What makes a histone variant a variant: Changing H2A to become H2A.Z.

Hilary T Brewis,Alice Y Wang,Peter C Stirling,Aline Gaub,Justine J Lau,Michael S Kobor,Robert Schneider

doi:10.1371/journal.pgen.1009950

Abstract

Chromatin structure and underlying DNA accessibility is modulated by the incorporation of histone variants. H2A.Z, a variant of the H2A core histone family, plays a distinct and essential role in a diverse set of biological functions including gene regulation and maintenance of heterochromatin-euchromatin boundaries. Although it is currently unclear how the replacement of H2A with H2A.Z can regulate gene expression, the variance in their amino acid sequence likely contributes to their functional differences. To tease apart regions of H2A.Z that confer its unique identity, a set of plasmids expressing H2A-H2A.Z hybrids from the native H2A.Z promoter were examined for their ability to recapitulate H2A.Z function. First, we found that the H2A.Z M6 region was necessary and sufficient for interaction with the SWR1-C chromatin remodeler. Remarkably, the combination of only 9 amino acid changes, the H2A.Z M6 region, K79 and L81 (two amino acids in the α2-helix), were sufficient to fully rescue growth phenotypes of the htz1Δ mutant. Furthermore, combining three unique H2A.Z regions (K79 and L81, M6, C-terminal tail) was sufficient for expression of H2A.Z-dependent heterochromatin-proximal genes and GAL1 derepression. Surprisingly, hybrid constructs that restored the transcription of H2A.Z-dependent genes, did not fully recapitulate patterns of H2A.Z-specific enrichment at the tested loci. This suggested that H2A.Z function in transcription regulation may be at least partially independent of its specific localization in chromatin. Together, this work has identified three regions that can confer specific H2A.Z-identity to replicative H2A, furthering our understanding of what makes a histone variant a variant.

Highlights

In eukaryotic cells, chromatin structure is a major modulator of genomic processes that require DNA accessibility
One modulator of chromatin structure is the incorporation of histone variants [2].Unlike the core histones, which are produced in equal amounts during S-phase by multiple genes, histone variants are encoded by one or two replication-independent genes, allowing variantspecific transcription and deposition throughout the cell cycle [3]
In order to determine which protein regions are involved in conferring H2A.Z-specific functions, we grouped all of the amino acids that differ between H2A.Z and H2A into nine regions (Fig 1)

Summary

Introduction

Chromatin structure is a major modulator of genomic processes that require DNA accessibility. Histone variants are distinct in their protein sequence and structure, which can lead to different post-translational modifications, recruitment of proteins to chromatin that interact with the variant, and changes to the stability and mobility of the nucleosome into which they are incorporated [4]. Through these properties, histone variants are capable of establishing unique chromatin neighbourhoods with distinct character and function in a regulated manner. H2A.Z has been associated with a diverse set of biological functions in mammals [9] including memory [10,11,12,13,14], the epithelial-to-mesenchymal transition [15,16], embryonic development [17], and cell proliferation in cancer [18,19,20,21]

Methods

Results

Discussion

Conclusion