Structure and dynamics of the yeast SWR1-nucleosome complex

Willhöft, Oliver; Ghoneim, Mohamed; Lin, Chia‐Liang; Chua, Eugene Y.D.; Wilkinson, M. K.; Chaban, Yuriy; Ayala, Rafael; McCormack, Elizabeth A.; Ocloo, Lorraine; Rueda, David; Wigley, Dale B.

doi:10.1126/science.aat7716

Cited by 140 publications

(211 citation statements)

References 48 publications

(72 reference statements)

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“…These locally filtered volumes were then modulated with a tau-factor falloff taken from the experimental SWR1-nucleosome dataset (Willhoft et al, 2018). The RELION utility relion_project was used to generate projections from the synthetic volumes, where the orientational distribution, CTF and noise parameters were taken from the experimental SWR1-nucleosome dataset (Willhoft et al, 2018) following a methodology similar to that previously reported for analysis of γ-secretase (Bai et al, 2015). The final projection images therefore represent a noisy, CTF-convoluted experimental dataset with a non-uniform distribution of projections exactly equivalent to the donor dataset.…”

Section: Generation Of Synthetic Data For Testingmentioning

confidence: 99%

Mitigating Local Over-fitting During Single Particle Reconstruction with SIDESPLITTER

Ramlaul¹,

Palmer

Aylett

2019

Preprint

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Abbreviations2D/3D -2/3-Dimensional; Cryo-EM -Electron Cryo-Microscopy; EM -Electron microscopy; FSC -Fourier shell correlation; LAFTER -Local Agreement Filter for Transmission EM Reconstructions; SNR -Signal to noise ratio. AbstractSingle particle analysis of cryo-EM images enables macromolecular structure determination at resolutions approaching the atomic scale. Experimental images are extremely noisy, however, and during iterative refinement it is possible to stably incorporate noise into the reconstructed density. Such "over-fitting" can lead to misinterpretation of the structure, and thereby flawed biological results. Several strategies are routinely used to prevent the spurious incorporation of noise within reconstructed volumes, the most common being independent refinement of two sides of a split dataset.In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise in reconstructed volumes refined using the half-set strategy. We propose a modified filtering process during refinement through the application of a local signal-to-noise filter, SIDESPLITTER, which we show to be capable of reducing over-fitting in both idealised and experimental settings, while maintaining independence between the two sides of a split refinement. SIDESPLITTER can also improve the final resolution in refinements of structures prone to severe over-fitting, such as membrane proteins in detergent micelles.

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Section: Generation Of Synthetic Data For Testingmentioning

confidence: 99%

Mitigating Local Over-fitting During Single Particle Reconstruction with SIDESPLITTER

Ramlaul¹,

Palmer

Aylett

2019

Preprint

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“…1). Binding at this location has also been observed for the chromatin remodellers Chd1 (Farnung et al, 2017;Sundaramoorthy et al, 2018), Snf2 (Liu et al, 2017), and Swr1 (Willhoft et al, 2018). The ATPase motor is in a closed, post-translocated state with AMP-PNP bound in the active site.…”

Section: Resultsmentioning

confidence: 72%

Nucleosome-CHD4 chromatin remodeller structure explains human disease mutations

Farnung

Ochmann

Cramer

2019

Preprint

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The chromatin remodelling enzyme CHD4 is a component of the NuRD and ChAHP complexes that are involved in gene repression. Here we report the cryo-electron microscopy (cryo-EM) structure of Homo sapiens CHD4 engaged with a nucleosome core particle in the presence of the non-hydrolysable ATP analogue AMP-PNP at an overall resolution of 3.1 Å. The ATPase motor of CHD4 binds and distorts nucleosomal DNA at superhelical location (SHL) +2, supporting the 'twist defect' model of chromatin remodelling. CHD4 does not induce unwrapping of terminal DNA, in contrast to its homologue Chd1, which functions in gene activation. Our results also rationalize the effect of CHD4 mutations that are associated with cancer or the intellectual disability disorder Sifrim-Hitz-Weiss syndrome.

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“…In yeast SWR1.C and human SRCAP.C, the ARP6 orthologs are indispensable for nucleo-some remodeling since they couple the ATPase motor to productive nucleosome sliding (Matsuda et al, 2010;Willhoft et al, 2018;Willhoft and Wigley, 2019;Wu et al, 2005). The Drosophila DOM-B.C is likely to employ a similar remodeling mechanism.…”

Section: Discussionmentioning

confidence: 99%

“…Since SWR1-type remodelers bind and hydrolyze ATP to incorporate H2A.Z variants (Hong et al, 2014;Willhoft et al, 2018), we wanted to confirm the ATP-requirement for in vivo incorporation of H2A.V by DOM-B. We devised an RNAi-based complementation strategy in which we rescued the effects of depleting endogenous dom-B mRNA by expression of RNAiresistant dom-B transgenes.…”

Section: Specific Effects Of Dom Isoforms On Transcriptionmentioning

confidence: 99%

“…H2A.Z is primarily found at active promoters and enhancers, where it is thought to be important to regulate transcription initiation and early elongation (Adam et al, 2001;Weber et al, 2010;Weber et al, 2014). In Saccharomyces cerevisiae, H2A.Z is introduced into chromatin by the SWR1 complex (SWR1.C), a multi-subunit ATP-dependent chromatin remodeler with the INO80-type ATPase Swr1 at its core (Mizuguchi et al, 2004;Ranjan et al, 2013;Wang et al, 2018a;Willhoft et al, 2018;Wu et al, 2005). In humans, the two Swr1 orthologs EP400 and SRCAP may also be involved in H2A.Z incorporation (Greenberg et al, 2019;Pradhan et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms

Scacchetti

Schauer²,

Reim

et al. 2020

Preprint

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SUMMARYHistone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene.

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Structure and dynamics of the yeast SWR1-nucleosome complex

Cited by 140 publications

References 48 publications

Mitigating Local Over-fitting During Single Particle Reconstruction with SIDESPLITTER

Mitigating Local Over-fitting During Single Particle Reconstruction with SIDESPLITTER

Nucleosome-CHD4 chromatin remodeller structure explains human disease mutations

Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms

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