RNAPII (Rpb3-FLAG) ChIP-seq during quiescence entry in Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJEB78738 | ENA |
REPOSITORIES: ENA
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Project description:ChIP-chip by array of Rpb3 localization in yeast with different CTD lenghts and with or without CDK8 deletion to determine the role of CTD length and Cdk8 on RNAPII localization
2013-12-30 | E-MTAB-1341 | biostudies-arrayexpress
Project description:Our structural and biochemical studies show that S. cerevisiae RNA Polymerase II (RNAPII) homodimerizes through the stalk domain (formed by the Rpb4-Rpb7 subunits). To explore the biological impact of disrupting this interaction we introduced a triple point mutation at the RNAPII dimerization interface in Rpb7 (Q96A, H97A, F109K). To test the impact of the dimerziation mutant on RNAPII occupancy, we performed ChIP-seq using a monoclonal antibody against the Rpb3 subunit (1Y26, abcam) of RNAPII, in WT and Rpb7-QHF cells.
2023-12-31 | E-MTAB-13369 | biostudies-arrayexpress
Project description:Cellular quiescence is coupled with cellular development, tissue homeostasis, and cancer progression. Both quiescence and cell cycle re-entry are controlled by active and precise regulation of gene expression. However, the roles of long noncoding RNAs (lncRNAs) during these processes remain to be elucidated. By performing a genome-wide transcriptome analyses, we identify thousands of differentially expressed lncRNAs, including ~30 of the less-characterized class of microRNA-host-gene lncRNAs (lnc-MIRHGs), during cellular quiescence and during serum-stimulation in human diploid cells. We observe that the mature MIR222HG display serum-stimulated induction due to enhanced pre-RNA splicing. Serum-stimulated binding of the pre-mRNA splicing factor SRSF1 to a micro-exon, which partially overlaps with the primary miR-222 precursor, facilitates enhanced MIR222HG splicing. In serum-stimulated cells, SRSF1 negatively regulates the Drosha/DGCR8-catalyzed cleavage of pri-miR-222, thereby increasing the cellular pool of the mature MIR222HG. Further, loss-of-function studies indicate that the mature MIR222HG facilitates the serum-stimulated cell cycle re-entry in a microRNA-independent manner. Mechanistically, MIR222HG, along with ILF3/2 complex, forms RNA:RNA duplex with DNM3OS lncRNA, thereby promoting DNM3OS stability. The current study identifies a mechanism in which the interplay between splicing versus microprocessor complex dictates the serum-induced expression of lnc-MIRHG MIR222HG for efficient cell cycle re-entry.
2020-09-07 | PXD017585 | Pride
Project description:Binding profiles for H3 and H4ac were determined as cells transition from log growth to quiescence. We found that massive chromatin changes that reflect global transcriptional repression occur after the diauxic shift in an Rpd3-dependent manner. Binding of Rpd3 is dramatically expanded to reflect binding at thousands of genes after quiescence entry, demonstrating an Rpd3-driven mechanism to change chromatin and repress transcription after entry into quiescence.
2015-08-20 | GSE67150 | GEO
Project description:The histone chaperone Spt6 is involved in promoting elongation of RNA polymerase II (RNAPII), maintaining chromatin structure, regulating co-transcriptional histone modifications, and controlling mRNA processing. These diverse functions of Spt6 are partly mediated through its interactions with RNAPII and other factors in the transcription elongation complex. In this study, we used mass spectrometry to characterize the differences in RNAPII interacting factors between wild-type cells and those depleted for Spt6, leading to the identification of proteins that depend on Spt6 for their interaction with RNAPII. In all, eight samples were processed - four genotypes (1. SPT6, RPB3-untagged; 2. SPT6, RPB3-tagged; 3. spt6-1004, RPB3-untagged; 4. spt6-1004; RPB3-tagged) in biological duplicates.
2021-12-05 | PXD027708 | Pride
Project description:ChIP on chip microarray experiment to decipher Rpb3 and Rpb4 recruitment in S.cerevesiae genome. Keywords: ChIP-chip
2007-11-15 | GSE9265 | GEO
Project description:Quiescence is a distinct cell cycle phase, termed G0, in which growth, transcription, translation, and replication are suppressed. Yeast cells enter G0 following glucose exhaustion but remain viable for an extended period and can re-enter the cell cycle when returned to glucose-rich medium. Quiescence is a feature of all organisms and is essential for the maintenance of stem cells and tissue renewal. Quiescence is also related to chronological lifespan (CLS) - or the capacity of post-mitotic quiescent cells to survive over time - and thus contributes to longevity. However, important questions remain to be answered regarding the mechanisms that control entry into quiescence, the maintenance of quiescence, and the re-entry of quiescent cells into the cell cycle. Histone acetylation is lost during the formation of quiescent yeast cells, and chromatin becomes highly condensed. This unique chromatin landscape plays a key role in supporting quiescence-specific transcriptional repression and has been linked to the formation and maintenance of quiescent cells. To ask if other chromatin features regulate quiescence, we conducted a comprehensive screen of histone H3 and H4 mutants. We identified several mutants that show altered quiescence entry and have characterized their chromatin phenotypes. None of these mutants retain histone acetylation, while several have altered chromatin condensation. Additionally, a screen for H3 and H4 mutants with altered chronological lifespan showed that CLS is highly correlated with quiescence entry.
2023-03-01 | GSE210305 | GEO
Project description:To determine the interactome of RNA Polymerase II (RNAPII), HA-tagged RPB3 was stably expressed in U2OS cells. The cells were harvested followed by the native stepwise isolation of chromatin-associated RNAPII complexes. HA-RPB3 was immunoprecipitated and interacting proteins analyzed by quantitative mass spectrometry. U2OS cells expressing no HA-tagged protein were used for comparison.
2024-12-20 | PXD054701 | Pride
Project description:Background: Although quiescence—reversible cell-cycle arrest—is a key part in the life history and fate of many mammalian cell types, the mechanisms of gene regulation in quiescent cells are poorly understood. We sought to clarify the role of microRNAs as regulators of the cellular functions of quiescent human fibroblasts. Results: Using microarrays, we discovered that the expression of the majority of profiled microRNAs differed between proliferating and quiescent fibroblasts. Fibroblasts induced into quiescence by contact inhibition or serum starvation had similar microRNA profiles, indicating common changes induced by distinct quiescence signals. By analyzing the gene expression patterns of microRNA target genes with quiescence, we discovered a strong regulatory function for miR-29, which is downregulated with quiescence. Using microarrays and immunoblotting, we confirmed that miR-29 targets genes encoding collagen and other extracellular matrix proteins and that those target genes are induced in quiescence. In addition, overexpression of miR-29 resulted in more rapid cell cycle re-entry from quiescence. We also found that let-7 and miR-125 were upregulated in quiescent cells. Overexpression of either one alone resulted in slower cell cycle re-entry from quiescence, while the combination of both together slowed cell cycle re-entry even further. Conclusions: microRNAs regulate key aspects of fibroblast quiescence including the proliferative state of the cells as well as their gene expression profiles, in particular, the induction of extracellular matrix proteins in quiescent fibroblasts. microRNAs in human neonatal dermal fibroblasts in 3 cell cycle conditions (proliferating, 4 days serum starved, 7 days contact inhibited) were analyzed by one color microarray. 3 separate fibroblast cell lines from different human donors were analyzed for each condition, with two separate labeling and hybridization samples for each cell line. In total, 18 samples were hybridized to the microRNA microarray.
2012-12-05 | E-GEOD-42593 | biostudies-arrayexpress
Project description:Background: Although quiescence—reversible cell-cycle arrest—is a key part in the life history and fate of many mammalian cell types, the mechanisms of gene regulation in quiescent cells are poorly understood. We sought to clarify the role of microRNAs as regulators of the cellular functions of quiescent human fibroblasts. Results: Using microarrays, we discovered that the expression of the majority of profiled microRNAs differed between proliferating and quiescent fibroblasts. Fibroblasts induced into quiescence by contact inhibition or serum starvation had similar microRNA profiles, indicating common changes induced by distinct quiescence signals. By analyzing the gene expression patterns of microRNA target genes with quiescence, we discovered a strong regulatory function for miR-29, which is downregulated with quiescence. Using microarrays and immunoblotting, we confirmed that miR-29 targets genes encoding collagen and other extracellular matrix proteins and that those target genes are induced in quiescence. In addition, overexpression of miR-29 resulted in more rapid cell cycle re-entry from quiescence. We also found that let-7 and miR-125 were upregulated in quiescent cells. Overexpression of either one alone resulted in slower cell cycle re-entry from quiescence, while the combination of both together slowed cell cycle re-entry even further. Conclusions: microRNAs regulate key aspects of fibroblast quiescence including the proliferative state of the cells as well as their gene expression profiles, in particular, the induction of extracellular matrix proteins in quiescent fibroblasts. mRNAs were analyzed by two color microarray from three separate human neonatal dermal fibroblasts cell lines transfected either with a miR-29b mimic or a control short dsRNA. One sample was labeled and analyzed in duplicate to ensure consistency in labeling and hybridization technique.
2012-12-05 | E-GEOD-42613 | biostudies-arrayexpress