Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

Sinha, Kalyan K.; Gross, John D.; Narlikar, Geeta J.

doi:10.1126/science.aaa3761

Cited by 106 publications

(107 citation statements)

References 71 publications

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“…As sfh1-13 alone did not induce Tf2 RNA, we speculate that Sfh1/RSC partly contribute to HIRA-dependent repression and in the absence of Sfh1/ RSC, Abp1 and partly active HIRA pathway cooperatively repress Tf2 transcription. RSC has been shown to function in eviction of nucleosome in vitro (Clapier et al, 2016;Sinha et al, 2017) and linked with active transcription because of its active role for formation of NDR at TSS (Badis et al, 2008;Hartley & Madhani, 2009;Parnell et al, 2008;Wippo et al, 2011;Yague-Sanz et al, 2017). In contrast, budding yeast RSC localizes at the histone HTA1/HTB promoter via corepressor complex containing HIRA and plays a role in redundant repression mechanisms (Ng, Robert, Young, & Struhl, 2002).…”

Section: Sfh1 Contributes To Repression Of Retrotransposons In Paramentioning

confidence: 99%

“…In addition, RSC contributes to generates nucleosome-depleted region (NDR), especially around transcription start sites in both yeasts (Badis et al, 2008;Hartley & Madhani, 2009;Parnell et al, 2008;Wippo et al, 2011;Yague-Sanz et al, 2017). Therefore, budding yeast RSC is shown to have nucleosome sliding and eviction activity in vitro (Clapier et al, 2016;Sinha et al, 2017). At fission yeast centromeric heterochromatin, histone deacetylase complex (HDAC) Clr3/SHREC eliminates NDR formation at particular site by antagonizing RSC.…”

Section: Introductionmentioning

confidence: 99%

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Sfh1, an essential component of the RSC chromatin remodeling complex, maintains genome integrity in fission yeast

et al. 2018

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Abp1 is a fission yeast CENP-B homologue that contributes to centromere function, silencing at pericentromeric heterochromatin and silencing of retrotransposons. We identified the sfh1 gene, encoding a core subunit of the fission yeast chromatin remodeling complex RSC as an Abp1-interacting protein. Because sfh1 is essential for growth, we isolated temperature-sensitive sfh1 mutants. These mutants showed defects in centromere functions, reflected by sensitivity to an inhibitor of spindle formation and minichromosome instability. Sfh1 localized at both kinetochore and pericentromeric heterochromatin regions. Although sfh1 mutations had minor effect on silencing at these regions, they decreased the levels of cohesin on centromeric heterochromatin. Sfh1 also localized at a retrotransposon, Tf2, in a partly Abp1-dependent manner, and assisted in silencing of Tf2 by Abp1 probably in the same pathway as a histone chaperon, HIRA, which is also known to involve in Tf2 repression. Furthermore, sfh1 mutants were sensitive to several DNA-damaging treatments (HU, MMS, UV and X-ray). Increase in spontaneous foci of Rad22, a recombination Mediator protein Rad52 homologue, in sfh1 mutant suggests that RSC functions in homologous recombination repair of double-stranded break downstream of the Rad22 recruitment. These results indicate that RSC plays multiple roles in the maintenance of genome integrity.

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Section: Sfh1 Contributes To Repression Of Retrotransposons In Paramentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sfh1, an essential component of the RSC chromatin remodeling complex, maintains genome integrity in fission yeast

et al. 2018

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“…Indeed, the intrinsic plasticity of the nucleosome is emerging as an important regulatory mechanism for chromatin transactions (90). For example, chromatin remodeling enzymes can transiently re-shape the nucleosome core via distortion during the remodeling reaction (91). It is thus possible that binding of FACT and Rtf1 at the acidic patch is regulated by changes to nucleosome structure that accompany transcription partly through the actions of chromatin remodeling factors and Pol II elongation complexes (92).…”

Section: Discussionmentioning

confidence: 99%

The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo

Cucinotta

Hildreth²,

McShane³

et al. 2019

Preprint

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The nucleosome core regulates DNA-templated processes through the highly conserved nucleosome acidic patch. While structural and biochemical studies have shown that the acidic patch controls chromatin factor binding and activity, few studies have elucidated its functions in vivo. We employed site-specific crosslinking to identify proteins that directly bind the acidic patch in Saccharomyces cerevisiae and demonstrated crosslinking of histone H2A to Paf1 complex subunit Rtf1 and FACT subunit Spt16. Rtf1 bound to nucleosomes through its histone modification domain, supporting its role as a cofactor in H2B K123 ubiquitylation. An acidic patch mutant showed defects in nucleosome positioning and occupancy genome-wide. Our results provide new information on the chromatin engagement of two central players in transcription elongation and emphasize the importance of the nucleosome core as a hub for proteins that regulate chromatin during transcription.Cucinotta et al.

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“…2 engineered in otherwise cysteine-free histones 1 . These crosslinks inhibited nucleosome sliding by SNF2h, suggesting that inhibition of sliding was due to restraining histone octamer dynamics.…”

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confidence: 99%

Histone dynamics within the nucleosome play a critical role in SNF2h-mediated nucleosome sliding

Gamarra

2020

Preprint

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Elucidating the mechanisms by which ATP-dependent chromatin remodeling enzymes disrupt nucleosome structure is essential to understanding how chromatin states are established and maintained. A key finding informing remodeler mechanism is the observation that the dynamics of protein residues buried within the histone core of the nucleosome are required by specific remodelers to mobilize the nucleosome 1 . Recently, a study obtaining cryo-electron microscopy (cryo-EM) structures of remodeler-nucleosome complexes failed to observe stable conformational rearrangements in the histone octamer 2 .The authors of this study also failed to replicate the finding that site-specifically restraining histone dynamics inhibits nucleosome sliding by ISWI-family remodelers 2 . In contrast, a recent cryo-EM structure detected asymmetric histone dynamics in an ISWI-nucleosome complex 3 . Here, using two different protocols, we replicate the original finding in Sinha et al. 1 that dynamics within the histone core are required for nucleosome sliding by the human ISWI remodeler, SNF2h. These results firmly establish histone dynamics as an essential feature of ISWI-mediated nucleosome sliding and highlight the care required in designing and performing biochemical experiments investigating nucleosome dynamics. Results and DiscussionIn previous work, dynamics in the histone core were demonstrated to be functionally important for nucleosome sliding by SNF2h using site-specific disulfide crosslinks

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Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

Cited by 106 publications

References 71 publications

Sfh1, an essential component of the RSC chromatin remodeling complex, maintains genome integrity in fission yeast

Sfh1, an essential component of the RSC chromatin remodeling complex, maintains genome integrity in fission yeast

The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo

Histone dynamics within the nucleosome play a critical role in SNF2h-mediated nucleosome sliding

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