CGGBP1 regulates chromatin barrier activity and CTCF occupancy at repeats

To study the role of CGGBP1 in regulation of CTCF occupancy, we performed CTCF ChIP-seq in HEK293T cells with three different levels of CGGBP1: (i) endogenous levels of CGGBP1 (ii) CGGBP1 knockdown, and (iii) CGGBP1 overexpression. Here, we show that CTCF binds to repeats as well as canonical CTCF-motifs and CGGBP1 determines the CTCF occupancy preference for repeats over canonical CTCF-motif. By combining CTCF ChIP-seq with histone modifications ChIP-seq (for H3K4me3, H3K9me3 and H3K27me3) under conditions of normal or CGGBP1 knockdown, we demonstrate that CTCF binding sites regulated by CGGBP1 correspond to chromatin barrier elements with profound effects on H3K9me3 distribution. In conclusion, these finding shows that CGGBP1 is a regulator of CTCF occupancy and serve as a regulator of barrier functions of CTCF-binding sites. Overall design: CTCF occupancy was compared in HEK293T cells through ChIP-seq under conditions of normal CGGBP1 expression, CGGBP1 knockdown and overexpression. Histone modifications ChIP-seq (H3K4me3, H3K9me3 and H3K27me3) were performed under endogenous levels of CGGBP1 and CGGBP1 knockdown.