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J Biol Chem. 2018 Feb 16;293(7):2498-2509. doi: 10.1074/jbc.RA117.000498. Epub 2017 Dec 29.

Recruitment and allosteric stimulation of a histone-deubiquitinating enzyme during heterochromatin assembly.

Author information

1
From the Department of Biochemistry and Molecular Genetics and.
2
Molecular Biology Program, University of Colorado, Denver-Anschutz Medical Campus, Aurora, Colorado 80045 and.
3
the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523.
4
From the Department of Biochemistry and Molecular Genetics and aaron.m.johnson@ucdenver.edu.

Abstract

Heterochromatin formation in budding yeast is regulated by the silent information regulator (SIR) complex. The SIR complex comprises the NAD-dependent deacetylase Sir2, the scaffolding protein Sir4, and the nucleosome-binding protein Sir3. Transcriptionally active regions present a challenge to SIR complex-mediated de novo heterochromatic silencing due to the presence of antagonistic histone post-translational modifications, including acetylation and methylation. Methylation of histone H3K4 and H3K79 is dependent on monoubiquitination of histone H2B (H2B-Ub). The SIR complex cannot erase H2B-Ub or histone methylation on its own. The deubiquitinase (DUB) Ubp10 is thought to promote heterochromatic silencing by maintaining low H2B-Ub at sub-telomeres. Here, we biochemically characterized the interactions between Ubp10 and the SIR complex machinery. We demonstrate that a direct interaction between Ubp10 and the Sir2/4 sub-complex facilitates Ubp10 recruitment to chromatin via a co-assembly mechanism. Using hydrolyzable H2B-Ub analogs, we show that Ubp10 activity is lower on nucleosomes compared with H2B-Ub in solution. We find that Sir2/4 stimulates Ubp10 DUB activity on nucleosomes, likely through a combination of targeting and allosteric regulation. This coupling mechanism between the silencing machinery and its DUB partner allows erasure of active PTMs and the de novo transition of a transcriptionally active DNA region to a silent chromatin state.

KEYWORDS:

SIR complex; chromatin; deubiquitylation (deubiquitination); epigenetics; heterochromatin; histone; sirtuin; ubiquitination; yeast

PMID:
29288197
PMCID:
PMC5818202
[Available on 2019-02-16]
DOI:
10.1074/jbc.RA117.000498

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