Promoter nucleosome dynamics regulated by signalling through the CTD code

Abstract

The phosphorylation of the RNA polymerase II C-terminal domain (CTD) plays a key role in delineating transcribed regions within chromatin by recruiting histone methylases and deacetylases. Using genome-wide nucleosome mapping, we show that CTD S2 phosphorylation controls nucleosome dynamics in the promoter of a subset of 324 genes, including the regulators of cell differentiation ste11 and metabolic adaptation inv1. Mechanistic studies on these genes indicate that during gene activation a local increase of phospho-S2 CTD nearby the promoter impairs the phospho-S5 CTD-dependent recruitment of Set1 and the subsequent recruitment of specific HDACs, which leads to nucleosome depletion and efficient transcription. The early increase of phospho-S2 results from the phosphorylation of the CTD S2 kinase Lsk1 by MAP kinase in response to cellular signalling. The artificial tethering of the Lsk1 kinase at the ste11 promoter is sufficient to activate transcription. Therefore, signalling through the CTD code regulates promoter nucleosomes dynamics.DOI: http://dx.doi.org/10.7554/eLife.09008.001

The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selection

“…S5A). In fact, Seb1 copurified with a GSTtagged version of the S. pombe CTD that was coexpressed in fission yeast (Materne et al 2015) but not with a control GST fusion protein (Fig. 4A, lanes 11,12), consistent with the notion that Seb1 can interact with the CTD of Rpb1.…”

A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions

“…As rightly pointed by the authors in their manuscript, it is possible that the inactivation of the snf21 - ts was not complete despite the fact that the strain has obvious phenotypes (see below), somehow masking an effect of most NDR. Supporting this possibility, we report here that while switching-off snf21 expression using a Tet-off system eventually results in cell death on plates (Materne et al 2015), it has a weak genome-wide effect on NDR formation when a short time point is used (Fig. 3a).…”

“…2b harbours the highest frequency of genes affected in the rsc1 mutant (Fig. 3c), including ste11 (Materne et al 2015, 2016). That cluster is characterized by an increase in occupancy over a broad region upstream of the TSS that may be typical of highly regulated genes relying on larger regulatory sequences, as typically seen for ste11 (Anandhakumar et al 2013).…”

“…Deletion of non-essential subunits of RSC or transcriptional switch-off of snf21 both impede ste11 expression and correlate with higher nucleosome occupancy at the ste11 NDR (Materne et al 2015, 2016). This effect led us to analyse the genome-wide effect of both RSC mutants on nucleosome positioning using MNase-Seq, which allows us to assess the conservation of the chromatin remodelling function of the RSC complex in budding and fission yeast.…”

“…a The profile of nucleosome occupancy ratios between fission yeast rsc1 deletion mutant ( rsc1Δ ) and control strains on the left panel (note that this panel is identical to Fig. 2b and repeated here for clarity), and between the fission yeast snf21 switch-off mutant [ tetO - snf21, 3 h of inhibition, (Materne et al 2015)] and control strains on the right panel are presented as a heatmap, where blue represents a gain in nucleosome occupancy and red represents a loss within a region ranging from −750 bp to +750 bp around the TSS at single nucleotide resolution. Rows represent genes and are organized into five groups by k -means clustering.…”