Nucleosome-interacting proteins regulated by DNA and histone methylation

Cell. 2010 Oct 29;143(3):470-84. doi: 10.1016/j.cell.2010.10.012.

Till Bartke ¹, Michiel Vermeulen, Blerta Xhemalce, Samuel C Robson, Matthias Mann, Tony Kouzarides

Affiliations

Affiliation

1 The Gurdon Institute, Department of Pathology, Cambridge, UK.

PMID: 21029866 DOI: 10.1016/j.cell.2010.10.012

Abstract

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.

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