Systematic identification of methyllysine-driven interactions for histone and nonhistone targets.
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.
Liu
Huadong
H
Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.
Galka
Marek
M
Iberg
Aimee
A
Wang
Zezhou
Z
Li
Lei
L
Voss
Courtney
C
Jiang
Xinfeng
X
Lajoie
Gilles
G
Huang
Zhiping
Z
Bedford
Mark T
MT
Li
Shawn S C
SS
D000090266:Chromobox Protein Homolog 5; D057890:Epigenomics; D006657:Histones / Q000032:analysis* / Q000378:metabolism; D006801:Humans; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D040081:Protein Array Analysis; D011485:Protein Binding; D016159:Tumor Suppressor Protein p53 / Q000032:analysis* / Q000378:metabolism
C000715593:CBX1 protein, human; D006657:Histones; D016159:Tumor Suppressor Protein p53; D000090266:Chromobox Protein Homolog 5; D008239:Lysine