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RNA polymerase II elongation study along yeast cell cycle.

ABSTRACT: RNA polymerase II elongation study along yeast cell cycle.

PROVIDER: PRJNA1164770 | ENA |

REPOSITORIES: ENA

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RNA polymerase II elongation study along yeast cell cycle.

Project description:Increasing evidence supports that the activity of RNA polymerase II (RNA pol II) during transcription elongation can be regulated to control transcription rates. Using genomic run-on (GRO) and RNA pol II chromatin immunoprecipitation (RPCC), we have respectively measured active and total RNA pol II present in the body of genes at 3 different stages of the mitotic cell cycle of Saccharomyces cerevisiae: G1, S and G2/M. Comparison of active and total RNA pol II values at these three points defined several gene clusters that reflect different patterns of transcription elongation control across the cell cycle. Previously defined cycling genes were overrepresented in some of these clusters, which showed cyclic average mRNA expression patterns. One of the clusters with most divergent GRO and RPCC patterns was significantly enriched in genes functionally related to ribosome biogenesis (RiBi). We confirmed that RiBi mRNA expression upregulates after START. Finally, we analysed the contribution of mRNA stability to each cluster and found that concerted control of RNA pol II activity and mRNA decay is needed to fully understand alternative strategies of gene expression across the cell cycle.

2025-03-21 | GSE277924 | GEO

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

Project description:During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle. Ribosome profiling, or sequencing of ribosome-protected mRNA fragments, in yeast. We assay ribosome footprint sizes and positions in three conditions: untreated yeast (3 replicates) and yeast treated with translation inhibitors cycloheximide (2 replicates) and anisomycin (2 biological replicates, one technical replicate). We also treat yeast with 3-aminotriazole to measure the effect of limited histidine tRNAs on ribosome footprint size and distribution (two treatment durations).

2014-06-10 | E-GEOD-58321 | biostudies-arrayexpress

Transcription profiling of yeast with a C-terminal deletion of the RNA polymerase II elongation factor Spt6 or overexpression of Spt6

Project description:Influence of a C-terminal deletion of the RNA polymerase II elongation factor Spt6 on the transcription of the yeast genome. In parallel the influence of a Spt6 overexpression on gene expression is analyzed.

2009-04-08 | E-MEXP-2123 | biostudies-arrayexpress

NDF Is a Transcription Factor that Stimulates Elongation by RNA Polymerase II

Project description:RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we find that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than does transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II-binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.

2022-03-10 | GSE185464 | GEO

Senataxin Promotes RNA Polymerase II Elongation [Hap1_DRBrelease_TTseq]

Project description:Senataxin Promotes RNA Polymerase II Elongation [Hap1_DRBrelease_TTseq]

| PRJNA1262997 | ENA

Senataxin Promotes RNA Polymerase II Elongation [PROseq]

Project description:Senataxin Promotes RNA Polymerase II Elongation [PROseq]

| PRJNA1175732 | ENA

Senataxin Promotes RNA Polymerase II Elongation [RChIPseq]

Project description:Senataxin Promotes RNA Polymerase II Elongation [RChIPseq]

| PRJNA1175733 | ENA

Senataxin Promotes RNA Polymerase II Elongation [DRBrelease_TTseq]

Project description:Senataxin Promotes RNA Polymerase II Elongation [DRBrelease_TTseq]