Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing

Yan Huang; Lu Sun; Leonidas Pierrakeas; Linchang Dai; Lu Pan; Ed Luk; Zheng Zhou

doi:10.1073/pnas.1914313117

New Research In

Edited by Song Tan, The Pennsylvania State University, University Park, PA, and accepted by Editorial Board Member Michael F. Summers December 30, 2019 (received for review August 19, 2019)

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Significance

Eukaryotic cells mobilize histones at specific locations along the chromosome to regulate genomic processes, such as transcription. DEF/Y motifs are short amino acid sequences that are known to bind to histones. We found that a tandem DEF/Y motif in the Swc5 subunit of the SWR complex is required for SWR’s nucleosome editing function, a process that involves the replacement of H2A within nucleosomes with the variant histone H2A.Z. Swc5 DEF/Y preferentially binds to histone H2A over H2A.Z. In yeast, the DEF/Y–histone interaction is partially dependent on SWR’s ATPase activity. We solved an X-ray crystal structure of Swc5 DEF/Y in complex with H2A, providing the structural basis for how Swc5 contributes to the directionality of the H2A-to-H2A.Z nucleosome editing process.

Abstract

The SWR complex edits the histone composition of nucleosomes at promoters to facilitate transcription by replacing the two nucleosomal H2A-H2B (A-B) dimers with H2A.Z-H2B (Z-B) dimers. Swc5, a subunit of SWR, binds to A-B dimers, but its role in the histone replacement reaction was unclear. In this study, we showed that Swc5 uses a tandem DEF/Y motif within an intrinsically disordered region to engage the A-B dimer. A 2.37-Å X-ray crystal structure of the histone binding domain of Swc5 in complex with an A-B dimer showed that consecutive acidic residues and flanking hydrophobic residues of Swc5 form a cap over the histones, excluding histone–DNA interaction. Mutations in Swc5 DEF/Y inhibited the nucleosome editing function of SWR in vitro. Swc5 DEF/Y interacts with histones in vivo, and the extent of this interaction is dependent on the remodeling ATPase of SWR, supporting a model in which Swc5 acts as a wedge to promote A-B dimer eviction. Given that DEF/Y motifs are found in other evolutionary unrelated chromatin regulators, this work provides the molecular basis for a general strategy used repeatedly during eukaryotic evolution to mobilize histones in various genomic functions.

Footnotes

↵¹To whom correspondence may be addressed. Email: ed.luk{at}stonybrook.edu or zhouzh{at}ibp.ac.cn.

Author contributions: Y.H., L.S., E.L., and Z.Z. designed research; Y.H., L.S., L. Pierrakeas, L.D., and L. Pan performed research; Y.H., E.L., and Z.Z. analyzed data; and Y.H., E.L., and Z.Z. wrote the paper.
The authors declare no competing interest.
This article is a PNAS Direct Submission. S.T. is a guest editor invited by the Editorial Board.
Data deposition: The atomic coordinate and structure factor of the Swc5/H2A-H2B complex has been deposited in the Protein Data Bank (accession no. 6KBB).
This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1914313117/-/DCSupplemental.

Published under the PNAS license.

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