Structure and mechanism of the chromatin remodelling factor ISW1a

Yamada, Keiko; Frouws, T.D.; Angst, Brigitte; Fitzgerald, Daniel J.; Deluca, C.I.; Schimmele, Kyoko; Sargent, David F.; Richmond, Timothy J.

doi:10.1038/nature09947

Cited by 168 publications

(184 citation statements)

References 53 publications

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“…These data were more consistent with a "protein ruler mechanism" derived from structural data for the Saccharomyces cerevisiae ISW1a remodeler in complex with nucleosomes (36), where linker length is suggested to result from simultaneous interactions of the remodeling complex with two neighboring nucleosomes. In particular, the HAND-SANT-SLIDE (HSS) domain of ISWI-type remodelers was suggested to be important for nucleosome spacing, e.g., as a "protein ruler" (36).…”

supporting

confidence: 78%

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Lieleg¹,

Ketterer

Nuebler

et al. 2015

Molecular and Cellular Biology

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Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI-and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the HAND-SANT-SLIDE (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.

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supporting

confidence: 78%

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Lieleg¹,

Ketterer

Nuebler

et al. 2015

Molecular and Cellular Biology

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“…This finding is clearly at odds with pure statistical positioning, which predicts an increased spacing for reduced nucleosome counts. Instead, Zhang et al (13) suggest an active packing mechanism mediated by remodeling enzymes, e.g., a dinucleosome packing mechanism of the type suggested for the imitation switch family remodeler ISW1a (30). We now explore the possibility that such a packing mechanism acts in addition to the mechanisms of the SNG model.…”

Section: Resultsmentioning

confidence: 87%

Toward a unified physical model of nucleosome patterns flanking transcription start sites

Möbius

Osberg

Tsankov

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Recent genome-wide maps of nucleosome positions in different eukaryotes revealed patterns around transcription start sites featuring a nucleosome-free region flanked by a periodic modulation of the nucleosome density. For Saccharomyces cerevisiae, the average in vivo pattern was previously shown to be quantitatively described by a "nucleosome gas" model based on the statistical positioning mechanism. However, this simple physical description is challenged by the fact that the pattern differs quantitatively between species and by recent experiments that appear incompatible with statistical positioning, indicating important roles for chromatin remodelers. We undertake a data-driven search for a unified physical model to describe the nucleosome patterns of 12 yeast species and also consider an extension of the model to capture remodeling effects. We are led to a nucleosome gas that takes into account nucleosome breathing, i.e., transient unwrapping of nucleosomal DNA segments. This known biophysical property of nucleosomes rationalizes a "pressure"-induced dependence of the effective nucleosome size that is suggested by the data. By fitting this model to the data, we find an average energy cost for DNA unwrapping consistent with previous biophysical experiments. Although the available data are not sufficient to reconstruct chromatin remodeling mechanisms, a minimal model extension by one mechanism yields an "active nucleosome gas" that can rationalize the behavior of systems with reduced histone-DNA ratio and remodeler knockouts. We therefore establish a basis for a physical description of nucleosome patterns that can serve as a null model for sequence-specific effects at individual genes and in models of transcription regulation.nucleosome maps | chromatin structure | quantitative biology

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“…Lowresolution (23-50 Å ) models of several yeast remodeling complexes derived from single-particle electron microscopy data have been reported (e.g. 1,2 ) and partial X-ray crystal structures have been reported for several components or domains or other complexes [3][4][5] but far less is known about CHD-family remodeling complexes, the best-described of which is the nucleosome remodeling and deacetylase (NuRD) complex.…”

Section: Introductionmentioning

confidence: 99%

The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7

et al. 2016

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The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed across multiple tissues in organisms ranging from mammals to nematode worms. In common with other chromatin-remodeling complexes, however, its molecular mechanism of action is not well understood and only limited structural information is available to show how the complex is assembled. As a step towards understanding the structure of the NuRD complex, we have characterized the interaction between two subunits: the metastasis associated protein MTA1 and the histone-binding protein RBBP4. We show that MTA1 can bind to two molecules of RBBP4 and present negative stain electron microscopy and chemical crosslinking data that allow us to build a low-resolution model of an MTA1-(RBBP4) 2 subcomplex. These data build on our understanding of NuRD complex structure and move us closer towards an understanding of the biochemical basis for the activity of this complex.

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Structure and mechanism of the chromatin remodelling factor ISW1a

Cited by 168 publications

References 53 publications

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Toward a unified physical model of nucleosome patterns flanking transcription start sites

The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7

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