Heterochromatin assembly by interrupted Sir3 bridges across neighboring nucleosomes

Behrouzi, Reza; Lu, Chenning; Currie, Mark A.; Jih, Gloria; Iglesias, Nahid; Moazed, Danesh

doi:10.7554/elife.17556

Cited by 37 publications

(54 citation statements)

References 111 publications

(188 reference statements)

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“…Sir2-dependent deacetylation is the sole erasure activity of the SIR complex, yet SIR complex binding is not severely affected by acetylated chromatin in the absence of deacetylase activity (10). Instead Sir3, the Sir protein important for spreading of the SIR complex, is particularly sensitive to histone acetylation and H3K79me (6,8,9,11,12,23,50). It remains unknown if H2B-Ub alone can directly inhibit or reduce SIR complex binding to the nucleosome.…”

Section: Sir2/4 Allosterically Stimulates Ubp10 Activity To Generate mentioning

confidence: 99%

“…This is exemplified by the specific recognition of the unmodified histone H4 tail by the silencing machinery (5)(6)(7). Additionally, methylation of histone H3 lysine 4 (H3K4me) and H3 lysine 79 (H3K79me) antagonize silencing (8)(9)(10)(11)(12). Heterochromatin assembly is coupled to enzymatic conversion of the histone code from the active to inactive state.…”

Section: Introductionmentioning

confidence: 99%

“…Several active marks are known to be anti-silencing, such as H3K4me3 and H3K79me3, as they interfere with SIR complex-mediated silencing and prevent association of the SIR complex with euchromatic regions (8)(9)(10)(11)(12)(21)(22)(23)(24) (Fig 1A). Tri-methylation of H3K4 and H3K79 are dependent on Rad6/Bre1-mediated mono-ubiquitination of H2BK123 (H2B-Ub) (25-27).…”

Section: Introductionmentioning

confidence: 99%

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

Zukowski

Al-Afaleq

Duncan

et al. 2018

Journal of Biological Chemistry

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Heterochromatin formation in budding yeast is regulated by the silent information regulator (SIR) complex. The SIR complex comprises the NADdependent 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 PTMs, including acetylation and methylation. Methylation of histone H3K4 and H3K79 are dependent on mono-ubiquitination 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 characterize 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 to 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.

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Section: Sir2/4 Allosterically Stimulates Ubp10 Activity To Generate mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Zukowski

Al-Afaleq

Duncan

et al. 2018

Journal of Biological Chemistry

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“…Crystal structure data indicate that K79 methylation would block hydrogen bond formation between K79 and the BAH of Sir3, thereby decreasing Sir3 affinity to nucleosomes (61,62) . In vitro, all three H3K79 methyl marks abolish the binding of Sir3 to H3 peptides (45,46) and reduced Sir3 affinity for reconstituted nucleosomes (62)(63)(64). In vivo, Sir3 was found associated with H3K79 mono and di methylation at active subtelomeric genes (62).…”

Section: End Of Extended Silent Domains: the Specific Role Of Dot1mentioning

confidence: 98%

Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

Hocher

Ruault

Kaferle

et al. 2017

Preprint

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The eukaryotic genome is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly and man. Heterochromatin generally initiates and spreads from defined loci, and diverse mechanisms prevent the ectopic spread of heterochromatin into euchromatin. Here, we overexpressed the silencing factor Sir3 at various levels in yeast, and found that Sir3 spreading into Extended Silent Domains (ESD) eventually reached saturation at subtelomeres. We observed that Sir3 spreading into ESDs covered zone associated with specific histone marks in wild-type cells and stopped at zones of histone mark transitions including H3K79 tri-methylation levels. The conserved enzyme Dot1 deposits H3K79 methylation, and we found that it is essential for viability upon overexpression of Sir3, but not of a spreading-defective mutant Sir3A2Q. These data suggest that H3K79 methylation actively blocks Sir3 spreading. Lastly, our metaanalysis uncovers previously uncharacterized discrete subtelomeric domains associated with specific chromatin features offering a new viewpoint on how to separate subtelomeres from the core chromosome.

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“…24 Additionally, the occusion of DNA linkers in Sir3 chromatin fibers requires its dimerization domain, 21 consistent with Sir3 dimerization bridging adjacent nucleosomes. 44 We propose that the Sir2/Sir4 complex reinforces the silencing properties of SIR heterochromatin by folding the SIR chromatin fiber into an inaccessible, condensed structure. Our analysis of SIR protein stoichiometry suggests a model in which one molecule of Sir2/4 binds primarily within each nucleosome linker and two molecules of Sir3 bind to each surface of the nucleosome, and fiber compaction is completed via cross-nucleosomal Sir3-Sir4 and Sir3-Sir3 interactions (Fig.…”

Section: The Shared Role Of Sir3 and Sir2/4 On Heterochromatin Formatmentioning

confidence: 99%

SIR proteins create compact heterochromatin fibers

Swygert

Senapati

Bolukbasi

et al. 2018

Preprint

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2 SummaryHeterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins --Sir3, believed to be the primary structural component of SIR heterochromatin, and the Sir2/4 complex, responsible for the targeted recruitment of SIR proteins and the deacetylation of lysine 16 of histone H4. Previously, we found that Sir3 binds but does not compact nucleosomal arrays. Here we reconstitute chromatin fibers with the complete complement of SIR proteins and use sedimentation velocity, molecular modeling, and atomic force microscopy to characterize the stoichiometry and conformation of SIR chromatin fibers. In contrast to previous studies, our results demonstrate that SIR arrays are highly compact. Strikingly, the condensed structure of SIR heterochromatin fibers requires both the integrity of H4K16 and an interaction between Sir3 and Sir4. We propose a model in which two molecules of Sir3 bridge and stabilize two adjacent nucleosomes, while a single Sir2/4 heterodimer binds the intervening linker DNA, driving fiber compaction. IntroductionEukaryotic cells regulate the accessibility of their genome to enzymatic processes by organizing it into two functionally distinct compartments, known as euchromatin and heterochromatin. Euchromatin consists of actively transcribed gene regions, whereas heterochromatin is refractory to external processes such as transcription and recombination 1 .Heterochromatin organizes and protects centromeres and telomeres, guards against the spreading of transposons, and prevents aberrant homologous recombination within repetitive regions that can lead to chromosomal abnormalities such as deletions, inversions, and translocations. [2][3][4] Additionally, heterochromatin formation is an essential developmental process All rights reserved. No reuse allowed without permission.

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Heterochromatin assembly by interrupted Sir3 bridges across neighboring nucleosomes

Cited by 37 publications

References 111 publications

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

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

Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

SIR proteins create compact heterochromatin fibers

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