{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T14:59:34Z","timestamp":1790953174916,"version":"4.1.0"},"reference-count":85,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2017,1,19]],"date-time":"2017-01-19T00:00:00Z","timestamp":1484784000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["5R01GM076507"],"award-info":[{"award-number":["5R01GM076507"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["5F32DK084706"],"award-info":[{"award-number":["5F32DK084706"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1006538","type":"journal-article","created":{"date-parts":[[2017,1,19]],"date-time":"2017-01-19T13:43:28Z","timestamp":1484833408000},"page":"e1006538","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":101,"title":["Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0075-8324","authenticated-orcid":true,"given":"Ian K.","family":"Quigley","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Kintner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,1,19]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1093\/emboj\/17.1.244","article-title":"Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome","volume":"17","author":"LA Cirillo","year":"1998","journal-title":"EMBO J"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1670","DOI":"10.1101\/gad.10.13.1670","article-title":"Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control","volume":"10","author":"R Gualdi","year":"1996","journal-title":"Genes Dev"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"S Heinz","year":"2010","journal-title":"Mol Cell"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1016\/j.cell.2008.01.018","article-title":"FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription","volume":"132","author":"M Lupien","year":"2008","journal-title":"Cell"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/ng1051","article-title":"Long-range chromatin regulatory interactions in vivo","volume":"32","author":"D Carter","year":"2002","journal-title":"Nat Genet"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nature12644","article-title":"A high-resolution map of the three-dimensional chromatin interactome in human cells","volume":"503","author":"F Jin","year":"2013","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nature14222","article-title":"Chromatin architecture reorganization during stem cell differentiation","volume":"518","author":"JR Dixon","year":"2015","journal-title":"Nature"},{"key":"ref8","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":"E Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"ref9","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":"SSP Rao","year":"2014","journal-title":"Cell"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nature12753","article-title":"Topology of mammalian developmental enhancers and their regulatory landscapes","volume":"502","author":"W de Laat","year":"2013","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1016\/j.cell.2016.01.004","article-title":"Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis","volume":"164","author":"L Luna-Zurita","year":"2016","journal-title":"Cell"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1242\/dev.074666","article-title":"Switching on cilia: transcriptional networks regulating ciliogenesis","volume":"141","author":"SP Choksi","year":"2014","journal-title":"Development"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"R973","DOI":"10.1016\/j.cub.2014.08.047","article-title":"Multiciliated cells","volume":"24","author":"ER Brooks","year":"2014","journal-title":"Curr Biol. Elsevier"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/1465-9921-14-70","article-title":"RFX3 modulation of FOXJ1 regulation of cilia genes in the human airway epithelium","volume":"14","author":"L Didon","year":"2013","journal-title":"Respir Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1016\/j.devcel.2012.05.010","article-title":"Forkhead transcription factor Fd3F cooperates with Rfx to regulate a gene expression program for mechanosensory cilia specialization","volume":"22","author":"FG Newton","year":"2012","journal-title":"Dev Cell"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.cell.2008.03.029","article-title":"Highly integrated single-base resolution maps of the epigenome in Arabidopsis","volume":"133","author":"R Lister","year":"2008","journal-title":"Cell"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1242\/dev.124.3.693","article-title":"The Xenopus homolog of Drosophila Suppressor of Hairless mediates Notch signaling during primary neurogenesis","volume":"124","author":"DA Wettstein","year":"1997","journal-title":"Development"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"4715","DOI":"10.1242\/dev.126.21.4715","article-title":"A two-step mechanism generates the spacing pattern of the ciliated cells in the skin of Xenopus embryos","volume":"126","author":"GA Deblandre","year":"1999","journal-title":"Development"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/ncb2406","article-title":"Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation","volume":"14","author":"JL Stubbs","year":"2012","journal-title":"Nat Cell Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"3410","DOI":"10.1242\/dev.108209","article-title":"Systematic discovery of novel ciliary genes through functional genomics in the zebrafish","volume":"141","author":"SP Choksi","year":"2014","journal-title":"Development"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e52166","DOI":"10.1371\/journal.pone.0052166","article-title":"Transcriptional program of ciliated epithelial cells reveals new cilium and centrosome components and links to human disease","volume":"7","author":"RA Hoh","year":"2012","journal-title":"PLoS One"},{"key":"ref22","first-page":"e01439","article-title":"Coordinated genomic control of ciliogenesis and cell movement by RFX2","volume":"3","author":"M-I Chung","year":"2014","journal-title":"Elife. eLife Sciences Publications Limited"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nbt.2057","article-title":"Genome architectures revealed by tethered chromosome conformation capture and population-based modeling","volume":"30","author":"R Kalhor","year":"2012","journal-title":"Nat Biotechnol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/s13059-015-0753-7","article-title":"Comparison of Hi-C results using in-solution versus in-nucleus ligation","volume":"16","author":"T Nagano","year":"2015","journal-title":"Genome Biol. BioMed Central"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1038\/ni.2432","article-title":"Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate","volume":"13","author":"YC Lin","year":"2012","journal-title":"Nat Immunol"},{"key":"ref26","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":"JR Dixon","year":"2012","journal-title":"Nature"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1234167","DOI":"10.1126\/science.1234167","article-title":"A switch between topological domains underlies HoxD genes collinearity in mouse limbs","volume":"340","author":"G Andrey","year":"2013","journal-title":"Science"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1073\/pnas.1317788111","article-title":"Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells","volume":"111","author":"J Zuin","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3119","DOI":"10.1038\/emboj.2013.237","article-title":"Cohesin-mediated interactions organize chromosomal domain architecture","volume":"32","author":"S Sofueva","year":"2013","journal-title":"EMBO J. European Molecular Biology Organization"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/nrm3949","article-title":"The selection and function of cell type-specific enhancers","volume":"16","author":"S Heinz","year":"2015","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1101\/gr.111724.110","article-title":"Nucleotide composition-linked divergence of vertebrate core promoter architecture","volume":"21","author":"SJ van Heeringen","year":"2011","journal-title":"Genome Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"D144","DOI":"10.1093\/nar\/gkr965","article-title":"AnimalTFDB: a comprehensive animal transcription factor database","volume":"40","author":"H-M Zhang","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1016\/j.tig.2013.05.010","article-title":"Human housekeeping genes, revisited","volume":"29","author":"E Eisenberg","year":"2013","journal-title":"Trends Genet"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"8549","DOI":"10.1038\/ncomms9549","article-title":"RFX transcription factors are essential for hearing in mice","volume":"6","author":"R Elkon","year":"2015","journal-title":"Nat Commun"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"12969","DOI":"10.1073\/pnas.0914241107","article-title":"Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals","volume":"107","author":"BP Piasecki","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref36","first-page":"233","article-title":"Metazoan promoters: emerging characteristics and insights into transcriptional regulation","volume":"13","author":"B Lenhard","year":"2012","journal-title":"Nat Rev Genet. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2594","DOI":"10.1101\/gr.1317703","article-title":"Nucleotide frequency variation across human genes","volume":"13","author":"E Louie","year":"2003","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2002-3-12-research0087","article-title":"Computational analysis of core promoters in the Drosophila genome","volume":"3","author":"U Ohler","year":"2002","journal-title":"Genome Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1454","DOI":"10.1038\/ng.267","article-title":"The forkhead protein Foxj1 specifies node-like cilia in Xenopus and zebrafish embryos","volume":"40","author":"JL Stubbs","year":"2008","journal-title":"Nat Genet"},{"key":"ref40","first-page":"1461","article-title":"Multicilin drives centriole biogenesis via E2f proteins","volume":"28","author":"L Ma","year":"2014","journal-title":"Genes Dev. Cold Spring Harbor Laboratory Press"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"4277","DOI":"10.1242\/dev.094102","article-title":"Myb promotes centriole amplification and later steps of the multiciliogenesis program","volume":"140","author":"FE Tan","year":"2013","journal-title":"Development"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/nature19840","article-title":"Genome evolution in the allotetraploid frog Xenopus laevis","volume":"538","author":"AM Session","year":"2016","journal-title":"Nature. Nature Research"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature07829","article-title":"Histone modifications at human enhancers reflect global cell-type-specific gene expression","volume":"459","author":"ND Heintzman","year":"2009","journal-title":"Nature"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1186\/s13059-015-0668-3","article-title":"Inferring regulatory element landscapes and transcription factor networks from cancer methylomes","volume":"16","author":"L Yao","year":"2015","journal-title":"Genome Biol. BioMed Central"},{"key":"ref45","article-title":"TAp73 is a central transcriptional regulator of airway multiciliogenesis","author":"A Nemajerova","year":"2016","journal-title":"Genes Dev"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1242\/dev.01775","article-title":"Analysis of xbx genes in C. elegans","volume":"132","author":"E Efimenko","year":"2005","journal-title":"Development"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"e1003019","DOI":"10.1371\/journal.pgen.1003019","article-title":"Evolutionarily ancient association of the FoxJ1 transcription factor with the motile ciliogenic program","volume":"8","author":"S Vij","year":"2012","journal-title":"PLoS Genet"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.ydbio.2011.12.029","article-title":"RFX2 is broadly required for ciliogenesis during vertebrate development","volume":"363","author":"M-I Chung","year":"2012","journal-title":"Dev Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1101\/gr.144840.112","article-title":"Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types","volume":"23","author":"J Ernst","year":"2013","journal-title":"Genome Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/ng.759","article-title":"Chromatin accessibility pre-determines glucocorticoid receptor binding patterns","volume":"43","author":"S John","year":"2011","journal-title":"Nat Genet. Nature Publishing Group"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"24504","DOI":"10.1074\/jbc.273.38.24504","article-title":"RFX1, a Single DNA-binding Protein with a Split Dimerization Domain, Generates Alternative Complexes","volume":"273","author":"Y Katan-Khaykovich","year":"1998","journal-title":"J Biol Chem"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1101\/gad.4.9.1528","article-title":"MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain","volume":"4","author":"W Reith","year":"1990","journal-title":"Genes Dev"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.stem.2015.11.007","article-title":"3D Chromosome Regulatory Landscape of Human Pluripotent Cells","volume":"18","author":"X Ji","year":"2015","journal-title":"Cell Stem Cell"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1186\/1471-2105-11-237","article-title":"ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data","volume":"11","author":"LJ Zhu","year":"2010","journal-title":"BMC Bioinformatics. BioMed Central"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/s00439-010-0922-4","article-title":"Gene expression studies in cells from primary ciliary dyskinesia patients identify 208 potential ciliary genes","volume":"129","author":"M Geremek","year":"2011","journal-title":"Hum Genet"},{"key":"ref56","article-title":"Rfx2 is required for spermatogenesis in the mouse","author":"W Shawlot","year":"2015","journal-title":"Genesis"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/1471-2148-8-226","article-title":"Identification and characterization of novel human tissue-specific RFX transcription factors","volume":"8","author":"S Aftab","year":"2008","journal-title":"BMC Evol Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"7145","DOI":"10.1073\/pnas.0701811104","article-title":"Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites","volume":"104","author":"X Xie","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1016\/j.bbrc.2004.09.207","article-title":"Foxj1 regulates asymmetric gene expression during left-right axis patterning in mice","volume":"324","author":"M Zhang","year":"2004","journal-title":"Biochem Biophys Res Commun"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"6874","DOI":"10.1093\/nar\/gkv274","article-title":"A new transcription factor for mitosis: in Schizosaccharomyces pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression","volume":"43","author":"A Garg","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/0092-8674(83)90015-6","article-title":"A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes","volume":"33","author":"J Banerji","year":"1983","journal-title":"Cell"},{"key":"ref62","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":"J Dostie","year":"2006","journal-title":"Genome Res"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.cell.2014.09.030","article-title":"Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes","volume":"159","author":"JM Dowen","year":"2014","journal-title":"Cell"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1016\/j.cell.2015.11.024","article-title":"CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription","volume":"163","author":"Z Tang","year":"2015","journal-title":"Cell"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1016\/j.molcel.2014.12.029","article-title":"Human promoters are intrinsically directional","volume":"57","author":"SHC Duttke","year":"2015","journal-title":"Mol Cell"},{"key":"ref66","article-title":"Microinjection of Xenopus oocytes","volume":"2010","author":"HL Sive","year":"2010","journal-title":"Cold Spring Harb Protoc"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1242\/dev.055699","article-title":"Specification of ion transport cells in the Xenopus larval skin","volume":"138","author":"IK Quigley","year":"2011","journal-title":"Development"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nmeth.2251","article-title":"Streaming fragment assignment for real-time analysis of sequencing experiments","volume":"10","author":"A Roberts","year":"2013","journal-title":"Nat Methods"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1093\/bioinformatics\/bth078","article-title":"Open source clustering software","volume":"20","author":"MJL de Hoon","year":"2004","journal-title":"Bioinformatics"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"3246","DOI":"10.1093\/bioinformatics\/bth349","article-title":"Java Treeview\u2014extensible visualization of microarray data","volume":"20","author":"AJ Saldanha","year":"2004","journal-title":"Bioinformatics"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1038\/nprot.2013.099","article-title":"Count-based differential expression analysis of RNA sequencing data using R and Bioconductor","volume":"8","author":"S Anders","year":"2013","journal-title":"Nat Protoc"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief Bioinform"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1126\/science.1139158","article-title":"Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization","volume":"317","author":"NH Putnam","year":"2007","journal-title":"Science"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Res"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1101\/gr.162529.113","article-title":"Evolutionary conservation of the eumetazoan gene regulatory landscape","volume":"24","author":"M Schwaiger","year":"2014","journal-title":"Genome Res"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1093\/molbev\/msv037","article-title":"Tree of life reveals clock-like speciation and diversification","volume":"32","author":"SB Hedges","year":"2015","journal-title":"Mol Biol Evol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nrc2439","article-title":"MYB function in normal and cancer cells","volume":"8","author":"RG Ramsay","year":"2008","journal-title":"Nat Rev Cancer"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"e1003778","DOI":"10.1371\/journal.pgen.1003778","article-title":"Regulation of the boundaries of accessible chromatin","volume":"9","author":"X Chai","year":"2013","journal-title":"PLoS Genet"},{"key":"ref81","first-page":"90","article-title":"Genome architectures revealed by tethered chromosome conformation capture and population-based modeling","volume":"30","author":"R Kalhor","year":"2012","journal-title":"Nat Biotechnol. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1126\/science.2402639","article-title":"Xotch, the Xenopus homolog of Drosophila notch","volume":"249","author":"C Coffman","year":"1990","journal-title":"Science"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1242\/dev.02417","article-title":"Radial intercalation of ciliated cells during Xenopus skin development","volume":"133","author":"JL Stubbs","year":"2006","journal-title":"Development"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.cell.2013.03.035","article-title":"Master transcription factors and mediator establish super-enhancers at key cell identity genes","volume":"153","author":"WA Whyte","year":"2013","journal-title":"Cell"}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1006538","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,22]],"date-time":"2022-07-22T00:51:55Z","timestamp":1658451115000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1006538"}},"subtitle":[],"editor":[{"given":"John","family":"Wallingford","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,1,19]]},"references-count":85,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,1,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1006538","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/085571","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,19]]}}}