Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement

Yang, Xiaofang; Zaurín, Roser; Beato, Miguel; Peterson, Craig L.

doi:10.1038/nsmb1238

Cited by 86 publications

(84 citation statements)

References 54 publications

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“…1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access…”

Section: Remodelers Slide Eject and Restructure Nucleosomesmentioning

confidence: 99%

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Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

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Chromatin remodelers are ATP-hydrolyzing machines specialized to restructure, mobilize or eject nucleosomes, allowing regulated exposure of DNA in chromatin. Recently, remodelers have been analyzed using single-molecule techniques in real time, revealing them to be complex DNA-pumping machines. The results both support and challenge aspects of current models of remodeling, supporting the idea that the remodeler translocates or pumps DNA loops into and around the nucleosome, while also challenging earlier concepts about loop formation, the character of the loop and how it propagates. Several complex behaviors were observed, such as reverse translocation and long translocation bursts of the remodeler, without appreciable DNA twist. This review presents and discusses revised models for nucleosome sliding and ejection that integrate this new information with the earlier biochemical studies.Many processes involving chromosomes are guided by DNA-binding proteins, and the access of these proteins to DNA is regulated by chromatin. Nucleosomes, the primary repeating unit of chromatin, package DNA by wrapping 147 base pairs (bp) around an octamer of histone proteins in ∼1.7 helical turns 1-3 . This packaging provides topological order but occludes one face of the DNA, which slows or prevents the recognition of DNA sequences by DNA-binding proteins. To maintain topological order, and also to allow rapid and regulated access to the DNA, cells have evolved a set of chromatin-remodeling machines that alter nucleosome position, presence and structure.Remodelers can be separated into several families on the basis of their composition and activities: SWI/SNF, ISWI, NURD/Mi-2/CHD and the 'split ATPases' INO80 and SWR1 (which bear an insertion within their ATPase domains). Rad54 may represent an additional family, as it perturbs chromatin in vitro, but it apparently lacks specific nucleosome-interacting domains 4,5 . The participation of remodelers in various chromosomal processes has been the subject of many reviews 6-9 . The present work focuses solely on remodeler mechanisms, and primarily on the function of their conserved catalytic subunit, a superfamily 2 (SF2) ATPdependent DNA translocase. Recently, single-molecule approaches have been used to examine several remodelers, providing many new insights into their behavior. Here I discuss these recent studies, compare them with previous biochemical studies and suggest refinements to existing models to account for some of the observations. Remodelers slide, eject and restructure nucleosomesRemodelers can affect nucleosomes in at least four ways ( Fig. 1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access

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Section: Remodelers Slide Eject and Restructure Nucleosomesmentioning

confidence: 99%

“…Specialization is further supported by the different roles and phenotypic effects of remodeler families in vivo 9 . Dimer ejection has been observed with all SWI/SNF remodelers tested, but with only a subset of ISWI remodelers 17,18 . Perhaps the most specialized function of remodelers involves histone-variant exchange.…”

mentioning

confidence: 94%

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

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“…The Snf2 ATPase is required in the SWI/SNF complex for Mec1 activation SWI/SNF is a large protein complex with 12 subunits, and many of the subunits are required for SWI/SNF chromatin remodeling activities (Cairns et al 1998;Yang et al 2007). To determine whether the mechanism of SWI/SNF-mediated Mec1 activation might be similar to or distinct from the SWI/SNF-mediated chromatin remodeling mechanism, we examined the subunit requirement in SWI/SNF for Mec1 activation during DNA damage response.…”

Section: Swi/snf Synergize With Known Mec1 Activation Pathwaysmentioning

confidence: 99%

Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex

et al. 2015

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ATP-dependent chromatin remodeling complexes alter chromatin structure through interactions with chromatin substrates such as DNA, histones, and nucleosomes. However, whether chromatin remodeling complexes have the ability to regulate nonchromatin substrates remains unclear. Saccharomyces cerevisiae checkpoint kinase Mec1 (ATR in mammals) is an essential master regulator of genomic integrity. Here we found that the SWI/SNF chromatin remodeling complex is capable of regulating Mec1 kinase activity. In vivo, Mec1 activity is reduced by the deletion of Snf2, the core ATPase subunit of the SWI/SNF complex. SWI/SNF interacts with Mec1, and cross-linking studies revealed that the Snf2 ATPase is the main interaction partner for Mec1. In vitro, SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dpb11. The subunit requirement of SWI/SNFmediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. Functionally, SWI/SNFmediated Mec1 regulation specifically occurs in S phase of the cell cycle. Together, these findings identify a novel regulator of Mec1 kinase activity and suggest that ATP-dependent chromatin remodeling complexes can regulate nonchromatin substrates such as a checkpoint kinase.

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“…23). Likewise, in human SWI-SNF, BAF53 and actin are tightly associated with the ATPase subunit BRG1 (ref.…”

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confidence: 99%

The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases

Szerlong

Hinata

Viswanathan

et al. 2008

Nat Struct Mol Biol

190

246

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We identify the helicase-SANT-associated (HSA) domain as the primary binding platform for nuclear actin-related proteins (ARPs) and actin. Individual HSA domains from chromatin remodelers (RSC, yeast SWI-SNF, human SWI-SNF, SWR1 and INO80) or modifiers (NuA4) reconstitute their respective ARP-ARP or ARP-actin modules. In RSC, the HSA domain resides on the catalytic ATPase subunit Sth1. The Sth1 HSA is essential in vivo, and its omission causes the specific loss of ARPs and a moderate reduction in ATPase activity. Genetic selections for arp suppressors yielded specific gain-of-function mutations in two new domains in Sth1, the post-HSA domain and protrusion 1, which are essential for RSC function in vivo but not ARP association. Taken together, we define the role of the HSA domain and provide evidence for a regulatory relationship involving the ARP-HSA module and two new functional domains conserved in remodeler ATPases that contain ARPs.Transcriptional regulation involves the concerted action of chromatin regulators, transcription factors and the basal transcription machinery. The two general types of chromatin regulators are chromatin remodelers, which reposition and restructure nucleosomes 1 , and chromatin modifiers, which add or remove covalent marks from the histone proteins 2 . These chromatin regulatory complexes work together to mark and move nucleosomes, which can either help silence or activate transcription, depending on the context. Remodelers bear a catalytic ATPase subunit required for ATP-dependent nucleosome repositioning 1,3,4 , whereas modifier complexes bear one or more subunits with histone-modification potential 2,5,6 . However, in both cases, most of the subunits of chromatin regulatory complexes are nonenzymatic. These attendant subunits are specialized for diverse tasks: targeting the complex to particular nucleosomes, enabling complex association with particular DNA binding proteins or other complexes, or helping to regulate enzymatic activity.Intriguingly, actin and ARPs are among the associated subunits of certain chromatinremodeling and chromatin-modifying complexes 7-9 . ARPs have been studied extensively in the budding yeast Saccharomyces cerevisiae, which contains ten ARPs 10 . Four ARPs (ARPs

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Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement

Cited by 86 publications

References 54 publications

Chromatin remodeling: insights and intrigue from single-molecule studies

Chromatin remodeling: insights and intrigue from single-molecule studies

Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex

The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases

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