Cell
Volume 143, Issue 3, 29 October 2010, Pages 470-484
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Article
Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

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Summary

Modifications on histones or on DNA recruit proteins that regulate chromatin function. Here, we use nucleosomes methylated on DNA and on histone H3 in an affinity assay, in conjunction with a SILAC-based proteomic analysis, to identify “crosstalk” between these two distinct classes of modification. Our analysis reveals proteins whose binding to nucleosomes is regulated by methylation of CpGs, H3K4, H3K9, and H3K27 or a combination thereof. We identify the origin recognition complex (ORC), including LRWD1 as a subunit, to be a methylation-sensitive nucleosome interactor that is recruited cooperatively by DNA and histone methylation. Other interactors, such as the lysine demethylase Fbxl11/KDM2A, recognize nucleosomes methylated on histones, but their recruitment is disrupted by DNA methylation. These data establish SILAC nucleosome affinity purifications (SNAP) as a tool for studying the dynamics between different chromatin modifications and provide a modification binding “profile” for proteins regulated by DNA and histone methylation.

Highlights

► Proteomics-based affinity purification identifies nucleosome-binding proteins ► Binding of proteins to chromatin is modulated by both DNA and histone modifications ► The origin recognition complex binds nucleosomes and includes LRWD1 as a subunit ► KDM2A binds H3K9me3-modified nucleosomes via HP1 and is blocked by CpG methylation

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Present address: Department of Physiological Chemistry and Cancer Genomics Centre, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands