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Unbiased proteomic screen for binding proteins to modified lysines on histone H3
Author(s) -
Chan Doug W.,
Wang Yi,
Wu Meng,
Wong Jiemin,
Qin Jun,
Zhao Yingming
Publication year - 2009
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200800600
Subject(s) - histone h3 , histone , lysine , bromodomain , phd finger , histone code , biology , computational biology , biochemistry , effector , acetylation , histone h2a , microbiology and biotechnology , transcription factor , nucleosome , amino acid , dna , gene , zinc finger
We report a sensitive peptide pull‐down approach in combination with protein identification by LC‐MS/MS and qualitative abundance measurements by spectrum counting to identify proteins binding to histone H3 tail containing dimethyl lysine 4 (H3K4me2), dimethyl lysine 9 (H3K9me2), or acetyl lysine 9 (H3K9ac). Our study identified 86 nuclear proteins that associate with the histone H3 tail peptides examined, including seven known direct binders and 16 putative direct binders with conserved PHD finger, bromodomain, and WD40 domains. The reliability of our proteomic screen is supported by the fact that more than one‐third of the proteins identified were previously described to associate with histone H3 tail directly or indirectly. To our knowledge, the results presented here are the most comprehensive analysis of H3K4me2, H3K9me2, and H3K9ac associated proteins and will provide a useful resource for researchers studying the mechanisms of histone code effector proteins.