{"doi":"10.1242/dev.200568","title":"Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication","abstract":"<jats:title>ABSTRACT</jats:title>\n                  <jats:p>The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors (e.g. CTCF) underlying topologically associating domains (TADs) leads to modest alterations in gene expression, whereas genomic rearrangements involving TAD boundaries disrupt normal gene expression and can lead to pathological phenotypes. Here, we targeted the TAD neighboring that of the noncoding transcript Xist, which controls X-chromosome inactivation. Inverting 245 kb within the TAD led to expected rearrangement of CTCF-based contacts but revealed heterogeneity in the ‘contact’ potential of different CTCF sites. Expression of most genes therein remained unaffected in mouse embryonic stem cells and during differentiation. Interestingly, expression of Xist was ectopically upregulated. The same inversion in mouse embryos led to biased Xist expression. Smaller inversions and deletions of CTCF clusters led to similar results: rearrangement of contacts and limited changes in local gene expression, but significant changes in Xist expression in embryos. Our study suggests that the wiring of regulatory interactions within a TAD can influence the expression of genes in neighboring TADs, highlighting the existence of mechanisms of inter-TAD communication.</jats:p>","journal":"Development","year":2022,"id":637901,"datarank":0.47032413238937254,"base_score":3.1354942159291497,"endowment":3.1354942159291497,"self_citation_contribution":0.47032413238937254,"citation_network_contribution":0.0,"self_endowment_contribution":0.47032413238937254,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":22,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1656538,"name":"Christel Picard","orcid":null,"position":1,"is_corresponding":false},{"id":88325,"name":"Nicolas Servant","orcid":"0000-0003-1678-7410","position":2,"is_corresponding":false},{"id":191573,"name":"Elphège P. Nora","orcid":null,"position":3,"is_corresponding":false},{"id":628641,"name":"Yinxiu Zhan","orcid":"0000-0001-7702-6207","position":4,"is_corresponding":false},{"id":1005574,"name":"Joke G. van Bemmel","orcid":"0000-0001-7034-3664","position":5,"is_corresponding":false},{"id":1518603,"name":"Fatima El Marjou","orcid":null,"position":6,"is_corresponding":false},{"id":1656539,"name":"Colin Johanneau","orcid":null,"position":7,"is_corresponding":false},{"id":1656540,"name":"Maud Borensztein","orcid":"0000-0002-4378-5018","position":8,"is_corresponding":false},{"id":1656541,"name":"Katia Ancelin","orcid":"0000-0002-2117-9754","position":9,"is_corresponding":false},{"id":628646,"name":"Luca Giorgetti","orcid":"0000-0002-9664-9087","position":10,"is_corresponding":false},{"id":44861,"name":"Édith Heard","orcid":"0000-0001-8052-7117","position":11,"is_corresponding":false},{"id":1028281,"name":"Rafael Galupa","orcid":"0000-0001-7319-043X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication","abstract":"<jats:title>ABSTRACT</jats:title>\n                  <jats:p>The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors (e.g. CTCF) underlying topologically associating domains (TADs) leads to modest alterations in gene expression, whereas genomic rearrangements involving TAD boundaries disrupt normal gene expression and can lead to pathological phenotypes. Here, we targeted the TAD neighboring that of the noncoding transcript Xist, which controls X-chromosome inactivation. Inverting 245 kb within the TAD led to expected rearrangement of CTCF-based contacts but revealed heterogeneity in the ‘contact’ potential of different CTCF sites. Expression of most genes therein remained unaffected in mouse embryonic stem cells and during differentiation. Interestingly, expression of Xist was ectopically upregulated. The same inversion in mouse embryos led to biased Xist expression. Smaller inversions and deletions of CTCF clusters led to similar results: rearrangement of contacts and limited changes in local gene expression, but significant changes in Xist expression in embryos. Our study suggests that the wiring of regulatory interactions within a TAD can influence the expression of genes in neighboring TADs, highlighting the existence of mechanisms of inter-TAD communication.</jats:p>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35502750","pmcid":null,"openalex_id":"https://openalex.org/W35502750","authors":[],"funders":[{"funder_name":"Région Ile-de-France","grant_id":"DIM Biothérapies Fellowship","title":null},{"funder_name":"European Research Council","grant_id":"ERC-2014-AdG no. 671027 Advanced Investigator award","title":null},{"funder_name":"La Ligue contre le cancer","grant_id":"Labélisation","title":null},{"funder_name":"Fondation pour la Recherche Médicale","grant_id":"DEI20151234398","title":null},{"funder_name":"Fondation pour la Recherche Médicale","grant_id":"FDT20160435295","title":null},{"funder_name":"Agence Nationale de la Recherche","grant_id":"DoseX 2017","title":null},{"funder_name":"Agence Nationale de la Recherche","grant_id":"ANR-11-BINF-0001","title":null},{"funder_name":"Labex DEEP","grant_id":"ANR-11-LBX-0044","title":null},{"funder_name":"Université de Recherche Paris Sciences et Lettres","grant_id":"ANR-10-IDEX-0001-02 PSL","title":null},{"funder_name":"French National Research Agency (ANR)","grant_id":"ANR-10-IDEX-0001","title":null},{"funder_name":"European Commission","grant_id":"671027","title":"Exploring mechanisms of gene repression and escape during X-chromosome inactivation"}],"total_grants":11,"fwci":0.0,"citation_percentile":0.00182643,"influential_citations":0,"citation_trend":[],"oa_status":"hybrid","license":"cc-by-nc-nd","oa_locations":[{"url":"http://hdl.handle.net/10481/22432","host_type":"repository"},{"url":"https://journals.biologists.com/dev/article-pdf/149/9/dev200568/2143292/dev200568.pdf","host_type":"publisher"},{"url":"https://journals.biologists.com/dev/article-pdf/doi/10.1242/dev.200568/2142628/dev200568.pdf","host_type":"publisher"},{"url":"https://journals.biologists.com/dev/article-pdf/doi/10.1242/dev.200568/3487023/dev200568.pdf","host_type":"publisher"},{"url":"https://digibug.ugr.es/bitstream/10481/22432/1/ManualNudistVivo8.pdf","host_type":""},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9148567","host_type":"repository"},{"url":"https://hal.science/hal-04266478","host_type":"repository"},{"url":"https://hdl.handle.net/2434/1156659","host_type":"repository"},{"url":"https://doi.org/10.1242/dev.200568","host_type":""},{"url":"https://doi.org/10.1101/2022.01.24.477495","host_type":""},{"url":"https://www.biorxiv.org/content/biorxiv/early/2022/01/24/2022.01.24.477495.full.pdf","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/35502750","host_type":""},{"url":"http://dx.doi.org/10.1242/dev.200568","host_type":""},{"url":"https://hal.science/hal-03746685v1","host_type":""},{"url":"https://hal.science/hal-03746685v1/document","host_type":""},{"url":"https://hal.science/hal-04266478v1","host_type":""},{"url":"https://hal.science/hal-04266478v1/document","host_type":""},{"url":"https://doi.org/https://doi.org/10.1242/dev.200568","host_type":""}],"fields_of_study":["Literary and Cultural Studies","Statistical Methods and Applications","0301 basic medicine","03 medical and health sciences","0303 health sciences","Animals","CCCTC-Binding Factor","Chromatin","Communication","Gene Expression","Genome","Mice","RNA, Long Noncoding","X Chromosome Inactivation"],"mesh_terms":["Animals","CCCTC-Binding Factor","Chromatin","Communication","Gene Expression","Genome","Mice","RNA, Long Noncoding","X Chromosome Inactivation"],"keywords":["Philosophy","Xist","570","CCCTC-Binding Factor","610","Gene Expression","[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry","Mice","X Chromosome Inactivation","[SDV.BDD] Life Sciences [q-bio]/Development Biology","Animals","Genomic engineering","TADs","[SDV.BDD]Life Sciences [q-bio]/Development Biology","Molecular Biology/Genomics [q-bio.GN]","Genome","Communication","Gene expression; 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