Research Article

Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

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Science  20 Jan 2017:
Vol. 355, Issue 6322, eaaa3761
DOI: 10.1126/science.aaa3761

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Deformation powers the nucleosome slide

In eukaryotes, DNA is packed onto nucleosomes. For transcription factors and other proteins to gain access to DNA, nucleosomes must be moved out of the way, or “remodeled”—but not disassembled. Nucleosomes are composed of histone protein octamers, the cores of which have generally been considered to be fairly rigid. Sinha et al. used nuclear magnetic resonance and protein cross-linking to show that one of the enzyme complexes that remodel nucleosomes, SNF2h, is able to distort the histone octamer (see the Perspective by Flaus and Owen-Hughes). Nucleosome deformation was important for this remodeler to be able to slide nucleosomes out of the way.

Science, this issue p. 10.1126/science.aaa3761 ; see also p. 245

Structured Abstract

INTRODUCTION

The establishment of specific gene expression states during the course of development, as well as their maintenance through the disruptive events of transcription, DNA replication, and DNA repair, requires rapid rearrangements of chromatin structure. Adenosine 5′-triphosphate (ATP)–dependent chromatin remodeling motors are the workhorses that enable dynamic changes in chromatin structure. These motors have the formidable task of mobilizing DNA in the context of a nucleosome, which contains ~150 base pairs of DNA tightly wrapped around an octamer of histone proteins. Yet, compared to other essential motors such as myosins and helicases, little is known about the biochemical mechanisms of chromatin remodeling motors, limiting an understanding of how their functions are regulated.

RATIONALE

Two classes of chromatin remodeling motors, the ISWI class and the SWI-SNF class, have proved to be powerful model systems for asking mechanistic questions. Notably, both the ISWI and SWI-SNF family motors can move DNA without disassembling the histone octamer. Further, recent studies indicate that ISWI family motors translocate DNA out of the nucleosome before feeding DNA into the nucleosome, a result that is difficult to reconcile with rigid Lego-block–like models of the histone octamer. One way the seemingly complex task of chromatin remodeling may be facilitated is by distorting the histone octamer. Here, we probe this possibility by carrying out methyl transverse relaxation–optimized nuclear magnetic resonance (methyl-TROSY NMR) experiments on the ~450-kilodalton complex of a nucleosome with an activated form of the major ISWI family remodeling motor from humans, SNF2h. Methyl-TROSY is a powerful tool capable of providing site-specific information on the dynamics of individual amino acid residues. We have further tested the functional relevance of information obtained from these NMR experiments in the context of chromatin remodeling reactions by introducing site-specific cysteine cross-links at the histone H3-H4 interface. These cross-links have provided a means to restrain backbone movements and thus, have allowed us to test the importance of octamer deformability during ATP-dependent remodeling reactions.

RESULTS

We show that the dynamics of buried isoleucine, leucine, and valine residues in histone H4 change when the nucleosome is bound to SNF2h in the presence of the nonhydrolyzable ATP analog ADP-BeFx. NMR studies following the isoleucine residues of histone H2A further indicate that the changes induced upon SNF2h binding extend across the nucleosome. These results indicate that the histone octamer is deformed in the presence of SNF2h. Using site-specific disulfide bridges at the H3-H4 interface, we show that interfering with octamer deformation can inhibit nucleosome sliding by SNF2h or alter the directionality of nucleosome sliding. We further show that different classes of remodeling enzymes respond differently to these disulfide restraints. Disulfide bridges that inhibit SNF2h-mediated sliding allow sliding by the INO80 complex and increase octamer eviction by the SWI-SNF family complex, RSC.

CONCLUSION

The histone core of a nucleosome is more plastic than previously imagined, and octamer deformation can play different roles based on the type of chromatin remodeling complex.

Model for role of octamer distortion in nucleosome sliding by SNF2h.

Octamer deformation near SHL2 (inhibited by sCx2 cross-link) promotes initiation of DNA translocation, while deformation near the dyad (inhibited by sCx1 cross-link) helps accommodate strain caused by DNA translocation. These conformational changes allow for a net translocation of DNA from the exit site before any DNA is drawn in from the entry site.

Abstract

Adenosine 5′-triphosphate (ATP)–dependent chromatin remodeling enzymes play essential biological roles by mobilizing nucleosomal DNA. Yet, how DNA is mobilized despite the steric constraints placed by the histone octamer remains unknown. Using methyl transverse relaxation–optimized nuclear magnetic resonance spectroscopy on a 450-kilodalton complex, we show that the chromatin remodeler, SNF2h, distorts the histone octamer. Binding of SNF2h in an activated ATP state changes the dynamics of buried histone residues. Preventing octamer distortion by site-specific disulfide linkages inhibits nucleosome sliding by SNF2h while promoting octamer eviction by the SWI-SNF complex, RSC. Our findings indicate that the histone core of a nucleosome is more plastic than previously imagined and that octamer deformation plays different roles based on the type of chromatin remodeler. Octamer plasticity may contribute to chromatin regulation beyond ATP-dependent remodeling.

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