The role of histone variant H2A.Z in co‐transcriptional splicing in Saccharomyces cerevisiae

Abstract

In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from pre‐messenger RNA (pre‐mRNA). Although RNA‐synthesis and RNA‐processing have typically been studied as biochemically distinct reactions, recent studies have shown these two processes to be spatio‐temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In S. cerevisiae, H2A.Z is deposited in to the chromatin by the SWR1‐complex and is typically found near the 5′ ends of protein‐coding genes. H2A.Z has been implicated in transcription elongation and polymerase processivity. Here we show that H2A.Z, encoded by HTZ1 in yeast, is important for efficient splicing of intron‐containing genes, and splicing in cells lacking H2A.Z is impaired under suboptimal conditions, such as mutant splicing complexes or suboptimal splice sites. HTZ1, is particularly dependent on an intact U2 snRNP, as it shows extensive genetic interactions with components of the U2 snRNP and U2 snRNP associated proteins. Consistent with this, H2A.Z is required for the splicing of introns containing a mutated splice site. RNA‐seq reveals that intron‐containing genes with non‐consensus branchpoint sequences are particularly sensitive to loss of H2A.Z. We find that deletion of HTZ1 results in persistent association of the U2 snRNP with nascent RNA, suggesting altered spliceosomal rearrangements in the absence of H2A.Z. Together, these results demonstrate that histone variant H2A.Z is required for efficient splicing of a subset of intron‐containing genes and indicate a role for H2A.Z in co‐transcriptional spliceosome assembly.Support or Funding InformationRuth L. Kirschstein National Research Service Award GM007185.