Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide levels of RNA polymerase II (RNAPII) in normally growing or heat-shocked wild-type and sumolyation-deficient ubc9-6 yeast strains

ABSTRACT: Many transcription-related proteins are known to be modified by SUMO post-translational modification in yeast, plants, humans and other eukaryotes. We are interested in understanding how cells use sumoylation to regulate transcription of specific genes and globally. To explore this, we carried out ChIP-seq analysis to determine how genomic levels of RNA polymerase II (RNAPII) change when cellular levels of sumoylation are greatly reduced in budding yeast. Compared to wild-type yeast, RNAP occupancy in the sumoylation-deficient ubc9-6 strain was significantly altered for hundreds of genes. Among the genes with the most elevated levels of RNAPII are those involved in translation and ribosome biogenesis, including most ribosomal protein genes. On the other hand, many genes involved in small molecule and amino acid metabolism and biosynthesis showed reduced RNAPII levels in ubc9-6. Exposure of yeast to heat shock is known to cause a widespread change to RNAPII occupancy across the genome. To examine whether cellular sumoylation plays a role in this process, RNAPII ChIP-seq was performed in wild-type and ubc9-6 strains after a brief heat shock. Strikingly, the sumoylation deficient strain showed a far more dramatic redistribution of RNAPII across the genome, with significantly more genes showing a heat-shock induced increase or decrease in RNAPII occupancy. These results imply that cellular sumoylation levels have a significant impact on the regulation of transcription genome-wide, and that normal sumoylation levels are needed to restrain the vast redistribution of RNAPII that occurs in response to heat shock.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE167424 | GEO | 2021/09/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis in sumoylation deficient (ubc9-6) budding yeast and in a strain with a sumoylation-impairing mutation in the TFIIF subunit, Tfg1

Project description:Transcription related proteins are among the most frequently identified targets of SUMO post-translational modification, but the gene-specific and genome-wide effects of transcription machinery sumoylation are not well-understood. To explore this, we examined whether dramatically reducing cellular sumoylation levels affects the levels of mRNAs in budding yeast. RNA-seq was performed using polyadenylate (polyA)-enriched RNAs from the sumoylation-deficient ubc9-6 strain and its wild-type parent. Indeed, the abundance of hundreds of mRNAs were upregulated or downregulated in the mutant strain, implying that sumoylation has a widespread influence on RNA polymerase II (RNAPII) transcription or mRNA stability. Interestingly, about one third of mRNAs that were significantly upregulated in the ubc9-6 strain encode proteins that are involved in small molecule metabolic processes, suggesting that sumoylation is normally involved in restricting these pathways. As part of our analysis of transcription-related sumoylation, we determined that the large subunit of TFIIF, Tfg1, is a major target of sumoylation among the general transcription factors (GTFs) of RNAPII. To determine whether sumoylation of Tfg1 specifically is involved in regulating mRNA levels, we performed RNA-seq on polyA-enriched RNAs derived from strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. However, with few exceptions, impairing Tfg1 sumoylation had no effect on the mRNA transcriptome. Together, our data demonstrate that gene expression is extensively regulated by sumoylation, but this likely involves the coordinated modification of multiple proteins at multiple levels.

2021-09-21 | GSE167427 | GEO

Effects of sumoylation-impairing mutation of TFIIF subunit Tfg1 on genome-wide RNA polymerase II (RNAPII) levels in budding yeast

Project description:Many transcription-related proteins, including components of the RNA polymerase II (RNAPII) general transcription factors (GTFs), have been shown through proteomics studies to be modifiable by SUMO conjugation. However, we determined that the large subunit of TFIIF, Tfg1, is likely the major target of sumoylation among GTFs in budding yeast. The primary site of sumoylation on Tfg1 is Lys residues 60 or 61, which lies in a region of the protein that is proximal to the Rpb2 subunit of RNAPII when the GTF-RNAPII preinitiation complex (PIC) assembles at promoters. As TFIIF and RNAPII are highly functionally and physically linked, we examined whether blocking Tfg1 sumoylation through Lys-to-Arg mutations could affect the recruitment or association of RNAPII with chromatin. RNAPII ChIP-seq was performed in strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. Indeed, nearly half of all protein-coding genes showed significantly reduced RNAPII levels in the mutant strain. These data suggest that sumoylation of TFIIF plays an important role in regulating the dynamics of RNAPII association with genes.

2021-09-21 | GSE167426 | GEO

RPRD1B is required for proper heat shock response [TTchem-seq]

Project description:The Heat Shock response (HSR) is a highly conserved transcriptional program induced by the exposure to a variety of environmental stressors. Following an insult, a small subset of genes, known as the Heat Shock genes, are rapidly induced by the Heat Shock Factors (HSFs) to maintain protein homeostasis and ensure cell survival. In this study, we demonstrate that the RNAPII interactor RPRD1B is required for proper transcription of heat shock induced genes and for survival to heat shock.

2022-09-08 | GSE197992 | GEO

RPRD1B is required for proper heat shock response [RNA-seq]

2022-09-08 | GSE197993 | GEO

Genome-wide localization of SUMO-modified proteins in untreated or heat-shocked budding yeast

Project description:Most SUMO-modified proteins in budding yeast and human cells are associated with chromatin. To determine specifically where sumoylated proteins are found across the genome, we performed ChIP-seq with a SUMO antibody in budding yeast. We identified 603 loci that each contain a stable SUMO peak. In agreement with a previous study, most of these sites correspond to tRNA genes or genes that encode ribosomal proteins (RPGs). However, 147 of the SUMO peaks in our analysis are found at promoters of protein-coding genes that are not RPGs (non-RPGs), many of which are among the most highly expressed genes. By comparing our data with other ChIP-seq studies, we determined that non-RPG SUMO peaks are situated precisely where general transcription factors (GTFs) assemble, but not where RNA polymerase II (RNAPII) or other promoter-proximal proteins bind. In support of this, we determined that the large subunit of TFIIF is the major SUMO target among GTFs and propose that its sumoylation controls the dynamics of RNAPII gene association. Additionally, we found that exposing yeast to a brief heat shock significantly reduces the intensity of SUMO peaks at most genes of all classes, which likely reflects the vast transcriptional reprogramming that occurs in response to temperature stress.

2021-09-21 | GSE167425 | GEO

H3K4me3 chromatin profiling in SUMOylation-competent and -deficient bone marrow derived dendritic cells unstimulated or stimulated with LPS

Project description:Purpose: To determine H3K4me3 chromatin profile in UBC9WT and UBC9KO BMDC before and after LPS stimulation. Methods: H3K4me3 chromatin profile was determined by sequencing UBC9 WT and UBC9 KO BMDC chromatin immunoprecipitated with antibody specific for H3K4me3. Results: We show differential chromatin profile for H3K4me3 on the ifnb1 locus between UBC9 KO cells and UBC9 WT. Conclusions: Loss of SUMOylation causes a deregulation of ifnb1 transcription activation mark. A study of H3K4me3 chromatin profile in UBC9 WT and UBC9 KO Bone Marrow derived Dendritic Cells.

2015-12-14 | E-GEOD-66338 | biostudies-arrayexpress

Protein SUMOylation is required for regulatory T cell expansion and function

Project description:Foxp3-expressing regulatory T (Treg) cells are essential regulators in the immune system; molecular mechanisms underlying Treg cell expansion and function are still not well understood. SUMOylation is an important post-translational modification characterized by covalent attachment of SUMO moieties to lysine within proteins. UBC9 is the only E2 conjugation enzyme involved in this process and loss of UBC9 completely impairs the SUMOylation pathway. Here we report that selective deletion of Ubc9 within the Treg cell lineage resulted in fatal early-onset autoimmunity as the Foxp3 mutant mice. Ubc9-deficient Treg cells exhibited severe defects in TCR-driven homeostatic proliferation, accompanied by impaired activation and compromised suppressor function. Importantly, TCR-enhanced SUMOylation of IRF4, a critical regulator of Treg cell function downstream of TCR signals, regulates its stability in Treg cells. Our data thus have demonstrated an essential role of SUMOylation in the expansion and function of Treg cells.

2016-05-31 | GSE82031 | GEO

UBC9 knockdown in bladder cancer T24 cell lines

Project description:UBC9 is the sole conjugating enzyme E2 in the sumoylation and plays a pivotal role in maintaining homeostasis and restraining stress reaction. Targeting UBC9 is emerging as a novel strategy for cancer therapy. However, the role of UBC9 in bladder cancer is not clear. Here, we sought to determine the alterations of trancriptome after shRNA-mediated knockdown UBC9 in T24 cell lines．

2018-12-25 | GSE117143 | GEO

Is transthyretin a regulator of Ubc9 SUMOylation?

Project description:Ageing and mutations of transthyretin (TTR), the thyroid hormones and retinol transporting protein lead to amyloidosis by destabilizing the structure of TTR. Because protein structure is regulated through posttranslational modifications, we investigated the Small Ubiquitin-like Modifier (SUMO)ylation of TTR. We chose the widely used Ubc9 fusion-directed SUMOylation system, which is based on a fusion of the SUMOylation substrate of interest with Ubc9, a sole SUMO conjugating enzyme. Surprisingly, despite our presumptions, we found that Ubc9 fused to TTR was SUMOylated at a unique set of lysine residues. Three unknown SUMOylation sites of Ubc9—K154, K18 and K65—were revealed by mass spectrometry (MS). The previously reported SUMOylation at K49 of Ubc9 was also observed. SUMOylation of the lysine residues of TTR fused to Ubc9 was hardly detectable. However, non-fused TTR was SUMOylated via trans-SUMOylation by Ubc9 fused to TTR. Interestingly, mutating the catalytic residue of Ubc9 fused to TTR did not result in complete loss of the SUMOylation signal, suggesting that Ubc9 linked to TTR is directly cross-SUMOylated by the SUMO-activating enzyme E1. Ubc9, TTR or fusion proteins composed of TTR and Ubc9 specifically affected the global SUMOylation of cellular proteins. TTR or Ubc9 alone increased global SUMOylation, whereas TTR and Ubc9 together decreased the amount of high-molecular weight (HMW) SUMO conjugates. Our data suggest that TTR may influence the SUMOylation of Ubc9, thereby altering signalling pathways in the cell.

2016-08-15 | PXD004515 | Pride

Protein SUMOylation is required for regulatory T cell expansion and function

Project description:Foxp3-expressing regulatory T (Treg) cells are essential regulators in the immune system; molecular mechanisms underlying Treg cell expansion and function are still not well understood. SUMOylation is an important post-translational modification characterized by covalent attachment of SUMO moieties to lysine within proteins. UBC9 is the only E2 conjugation enzyme involved in this process and loss of UBC9 completely impairs the SUMOylation pathway. Here we report that selective deletion ofÂ Ubc9Â within the Treg cell lineage resulted in fatal early-onset autoimmunity as the Foxp3 mutant mice. Ubc9-deficient Treg cells exhibited severe defects in TCR-driven homeostatic proliferation, accompanied by impaired activation and compromised suppressor function. Importantly, TCR-enhanced SUMOylation of IRF4, a critical regulator of Treg cell function downstream of TCR signals, regulates its stability in Treg cells. Our data thus have demonstrated an essential role of SUMOylation in the expansion and function of Treg cells. RNA-seq library was generated using mRNA of CD4+ YFP+ Treg cells sorted from lymph nodes and spleen of Foxp3cre/wtUbc9fl/wt or Foxp3cre/wtUbc9fl/fl mice, each sample contained pooled Treg cells from 5~10 mice.

2016-05-31 | E-GEOD-82031 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data