CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands

Epigenetics & Chromatin
Louie N van de LagemaatDouglas Vernimmen

Abstract

The mechanism by which protein complexes interact to regulate the deposition of post-translational modifications of histones remains poorly understood. This is particularly important at regulatory regions, such as CpG islands (CGIs), which are known to recruit Trithorax (TrxG) and Polycomb group proteins. The CxxC zinc finger protein 1 (CFP1, also known as CGBP) is a subunit of the TrxG SET1 protein complex, a major catalyst of trimethylation of H3K4 (H3K4me3). Here, we used ChIP followed by high-throughput sequencing (ChIP-seq) to analyse genomic occupancy of CFP1 in two human haematopoietic cell types. We demonstrate that CFP1 occupies CGIs associated with active transcription start sites (TSSs), and is mutually exclusive with H3K27 trimethylation (H3K27me3), a marker of polycomb repressive complex 2. Strikingly, rather than being restricted to active CGI TSSs, CFP1 also occupies a substantial fraction of active non-CGI TSSs and enhancers of transcribed genes. However, relative to other TrxG subunits, CFP1 was specialised to TSSs. Finally, we found enrichment of CpG-containing DNA motifs in CFP1 peaks at CGI promoters. We found that CFP1 is not solely recruited to CpG islands as it was originally defined, but also other regio...Continue Reading

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Datasets Mentioned

BETA
GSE50893
GM12878
GSE114084
GSE70660
GSE30611

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
ChIP
RNA-seq
co-immunoprecipitation
PCR
ChIPs
Assay

Software Mentioned

Rsubread
Phantompeakqualtools
bamCompare
R
deepTools bamCompare
deepTools
ENCODE
bedtools
hisat2 aligner
ChIPpeakAnno

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