{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T08:49:10Z","timestamp":1775983750024,"version":"3.50.1"},"posted":{"date-parts":[[2025,3,29]]},"group-title":"Molecular Biology","reference-count":87,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T00:00:00Z","timestamp":1743206400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,3,29]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                <jats:p>\n                  Spiral ganglion neurons (SGNs) are crucial for hearing, and the loss of SGNs causes hearing loss. Stem cell-based therapies offer a promising approach for SGN regeneration and require understanding the mechanisms governing SGN differentiation. We investigated the chromatin remodeler CHD7 in neuronal differentiation using immortalized multipotent otic progenitor (iMOP) cells. We demonstrated that CHD7 knockdown impaired neuronal differentiation. Genome-wide analysis revealed CHD7 binding at diverse\n                  <jats:italic>cis<\/jats:italic>\n                  -regulatory elements, with notable enrichment at sites marked by the insulator-binding protein CTCF between topologically associating domains (TADs). Insulators marked by the enrichment of CHD7 and CTCF resided near genes critical for neuronal differentiation, including\n                  <jats:italic>Mir9-2<\/jats:italic>\n                  . Targeting these regulatory regions in iMOPs with CRISPR interference (CRISPRi) and activation (CRISPRa) increased miR-9 transcription, irrespective of the method. Blocking the CHD7 and CTCF marked sites suggested that the elements function as insulators to regulate gene expression. The study highlights CHD7 activity at insulators and underscores an unreported mechanism for promoting neuronal differentiation.\n                <\/jats:p>","DOI":"10.1101\/2025.03.28.646031","type":"posted-content","created":{"date-parts":[[2025,3,30]],"date-time":"2025-03-30T02:38:56Z","timestamp":1743302336000},"source":"Crossref","is-referenced-by-count":0,"title":["CHD7 binds to insulators during neuronal differentiation"],"prefix":"10.64898","author":[{"given":"Jingyun","family":"Qiu","sequence":"first","affiliation":[{"name":"Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"},{"name":"Stem Cell Research Center and Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Azadeh","family":"Jadali","sequence":"additional","affiliation":[{"name":"Sampled, Piscataway, NJ 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edward","family":"Martinez","sequence":"additional","affiliation":[{"name":"Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"},{"name":"Stem Cell Research Center and Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhichao","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie Z.","family":"Ni","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8617-5543","authenticated-orcid":false,"given":"Kelvin Y.","family":"Kwan","sequence":"additional","affiliation":[{"name":"Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"},{"name":"Stem Cell Research Center and Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026041201213369000_2025.03.28.646031v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-021-02788-6"},{"key":"2026041201213369000_2025.03.28.646031v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.06.007"},{"key":"2026041201213369000_2025.03.28.646031v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nature07242"},{"key":"2026041201213369000_2025.03.28.646031v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/nature08733"},{"key":"2026041201213369000_2025.03.28.646031v1.5","doi-asserted-by":"crossref","unstructured":"Blighe K, R. S. , Lewis M (2024). \"EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling.\" https:\/\/github.com\/kevinblighe\/EnhancedVolcano.","DOI":"10.32614\/CRAN.package.ggvolcano"},{"key":"2026041201213369000_2025.03.28.646031v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.09.043"},{"key":"2026041201213369000_2025.03.28.646031v1.7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1213825109"},{"key":"2026041201213369000_2025.03.28.646031v1.8","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1519207"},{"key":"2026041201213369000_2025.03.28.646031v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-41265-y"},{"key":"2026041201213369000_2025.03.28.646031v1.10","first-page":"4","article-title":"Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair","volume":"25","year":"2024","journal-title":"Brief Bioinform"},{"key":"2026041201213369000_2025.03.28.646031v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/nature11415"},{"key":"2026041201213369000_2025.03.28.646031v1.12","doi-asserted-by":"publisher","DOI":"10.3389\/fncel.2013.00220"},{"key":"2026041201213369000_2025.03.28.646031v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2012.03.003"},{"key":"2026041201213369000_2025.03.28.646031v1.14","doi-asserted-by":"publisher","DOI":"10.1002\/neu.20310"},{"key":"2026041201213369000_2025.03.28.646031v1.15","doi-asserted-by":"publisher","DOI":"10.1038\/nature11082"},{"key":"2026041201213369000_2025.03.28.646031v1.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.04.005"},{"key":"2026041201213369000_2025.03.28.646031v1.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-019-0142-2"},{"key":"2026041201213369000_2025.03.28.646031v1.18","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0018195"},{"key":"2026041201213369000_2025.03.28.646031v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/ng.825"},{"key":"2026041201213369000_2025.03.28.646031v1.20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0812446106"},{"key":"2026041201213369000_2025.03.28.646031v1.21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0086679"},{"key":"2026041201213369000_2025.03.28.646031v1.22","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2311720121"},{"key":"2026041201213369000_2025.03.28.646031v1.23","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.2910310104"},{"key":"2026041201213369000_2025.03.28.646031v1.24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac808"},{"key":"2026041201213369000_2025.03.28.646031v1.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2022.04.008"},{"key":"2026041201213369000_2025.03.28.646031v1.26","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2010.05.004"},{"key":"2026041201213369000_2025.03.28.646031v1.27","unstructured":"https:\/\/broadinstitute.github.io\/picard\/ ( 2019). \"Picard Toolkit.\" Broad Institute, GitHub repository."},{"key":"2026041201213369000_2025.03.28.646031v1.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.heares.2011.08.005"},{"key":"2026041201213369000_2025.03.28.646031v1.29","doi-asserted-by":"publisher","DOI":"10.1007\/s00335-006-0107-6"},{"key":"2026041201213369000_2025.03.28.646031v1.30","doi-asserted-by":"publisher","DOI":"10.1242\/dev.047894"},{"key":"2026041201213369000_2025.03.28.646031v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2006.08.008"},{"key":"2026041201213369000_2025.03.28.646031v1.32","doi-asserted-by":"publisher","DOI":"10.1126\/science.1069473"},{"key":"2026041201213369000_2025.03.28.646031v1.33","unstructured":"Jadali, A. , Z. Song , A. S. Laureano , A. Toro-Ramos and K. Kwan (2016). \"Initiating Differentiation in Immortalized Multipotent Otic Progenitor Cells.\" J Vis Exp(107)."},{"key":"2026041201213369000_2025.03.28.646031v1.34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48523-7"},{"key":"2026041201213369000_2025.03.28.646031v1.35","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq351"},{"key":"2026041201213369000_2025.03.28.646031v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3317"},{"key":"2026041201213369000_2025.03.28.646031v1.37","doi-asserted-by":"crossref","unstructured":"Kim, J. , E. Martinez , J. Qiu , J. Zhouli Ni and K. Y. Kwan (2024). \"Chromatin remodeling protein CHD4 regulates axon guidance of spiral ganglion neurons in developing cochlea.\" bioRxiv.","DOI":"10.1101\/2024.01.31.578202"},{"key":"2026041201213369000_2025.03.28.646031v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2024.02.007"},{"key":"2026041201213369000_2025.03.28.646031v1.39","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.12.048"},{"key":"2026041201213369000_2025.03.28.646031v1.40","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth843"},{"key":"2026041201213369000_2025.03.28.646031v1.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.02.005"},{"key":"2026041201213369000_2025.03.28.646031v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-020-00539-5)"},{"key":"2026041201213369000_2025.03.28.646031v1.43","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.4985-05.2006"},{"key":"2026041201213369000_2025.03.28.646031v1.44","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.2845-09.2009"},{"key":"2026041201213369000_2025.03.28.646031v1.45","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2009.22"},{"key":"2026041201213369000_2025.03.28.646031v1.46","doi-asserted-by":"publisher","DOI":"10.1016\/j.stemcr.2014.11.001"},{"key":"2026041201213369000_2025.03.28.646031v1.47","doi-asserted-by":"publisher","DOI":"10.1016\/S0960-9822(02)00809-6"},{"key":"2026041201213369000_2025.03.28.646031v1.48","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"2026041201213369000_2025.03.28.646031v1.49","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.01.015"},{"key":"2026041201213369000_2025.03.28.646031v1.50","doi-asserted-by":"crossref","unstructured":"Li, C. , X. Li , Z. Bi , K. Sugino , G. Wang , T. Zhu and Z. Liu (2020). \"Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages.\" Elife 9.","DOI":"10.7554\/eLife.50491"},{"key":"2026041201213369000_2025.03.28.646031v1.51","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"2026041201213369000_2025.03.28.646031v1.52","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1218072110"},{"key":"2026041201213369000_2025.03.28.646031v1.53","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"2026041201213369000_2025.03.28.646031v1.54","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.2358-11.2011"},{"key":"2026041201213369000_2025.03.28.646031v1.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.04.004"},{"key":"2026041201213369000_2025.03.28.646031v1.56","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M117.779470"},{"key":"2026041201213369000_2025.03.28.646031v1.57","doi-asserted-by":"publisher","DOI":"10.1186\/s13072-019-0287-4"},{"key":"2026041201213369000_2025.03.28.646031v1.58","doi-asserted-by":"publisher","DOI":"10.1038\/ng.905"},{"key":"2026041201213369000_2025.03.28.646031v1.59","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02108-x"},{"key":"2026041201213369000_2025.03.28.646031v1.60","doi-asserted-by":"publisher","DOI":"10.1038\/nature722"},{"key":"2026041201213369000_2025.03.28.646031v1.61","doi-asserted-by":"publisher","DOI":"10.3727\/096368911X623907"},{"key":"2026041201213369000_2025.03.28.646031v1.62","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-4781(98)00128-6"},{"key":"2026041201213369000_2025.03.28.646031v1.63","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.05.004"},{"key":"2026041201213369000_2025.03.28.646031v1.64","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31580-1"},{"key":"2026041201213369000_2025.03.28.646031v1.65","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"2026041201213369000_2025.03.28.646031v1.66","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku365"},{"key":"2026041201213369000_2025.03.28.646031v1.67","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.11.021"},{"key":"2026041201213369000_2025.03.28.646031v1.68","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"2026041201213369000_2025.03.28.646031v1.69","doi-asserted-by":"publisher","DOI":"10.1002\/emmm.201100922"},{"key":"2026041201213369000_2025.03.28.646031v1.70","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2203935119"},{"key":"2026041201213369000_2025.03.28.646031v1.71","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-27293-6"},{"key":"2026041201213369000_2025.03.28.646031v1.72","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaa1738"},{"key":"2026041201213369000_2025.03.28.646031v1.73","doi-asserted-by":"publisher","DOI":"10.1101\/gr.086983.108"},{"key":"2026041201213369000_2025.03.28.646031v1.74","doi-asserted-by":"publisher","DOI":"10.1038\/nature07228"},{"key":"2026041201213369000_2025.03.28.646031v1.75","doi-asserted-by":"publisher","DOI":"10.1016\/j.heares.2013.01.017"},{"key":"2026041201213369000_2025.03.28.646031v1.76","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.5085-10.2011"},{"key":"2026041201213369000_2025.03.28.646031v1.77","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2009.01.037"},{"key":"2026041201213369000_2025.03.28.646031v1.78","doi-asserted-by":"publisher","DOI":"10.1038\/47412"},{"key":"2026041201213369000_2025.03.28.646031v1.79","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12166-w"},{"key":"2026041201213369000_2025.03.28.646031v1.80","doi-asserted-by":"crossref","unstructured":"Thelin, J. W. and J. C. Fussner (2005). \"Factors related to the development of communication in CHARGE syndrome.\" Am J Med Genet A 133A(3): 282-290.","DOI":"10.1002\/ajmg.a.30550"},{"key":"2026041201213369000_2025.03.28.646031v1.81","doi-asserted-by":"publisher","DOI":"10.1016\/S0165-5876(86)80072-6"},{"key":"2026041201213369000_2025.03.28.646031v1.82","doi-asserted-by":"publisher","DOI":"10.1038\/ng1407"},{"key":"2026041201213369000_2025.03.28.646031v1.83","doi-asserted-by":"publisher","DOI":"10.1016\/j.brainres.2006.07.006"},{"key":"2026041201213369000_2025.03.28.646031v1.84","doi-asserted-by":"crossref","unstructured":"Xiao, J. Y. , A. Hafner and A. N. Boettiger (2021). \"How subtle changes in 3D structure can create large changes in transcription.\" Elife 10.","DOI":"10.7554\/eLife.64320"},{"key":"2026041201213369000_2025.03.28.646031v1.85","doi-asserted-by":"publisher","DOI":"10.4161\/rna.8.4.16019"},{"key":"2026041201213369000_2025.03.28.646031v1.86","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-39043-x"},{"key":"2026041201213369000_2025.03.28.646031v1.87","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.a.33323"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.03.28.646031","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T08:21:41Z","timestamp":1775982101000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.03.28.646031"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,29]]},"references-count":87,"URL":"https:\/\/doi.org\/10.1101\/2025.03.28.646031","relation":{},"subject":[],"published":{"date-parts":[[2025,3,29]]},"subtype":"preprint"}}