Systematic Identification of Methyllysine-Driven Interactions for Histone and Nonhistone Targets

Authors

Huadong Liu, The University of Western Ontario
Marek Galka, The University of Western Ontario
Aimee Iberg, The University of Texas M.D. Anderson Cancer Center
Zezhou Wang, The University of Western Ontario
Lei Li, The University of Western Ontario
Courtney Voss, The University of Western Ontario
Xinfeng Jiang, The University of Western Ontario
Gilles Lajoie, The University of Western Ontario
Zhiping Huang, Institute of Chemical Defense, Beijing, China
Mark T. Bedford, The University of Texas M.D. Anderson Cancer Center
Shawn S. C. Li, The University of Western Ontario

Document Type

Article

Publication Date

11-5-2010

Journal

Journal of Proteome Research

Volume

9

Issue

11

First Page

5827

Last Page

5836

URL with Digital Object Identifier

http://dx.doi.org/10.1021/pr100597b

Abstract

An important issue in epigenetic research is to understand how the numerous methylation marks associated with histone and certain nonhistone proteins are recognized and interpreted by the hundreds of chromatin-binding modules (CBMs) in a cell to control chromatin state, gene expression, and other cellular functions. We have assembled a peptide chip that represents known and putative lysine methylation marks on histones and p53 and probed the chip for binding to a group of CBMs to obtain a comprehensive interaction network mediated by lysine methylation. Interactions revealed by the peptide array screening were validated by in-solution binding assays. This study not only recapitulated known interactions but also uncovered new ones. A novel heterochromatin protein 1 beta (HP1β) chromodomain-binding site on histone H3, H3K23me, was discovered from the peptide array screen and subsequently verified by mass spectrometry. Data from peptide pull-down and colocalization in cells suggest that, besides the H3K9me mark, H3K23me may play a role in facilitating the recruitment of HP1β to the heterochromatin. Extending the peptide array and mass spectrometric approach presented here to more histone marks and CBMs would eventually afford a comprehensive specificity and interaction map to aid epigenetic studies.