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CpG islands influence chromatin structure via the CpG-binding protein Cfp1

Abstract

CpG islands (CGIs) are prominent in the mammalian genome owing to their GC-rich base composition and high density of CpG dinucleotides1,2. Most human gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3), irrespective of transcriptional activity3,4. In spite of these intriguing correlations, the functional significance of non-methylated CGI sequences with respect to chromatin structure and transcription is unknown. By performing a search for proteins that are common to all CGIs, here we show high enrichment for Cfp1, which selectively binds to non-methylated CpGs in vitro5,6. Chromatin immunoprecipitation of a mono-allelically methylated CGI confirmed that Cfp1 specifically associates with non-methylated CpG sites in vivo. High throughput sequencing of Cfp1-bound chromatin identified a notable concordance with non-methylated CGIs and sites of H3K4me3 in the mouse brain. Levels of H3K4me3 at CGIs were markedly reduced in Cfp1-depleted cells, consistent with the finding that Cfp1 associates with the H3K4 methyltransferase Setd1 (refs 7, 8). To test whether non-methylated CpG-dense sequences are sufficient to establish domains of H3K4me3, we analysed artificial CpG clusters that were integrated into the mouse genome. Despite the absence of promoters, the insertions recruited Cfp1 and created new peaks of H3K4me3. The data indicate that a primary function of non-methylated CGIs is to genetically influence the local chromatin modification state by interaction with Cfp1 and perhaps other CpG-binding proteins.

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Figure 1: Cfp1 is enriched in non-methylated CpG island chromatin.
Figure 2: Genome-wide ChIP sequencing shows a tight association between Cfp1 and H3K4me3 at CGIs.
Figure 3: Depletion of Cfp1 results in reduced H3K4 trimethylation levels at CpG islands.
Figure 4: Artificial promoterless CpG-rich sequences recruit Cfp1 and generate new H3K4me3 peaks in mouse ES cells.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

High throughput sequencing data has been deposited in the Gene Expression Omnibus (GEO) under the accession number GSE18578.

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Acknowledgements

We are grateful to D. Skalnik for the gift of a Cfp1 antibody, I. Chambers for the TβC44 ES cell line, R. Klose for discussions, E. Sheridan for testing the DNA sequencing protocol, and K. Auger and J. Parkhill for coordinating the DNA sequencing. We also thank R. Ekiert and J. Connelly for comments on the manuscript. This work was funded by a Cancer Research UK studentship to J.P.T. and by grants from the Wellcome Trust, the Medical Research Council and the European Union ‘Epigenome’ Network of Excellence.

Author Contributions J.P.T. and P.J.S. performed the ChIP, knockdown and bisulphite analysis. T.C. did preliminary ChIP analysis. J.S. and J.G. generated the MeCP2-eGFP cell line. J.S. performed bisulphite analysis of the TβC44 ES cell line. R.I. prepared samples for sequencing. K.D.J., D.J.T. and R.A. performed the sequencing and mapping. S.W., A.R.W.K., A.D. and R.I. performed the bioinformatic analysis. J.P.T., P.J.S., T.C., R.I. and A.B. wrote the manuscript.

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Correspondence to Adrian Bird.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1 - S4 with legends and reference for Supplementary Figure S2, legend for Supplementary Table S1 (see separate Supplementary Table file) and Supplementary Tables S2 - S3. (PDF 558 kb)

Supplementary Table 1

This table shows the association of Cfp1, histone H3K4me3, H3K27me3 and RNA polymerase II with non-methylated CGIs. (see Supplementary Information file for full legend). (XLS 1090 kb)

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Thomson, J., Skene, P., Selfridge, J. et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464, 1082–1086 (2010). https://doi.org/10.1038/nature08924

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