Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation

Elife. 2020 Feb 28;9:e53375. doi: 10.7554/eLife.53375.


The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is encoded by two genes expressing two isoforms, H2A.Z.1 and H2A.Z.2 differing by three amino acids. Here, we undertook an integrated analysis of their functions in gene expression using endogenously-tagged proteins. RNA-Seq analysis in untransformed cells showed that they can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner. Furthermore, they have similar or antagonistic function depending on genes. H2A.Z.1 and H2A.Z.2 can replace each other at Transcription Start Sites, providing a molecular explanation for this interplay. Mass spectrometry analysis showed that H2A.Z.1 and H2A.Z.2 have specific interactors, which can mediate their functional antagonism. Our data indicate that the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important to regulate specific gene expression, providing an additional layer of complexity to the control of gene expression by histone variants.

Keywords: H2A.Z histone variant; chromosomes; gene expression; genome-wide analyses; human.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Gene Expression Regulation* / genetics
  • Genes / physiology
  • Histones / physiology*
  • Humans
  • Promoter Regions, Genetic
  • Protein Isoforms / physiology
  • Transcription, Genetic / physiology


  • Histones
  • Protein Isoforms
  • histone H2A.F-Z

Associated data

  • GEO/GSE131579
  • GEO/GSE134532