Histone Variant H2A.Z and RNA Polymerase II Transcription Elongation

Abstract

Nucleosomes containing histone variant H2A.Z (Htz1) serve to poise quiescent genes for activation and transcriptional initiation. However, little is known about their role in transcription elongation. Here we show that dominant mutations in the elongation genes SPT5 and SPT16 suppress the hypersensitivity of htz1⌬ strains to drugs that inhibit elongation, indicating that Htz1 functions at the level of transcription elongation. Direct kinetic measurements of RNA polymerase II (Pol II) movement across the 9.5-kb GAL10p-VPS13 gene revealed that the elongation rate of polymerase is 24% slower in the absence of Htz1. We provide evidence for two nonexclusive mechanisms. First, we observed that both the phospho-Ser2 levels in the elongating isoform of Pol II and the loading of Spt5 and Elongator over the GAL1 open reading frame (ORF) depend on Htz1. Second, in the absence of Htz1, the density of nucleosome occupancy is increased over the GAL10p-VPS13 ORF and the chromatin is refractory to remodeling during active transcription. These results establish a mechanistic role for Htz1 in transcription elongation and suggest that Htz1-containing nucleosomes facilitate Pol II passage by affecting the correct assembly and modification status of Pol II elongation complexes and by favoring efficient nucleosome remodeling over the gene.Transcription by RNA polymerase II (Pol II) takes place on a compositionally and topologically complex chromatin template at multiple steps, including promoter activation, transcription initiation, elongation, and termination. A number of mechanisms facilitate the initiation of gene transcription on chromatin templates. Two of the most prominent of these are the remodeling of nucleosomes by DNA-dependent ATPase complexes and the covalent posttranslational modification of histone proteins (20,90). At a minimum, these pathways are thought to act by establishing a permissive chromatin structure at gene promoters, allowing access of site-specific transcription factors and the subsequent recruitment of polymerase and the general factors (25,69).

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

“…37,38 Altogether, this provides a logic for H2A.Z detection in MNase LiDs. Additionally, although H2A.Z is positively involved in transcription, 30,[38][39][40] it also localizes to poised promoters bound by the Polycomb repressor 2 complex. 41,42 This is in line with the enrichment of MNase LiDs in H3K27me3 and in the H3K27 methyltransferase EZH2, a component of this complex.…”

Rho and NusG suppress pervasive antisense transcription in Escherichia coli

“…Together with Nrd1 and Nab, which confer both RNA recognition (Carroll et al 2007) and early elongation phase-specific RNAPII CTD recognition (Vasiljeva et al 2008), Sen1, like Rho, terminates cryptic, untranslated transcripts, including antisense transcripts (Arigo et al 2006;Brow 2011). Both histone modifications and nucleosome composition affect these processes in eukaryotes (Carrozza et al 2005;Santisteban et al 2011), and some histone modifications appear to aid Sen1 action (Terzi et al 2011). Furthermore, the evolutionarily conserved Spt5 (NusG) elongation factor both aids transcript elongation (Hirtreiter et al 2010) and, through its multiple C-terminal KOW domains, recruits elongation factors (Zhang et al 2005), apparently including Nrd1 (Vasiljeva and Buratowski 2006;Lepore and Lafontaine 2011).…”

Histone variants: dynamic punctuation in transcription

“…In addition to roles in activation and initiation, H2A.Z has been found to promote elongation (Santisteban et al 2011). To explore the molecular basis for this role, we developed a single-base-resolution method to map the position of RNAPII through the 39 end of nascent transcripts (39 NT) in Drosophila.…”