Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome

Lorch, Yahli; Maier-Davis, Barbara; Kornberg, Roger D.

doi:10.1016/j.molcel.2018.09.030

Cited by 22 publications

(23 citation statements)

References 45 publications

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“…The strength of the SnAC-histone octamer contact may be influenced by the N-terminal tail of histone H4, which binds at the interface of the SnAC and ATPase motor of Sth1 ( Figure 3a ). Since histone acetylation can impair octamer transfer by RSC to the histone chaperone Nap1 22 , histone acetylation may modulate the sandwiching contacts, maybe influencing nucleosome eviction or sliding.…”

Section: Nucleosome Sandwiching and Slidingmentioning

confidence: 99%

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Wagner

Dienemann

Wang

et al. 2020

Nature

121

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Chromatin remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs) 1 , 2 . The essential Saccharomyces cerevisiae SWI/SNF complex RSC 3 contains 16 subunits, including the ATP-dependent DNA translocase Sth1 4 , 5 . RSC removes nucleosomes from promoter regions 6 , 7 and positions the specialized +1 and –1 nucleosomes that flank NDRs 8 , 9 . Here, we present the cryo-EM structure of RSC in complex with a nucleosome substrate. The structure reveals that RSC forms five protein modules and suggests key features of the remodelling mechanism. The body module serves as a scaffold for the four flexible modules that we call DNA-interacting, ATPase, arm and ARP modules. The DNA-interacting module binds extra-nucleosomal DNA and is involved in the recognition of promoter DNA elements 8 , 10 , 11 that influence RSC functionality 12 . The ATPase and arm modules sandwich the nucleosome disc with their ‘SnAC’ and ‘finger’ elements, respectively. The translocase motor of the ATPase module engages with the edge of the nucleosome at superhelical location +2. The mobile ARP module may modulate translocase-nucleosome interactions to regulate RSC activity 5 . The RSC-nucleosome structure provides a basis for understanding NDR formation and the structure and function of human SWI/SNF complexes that are frequently mutated in cancer 13 .

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Section: Nucleosome Sandwiching and Slidingmentioning

confidence: 99%

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Wagner

Dienemann

Wang

et al. 2020

Nature

121

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“…Relatively little is known about the roles of the ancillary subunits, given that the ATPase subunit contains the remodeling activity. These subunits may have regulatory functions, such as targeting a remodeler to specific DNA sequences (e.g., the Rsc3 and Rsc30 subunits of RSC [ 29 ]), or to nucleosomes carrying specific histone modifications (e.g., RSC has many bromodomains [ 30 , 31 , 32 ]).…”

Section: The Atp-dependent Chromatin Remodelersmentioning

confidence: 99%

Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast

Prajapati

Ocampo

Clark

2020

Biology

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Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent remodeling enzymes that are capable of moving nucleosomes along DNA, or of evicting nucleosomes altogether. In yeast, the nucleosome-spacing enzymes are ISW1 (Imitation SWitch protein 1), Chromodomain-Helicase-DNA-binding (CHD)1, ISW2 (Imitation SWitch protein 2) and INOsitol-requiring 80 (INO80); the nucleosome eviction enzymes are the SWItching/Sucrose Non-Fermenting (SWI/SNF) family, the Remodeling the Structure of Chromatin (RSC) complexes and INO80. We discuss the contributions of each set of enzymes to chromatin organisation. ISW1 and CHD1 are the major spacing enzymes; loss of both enzymes results in major chromatin disruption, partly due to the appearance of close-packed di-nucleosomes. ISW1 and CHD1 compete to set nucleosome spacing on most genes. ISW1 is dominant, setting wild type spacing, whereas CHD1 sets short spacing and may dominate on highly-transcribed genes. We propose that the competing remodelers regulate spacing, which in turn controls the binding of linker histone (H1) and therefore the degree of chromatin folding. Thus, genes with long spacing bind more H1, resulting in increased chromatin compaction. RSC, SWI/SNF and INO80 are involved in NDR formation, either directly by nucleosome eviction or repositioning, or indirectly by affecting the size of the complex that resides in the NDR. The nature of this complex is controversial: some suggest that it is a RSC-bound “fragile nucleosome”, whereas we propose that it is a non-histone transcription complex. In either case, this complex appears to serve as a barrier to nucleosome formation, resulting in the formation of phased nucleosomal arrays on both sides.

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“…The strength of the SnAC-histone octamer contact may be influenced by the N-terminal tail of histone H4, which binds at the interface of the SnAC and ATPase motor of Sth1 (Figure 4a). Since histone acetylation can impair octamer transfer by RSC to the histone chaperone Nap1 34 , this leads to the intriguing model that histone acetylation may strengthen the sandwiching contacts, thereby impairing octamer eviction and favouring nucleosome sliding.…”

Section: Nucleosome Sandwiching and Slidingmentioning

confidence: 99%

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Wagner

Dienemann

Wang

et al. 2019

Preprint

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13 Chromatin remodelling complexes of the SWI/SNF family function in the formation of 14 nucleosome-depleted regions and transcriptionally active promoters in the eukaryote 15 genome. The structure of the Saccharomyces cerevisiae SWI/SNF family member RSC in 16 complex with a nucleosome substrate reveals five protein modules and suggests key 17 features of the remodelling mechanism. A DNA-interacting module grasps extra-18 nucleosomal DNA and helps to recruit RSC to promoters. The ATPase and arm modules 19 sandwich the nucleosome disc with their 'SnAC' and 'finger' elements, respectively. The 20 translocase motor engages with the edge of the nucleosome at superhelical location +2 to 21 pump DNA along the nucleosome, resulting in a sliding of the histone octamer along DNA. 22

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Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome

Cited by 22 publications

References 45 publications

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

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