CGGBP1 regulates CTCF occupancy at repeats

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...

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Bibliographic Details
Published in:Epigenetics & chromatin 2019-09, Vol.12 (1), p.57-57, Article 57
Main Authors: Patel, Divyesh, Patel, Manthan, Datta, Subhamoy, Singh, Umashankar
Format: Article
Language:English
Subjects:
Analysis
Binding Sites
Biochemistry
CCCTC-Binding Factor - chemistry
CCCTC-Binding Factor - metabolism
Cell cycle
Cell Line
Cell Nucleus - metabolism
Cell proliferation
Chromatin
Chromatin - metabolism
Cytosine
DNA
DNA damage
DNA methylation
DNA sequencing
DNA-Binding Proteins - antagonists & inhibitors
DNA-Binding Proteins - genetics
DNA-Binding Proteins - metabolism
Enzymes
Fibroblasts
Gene expression
Genes
Genomes
Histones - metabolism
Humans
Methylation
Occupancy
Polyclonal antibodies
Protein binding
Protein Processing, Post-Translational
Proteins
Pyrimidines
RNA Interference
RNA, Small Interfering - metabolism
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Summary: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. 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. CGGBP1 affects the pattern of CTCF occupancy. Our results posit CGGBP1 as a regulator of CTCF and its binding sites in interspersed repeats.
ISSN:1756-8935
1756-8935
DOI:10.1186/s13072-019-0305-6