Mediator-Regulated Transcription through the +1 Nucleosome

Abstract

SUMMARY Many genes are regulated at the level of a Pol II that is recruited to a nucleosome-free region upstream of the +1 nucleosome. How the Mediator coactivator complex, which functions at multiple steps, affects transcription through the promoter proximal region, including this nucleosome, remains largely unaddressed. We have established a fully defined in vitro assay system to delineate mechanisms for Pol II transit across the +1 nucleosome. Our results reveal cooperative functions of multiple cofactors, particularly of Mediator and elongation factor SII, in transcribing into this nucleosome. This is achieved, in part, through an unusual activity of SII that alters the intrinsic catalytic properties of promoter-proximal Pol II and, in concert with the Mediator, leads to enhancement in transcription of nucleosomal DNA. Our data provide additional mechanistic bases for Mediator function after recruitment of Pol II and, potentially, for regulation of genes controlled via nucleosome-mediated promoter-proximal pausing.

Histone H2A.Z subunit exchange controls consolidation of recent and remote memory

“…2), suggesting that H2A.Z at the +1 nucleosome restricts transcription. These findings are consistent with reports of stimulus-induced H2A.Z eviction 16–20 and evidence for the +1 nucleosome acting as a transcriptional barrier 15,21 .Given that our data are normalized to histone H3 to correct for potential changes in nucleosome occupancy, we conclude that H2A.Z eviction in particular is associated with activity-induced gene expression.…”

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

“…Moreover, Arabidopsis SSRP1, but not SPT16, is required for the action of the DNA demethylase DME in the central cell of the female gametophyte (Ikeda et al, 2011). FACT and TFIIS can help RNAPII transcribe through nucleosomes (Belotserkovskaya et al, 2003;Bondarenko et al, 2006;Nock et al, 2012), and they might collaborate regarding this function, which may explain the impaired growth of the tfIIs ssrp1 mutants relative to the respective single mutants. In metazoa, PAF1-C and FACT can apparently recruit each other to sites of transcription (Adelman et al, 2006;Pavri et al, 2006), and yeast cells lacking both PAF1 and SPT16 exhibit synthetic growth defects (Squazzo et al, 2002).…”

The Mediator complex: a central integrator of transcription

“…In addition to POLR2M and the SEC, other factors involved in regulating pol II pausing and elongation have been shown to have mechanistic links to Mediator, including cohesin 101,102 , ELL3 103 , TFIIS 104-106 , and DSIF 107 . This elaborate and expanding network of factors, whose regulatory roles are still emerging, coupled with the dynamic and apparently combinatorial nature of the pol II initiation and elongation machinery, suggests that delineation of specific mechanistic details will require structural, cellular, and biochemical assays, including studies with reconstituted in vitro transcription systems.…”

“…This model is analogous to results in D. melanogaster , in which paused promoter-proximal pol II complexes helped maintain nucleosome-free regions to promote transcription activation 117 . Mediator also interacts with the SWI/SNF and CHD1 chromatin remodeling complexes 118-120 and appears to contribute to nucleosome displacement during transcription activation in both yeast and humans 92,106 .…”