Research Article

Structure and dynamics of the yeast SWR1-nucleosome complex

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Science  12 Oct 2018:
Vol. 362, Issue 6411, eaat7716
DOI: 10.1126/science.aat7716

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From DNA unwrapping to histone exchange

The yeast SWR1 complex, a member of the INO80 family of nucleosome remodelers, exchanges the H2A-H2B histone dimer for the Htz1 variant–containing dimer. Unlike all other remodelers, SWR1 does not translocate the nucleosome. Willhoft et al. applied structural and single-molecule analyses to show that the interaction between SWR1 and the nucleosome destabilizes the DNA wrapped around the histone core. This SWR1-catalyzed partial unwrapping of the DNA was regulated by adenosine triphosphate (ATP) binding but did not require ATP hydrolysis.

Science, this issue p. eaat7716

Structured Abstract

INTRODUCTION

Canonical nucleosomes contain two copies of each of four histone proteins: H2A, H2B, H3, and H4. However, variants of these histones can be inserted by adenosine triphosphate (ATP)–dependent chromatin-remodeling machines. The yeast SWR1 chromatin-remodeling complex, a member of the INO80 remodeler family, catalyzes the exchange of H2A-H2B dimers for dimers containing Htz1 (H2A.Z in human) in an ATP-dependent manner. However, the mechanism by which SWR1 exchanges histones is poorly understood. Despite having a DNA translocase subunit similar to that in the INO80 complex that slides nucleosomes, no net translocation of nucleosomes has been reported for SWR1. Consequently, the function of the ATPase activity, which is required for histone exchange in SWR1, has remained enigmatic.

RATIONALE

To obtain sufficient quantities for structural analysis, we generated the complete 14-subunit yeast SWR1 complex in insect cells. Binding of nucleosomes to SWR1 is stabilized in the presence of an ATP analog (ADP•BeF3), which we used to prepare a complex with a canonical yeast H2A-containing nucleosome. Structural analysis was undertaken by cryo–electron microscopy (cryo-EM). We also used single-molecule FRET (smFRET) techniques to probe the dynamics of nucleosomes bound to SWR1. Fluorescent probes were positioned on the H2A histones and the end of the DNA to monitor changes in nucleosome dynamics upon binding of SWR1 and ATP (or ATP analogs).

RESULTS

We determined the cryo-EM structure of the SWR1-nucleosome complex at 3.6-Å resolution. The architecture of the complex shows how the SWR1 complex is assembled around a heterohexameric core of the RuvBL1 and RuvBL2 subunits. The Swr1 motor subunit binds at superhelical location 2 (SHL2), a position it shares in common with other remodelers but not with its most closely related complex, INO80, which binds at SHL6-SHL7. Binding of ATP or ADP•BeF3 to the SWR1-nucleosome complex induces substantial unwrapping of the DNA wrap. Conformational changes in the motor domains of the Swr1 subunit drive a single–base pair translocation of the DNA wrap from the DNA entry site. The single–base pair DNA translocation accompanies conformational changes in the histone core that begin to destabilize the histone dimer interface. Using smFRET methods, we further probed these conformational changes to show how an increase in the dynamics of the SWR1-bound nucleosomes is dependent on binding of ATP but not hydrolysis.

CONCLUSION

The cryo-EM structure of the SWR1 complex bound to a nucleosome reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at SHL2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core that likely destabilize the dimer interface. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to the SWR1 complex. Single-molecule data monitor this unwrapping and show how the dynamics are altered by ATP binding prior to hydrolysis.

Structure of the SWR1-nucleosome complex.

(A) 3.6-Å SWR1-nucleosome map. (B) Binding of SWR1-ADP•BeF3 to the nucleosome induces multiple changes: (i) The DNA wrap is peeled away by ~2.5 turns, (ii) DNA is translocated by one base pair, and (iii) SHL2 is distorted as a consequence of motor domain closure. These distortions are a precursor to histone exchange and can be monitored by smFRET.

Abstract

The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo–electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at superhelical location 2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to SWR1 complex. The unwrapping, as monitored by single-molecule data, is stabilized and has its dynamics altered by adenosine triphosphate binding but does not require hydrolysis.

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