CTCF loss mediates unique DNA hypermethylation landscapes in human cancers

Abstract

Background: The chromatin insulator CCCTC-binding factor (CTCF) displays tissue-specific DNA binding sites that regulate transcription and chromatin organization. Despite evidence linking CTCF to the protection of epigenetic states through barrier insulation, the impact of CTCF loss on genome-wide DNA methylation sites in human cancer remains undefined. Results: Here, we demonstrate that prostate and breast cancers within The Cancer Genome Atlas (TCGA) exhibit frequent copy number loss of CTCF and that this loss is associated with increased DNA methylation events that occur preferentially at CTCF binding sites. CTCF sites differ among tumor types and result in tissue-specific methylation patterns with little overlap between breast and prostate cancers. DNA methylation and transcriptome profiling in vitro establish that forced downregulation of CTCF leads to spatially distinct DNA hypermethylation surrounding CTCF binding sites, loss of CTCF binding, and decreased gene expression that is also seen in human tumors. DNA methylation inhibition reverses loss of expression at these CTCF-regulated genes. Conclusion: These findings establish CTCF loss as a major mediator in directing localized DNA hypermethylation events in a tissue-specific fashion and further support its role as a driver of the cancer phenotype.

Epigenetic Regulation of Genomic Stability by Vitamin C

“…DNA hypermethylation caused by loss of TET activity increases nucleosome occupancy, and subsequently, loss of CTCF binding and a block in the downstream recruitment of the cohesin complex, reducing the formation of CTCF/cohesion-mediated chromatin loops thereby downregulating the expression of neighboring genes ( Wiehle et al, 2019 ; Nanavaty et al, 2020 ). Loss of CTCF itself can also induce DNA hypermethylation at CTCF binding sites and the fusion of TAD boundaries that establish oncogenic expression patterns and increased cancer progression ( Akdemir et al, 2020 ; Damaschke et al, 2020 ). TETs also regulate chromosomal architecture by protecting large undermethylated genomic regions known as DNA methylation “canyons” from becoming hypermethylated ( Wiehle et al, 2016 ; Zhang X. et al, 2016 ).…”

CTCF as a regulator of alternative splicing: new tricks for an old player

“…While CTCF binding is inhibited by DNA methylation ( 94–98 ), CTCF itself regulates DNA methylation and preserves methylation-free regions throughout the genome ( 115–117 ). Moreover, CTCF knockdown induces global hypermethylation, particularly at CTCF binding sites, as well as loss of CTCF binding associated with altered expression of CTCF-regulated genes ( 118 ). Interestingly, two individuals with an intellectual disability and diagnosed with CTCF heterozygous deletions exhibited hypermethylation at nearly 300 CTCF binding sites genome-wide ( 119 ).…”

“…Knowing that Ctcf haploinsufficiency ( 119 , 120 ) or knockdown ( 118 ) induces hypermethylation, we proposed that Ctcf haploinsufficiency increased intron retention through a methylation-dependent mechanism ( 45 ), which may involve altering the kinetics of RNAPII elongation or chromatin looping. However, this hypothesis requires further direct experimental validation, considering possible indirect effects of decreased Ctcf levels.…”

Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF

“…In other contexts, CTCF loss mediates unique DNA hypermethylation surrounding CTCF binding sites in a variety of human cancers [ 38 ]. In the prostate, the Igf2-H19 locus experiences DNA methylation with CTCF downregulation at multiple intergenic CTCF sites [ 39 ].…”