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Mol Cell Proteomics. 2014 Jul;13(7):1855-65. doi: 10.1074/mcp.O113.036335. Epub 2014 Apr 16.

Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk.

Author information

1
From the Department of Biochemistry and Molecular Biology University of Southern Denmark Campusvej 55 DK-5230 Odense M, Denmark veitveit@bmb.sdu.dk.
2
From the Department of Biochemistry and Molecular Biology University of Southern Denmark Campusvej 55 DK-5230 Odense M, Denmark.

Abstract

Mass spectrometry (MS) is a powerful analytical method for the identification and quantification of co-existing post-translational modifications in histone proteins. One of the most important challenges in current chromatin biology is to characterize the relationships between co-existing histone marks, the order and hierarchy of their deposition, and their distinct biological functions. We developed the database CrossTalkDB to organize observed and reported co-existing histone marks as revealed by MS experiments of histone proteins and their derived peptides. Statistical assessment revealed sample-specific patterns for the co-frequency of histone post-translational modifications. We implemented a new method to identify positive and negative interplay between pairs of methylation and acetylation marks in proteins. Many of the detected features were conserved between different cell types or exist across species, thereby revealing general rules for cross-talk between histone marks. The observed features are in accordance with previously reported examples of cross-talk. We observed novel types of interplay among acetylated residues, revealing positive cross-talk between nearby acetylated sites but negative cross-talk for distant ones, and for discrete methylation states at Lys-9, Lys-27, and Lys-36 of histone H3, suggesting a more differentiated functional role of methylation beyond the general expectation of enhanced activity at higher methylation states.

PMID:
24741113
PMCID:
PMC4083120
DOI:
10.1074/mcp.O113.036335
[Indexed for MEDLINE]
Free PMC Article
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