title: Induced DNA demethylation can reshape chromatin topology at the IGF2-H19 locus.
abstract: Choriocarcinomas are embryonal tumours with loss of imprinting and hypermethylation at the insulin-like growth factor 2 (IGF2)-H19 locus. The DNA methyltransferase inhibitor, 5-Aza-2'deoxycytidine (5-AzaCdR) is an approved epigenetic cancer therapy. However, it is not known to what extent 5-AzaCdR influences other epigenetic marks. In this study, we set out to determine whether 5-AzaCdR treatment can reprogram the epigenomic organization of the IGF2-H19 locus in a choriocarcinoma cancer cell line (JEG3). We found that localized DNA demethylation at the H19 imprinting control region (ICR) induced by 5-AzaCdR, reduced IGF2, increased H19 expression, increased CTCF and cohesin recruitment and changed histone modifications. Furthermore chromatin accessibility was increased locus-wide and chromatin looping topography was altered such that a CTCF site downstream of the H19 enhancers switched its association with the CTCF site upstream of the IGF2 promoters to associate with the ICR. We identified a stable chromatin looping domain, which forms independently of DNA methylation. This domain contains the IGF2 gene and is marked by a histone H3 lysine 27 trimethylation block between CTCF site upstream of the IGF2 promoters and the Centrally Conserved Domain upstream of the ICR. Together, these data provide new insights into the responsiveness of chromatin topography to DNA methylation changes.
authors.affiliation: Department of Oncology, University of Cambridge, CRUK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Ito
authors.forename: Raffaella
authors.initials: R
authors.lastname: Nativio
authors.forename: Adele
authors.initials: A
authors.lastname: Murrell
mesh_terms: D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins / Q000378:metabolism; D045744:Cell Line, Tumor; D002843:Chromatin / Q000737:chemistry*; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism; D019175:DNA Methylation / Q000187:drug effects; D000077209:Decitabine; D015536:Down-Regulation; D004742:Enhancer Elements, Genetic; D004791:Enzyme Inhibitors / Q000494:pharmacology; D015870:Gene Expression; D056426:Genetic Loci; D018392:Genomic Imprinting; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007335:Insulin-Like Growth Factor II / Q000235:genetics*; D008745:Methylation; D009088:Mucoproteins / Q000378:metabolism; D009363:Neoplasm Proteins; D009707:Nucleosomes / Q000737:chemistry; D063151:Polycomb Repressive Complex 2 / Q000378:metabolism; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics*; D012097:Repressor Proteins / Q000378:metabolism; D014157:Transcription Factors; D000097722:Cohesins
chemical_list: D001374:Azacitidine; D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D000077209:Decitabine; D004791:Enzyme Inhibitors; D006657:Histones; D007335:Insulin-Like Growth Factor II; D009088:Mucoproteins; D009363:Neoplasm Proteins; D009707:Nucleosomes; D063151:Polycomb Repressive Complex 2; D062085:RNA, Long Noncoding; D012097:Repressor Proteins; D014157:Transcription Factors; D000097722:Cohesins; C000619697:CTCF protein, human; C094335:H19 long non-coding RNA; C035170:IGF2 protein, human; C430461:SUZ12 protein, human; C010393:lysin, gastropoda