Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

Sundaramoorthy, Ramasubramanian; Hughes, Amanda L.; Singh, Vijender; Wiechens, Nicola; Ryan, Daniel P.; Mkami, Hassane El; Petoukhov, Maxim V.; Svergun, Dmitri I.; Treutlein, Barbara; Quack, Salina; Fischer, Monika; Michaelis, Jens; Böttcher, Bettina; Norman, D.; Owen-Hughes, Tom

doi:10.7554/elife.22510

Cited by 56 publications

(59 citation statements)

References 82 publications

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“…Similar to observations for the Swi2/Snf2 ATPase domain and Chd1, our structure implies a large conformational rearrangement in the RecA lobes of SNF2h upon nucleosome binding (Farnung et al, 2017; Hauk et al, 2010; Liu et al, 2017; Sundaramoorthy et al, 2018; 2017; Xia et al, 2016; Yan et al, 2016) (Figure 3B, Figure 3-supplement 2). A large conformational change is also implied for the brace helix extending from lobe 2 (Figure 3-supplement 3A, orange helices) (Liu et al, 2017; Yan et al, 2016).…”

Section: The Role Of Snf2h-nucleosome Interactions In Nucleosome Slidingsupporting

confidence: 83%

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

Armache¹,

Gamarra²,

Sl³

et al. 2019

Preprint

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18The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two 19 protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer 20 deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here 21 we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture 22 two reaction intermediates. In one structure, histone residues near the dyad and in the H2A- 23H2B acidic patch, distal to the active SNF2h protomer, are disordered. The disordered acidic 24 patch is expected to inhibit the second SNF2h promoter, while disorder near the dyad is 25 expected to promote DNA translocation. The other structure doesn't show octamer deformation, 26but surprisingly shows a 2bp translocation. FRET studies indicate that ADP-BeFx predisposes 27 SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for 28 allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric 29 octamer deformation to inhibit the second protomer, while stimulating directional DNA 30 translocation. 31 32 One sentence summary: Cryo-EM structures capture different conformational states of 33 chromatin remodeler-nucleosome complexes. 34 35 65 complex: a state with an unexpectedly translocated nucleosome (Figure 1, Figure 1-supplement 66 1-6), a state with two SNF2h protomers bound to a nucleosome (Figure 2A, Figure 2-67 supplement 1) and a state with one protomer bound to a nucleosome that shows increased 68 disorder within the histone core (Figure 2B). The locations of histone disorder strongly suggest a 69 4 role for octamer deformation in protomer coordination and directional DNA translocation. In 70 addition, we detect new ISWI-histone contacts that make significant contributions to 71 nucleosome sliding and help explain why ISWI may differ in mechanism from Swi2/Snf2 (Figure 72 3) (Liu et al., 2017).73 74 Overview of SNF2h-nucleosome structures 75 Like most ISWI remodelers, SNF2h slides mono-nucleosomes assembled on short stretches of 76 DNA towards the center of the DNA (Clapier and Cairns, 2009; Narlikar et al., 2013; Zhou et al., 77 2016). In previous studies we have found that while a monomer of SNF2h can slide 78 nucleosomes, SNF2h functions most optimally as a dimer (Leonard and Narlikar, 2015; Racki et 79 al., 2009). In these studies, we were able to visualize both singly bound and doubly bound 80 SNF2h using negative stain EM (Racki et al., 2009). Previous studies have further shown that 81 binding of the ATP analog, ADP-BeF x , promotes a restricted conformation of the ATPase active 82 site in a manner that is dependent on the H4 tail (Racki et al., 2014). The restricted 83 conformation is consistent with observations showing an activating role for the H4 tail (Clapier et 84 al., 2001; 2002; Hamiche et al., 2001). Further, binding of ADP-BeF x to SNF2h promotes 85 conformational flexibility of buried histone residues (Sinha et al., 2017). This conformational 86 flexibility is functionally important ...

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Section: The Role Of Snf2h-nucleosome Interactions In Nucleosome Slidingsupporting

confidence: 83%

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

Armache¹,

Gamarra²,

Sl³

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…The ATPase motor is in a closed, post-translocated state with AMP-PNP bound in the active site. A similar state was observed for Chd1 when bound to ADP·BeF 3 (Farnung et al, 2017;Sundaramoorthy et al, 2018Sundaramoorthy et al, , 2017. The double chromodomain is located at SHL +1 and contacts the nucleosomal DNA phosphate backbone via electrostatic interactions, in a fashion similar to that observed for S. cerevisiae Chd1 ( Fig.…”

Section: Resultssupporting

confidence: 76%

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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“…The tetramer structure of histone chaperones in solution was modelled from an XRD-based dimer structure and DEER restraints, whereas SAXS curve fitting was used for testing for the correct global shape [64]. A similar approach was applied to a chromatin-remodelling enzyme [65]. Integration of SAXS and DEER data in modelling a minimal ensemble of conformations, combined with tests against single-molecule fluorescence resonance energy transfer data, was performed by unbiased replica exchange Monte Carlo simulations [66].…”

Section: Integrative Modellingmentioning

confidence: 99%

The contribution of modern EPR to structural biology

Jeschke

2018

Emerging Topics in Life Sciences

111

133

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Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron-electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

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Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

Cited by 56 publications

References 82 publications

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

Nucleosome-CHD4 chromatin remodeller structure explains human disease mutations

The contribution of modern EPR to structural biology

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