{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T04:23:33Z","timestamp":1772943813375,"version":"3.50.1"},"reference-count":149,"publisher":"Canadian Science Publishing","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/deed.en_GB"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"crossref","award":["PJT"],"award-info":[{"award-number":["PJT"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"crossref","award":["180312"],"award-info":[{"award-number":["180312"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["cdnsciencepub.com"],"crossmark-restriction":false},"short-container-title":["Biochem. Cell Biol."],"published-print":{"date-parts":[[2026,1,1]]},"abstract":"<jats:p>Transcription factor SOX2 is essential for a number of biological processes, including mammalian nervous system development and adult brain stem cell maintenance. Expression of this gene requires precise control by a complex network of regulatory elements, which still remains poorly understood. Years of research by different groups have generated a large amount of data on multiple SOX2 enhancers, with varying levels of evidence for their activity across species and tissues. However, the volume of information in the field and inconsistent nomenclature, with the same enhancer referred to by different study-specific names, make understanding progress in SOX2 enhancer regulation challenging. In this review, we brought together current knowledge on predicted and experimentally validated SOX2 enhancers, highlighting links between conserved elements studied in different species. We also propose a unified enhancer naming system based on the distance from the SOX2 transcription start site in the genome of interest, aiming to improve consistency and make communication in the field more straightforward.<\/jats:p>","DOI":"10.1139\/bcb-2025-0375","type":"journal-article","created":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T21:34:32Z","timestamp":1769895272000},"page":"1-15","update-policy":"https:\/\/doi.org\/10.1139\/csp-crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["<i>SOX2<\/i>\n                    transcriptional regulation by enhancer elements: a comprehensive review with a unified enhancer nomenclature"],"prefix":"10.1139","volume":"104","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-3996-3615","authenticated-orcid":false,"given":"Mariia","family":"Cherednychenko","sequence":"first","affiliation":[{"name":"University of Toronto","place":["Toronto, Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6857-3083","authenticated-orcid":false,"given":"Natalia A.","family":"Gajewska","sequence":"additional","affiliation":[{"name":"University of Toronto","place":["Toronto, Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7147-4604","authenticated-orcid":false,"given":"Jennifer A.","family":"Mitchell","sequence":"additional","affiliation":[{"name":"University of Toronto","place":["Toronto, Canada"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"155","reference":[{"key":"refg1\/ref1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad734"},{"key":"refg2\/ref2","doi-asserted-by":"publisher","DOI":"10.1139\/bcb-2024-0287"},{"key":"refg3\/ref3","doi-asserted-by":"publisher","DOI":"10.1101\/gad.224503"},{"key":"refg4\/ref4","doi-asserted-by":"publisher","DOI":"10.1136\/bjo.2007.117929"},{"key":"refg5\/ref5","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(81)90413-x"},{"issue":"1","key":"refg6\/ref6","first-page":"1","volume":"1","author":"Barone C.","year":"2018","journal-title":"Insights Neuro Oncol."},{"key":"refg7\/ref7","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2016.04.004"},{"key":"refg8\/ref8","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215160.116"},{"key":"refg9\/ref9","doi-asserted-by":"publisher","DOI":"10.1101\/gad.3.9.1288"},{"key":"refg10\/ref10","doi-asserted-by":"publisher","DOI":"10.1016\/S1097-2765(00)80433-5"},{"key":"refg11\/ref11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18035-1"},{"key":"refg12\/ref12","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.231608898"},{"key":"refg13\/ref13","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2017-11-737379"},{"key":"refg14\/ref14","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2009.10.019"},{"key":"refg15\/ref15","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.11.030"},{"key":"refg16\/ref16","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.09.002"},{"key":"refg17\/ref17","doi-asserted-by":"publisher","DOI":"10.3390\/neurolint13040054"},{"key":"refg18\/ref18","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.09.043"},{"key":"refg19\/ref19","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.02.027"},{"key":"refg20\/ref20","doi-asserted-by":"publisher","DOI":"10.1038\/nature14590"},{"key":"refg21\/ref21","doi-asserted-by":"publisher","DOI":"10.1038\/nn1131"},{"key":"refg22\/ref22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2015.11.034"},{"key":"refg23\/ref23","doi-asserted-by":"publisher","DOI":"10.1038\/ng1051"},{"key":"refg24\/ref24","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M405514200"},{"key":"refg25\/ref25","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-022-01295-6"},{"key":"refg26\/ref26","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-152"},{"key":"refg27\/ref27","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar4199"},{"key":"refg28\/ref28","doi-asserted-by":"publisher","DOI":"10.1242\/dev.122.2.509"},{"key":"refg29\/ref29","doi-asserted-by":"publisher","DOI":"10.1126\/science.1231143"},{"key":"refg30\/ref30","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1016071107"},{"key":"refg31\/ref31","doi-asserted-by":"publisher","DOI":"10.1126\/science.1067799"},{"key":"refg32\/ref32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.03.051"},{"key":"refg33\/ref33","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.09.023"},{"key":"refg34\/ref34","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.07.013"},{"key":"refg35\/ref35","doi-asserted-by":"publisher","DOI":"10.1038\/nature11082"},{"key":"refg36\/ref36","doi-asserted-by":"publisher","DOI":"10.1126\/science.ads6552"},{"key":"refg37\/ref37","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2013.10.012"},{"key":"refg38\/ref38","doi-asserted-by":"publisher","DOI":"10.1159\/000082134"},{"key":"refg39\/ref39","doi-asserted-by":"publisher","DOI":"10.1038\/ng1120"},{"key":"refg40\/ref40","doi-asserted-by":"publisher","DOI":"10.1038\/nn.2397"},{"key":"refg41\/ref41","doi-asserted-by":"publisher","DOI":"10.1038\/ncb1181"},{"key":"refg42\/ref42","doi-asserted-by":"publisher","DOI":"10.1242\/dev.01204"},{"key":"refg43\/ref43","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-313X.2006.02859.x"},{"key":"refg44\/ref44","doi-asserted-by":"publisher","DOI":"10.1002\/wdev.395"},{"key":"refg45\/ref45","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-023-01391-1"},{"key":"refg46\/ref46","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2008.02.035"},{"key":"refg47\/ref47","doi-asserted-by":"publisher","DOI":"10.1016\/S0896-6273(03)00497-5"},{"key":"refg48\/ref48","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1589-8"},{"key":"refg49\/ref49","doi-asserted-by":"publisher","DOI":"10.1038\/346245a0"},{"key":"refg50\/ref50","doi-asserted-by":"publisher","DOI":"10.3390\/cells10040727"},{"key":"refg51\/ref51","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3605"},{"key":"refg52\/ref52","doi-asserted-by":"publisher","DOI":"10.1038\/ng1966"},{"key":"refg53\/ref53","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19452-y"},{"key":"refg54\/ref54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0020164"},{"key":"refg55\/ref55","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1313"},{"key":"refg56\/ref56","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00863-6"},{"key":"refg57\/ref57","doi-asserted-by":"publisher","DOI":"10.1111\/gtc.12753"},{"key":"refg58\/ref58","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2443.2007.01114.x"},{"key":"refg59\/ref59","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2010.12.027"},{"key":"refg60\/ref60","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2016.03.001"},{"key":"refg61\/ref61","doi-asserted-by":"publisher","DOI":"10.1038\/nature15740"},{"key":"refg62\/ref62","doi-asserted-by":"publisher","DOI":"10.1038\/nature09380"},{"key":"refg63\/ref63","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09982-5"},{"key":"refg64\/ref64","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(83)90410-5"},{"key":"refg65\/ref65","doi-asserted-by":"publisher","DOI":"10.1038\/nature03487"},{"key":"refg66\/ref66","doi-asserted-by":"publisher","DOI":"10.1634\/stemcells.2007-0951"},{"key":"refg67\/ref67","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.09.028"},{"key":"refg68\/ref68","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2013.132"},{"key":"refg69\/ref69","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2011.12.014"},{"key":"refg70\/ref70","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2012.09.014"},{"key":"refg71\/ref71","doi-asserted-by":"publisher","DOI":"10.1126\/science.adi5516"},{"key":"refg72\/ref72","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0114485"},{"key":"refg73\/ref73","doi-asserted-by":"publisher","DOI":"10.1016\/j.cellsig.2013.02.013"},{"key":"refg74\/ref74","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2023.104870"},{"key":"refg75\/ref75","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-22-1858"},{"key":"refg76\/ref76","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27055-4"},{"key":"refg77\/ref77","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.09.018"},{"key":"refg78\/ref78","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2012.12.001"},{"key":"refg79\/ref79","doi-asserted-by":"publisher","DOI":"10.1242\/dev.055178"},{"key":"refg80\/ref80","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2137"},{"key":"refg81\/ref81","doi-asserted-by":"publisher","DOI":"10.3390\/cells11101604"},{"key":"refg82\/ref82","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0049274"},{"key":"refg83\/ref83","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.24.10.4207-4220.2004"},{"key":"refg84\/ref84","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M512669200"},{"key":"refg85\/ref85","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2017115118"},{"key":"refg86\/ref86","doi-asserted-by":"publisher","DOI":"10.1101\/gr.210930.116"},{"key":"refg87\/ref87","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/9.22.6047"},{"key":"refg88\/ref88","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.10.039"},{"key":"refg89\/ref89","doi-asserted-by":"publisher","DOI":"10.1016\/j.semcancer.2019.08.007"},{"key":"refg90\/ref90","doi-asserted-by":"publisher","DOI":"10.1111\/dgd.12185"},{"key":"refg91\/ref91","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2024.04.013"},{"key":"refg92\/ref92","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2022.995388"},{"key":"refg93\/ref93","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-01560-x"},{"key":"refg94\/ref94","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1589"},{"key":"refg95\/ref95","doi-asserted-by":"publisher","DOI":"10.1038\/nature05295"},{"key":"refg96\/ref96","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-437X(97)80147-5"},{"key":"refg97\/ref97","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocel.2009.08.018"},{"key":"refg98\/ref98","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2005.02.006"},{"key":"refg99\/ref99","doi-asserted-by":"publisher","DOI":"10.1242\/dev.003855"},{"key":"refg100\/ref100","doi-asserted-by":"publisher","DOI":"10.1242\/dev.034629"},{"key":"refg101\/ref101","doi-asserted-by":"publisher","DOI":"10.1038\/nature09692"},{"key":"refg102\/ref102","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.a.30642"},{"key":"refg103\/ref103","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.11.021"},{"key":"refg104\/ref104","doi-asserted-by":"publisher","DOI":"10.1126\/science.290.5500.2306"},{"key":"refg105\/ref105","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar3958"},{"key":"refg106\/ref106","doi-asserted-by":"publisher","DOI":"10.3390\/cancers13071574"},{"key":"refg107\/ref107","doi-asserted-by":"publisher","DOI":"10.1038\/nature11279"},{"key":"refg108\/ref108","doi-asserted-by":"publisher","DOI":"10.1002\/jnr.21635"},{"key":"refg109\/ref109","doi-asserted-by":"publisher","DOI":"10.1007\/s10549-010-1169-4"},{"key":"refg110\/ref110","doi-asserted-by":"publisher","DOI":"10.1038\/346240a0"},{"key":"refg111\/ref111","doi-asserted-by":"publisher","DOI":"10.1101\/gr.272468.120"},{"key":"refg112\/ref112","doi-asserted-by":"publisher","DOI":"10.1111\/j.1528-1167.2006.00464.x"},{"key":"refg113\/ref113","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.21856"},{"key":"refg114\/ref114","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.07.024"},{"key":"refg115\/ref115","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.11.019"},{"key":"refg116\/ref116","doi-asserted-by":"publisher","DOI":"10.1242\/dev.02196"},{"key":"refg117\/ref117","doi-asserted-by":"publisher","DOI":"10.1038\/nature09729"},{"key":"refg118\/ref118","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1407906"},{"key":"refg119\/ref119","doi-asserted-by":"publisher","DOI":"10.1101\/gad.349489.122"},{"key":"refg120\/ref120","doi-asserted-by":"publisher","DOI":"10.1242\/bio.048728"},{"key":"refg121\/ref121","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001046"},{"key":"refg122\/ref122","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2024.11.008"},{"key":"refg123\/ref123","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2011.05.017"},{"key":"refg124\/ref124","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkaf012"},{"key":"refg125\/ref125","doi-asserted-by":"publisher","DOI":"10.1016\/S1097-2765(02)00781-5"},{"key":"refg126\/ref126","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf435"},{"key":"refg127\/ref127","doi-asserted-by":"publisher","DOI":"10.1016\/j.stemcr.2024.03.003"},{"key":"refg128\/ref128","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.86.8.2554"},{"key":"refg129\/ref129","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-800352-7.00007-4"},{"key":"refg130\/ref130","doi-asserted-by":"publisher","DOI":"10.1016\/S1534-5807(03)00088-1"},{"key":"refg131\/ref131","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl822"},{"key":"refg132\/ref132","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.12.041"},{"key":"refg133\/ref133","doi-asserted-by":"publisher","DOI":"10.1126\/science.1246981"},{"key":"refg134\/ref134","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.111842"},{"key":"refg135\/ref135","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.03.035"},{"key":"refg136\/ref136","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(00)00086-X"},{"key":"refg137\/ref137","doi-asserted-by":"publisher","DOI":"10.1126\/science.aax8137"},{"key":"refg138\/ref138","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0030007"},{"key":"refg139\/ref139","doi-asserted-by":"publisher","DOI":"10.1126\/science.1465613"},{"key":"refg140\/ref140","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.16570"},{"key":"refg141\/ref141","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2660"},{"key":"refg142\/ref142","doi-asserted-by":"publisher","DOI":"10.1126\/science.1151526"},{"key":"refg143\/ref143","doi-asserted-by":"publisher","DOI":"10.1242\/dev.127.11.2367"},{"key":"refg144\/ref144","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.a.31384"},{"key":"refg145\/ref145","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-020-00242-3"},{"key":"refg146\/ref146","doi-asserted-by":"publisher","DOI":"10.15252\/embr.201540945"},{"key":"refg147\/ref147","doi-asserted-by":"publisher","DOI":"10.1101\/gad.248526.114"},{"key":"refg148\/ref148","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.12.033"},{"key":"refg149\/ref149","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04570-y"}],"container-title":["Biochemistry and Cell Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdnsciencepub.com\/doi\/full-xml\/10.1139\/bcb-2025-0375","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdnsciencepub.com\/doi\/pdf\/10.1139\/bcb-2025-0375","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T12:50:45Z","timestamp":1772887845000},"score":1,"resource":{"primary":{"URL":"https:\/\/cdnsciencepub.com\/doi\/10.1139\/bcb-2025-0375"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,1]]},"references-count":149,"alternative-id":["10.1139\/bcb-2025-0375"],"URL":"https:\/\/doi.org\/10.1139\/bcb-2025-0375","relation":{},"ISSN":["0829-8211","1208-6002"],"issn-type":[{"value":"0829-8211","type":"print"},{"value":"1208-6002","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,1]]},"assertion":[{"value":"2026-03-04","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}