CTCF loss mediates unique DNA hypermethylation landscapes in human cancers

Nathan A. Damaschke,John Svaren,Mele Avilla,Bing Yang,Joseph Gawdzik,Jian-Hua Luo,Avtar Roopra,Yan P. Yu,Sunduz Keles,David F. Jarrard

doi:10.1186/s13148-020-00869-7

Abstract

BackgroundThe 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.ResultsHere, 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.ConclusionThese 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.

Highlights

The chromatin insulator CCCTC-binding factor (CTCF) displays tissue-specific DNA binding sites that regulate transcription and chromatin organization
DNA hypermethylation occurs at CTCF binding sites within downregulated genes after CTCF knockdown To further define the role of DNA methylation at these CTCF regulated genes, we examined whether CTCF knockdown would lead to promoter-CTCF binding site associated gains of DNA methylation after transcriptional silencing of target genes
Decreases in CTCF expression alter the DNA methylation landscape in prostate and breast cancer, two of the most common human tumors. These findings are of importance in explaining epigenetic alterations in other tissues and tumor types since CTCF function may be modulated through other mechanisms besides deletion

Summary

Introduction

The chromatin insulator CCCTC-binding factor (CTCF) displays tissue-specific DNA binding sites that regulate transcription and chromatin organization. Gene silencing precedes DNA hypermethylation, where evacuation of activating transcription factors is associated with alterations to chromatin structure [2, 3]. Understanding the drivers associated with nuclear organization, DNA methylation, and gene expression are key to our understanding of disease including the important question of why DNA patterns vary between cancers of different tissues. CTCF functions in gene transcription and repression and as an insulator that interferes with enhancerpromoter interactions [4, 5]. CTCF recruits cohesin to assist in these chromatin organization functions, including in long-range interactions between genes [6]

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Conclusion