{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T08:44:00Z","timestamp":1776847440953,"version":"3.51.2"},"reference-count":41,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2022,6,23]],"date-time":"2022-06-23T00:00:00Z","timestamp":1655942400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"French foundation \u201cLa Fondation pour l\u2019Audition\u201d","award":["FPARD-2018-9"],"award-info":[{"award-number":["FPARD-2018-9"]}]},{"name":"the \u201cR\u00e9gion Bretagne\u201d","award":["FPARD-2018-9"],"award-info":[{"award-number":["FPARD-2018-9"]}]},{"name":"association \u201cGa\u00e9tan Sala\u00fcn\u201d","award":["FPARD-2018-9"],"award-info":[{"award-number":["FPARD-2018-9"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The human genome is covered by 8% of candidate cis-regulatory elements. The identification of distal acting regulatory elements and an understanding of their action are crucial to determining their key role in gene expression. Disruptions of such regulatory elements and\/or chromatin conformation are likely to play a critical role in human genetic diseases. Non-syndromic hearing loss (i.e., DFNB1) is mostly due to GJB2 (Gap Junction Beta 2) variations and DFNB1 large deletions. Although several GJB2 cis-regulatory elements (CREs) have been described, GJB2 gene regulation remains not well understood. We investigated the endogenous effect of these CREs with CRISPR (clustered regularly interspaced short palindromic repeats) disruptions and observed GJB2 expression. To decipher the GJB2 regulatory landscape, we used the 4C-seq technique and defined new chromatin contacts inside the DFNB1 locus, which permit DNA loops and long-range regulation. Moreover, through ChIP-PCR, we determined the involvement of the MEIS1 transcription factor in GJB2 expression. Taken together, the results of our study enable us to describe the 3D DFNB1 regulatory landscape.<\/jats:p>","DOI":"10.3390\/ijms23136964","type":"journal-article","created":{"date-parts":[[2022,6,23]],"date-time":"2022-06-23T21:25:00Z","timestamp":1656019500000},"page":"6964","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["3D Chromatin Organization Involving MEIS1 Factor in the cis-Regulatory Landscape of GJB2"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9921-1064","authenticated-orcid":false,"given":"Ana\u00efs","family":"Le Nabec","sequence":"first","affiliation":[{"name":"University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clara","family":"Blotas","sequence":"additional","affiliation":[{"name":"University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alin\u00e9or","family":"Briset","sequence":"additional","affiliation":[{"name":"University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5396-8723","authenticated-orcid":false,"given":"M\u00e9gane","family":"Collobert","sequence":"additional","affiliation":[{"name":"University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claude","family":"F\u00e9rec","sequence":"additional","affiliation":[{"name":"University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phanie","family":"Moisan","sequence":"additional","affiliation":[{"name":"University Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France"},{"name":"Laboratoire de G\u00e9n\u00e9tique Mol\u00e9culaire et d\u2019Histocompatibilit\u00e9, CHRU Brest, UMR 1078, F-29200 Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"The ENCODE Project Consortium, Moore, J.E., Purcaro, M.J., Pratt, H.E., Epstein, C.B., Shoresh, N., Adrian, J., Kawli, T., Davis, C.A., and Dobin, A. (2020). Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 583, 699\u2013710.","DOI":"10.1038\/s41586-020-2493-4"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1038\/nsmb.2784","article-title":"Enhancer biology and enhanceropathies","volume":"21","author":"Smith","year":"2014","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/nbt.3863","article-title":"Characterization of noncoding regulatory DNA in the human genome","volume":"35","author":"Elkon","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1016\/j.tcb.2018.04.003","article-title":"Enhancer Logic and Mechanics in Development and Disease","volume":"28","author":"Rickels","year":"2018","journal-title":"Trends Cell Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1016\/j.molmed.2021.07.012","article-title":"Enhancers in disease: Molecular basis and emerging treatment strategies","volume":"27","author":"Claringbould","year":"2021","journal-title":"Trends Mol. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/s41576-019-0209-0","article-title":"Towards a comprehensive catalogue of validated and target-linked human enhancers","volume":"21","author":"Gasperini","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1016\/j.molcel.2019.05.032","article-title":"Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D","volume":"74","author":"Robson","year":"2019","journal-title":"Mol. Cell"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.lpm.2017.09.005","article-title":"Les surdit\u00e9s d\u2019origine g\u00e9n\u00e9tique","volume":"46","author":"Marlin","year":"2017","journal-title":"Presse Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1002\/ajmg.a.20588","article-title":"Large deletion of the GJB6 gene in deaf patients heterozygous for the GJB2 gene mutation: Genotypic and phenotypic analysis","volume":"127","author":"Feldmann","year":"2004","journal-title":"Am. J. Med. Genet. Part A"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/S0378-1119(97)00365-X","article-title":"Upstream genomic sequence of the human connexin26 gene","volume":"199","author":"Kiang","year":"1997","journal-title":"Gene"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"909","DOI":"10.4267\/10608\/848","article-title":"Connexines, canaux jonctionnels et communications cellulaires","volume":"12","author":"Meda","year":"1996","journal-title":"M\u00e9decine\/Science"},{"key":"ref_12","first-page":"354","article-title":"Aberrant Cx26 hemichannels and keratitis-ichthyosis-deafness syndrome: Insights into syndromic hearing loss","volume":"8","author":"Verselis","year":"2014","journal-title":"Front. Cell. Neurosci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1007\/s00441-014-2029-z","article-title":"Connexins and gap junctions in the inner ear--it\u2019s not just about K+ recycling","volume":"360","author":"Jagger","year":"2015","journal-title":"Cell Tissue Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1165\/ajrcmb.18.1.2789","article-title":"Connexin 26 expression in human and ferret airways and lung during development","volume":"18","author":"Carson","year":"1998","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1007\/s00439-019-02068-8","article-title":"Characterization of GJB2 cis-regulatory elements in the DFNB1 locus","volume":"138","author":"Moisan","year":"2019","journal-title":"Hum. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.ejmg.2008.11.006","article-title":"A new large deletion in the DFNB1 locus causes nonsyndromic hearing loss","volume":"52","author":"Feldmann","year":"2009","journal-title":"Eur. J. Med. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1134\/S1022795414020045","article-title":"New recurrent large deletion, encompassing both GJB2 and GB6 genes, results in isolated sensorineural hearing impairment with autosomal recessive mode of inheritance","volume":"50","author":"Bliznetz","year":"2014","journal-title":"Russ. J. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1002\/humu.1222","article-title":"A deletion mutation in GJB6 cooperating with a GJB2 mutation in trans in non-syndromic deafness: A novel founder mutation in Ashkenazi Jews","volume":"18","author":"Lerer","year":"2001","journal-title":"Hum. Mutat."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1056\/NEJMoa012052","article-title":"A Deletion Involving the Connexin 30 Gene in Nonsyndromic Hearing Impairment","volume":"346","author":"Villamar","year":"2002","journal-title":"New Engl. J. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1038\/sj.ejhg.5200762","article-title":"A large deletion including most of GJB6 in recessive non syndromic deafness: A digenic effect?","volume":"10","author":"Blanchet","year":"2002","journal-title":"Eur. J. Hum. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1136\/jmg.2004.028324","article-title":"A novel deletion involving the connexin-30 gene, del(GJB6-d13s1854), found in trans with mutations in the GJB2 gene (connexin-26) in subjects with DFNB1 non-syndromic hearing impairment","volume":"42","author":"Alvarez","year":"2005","journal-title":"J. Med. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.1399-0004.2010.01387.x","article-title":"A novel DFNB1 deletion allele supports the existence of a distant cis-regulatory region that controls GJB2 and GJB6 expression","volume":"78","author":"Wilch","year":"2010","journal-title":"Clin. Genet."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1002\/humu.22912","article-title":"Targeted Droplet-Digital PCR as a Tool for Novel Deletion Discovery at the DFNB1 Locus","volume":"37","author":"Tayoun","year":"2015","journal-title":"Hum. Mutat."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2111","DOI":"10.1002\/ccr3.1800","article-title":"Diagnostic pitfalls for GJB2 -related hearing loss: A novel deletion detected by Array-CGH analysis in a Japanese patient with congenital profound hearing loss","volume":"6","author":"Abe","year":"2018","journal-title":"Clin. Case Rep."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Safka Brozkova, D., Uhrova Meszarosova, A., Lassuthova, P., Varga, L., Stan\u011bk, D., Boreck\u00e1, S., La\u0161t\u016fvkov\u00e1, J., \u010cejnov\u00e1, V., Ra\u0161kov\u00e1, D., and Lhota, F. (2021). The Cause of Hereditary Hearing Loss in GJB2 Heterozygotes\u2014A Comprehensive Study of the GJB2\/DFNB1 Region. Genes, 12.","DOI":"10.3390\/genes12050684"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1111\/j.1365-2230.2005.01878.x","article-title":"Specific loss of connexin 26 expression in ductal sweat gland epithelium associated with the deletion mutation del(GJB6-D13S1830)","volume":"30","author":"Common","year":"2005","journal-title":"Clin. Exp. Dermatol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.bbrc.2009.08.152","article-title":"The digenic hypothesis unraveled: The GJB6 del(GJB6-D13S1830) mutation causes allele-specific loss of GJB2 expression in cis","volume":"389","author":"Schrijver","year":"2009","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Rodriguez-Paris, J., Tamayo, M.L., Gelvez, N., and Schrijver, I. (2011). Allele-Specific Impairment of GJB2 Expression by GJB6 Deletion del(GJB6-D13S1854). PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0021665"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/nrm.2015.2","article-title":"Beyond editing: Repurposing CRISPR\u2013Cas9 for precision genome regulation and interrogation","volume":"17","author":"Dominguez","year":"2015","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_30","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":"2014","journal-title":"Nature"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"ev174706","DOI":"10.1242\/dev.174706","article-title":"MEIS transcription factors in development and disease","volume":"146","author":"Schulte","year":"2019","journal-title":"Development"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature06008","article-title":"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells","volume":"448","author":"Mikkelsen","year":"2007","journal-title":"Nature"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1016\/S1569-1993(16)30090-X","article-title":"WS06.1 Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements","volume":"15","author":"Moisan","year":"2016","journal-title":"J. Cyst. Fibros."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1530\/JME-19-0100","article-title":"HOXA10 co-factor MEIS1 is required for the decidualization in human endometrial stromal cell","volume":"64","author":"Xu","year":"2020","journal-title":"J. Mol. Endocrinol."},{"key":"ref_35","first-page":"1","article-title":"Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing","volume":"11","author":"Li","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Hazan, J., and Bester, A.C. (2021). CRISPR-Based Approaches for the High-Throughput Characterization of Long Non-Coding RNAs. Non-Coding RNA, 7.","DOI":"10.3390\/ncrna7040079"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/S1097-2765(02)00459-8","article-title":"Opening of Compacted Chromatin by Early Developmental Transcription Factors HNF3 (FoxA) and GATA-4","volume":"9","author":"Cirillo","year":"2002","journal-title":"Mol. Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2513","DOI":"10.1101\/gad.1446006","article-title":"A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer","volume":"20","author":"Eeckhoute","year":"2006","journal-title":"Genes Dev."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2166","DOI":"10.1016\/j.molcel.2021.03.008","article-title":"Enhancers are activated by p300\/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release","volume":"81","author":"Narita","year":"2021","journal-title":"Mol. Cell"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/s41594-020-00539-5","article-title":"Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation","volume":"28","author":"Kubo","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.ymeth.2019.07.014","article-title":"4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis","volume":"170","author":"Krijger","year":"2020","journal-title":"Methods"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/13\/6964\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:38:32Z","timestamp":1760139512000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/13\/6964"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,23]]},"references-count":41,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2022,7]]}},"alternative-id":["ijms23136964"],"URL":"https:\/\/doi.org\/10.3390\/ijms23136964","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,23]]}}}