title: Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island.
abstract: Repression of many tumor suppressor genes in cancer is concurrent with aberrantly increased DNA methylation levels at promoter CpG islands (CGIs). About one-fourth of empirically defined human promoters are surrounded by or contain clustered repetitive elements. It was previously observed that a sharp transition of methylation exists between highly methylated repetitive elements and unmethylated promoter-CGIs in normal tissues. The factors that lead to aberrant CGI hypermethylation in cancer remain poorly understood. Here, we established a site-specific integration system with enforced local transcriptional repression in colorectal cancer cells and monitored the occurrence of initial de novo methylation at specific CG sites adjacent to the CGI of the INSL6 promoter, which could be accelerated by binding a KRAB-containing transcriptional factor. Additional repetitive elements from P16 and RIL (PDLIM4), if situated adjacent to the promoter of INSL6, could confer DNA methylation spreading into the CGI particularly in the setting of KRAB-factor binding. However, a repressive chromatin alone was not sufficient to initiate DNA methylation, which required specific DNA sequences and was integration-site (and/or cell-line) specific. Overall, these results demonstrate a requirement for specific DNA sequences to trigger de novo DNA methylation, and repetitive elements as cis-regulatory factors to cooperate with advanced transcriptional repression in promoting methylation spreading.
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jingmin
authors.initials: J
authors.lastname: Shu
authors.forename: Jiali
authors.initials: J
authors.lastname: Si
authors.forename: Lanlan
authors.initials: L
authors.lastname: Shen
authors.forename: Marcos R H
authors.initials: MR
authors.lastname: Estecio
authors.forename: Jean-Pierre J
authors.initials: JP
authors.lastname: Issa
mesh_terms: D045744:Cell Line, Tumor; D002843:Chromatin / Q000378:metabolism; D018899:CpG Islands; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D020868:Gene Silencing; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D014158:Transcription, Genetic; D019076:Transgenes
chemical_list: D002843:Chromatin; D036341:Intercellular Signaling Peptides and Proteins; D004247:DNA