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Multivalent di‐nucleosome recognition enables the Rpd3S histone deacetylase complex to tolerate decreased H3K36 methylation levels
Author(s) -
Huh JaeWan,
Wu Jun,
Lee ChulHwan,
Yun Miyong,
Gilada Daniel,
Brautigam Chad A,
Li Bing
Publication year - 2012
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1038/emboj.2012.221
Subject(s) - nucleosome , biology , chromatin , histone code , acetylation , histone , histone methylation , microbiology and biotechnology , histone octamer , histone h3 , genetics , computational biology , dna , dna methylation , gene , gene expression
The Rpd3S histone deacetylase complex represses cryptic transcription initiation within coding regions by maintaining the hypo‐acetylated state of transcribed chromatin. Rpd3S recognizes methylation of histone H3 at lysine 36 (H3K36me), which is required for its deacetylation activity. Rpd3S is able to function over a wide range of H3K36me levels, making this a unique system to examine how chromatin regulators tolerate the reduction of their recognition signal. Here, we demonstrated that Rpd3S makes histone modification‐independent contacts with nucleosomes, and that Rpd3S prefers di‐nucleosome templates since two binding surfaces can be readily accessed simultaneously. Importantly, this multivalent mode of interaction across two linked nucleosomes allows Rpd3S to tolerate a two‐fold intramolecular reduction of H3K36me. Our data suggest that chromatin regulators utilize an intrinsic di‐nucleosome‐recognition mechanism to prevent compromised function when their primary recognition modifications are diluted.