Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA259340 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The carboxy-terminal domain of RPB1 subunit of RNA Polymerase II (CTD) plays an essential function in the regulation of gene expression and the coordination of co-transcriptional processes. CTD consists of hepta-amino acid repeats varying in number from 52 in humans to 26 in yeast and its length is crucial for spatial organization of transcriptional machinery in the nucleus. We found that the proximal half of the CTD is sufficient to support RNA metabolism and co-transcriptional processing in steady state conditions in human cells. Signal induced transcription, however, is severely impaired upon CTD shortening. Our data suggest that CTD length increased in evolution to allow for spatio-temporal control of gene expression patterns at least in part by facilitating enhancer function.
2021-01-04 | GSE159092 | GEO
Project description:The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight CTD’s pivotal role in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
2024-02-09 | GSE252260 | GEO
Project description:The C-terminal domain of RPB1 (CTD) orchestrates transcription by recruiting regulators to RNA Pol II upon phosphorylation. Recent insights highlight CTD’s pivotal role in driving condensate formation on gene loci. Yet, the molecular mechanism behind how CTD-mediated recruitment of transcriptional regulators influences condensates formation remains unclear. Our study unveils that phosphorylation reversibly dissolves phase separation induced by the unphosphorylated CTD. Phosphorylated CTD, upon specific association with transcription regulatory proteins, forms distinct condensates from unphosphorylated CTD. Function studies demonstrate CTD variants with diverse condensation properties in vitro exhibit difference in promoter binding and mRNA co-processing in cells. Notably, varying CTD lengths lead to alternative splicing outcomes impacting cellular growth, linking the evolution of CTD variation/length with the complexity of splicing from yeast to human. These findings provide compelling evidence for a model wherein post-translational modification enables the transition of functionally specialized condensates, highlighting a co-evolution link between CTD condensation and splicing.
2024-02-09 | GSE252258 | GEO
Project description:The modification of Ser 5 is important for the relocalization of RNAP II upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. The 5A strain carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with alanine followed by 7 wild-type-sequenced repeats.
2014-12-03 | GSE60707 | GEO
Project description:The modification of Ser 5 is important for the relocalization of RNAP II upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. The 5A strain carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with alanine followed by 7 wild-type-sequenced repeats. Two-color fluorescence arrays reporting on Rpb3 localization abundance in strains (input vs. IP) before and at 20 min after a shock with 0.7M NaCl
2014-12-03 | E-GEOD-60707 | biostudies-arrayexpress
Project description:In fission yeast, the nuclear-localized Lsk1p-Lsc1p-Lsg1p cyclin dependent kinase complex is required for the reliable execution of cytokinesis and is also required for Ser-2 phosphorylation RNA pol II carboxy terminal domain. To address whether alterations in CTD phosphorylation might selectively alter expression of cytokinesis genes, expression profiling of site-directed CTD mutants was performed. Strains bearing the rpb1-12XCTD and rpb1-12XS2ACTD mutations were grown to mid-log phase in YES media and treated with 0.5uM LatA (or the solvent control, DMSO) for three hours at 30C. Three biological replicates were performed.
2011-08-31 | E-GEOD-31369 | biostudies-arrayexpress
Project description:Transctriptome profiling of CTD-14 repeats, 2A, 5A mutants responding to 0.7N NaCl for 30mins. The study shows that phosphorylation at Ser5 sites plays a role in normal induction and repression of genes upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. 5A strains carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with Ala followed by 7 wild-type-sequenced repeats. The 2A strains carrys 8 repeats of CTD-serine 2 substituted with alanine followed by 7 wild-type-sequenced repeats.
2014-12-03 | GSE60700 | GEO
Project description:Transctriptome profiling of CTD-14 repeats, 2A, 5A mutants responding to 0.7N NaCl for 30mins. The study shows that phosphorylation at Ser5 sites plays a role in normal induction and repression of genes upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. 5A strains carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with Ala followed by 7 wild-type-sequenced repeats. The 2A strains carrys 8 repeats of CTD-serine 2 substituted with alanine followed by 7 wild-type-sequenced repeats. Two-color fluorescence arrays reporting on mRNA abunance in strains before and after 30 min with 0.7M NaCl treatment
2014-12-03 | E-GEOD-60700 | biostudies-arrayexpress
Project description:We report calibrated transcriptome of rpb1-CTD-S2A and WT of S. pombe cells. Phosphorylation of the RNA polymerase II (Pol II) C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that alanine substitution of all Ser2 in CTD result in increased antisense transcription.
2021-08-26 | GSE171307 | GEO
Project description:The carboxy-terminal domain (CTD) of Rpb1, the largest component of the 12-subunit RNA polymerase II, consists of repeating Y1S2P3T4S5P6S7 heptapeptides (26 repeats in budding yeast). Each stage of transcription relies on the ordered recruitment and exchange of specific protein complexes that act on RNA polymerase II, its nascent transcripts, and the underlying chromatin. This dynamic process is orchestrated via patterned post-translational modifications of the CTD. To characterize the role of phosphorylation on Thr4, we examined the effect of Rpb1 alleles in which Thr4 was substituted with an alanine (T4A) or the phospho-mimic glutamate (T4E). Substitutions were made across all heptad repeats of the CTD.
We affinity purified HA-tagged Rpb1 from Saccharomyces cerevisiae strains bearing WT, T4A, and T4E CTDs. A control strain (Z26) lacking the HA-tagged Rpb1 was subjected to an identical affinity enrichment procedure. Three biological replicates were acquired for each type of affinity purification and analyzed independently. After TCA-precipitation, proteins were urea-denatured, reduced, alkylated, then digested with endoproteinase LysC followed by trypsin. The resulting peptide mixtures were analyzed by Multidimensional Protein Identification Technology (MudPIT). Label-free quantitative proteomics was used to identify and quantify the relative abundance of affinity-enriched complexes.
2017-02-24 | MSV000080573 | MassIVE