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Mouton Pro Retina & Marie-Claire Li\u00e9naert"},{"name":"Ghent University Fund Alzheimer and Neurodegenerative Diseases","id":[{"id":"https:\/\/ror.org\/00cv9y106","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100011011","name":"Junta de Andaluc\u00eda","doi-asserted-by":"publisher","award":["DOC_00397"],"award-info":[{"award-number":["DOC_00397"]}],"id":[{"id":"10.13039\/501100011011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiotemporal expression within these interconnected retinal components through the local recruitment of\n                      <jats:italic>cis<\/jats:italic>\n                      -regulatory elements (CREs) in 3D nuclear space.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      To understand the role of differential chromatin architecture in establishing tissue-specific expression at inherited retinal disease loci, we mapped genome-wide chromatin interactions using in situ Hi-C and H3K4me3 HiChIP on neural retina and RPE\/choroid from human adult donor eyes. We observed chromatin looping between active promoters and 32,425 and 8060 candidate CREs in the neural retina and RPE\/choroid, respectively. A comparative 3D genome analysis between these two retinal tissues revealed that 56% of 290 known inherited retinal disease genes were marked by differential chromatin interactions. One of these was\n                      <jats:italic>ABCA4<\/jats:italic>\n                      , which is implicated in the most common autosomal recessive inherited retinal disease. We zoomed in on retina- and RPE-specific\n                      <jats:italic>cis<\/jats:italic>\n                      -regulatory interactions at the\n                      <jats:italic>ABCA4<\/jats:italic>\n                      locus using high-resolution UMI-4C. Integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish revealed tissue-specific CREs interacting with\n                      <jats:italic>ABCA4<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Through comparative 3D genome mapping, based on genome-wide, promoter-centric, and locus-specific assays of human neural retina and RPE, we have shown that gene regulation at key inherited retinal disease loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes at retinal disease loci, but also delineate the search space for non-coding genomic variation underlying unsolved inherited retinal diseases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Graphical Abstract<\/jats:title>\n                  <\/jats:sec>","DOI":"10.1186\/s13059-024-03250-6","type":"journal-article","created":{"date-parts":[[2024,5,17]],"date-time":"2024-05-17T03:02:24Z","timestamp":1715914944000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci"],"prefix":"10.1186","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5936-8294","authenticated-orcid":false,"given":"Eva","family":"D\u2019haene","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4621-7547","authenticated-orcid":false,"given":"V\u00edctor","family":"L\u00f3pez-Soriano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2119-2465","authenticated-orcid":false,"given":"Pedro Manuel","family":"Mart\u00ednez-Garc\u00eda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7028-8067","authenticated-orcid":false,"given":"Soraya","family":"Kalayanamontri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4456-6159","authenticated-orcid":false,"given":"Alfredo Due\u00f1as","family":"Rey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6457-5397","authenticated-orcid":false,"given":"Ana","family":"Sousa-Ortega","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4529-3332","authenticated-orcid":false,"given":"Silvia","family":"Naranjo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3294-0668","authenticated-orcid":false,"given":"Stijn","family":"Van de Sompele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lies","family":"Vantomme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quinten","family":"Mahieu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0816-6262","authenticated-orcid":false,"given":"Sarah","family":"Vergult","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4670-034X","authenticated-orcid":false,"given":"Ana","family":"Neto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5125-4332","authenticated-orcid":false,"given":"Jos\u00e9 Luis","family":"G\u00f3mez-Skarmeta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4650-4293","authenticated-orcid":false,"given":"Juan Ram\u00f3n","family":"Mart\u00ednez-Morales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0402-9006","authenticated-orcid":false,"given":"Miriam","family":"Bauwens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8165-7984","authenticated-orcid":false,"given":"Juan Jes\u00fas","family":"Tena","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5609-6895","authenticated-orcid":false,"given":"Elfride","family":"De Baere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,17]]},"reference":[{"key":"3250_CR1","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/nrg2717","volume":"11","author":"AF Wright","year":"2010","unstructured":"Wright AF, Chakarova CF, Abd El-Aziz MM, Bhattacharya SS. 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