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Rtr1 regulates global levels of RNA Polymerase II CTD phosphorylation during transcription elongation

ABSTRACT: RNA Polymerase Serine 5 phosphorylation (H14 antibody) is examined in wt and rtr1 deletion conditions to see if deletion of rtr1 causes a redistribution of these marks across open reading frames.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE68181 | GEO | 2016/06/07

SECONDARY ACCESSION(S): PRJNA281987

REPOSITORIES: GEO

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Sexual differentiation controlled by RNA polymerase II CTD phosphorylation on serine 2

Project description:The switch from cellular proliferation to differentiation occurs to a large extend through specific programs of gene expression. In fission yeast, the high-mobility-group transcription factor Ste11 is the master regulator of sexual differentiation. ste11 is induced by environmental conditions, mostly nitrogen starvation, leading to mating and meiosis 1. We have used ChIP-chip and gene expression profiling to show that CDK-dependent phosphorylation of serine 2 in the C-terminal domain (CTD) of the largest subunit of the RNA polymerase II (PolII) holoenzyme plays a critical role in the induction of ste11 transcription during sexual differentiation while it has a minor impact on gene expression during vegetative growth. Moreover, we demonstrate that both the recruitment of the CTD serine 2 kinase and the phosphorylation event initiate at the promoter region of ste11 in contrast to the classical case where serine 2 phosphorylation occurs across the coding region 2. In the absence of CTD serine 2 phosphorylation, both PolII occupancy at the ste11 locus, and ste11 expression are impaired. This results in sterility that is rescued when ste11 is expressed from the canonical adh promoter. We conclude that a modification of the RNA polymerase II holoenzyme plays a specific and pivotal role in the sexual differentiation. For the ChIP-chip experiments, 3-4 biological replicates were performed for each tagged protein of interest. For the expression experiments, two biological samples were hybridized for each mutant strain (replicates 1 and 2), with two dye-swap technical replicates per sample (replicates 3 and 4).

2010-01-01 | E-GEOD-16498 | biostudies-arrayexpress

Gene-specific RNA polymerase II phosphorylation and the CTD code.

Project description: Not available

| S-EPMC3048030 | biostudies-literature

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation.

Project description: Not available

| S-EPMC4081074 | biostudies-literature

Structure of TFIIK for phosphorylation of CTD of RNA polymerase II.

Project description: Not available

| S-EPMC8026125 | biostudies-literature

Heptad-specific phosphorylation of RNA polymerase II CTD

Project description:The carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) consists of heptad repeats with the consensus motif Y1-S2-P3-T4-S5-P6-S7. Dynamic phosphorylation of the CTD coordinates Pol II progression through the transcription cycle. Monoclonal antibodies have been used to study in vivo the potentially phosphorylated CTD amino acids (Y1, S2, T4, S5 and S7). However, the epitopes detected by antibodies can be masked by proteins or modifications at neighbouring sites. Therefore, the effectiveness of antibodies in western blot or ChIP analysis reflects the number of accessible CTD phosphorylation marks, but not the total number of phosphorylations. Most importantly, CTD phospho-specific antibodies do not provide any heptad - (location) specific information of CTD phosphorylation. Due to these limitations, the principles and patterns of CTD phosphorylation remained elusive. Here, we use genetic and mass spectrometric approaches to directly detect and map phosphosites along the entire CTD. We confirm phosphorylation of CTD residues Y1, S2, T4, S5 and S7 in mammalian and yeast cells. Although specific phosphorylation signatures dominate, adjacent CTD repeats can be differently phosphorylated, leading to a high variation of coexisting phosphosites in mono- and di-heptad CTD repeats. Inhibition of CDK9 kinase specifically reduces S2 phosphorylation levels within the CTD.

2016-01-25 | PXD003159 | Pride

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

Project description:Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and tRNA adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared to other transcripts with equally high ribosome densities.

2019-09-10 | PXD014357 | Pride

Pervasive functional translation of noncanonical open reading frames

Project description:Pervasive functional translation of noncanonical open reading frames

| PRJNA544411 | ENA

Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression.

Project description: Not available

| S-EPMC4893663 | biostudies-literature

How an mRNA capping enzyme reads distinct RNA polymerase II and Spt5 CTD phosphorylation codes.

Project description: Not available

| S-EPMC4066402 | biostudies-literature

A gene-specific requirement of RNA polymerase II CTD phosphorylation on serine 2 for sexual differentiation in fission yeast

Project description:The switch from cellular proliferation to differentiation occurs to a large extent through specific programs of gene expression. In fission yeast, the master regulator of sexual differentiation, ste11, is induced by environmental conditions leading to mating and meiosis. We show that phosphorylation of serine 2 (S2P) in the C-terminal domain (CTD) of the largest subunit of the RNA polymerase II (PolII) enzyme by the Lsk1 cyclin dependent kinase has only a minor impact on global gene expression during vegetative growth but is critical for the induction of ste11 transcription during sexual differentiation. The recruitment of the Lsk1 kinase initiates in the vicinity of the transcription start site of ste11, resulting in a marked increase of S2P on the ste11 unit including an extended 5’-untranslated region (5’-UTR). This pattern contrasts with the classical gradient of S2P towards the 3’ region. In the absence of S2P, both PolII occupancy at the ste11 locus and ste11 expression are impaired. This results in sterility which is rescued by expression of the ste11 coding sequence from the adh1 promoter. Thus, the S2P polymerase plays a specific, regulatory role in cell differentiation through the induction of ste11.

2010-01-01 | GSE16498 | GEO

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