A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin.

Michael S Kobor,Andrew J Link,Marc D Meneghini,Jennifer W Gin,Shivkumar Venkatasubrahmanyam,Hiten D Madhani,Jasper Rine,Jennifer L Jennings,Peter Becker Peter Becker

doi:10.1371/journal.pbio.0020131

Abstract

The conserved histone variant H2A.Z functions in euchromatin to antagonize the spread of heterochromatin. The mechanism by which histone H2A is replaced by H2A.Z in the nucleosome is unknown. We identified a complex containing 13 different polypeptides associated with a soluble pool of H2A.Z in Saccharomyces cerevisiae. This complex was designated SWR1-Com in reference to the Swr1p subunit, a Swi2/Snf2-paralog. Swr1p and six other subunits were found only in SWR1-Com, whereas six other subunits were also found in the NuA4 histone acetyltransferase and/or the Ino80 chromatin remodeling complex. H2A.Z and SWR1 were essential for viability of cells lacking the EAF1 component of NuA4, pointing to a close functional connection between these two complexes. Strikingly, chromatin immunoprecipitation analysis of cells lacking Swr1p, the presumed ATPase of the complex, revealed a profound defect in the deposition of H2A.Z at euchromatic regions that flank the silent mating type cassette HMR and at 12 other chromosomal sites tested. Consistent with a specialized role for Swr1p in H2A.Z deposition, the majority of the genome-wide transcriptional defects seen in swr1Δ cells were also found in htz1Δ cells. These studies revealed a novel role for a member of the ATP-dependent chromatin remodeling enzyme family in determining the region-specific histone subunit composition of chromatin in vivo and controlling the epigenetic state of chromatin. Metazoan orthologs of Swr1p (Drosophila Domino; human SRCAP and p400) may have analogous functions.

Highlights

Histones are the major constituent of chromatin and exert a profound influence on most if not all aspects of chromosome behavior
We have shown previously that an important function of H2A.Z in S. cerevisiae is to prevent the spreading of silent chromatin, termed heterochromatin, into adjacent euchromatic regions (Meneghini et al 2003)
H2A.Z is important for specifying euchromatic regions in the genome of S. cerevisiae (Meneghini et al 2003)

Summary

Introduction

Histones are the major constituent of chromatin and exert a profound influence on most if not all aspects of chromosome behavior. The functional state of chromatin is regulated, in part, by histone modifying enzymes and ATPdependent chromatin remodeling enzymes Members of the latter enzyme class alter the structure of nucleosomes or slide them along DNA in vitro (reviewed in Becker and Horz 2002; Peterson 2002). In yeast cells lacking H2A.Z, the Sir complex spreads beyond its normal boundaries at HMR and into neighboring euchromatin, resulting in the repression of gene expression (Meneghini et al 2003). This repression is reversed by a deletion of SIR2 or a deletion of the nucleation sites for silencing at HMR.

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Results

Conclusion