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

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

doi:10.7554/eLife.22510

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

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

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.

Original language	English
Article number	e22510
Journal	eLife
Volume	6
DOIs	https://doi.org/10.7554/eLife.22510
Publication status	Published - 2017

Funding

We thank David Bhella and Saskia Hutten (University of Glasgow), Joanna Brown (University of Edin-burgh), and Linas Urnavicius and Andrew Carter (University of Cambridge) for assistance in screening cryo grids. High resolution data was collected at NeCEN with assistance from Ludo Renault and Christoph Diebolder. We thank Sara Ten Have and Kelly Hodge for assistance with analysis of crosslink MS data. This work was funded by Wellcome Senior Fellowship 095062, Wellcome Trust grants 094090, 099149 and 097945. ALH was funded by and EMBO long-term fellowship ALTF 380–2015 co-funded by the European Commission (LTFCOFUND2013, GA-2013–609409). Finally we would like to thank reviewers for useful suggestions in revising the manuscript. Wellcome 095062 Ramasubramanian Sundaramoorthy Amanda L Hughes Vijender Singh Nicola Wiechens Tom Owen-Hughes Wellcome 097945/B/11/Z Ramasubramanian Sundaramoorthy Amanda L Hughes Vijender Singh Nicola Wiechens Tom Owen-Hughes Wellcome 099149/Z/12/Z Ramasubramanian Sundaramoorthy Hassane El-Mkami David G Norman Tom Owen-Hughes Wellcome 097945 Ramasubramanian Sundaramoorthy Amanda L Hughes Nicola Wiechens Daniel P Ryan David G Norman Tom Owen-Hughes European Molecular Biology Organization ALTF 380-2015 Amanda L Hughes The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Funders	Funder number
European Molecular Biology Organization
Wellcome Trust	099149, 095062, 094090, 097945
Seventh Framework Programme	609409
Biotechnology and Biological Sciences Research Council	BB/E022286/1
University of Cambridge
European Commission	GA-2013–609409, LTFCOFUND2013
University of Glasgow

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Sundaramoorthy, R., Hughes, A. L., Singh, V., Wiechens, N., Ryan, D. P., El-Mkami, H., Petoukhov, M., Svergun, D. I., Treutlein, B., Quack, S., Fischer, M., Michaelis, J., Böttcher, B., Norman, D. G., & Owen-Hughes, T. (2017). Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife, 6, Article e22510. https://doi.org/10.7554/eLife.22510

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title = "Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes",

abstract = "The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.",

author = "Ramasubramanian Sundaramoorthy and Hughes, {Amanda L.} and Vijender Singh and Nicola Wiechens and Ryan, {Daniel P.} and Hassane El-Mkami and Maxim Petoukhov and Svergun, {Dmitri I.} and Barbara Treutlein and Salina Quack and Monika Fischer and Jens Michaelis and Bettina B{\"o}ttcher and Norman, {David G.} and Tom Owen-Hughes",

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AU - Sundaramoorthy, Ramasubramanian

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AU - Singh, Vijender

AU - Wiechens, Nicola

AU - Ryan, Daniel P.

AU - El-Mkami, Hassane

AU - Petoukhov, Maxim

AU - Svergun, Dmitri I.

AU - Treutlein, Barbara

AU - Quack, Salina

AU - Fischer, Monika

AU - Michaelis, Jens

AU - Böttcher, Bettina

AU - Norman, David G.

AU - Owen-Hughes, Tom

PY - 2017

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AB - The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.

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ER -

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

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