CGGBP1 regulates CTCF occupancy at repeats

Abstract

Background CGGBP1 is a repeat-binding protein with diverse functions in the regulation of gene expression, cytosine methylation, repeat silencing and genomic integrity. CGGBP1 has also been identified as a cooperator of histone-modifying enzymes and as a component of CTCF-containing complexes that regulate the enhancer–promoter looping. CGGBP1–CTCF cross talk in chromatin regulation has been hitherto unknown. Results Here, we report that the occupancy of CTCF at repeats depends on CGGBP1. Using ChIP-sequencing for CTCF, we describe its occupancy at repetitive DNA. Our results show that endogenous level of CGGBP1 ensures CTCF occupancy preferentially on repeats over canonical CTCF motifs. By combining CTCF ChIP-sequencing results with ChIP sequencing for three different kinds of histone modifications (H3K4me3, H3K9me3 and H3K27me3), we show that the CGGBP1-dependent repeat-rich CTCF-binding sites regulate histone marks in flanking regions. Conclusion CGGBP1 affects the pattern of CTCF occupancy. Our results posit CGGBP1 as a regulator of CTCF and its binding sites in interspersed repeats.

HDAC inhibitor Givinostat targets DNA-binding of human CGGBP1

“…Most interestingly, the normal and cancer cells exhibit different responses to CGGBP1 knockdown: cancer cells undergo G1/S block whereas normal fibroblasts progress through through the S phase slowly arrest in the G2/M phase [3] . Recent works implicate CTCF in regulation of CTCF binding at repeats and regulation of chromatin function [4] . The differential dependence of normal and cancer cells on CGGBP1 suggests that inhibiting it may be a useful means to target cancer cells.…”

CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity

“…Non-targeting (CT) or CGGBP1-targeting (KD) shRNA were expressed in HEK293T cells as described elsewhere [20] (Fig S1). DNA fragments were enriched using methylcytosine antibody and the methylated DNA (hereafter the DNA with cytosine methylation is referred to as methylated DNA) sequenced on the Ion Torrent platform with mean read lengths of 150 bp.…”

“…By maintaining the balance between CTCF at repeats or motifs, CGGBP1 acts as a regulator of CTCF binding pattern genome-wide. Data suggests that the repeat binding of CTCF takes place in cooperation with CGGBP1 [20] . Thus, while CGGBP1 depletion directly affects CTCF association with repetitive sequences, the gain of binding at motifs seems like an indirect consequence of CTCF displacement from the repeats.…”

“…However, CGGBP1 depletion leads to an imbalance in the DNA-binding preference of CTCF. Upon CGGBP1 knockdown the repeat binding of CTCF is diminished and the CTCF-binding gets limited to the motifs [20] . Interestingly, like CTCF, CGGBP1 itself is a methylation-sensitive DNA-binding protein [20][21][22][23][24][25] .…”

“…Upon CGGBP1 knockdown the repeat binding of CTCF is diminished and the CTCF-binding gets limited to the motifs [20] . Interestingly, like CTCF, CGGBP1 itself is a methylation-sensitive DNA-binding protein [20][21][22][23][24][25] . However, there is evidence that CGGBP1 binding to the target sequences prevents methylation from taking place [25,26] .…”