3D chromatin remodeling potentiates transcriptional programs driving cell invasion

Abstract

The contribution of deregulated chromatin architecture, including topologically associated domains (TADs), to cancer progression remains ambiguous. CCCTC-binding factor (CTCF) is a central regulator of higher-order chromatin structure that undergoes copy number loss in over half of all breast cancers, but the impact of this defect on epigenetic programming and chromatin architecture remains unclear. We find that under physiological conditions, CTCF organizes subTADs to limit the expression of oncogenic pathways, including phosphatidylinositol 3-kinase (PI3K) and cell adhesion networks. Loss of a single CTCF allele potentiates cell invasion through compromised chromatin insulation and a reorganization of chromatin architecture and histone programming that facilitates de novo promoter-enhancer contacts. However, this change in the higher-order chromatin landscape leads to a vulnerability to inhibitors of mTOR. These data support a model whereby subTAD reorganization drives both modification of histones at de novo enhancer-promoter contacts and transcriptional up-regulation of oncogenic transcriptional networks.

DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity

“…To understand the interplay between CTCF expression and binding, we analyzed the publicly available CTCF ChIP-seq data of CTCF knockdown in MCF10A from Lebeau et al. ( 55 ), in which they showed a 50–60% reduction in CTCF protein, and the overall CTCF binding of the cells remained largely unchanged, with a small number of lost CTCF binding sites, and even smaller number of gained CTCF binding sites ( 55 ). Reanalyzing their CTCF ChIP-seq data (alignment to the human GRCh38/hg38 build genome) and filtering out non-CTCF motif-containing binding sites, we found very similar results with a total of 38 875 CTCF peaks, of which 3270 were significantly lost (FDR < 0.01, log 2 FC < −1) and 504 CTCF peaks significantly gained (FDR < 0.01, log 2 FC > 1) in the CTCF knockdown cells, while the rest of CTCF binding peaks ( n = 35 101) remained statistically unchanged ( 55 ) (Figure 4A ).…”

“…The publicly available data for CTCF chromatin immunoprecipitation sequencing (ChIP-seq) from HeLa ( 45 ), GM12878 ( 45 ), MCF10A ( 54 , 55 ), Jurkat ( 56 ), NPCs ( 45 ) and RPE-1 ( 45 ), and each associated input control data, were downloaded and aligned to the GRCh38/hg38 genome using bowtie2 (v. 2.3.4.1). Binding peaks were called by the macs2 tool (v. 2.2.9.1) using the default setting with each dataset controlled for the matching input data (-c).…”

“…CTCF ChIP-seq data from MCF10A CTCF wild-type (WT) and knockdown (KD) cells ( 55 ) were downloaded and processed as described earlier. Binding peaks with CTCF motifs were used for further analysis to identify differentially binding regions using DiffBind 3.0 with the same parameters as described in Lebeau et al.…”

“…Binding peaks with CTCF motifs were used for further analysis to identify differentially binding regions using DiffBind 3.0 with the same parameters as described in Lebeau et al. ( 55 ). Briefly, bam and narrowPeak files for each sample and bam files of the associated input were used.…”

The CTCF-H3K27me3 axis supports melanoma cell migration by repressing cholesterol biosynthesis

“…CTCF involvement in cell migration is ambiguous; on one hand it was shown to repress breast cancer cell migration and invasion 35,36 , while on the other hand it was shown to support migration and/or invasion of various primary and cancerous cells including human corneal epithelial cells 37,38 , cortical neurons 39 , skin-resident dendritic cells 40 , prostate cancer cells 41,42 , ovarian cancer cells 43 , gastric cancer cells 44 and melanoma cells 45 . Although it is assumed that CTCF affects cell migration by its ability to regulate transcription, the exact mechanism by which CTCF controls transcription to control cell migration has not been determined yet.…”