal ganglion cells following axotomy: effects of osteopontin and mTOR signaling. Neuron. 2015;85(6):1244\u201356. https:\/\/doi.org\/10.1016\/j.neuron.2015.02.017.","journal-title":"Neuron"},{"issue":"1","key":"8050_CR14","doi-asserted-by":"publisher","first-page":"17359","DOI":"10.1038\/s41598-020-71460-6","volume":"10","author":"KB VanderWall","year":"2020","unstructured":"VanderWall KB, Lu B, Alfaro JS, Allsop AR, Carr AS, Wang S, et al. Differential susceptibility of retinal ganglion cell subtypes in acute and chronic models of injury and disease. Sci Rep. 2020;10(1):17359. https:\/\/doi.org\/10.1038\/s41598-020-71460-6.","journal-title":"Sci Rep"},{"issue":"3","key":"8050_CR15","doi-asserted-by":"publisher","first-page":"e93274","DOI":"10.1371\/journal.pone.0093274","volume":"9","author":"L Perez de Sevilla Muller","year":"2014","unstructured":"Perez de Sevilla Muller L, Sargoy A, Rodriguez AR, Brecha NC. Melanopsin ganglion cells are the most resistant retinal ganglion cell type to axonal injury in the rat retina. Plos One. 2014;9(3):e93274.","journal-title":"Plos One"},{"key":"8050_CR16","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/j.preteyeres.2018.11.006","volume":"71","author":"M Berry","year":"2019","unstructured":"Berry M, Ahmed Z, Logan A. Return of function after CNS axon regeneration: lessons from injury-responsive intrinsically photosensitive and alpha retinal ganglion cells. Prog Retin Eye Res. 2019;71:57\u201367. https:\/\/doi.org\/10.1016\/j.preteyeres.2018.11.006.","journal-title":"Prog Retin Eye Res"},{"issue":"3","key":"8050_CR17","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1007\/s00018-020-03641-5","volume":"78","author":"ML Aranda","year":"2020","unstructured":"Aranda ML, Schmidt TM. Diversity of intrinsically photosensitive retinal ganglion cells: circuits and functions. Cell Mol Life Sci. 2020;78(3):889\u2013907. https:\/\/doi.org\/10.1007\/s00018-020-03641-5.","journal-title":"Cell Mol Life Sci"},{"issue":"2","key":"8050_CR18","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1016\/j.neuron.2019.07.016","volume":"104","author":"MTH Do","year":"2019","unstructured":"Do MTH. Melanopsin and the intrinsically photosensitive retinal ganglion cells: biophysics to behavior. Neuron. 2019;104(2):205\u201326. https:\/\/doi.org\/10.1016\/j.neuron.2019.07.016.","journal-title":"Neuron"},{"key":"8050_CR19","first-page":"59","volume":"162","author":"GE Pickard","year":"2012","unstructured":"Pickard GE, Sollars PJ. Intrinsically photosensitive retinal ganglion cells. Rev Physiol Biochem Pharmacol. 2012;162:59\u201390.","journal-title":"Rev Physiol Biochem Pharmacol"},{"issue":"1","key":"8050_CR20","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1749-8104-6-8","volume":"6","author":"DS McNeill","year":"2011","unstructured":"McNeill DS, Sheely CJ, Ecker JL, Badea TC, Morhardt D, Guido W, et al. Development of melanopsin-based irradiance detecting circuitry. Neural Dev. 2011;6(1):8. https:\/\/doi.org\/10.1186\/1749-8104-6-8.","journal-title":"Neural Dev"},{"issue":"1","key":"8050_CR21","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1146\/annurev-neuro-071714-034120","volume":"38","author":"JR Sanes","year":"2015","unstructured":"Sanes JR, Masland RH. The types of retinal ganglion cells: current status and implications for neuronal classification. Annu Rev Neurosci. 2015;38(1):221\u201346. https:\/\/doi.org\/10.1146\/annurev-neuro-071714-034120.","journal-title":"Annu Rev Neurosci"},{"key":"8050_CR22","volume-title":"Webvision","author":"J Liu","year":"1995","unstructured":"Liu J. The Anatomy and Physiology of Direction-Selective Retinal Ganglion Cells. In: Kolb H, Fernandez E, Nelson R, editors. Webvision. Salt Lake City: The Organization of the Retina and Visual System; 1995."},{"issue":"3764","key":"8050_CR23","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1126\/science.155.3764.841","volume":"155","author":"CW Oyster","year":"1967","unstructured":"Oyster CW, Barlow HB. Direction-selective units in rabbit retina: distribution of preferred directions. Science. 1967;155(3764):841\u20132. https:\/\/doi.org\/10.1126\/science.155.3764.841.","journal-title":"Science"},{"issue":"1","key":"8050_CR24","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1523\/JNEUROSCI.1784-18.2018","volume":"39","author":"OS Dhande","year":"2019","unstructured":"Dhande OS, Stafford BK, Franke K, El-Danaf R, Percival KA, Phan AH, et al. Molecular fingerprinting of on-off direction-selective retinal ganglion cells across species and relevance to primate visual circuits. J Neurosci. 2019;39(1):78\u201395. https:\/\/doi.org\/10.1523\/JNEUROSCI.1784-18.2018.","journal-title":"J Neurosci"},{"issue":"1","key":"8050_CR25","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15\u201321. https:\/\/doi.org\/10.1093\/bioinformatics\/bts635.","journal-title":"Bioinformatics"},{"issue":"1","key":"8050_CR26","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1186\/s13059-019-1910-1","volume":"20","author":"S Kovaka","year":"2019","unstructured":"Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019;20(1):278. https:\/\/doi.org\/10.1186\/s13059-019-1910-1.","journal-title":"Genome Biol"},{"key":"8050_CR27","doi-asserted-by":"publisher","first-page":"132","DOI":"10.3389\/fgene.2018.00132","volume":"9","author":"LF daSilva","year":"2018","unstructured":"daSilva LF, Beckedorff FC, Ayupe AC, Amaral MS, Mesel V, Videira A, et al. Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs. Front Genet. 2018;9:132.","journal-title":"Front Genet"},{"issue":"W1","key":"8050_CR28","doi-asserted-by":"publisher","first-page":"W12","DOI":"10.1093\/nar\/gkx428","volume":"45","author":"YJ Kang","year":"2017","unstructured":"Kang YJ, Yang DC, Kong L, Hou M, Meng YQ, Wei L, et al. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 2017;45(W1):W12\u2013W6. https:\/\/doi.org\/10.1093\/nar\/gkx428.","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"8050_CR29","doi-asserted-by":"publisher","first-page":"e74","DOI":"10.1093\/nar\/gkt006","volume":"41","author":"L Wang","year":"2013","unstructured":"Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41(6):e74. https:\/\/doi.org\/10.1093\/nar\/gkt006.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"8050_CR30","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12(1):323. https:\/\/doi.org\/10.1186\/1471-2105-12-323.","journal-title":"BMC Bioinformatics"},{"issue":"12","key":"8050_CR31","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. https:\/\/doi.org\/10.1186\/s13059-014-0550-8.","journal-title":"Genome Biol"},{"issue":"8","key":"8050_CR32","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1080\/15476286.2015.1062960","volume":"12","author":"AC Ayupe","year":"2015","unstructured":"Ayupe AC, Tahira AC, Camargo L, Beckedorff FC, Verjovski-Almeida S, Reis EM. Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome. RNA Biol. 2015;12(8):877\u201392. https:\/\/doi.org\/10.1080\/15476286.2015.1062960.","journal-title":"RNA Biol"},{"issue":"1","key":"8050_CR33","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"W Huang da","year":"2009","unstructured":"Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44\u201357. https:\/\/doi.org\/10.1038\/nprot.2008.211.","journal-title":"Nat Protoc"},{"key":"8050_CR34","doi-asserted-by":"publisher","first-page":"e01749","DOI":"10.7554\/eLife.01749","volume":"2","author":"M Sauvageau","year":"2013","unstructured":"Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2013;2:e01749. https:\/\/doi.org\/10.7554\/eLife.01749.","journal-title":"Elife"},{"issue":"Unit3","key":"8050_CR35","first-page":"22","volume":"Chapter 3","author":"V Grozdanov","year":"2010","unstructured":"Grozdanov V, Muller A, Sengottuvel V, Leibinger M, Fischer D. A method for preparing primary retinal cell cultures for evaluating the neuroprotective and neuritogenic effect of factors on axotomized mature CNS neurons. Curr Protoc Neurosci. 2010;Chapter 3(Unit3):22.","journal-title":"Curr Protoc Neurosci"},{"issue":"1","key":"8050_CR36","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1186\/s12864-019-5903-y","volume":"20","author":"Y Wan","year":"2019","unstructured":"Wan Y, Liu XY, Zheng DW, Wang YY, Chen H, Zhao XF, et al. Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing. BMC Genomics. 2019;20(1):559. https:\/\/doi.org\/10.1186\/s12864-019-5903-y.","journal-title":"BMC Genomics"},{"issue":"9","key":"8050_CR37","doi-asserted-by":"publisher","first-page":"1775","DOI":"10.1101\/gr.132159.111","volume":"22","author":"T Derrien","year":"2012","unstructured":"Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22(9):1775\u201389. https:\/\/doi.org\/10.1101\/gr.132159.111.","journal-title":"Genome Res"},{"issue":"2","key":"8050_CR38","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1038\/s41576-019-0184-5","volume":"21","author":"N Gil","year":"2020","unstructured":"Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet. 2020;21(2):102\u201317. https:\/\/doi.org\/10.1038\/s41576-019-0184-5.","journal-title":"Nat Rev Genet"},{"issue":"2","key":"8050_CR39","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1006\/dbio.1999.9280","volume":"210","author":"L Gan","year":"1999","unstructured":"Gan L, Wang SW, Huang Z, Klein WH. POU domain factor Brn-3b is essential for retinal ganglion cell differentiation and survival but not for initial cell fate specification. Dev Biol. 1999;210(2):469\u201380. https:\/\/doi.org\/10.1006\/dbio.1999.9280.","journal-title":"Dev Biol"},{"issue":"4","key":"8050_CR40","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1002\/cne.22765","volume":"520","author":"V Jain","year":"2012","unstructured":"Jain V, Ravindran E, Dhingra NK. Differential expression of Brn3 transcription factors in intrinsically photosensitive retinal ganglion cells in mouse. J Comp Neurol. 2012;520(4):742\u201355. https:\/\/doi.org\/10.1002\/cne.22765.","journal-title":"J Comp Neurol"},{"issue":"3","key":"8050_CR41","doi-asserted-by":"publisher","first-page":"e93258","DOI":"10.1371\/journal.pone.0093258","volume":"9","author":"M Yasuda","year":"2014","unstructured":"Yasuda M, Tanaka Y, Ryu M, Tsuda S, Nakazawa T. RNA Sequence Reveals Mouse Retinal Transcriptome Changes Early after Axonal Injury. Plos One. 2014;9(3):e93258.","journal-title":"Plos One"},{"issue":"5","key":"8050_CR42","doi-asserted-by":"publisher","first-page":"2205","DOI":"10.1523\/JNEUROSCI.2635-12.2013","volume":"33","author":"AM Wilson","year":"2013","unstructured":"Wilson AM, Morquette B, Abdouh M, Unsain N, Barker PA, Feinstein E, et al. ASPP1\/2 regulate p53-dependent death of retinal ganglion cells through PUMA and Fas\/CD95 activation in vivo. J Neurosci. 2013;33(5):2205\u201316. https:\/\/doi.org\/10.1523\/JNEUROSCI.2635-12.2013.","journal-title":"J Neurosci"},{"issue":"3","key":"8050_CR43","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/j.cell.2018.01.011","volume":"172","author":"F Kopp","year":"2018","unstructured":"Kopp F, Mendell JT. Functional classification and experimental dissection of long noncoding RNAs. Cell. 2018;172(3):393\u2013407. https:\/\/doi.org\/10.1016\/j.cell.2018.01.011.","journal-title":"Cell"},{"issue":"7","key":"8050_CR44","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1016\/j.cell.2007.05.022","volume":"129","author":"JL Rinn","year":"2007","unstructured":"Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007;129(7):1311\u201323. https:\/\/doi.org\/10.1016\/j.cell.2007.05.022.","journal-title":"Cell"},{"issue":"28","key":"8050_CR45","doi-asserted-by":"publisher","first-page":"11667","DOI":"10.1073\/pnas.0904715106","volume":"106","author":"AM Khalil","year":"2009","unstructured":"Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009;106(28):11667\u201372. https:\/\/doi.org\/10.1073\/pnas.0904715106.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"8050_CR46","doi-asserted-by":"publisher","first-page":"e1003705","DOI":"10.1371\/journal.pgen.1003705","volume":"9","author":"FC Beckedorff","year":"2013","unstructured":"Beckedorff FC, Ayupe AC, Crocci-Souza R, Amaral MS, Nakaya HI, Soltys DT, et al. The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation. PLoS Genet. 2013;9(8):e1003705. https:\/\/doi.org\/10.1371\/journal.pgen.1003705.","journal-title":"PLoS Genet"},{"issue":"1","key":"8050_CR47","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s12964-020-00691-x","volume":"19","author":"A Videira","year":"2021","unstructured":"Videira A, Beckedorff FC, daSilva LF, Verjovski-Almeida S. PVT1 signals an androgen-dependent transcriptional repression program in prostate cancer cells and a set of the repressed genes predicts high-risk tumors. Cell Commun Signal. 2021;19(1):5.","journal-title":"Cell Commun Signal"},{"issue":"10","key":"8050_CR48","doi-asserted-by":"publisher","first-page":"3943","DOI":"10.1167\/iovs.18-23784","volume":"59","author":"K Sato","year":"2018","unstructured":"Sato K, Shiga Y, Nakagawa Y, Fujita K, Nishiguchi KM, Tawarayama H, et al. Ecel1 knockdown with an AAV2-mediated CRISPR\/Cas9 system promotes optic nerve damage-induced RGC death in the mouse retina. Invest Ophthalmol Vis Sci. 2018;59(10):3943\u201351. https:\/\/doi.org\/10.1167\/iovs.18-23784.","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"6","key":"8050_CR49","doi-asserted-by":"publisher","first-page":"e2847","DOI":"10.1038\/cddis.2017.212","volume":"8","author":"A Kaneko","year":"2017","unstructured":"Kaneko A, Kiryu-Seo S, Matsumoto S, Kiyama H. Damage-induced neuronal endopeptidase (DINE) enhances axonal regeneration potential of retinal ganglion cells after optic nerve injury. Cell Death Dis. 2017;8(6):e2847. https:\/\/doi.org\/10.1038\/cddis.2017.212.","journal-title":"Cell Death Dis"},{"issue":"6","key":"8050_CR50","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1007\/s11064-018-2665-x","volume":"44","author":"S Kiryu-Seo","year":"2019","unstructured":"Kiryu-Seo S, Nagata K, Saido TC, Kiyama H. New insights of a neuronal peptidase DINE\/ECEL1: nerve development, nerve regeneration and neurogenic pathogenesis. Neurochem Res. 2019;44(6):1279\u201388. https:\/\/doi.org\/10.1007\/s11064-018-2665-x.","journal-title":"Neurochem Res"},{"key":"8050_CR51","doi-asserted-by":"publisher","first-page":"59","DOI":"10.3389\/fnint.2019.00059","volume":"13","author":"J Chen","year":"2019","unstructured":"Chen J, Zhang L, Liu L, Yang X, Wu F, Gan X, et al. Acupuncture treatment reverses retinal gene expression induced by optic nerve injury via RNA sequencing analysis. Front Integr Neurosci. 2019;13:59. https:\/\/doi.org\/10.3389\/fnint.2019.00059.","journal-title":"Front Integr Neurosci"},{"issue":"1","key":"8050_CR52","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1186\/s13287-019-1487-3","volume":"10","author":"Y Cui","year":"2019","unstructured":"Cui Y, Yin Y, Xiao Z, Zhao Y, Chen B, Yang B, et al. LncRNA Neat1 mediates miR-124-induced activation of Wnt\/beta-catenin signaling in spinal cord neural progenitor cells. Stem Cell Res Ther. 2019;10(1):400. https:\/\/doi.org\/10.1186\/s13287-019-1487-3.","journal-title":"Stem Cell Res Ther"},{"key":"8050_CR53","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.neuroscience.2016.12.020","volume":"343","author":"AK Patel","year":"2017","unstructured":"Patel AK, Park KK, Hackam AS. Wnt signaling promotes axonal regeneration following optic nerve injury in the mouse. Neuroscience. 2017;343:372\u201383. https:\/\/doi.org\/10.1016\/j.neuroscience.2016.12.020.","journal-title":"Neuroscience"},{"issue":"1","key":"8050_CR54","doi-asserted-by":"publisher","first-page":"e54462","DOI":"10.1371\/journal.pone.0054462","volume":"8","author":"S Dupraz","year":"2013","unstructured":"Dupraz S, Grassi D, Karnas D, Guil AFN, Hicks D, Quiroga S. The Insulin-Like Growth Factor 1 Receptor Is Essential for Axonal Regeneration in Adult Central Nervous System Neurons. Plos One. 2013;8(1):e54462.","journal-title":"Plos One"},{"issue":"3","key":"8050_CR55","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/s41419-018-1289-z","volume":"10","author":"H Huang","year":"2019","unstructured":"Huang H, Miao L, Yang L, Liang F, Wang Q, Zhuang P, et al. AKT-dependent and -independent pathways mediate PTEN deletion-induced CNS axon regeneration. Cell Death Dis. 2019;10(3):203. https:\/\/doi.org\/10.1038\/s41419-018-1289-z.","journal-title":"Cell Death Dis"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-021-08050-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-021-08050-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-021-08050-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,14]],"date-time":"2021-10-14T16:22:07Z","timestamp":1634228527000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-021-08050-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,14]]},"references-count":55,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["8050"],"URL":"https:\/\/doi.org\/10.1186\/s12864-021-08050-x","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,14]]},"assertion":[{"value":"14 January 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 September 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 October 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All methods were carried out in accordance with relevant institutional guidelines and regulations. Mouse procedures were performed in compliance with protocols approved by the Institutional Animal Care and Use Committee (IACUC) at University of Miami Miller School of Medicine (Permit Number: 19\u2013150). This study was carried out in compliance with the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"No potential conflict of interest was reported by the authors.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"741"}}