CGGBP1 regulates chromatin barrier activity and CTCF occupancy at repeats

Abstract

CGGBP1 is a repeat-binding protein with diverse functions in regulation of gene expression, cytosine methylation, repeat silencing and genomic integrity. CGGBP1 has also been identified as a cooperator factor in histone modifying complexes and as a component of protein complexes that form the enhancer-promoter loops. Here we report that the occupancy of CTCF at repeats and the chromatin barrier function of these repeat sequences depends on CGGBP1. Using ChIP-sequencing for CTCF we describe CTCF binding on repetitive DNA. Our results show that CGGBP1 determines the CTCF occupancy preference for repeats over canonical CTCF-motif. By combining CTCF ChIP-sequencing results with ChIP-sequencing for three different kinds of histone modifications (H3K4me3, H3K9me3 and H3K27me3) we uncover insulator-like chromatin barrier activities of the repeat-rich CTCF-binding sites. This work shows that CGGBP1 is a regulator of CTCF occupancy and posits it as a regulator of barrier functions of CTCF-binding sites.