Reprogramming mRNA expression in response to defect in RNA polymerase III assembly in the yeast Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA702291 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13729838_1.fastq.gz | Fastqsanger.gz | |||
| SRR13729838_2.fastq.gz | Fastqsanger.gz | |||
| SRR13729839_1.fastq.gz | Fastqsanger.gz | |||
| SRR13729839_2.fastq.gz | Fastqsanger.gz | |||
| SRR13729840_1.fastq.gz | Fastqsanger.gz |
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Project description:Interplay between nuclear RNA polymerases is key to growth control. Here, we explored the ways in which mRNA transcription by polymerase II (Pol II) is influenced by a defect in the biogenesis of Pol III. We used the cold-sensitive yeast mutant rpc128-1007, which prevents assembly of the Pol III complex and consequently leads to low tRNA levels. mRNA upregulation in rpc128-1007 cells was generally stronger and involved more genes than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the de-repression of general control transcription factor Gcn4. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. We also investigated the ways in which the reprogramming of Pol II genes is influenced by the rpc128-1007 suppressors RBS1 and PRT1, which encode the Pol III assembly factor and the subunit of translation initiation factor eIF3, respectively. Both of the suppressor genes countered the effects of rpc128-1007 on the expression of Gcn4-dependent genes and the effects of PRT1 were stronger than the effects of RBS1. Additionally, Rbs1 modulates Gcn4 activity in a manner that depends on of the Pho85 cyclin Pcl5. We have shown that the downregulation of Pcl5 protein levels by Rbs1 overproduction leads to a Gcn4 response that is likely related to the stabilization of Gcn4 protein. Altogether, our data contribute to the regulatory network which links transcription of different RNA classes
2021-07-28 | GSE166918 | GEO
Project description:The coordinated transcription of the genome is the fundamental mechanism in molecular biology. Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. The purpose of this study was to determine the mRNA levels in the yeast mutant rpc128-1007 and its overdose suppressors, RBS1 and PRT1. The rpc128-1007 mutant prevents assembly of the Pol III complex and functionally mimics similar mutations in human Pol III, which cause hypomyelinating leukodystrophies. We applied RNAseq followed by the hierarchical clustering of our complete RNA-seq transcriptome and functional analysis of genes from the clusters. mRNA upregulation in rpc128-1007 cells was generally stronger than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the derepression of general transcription factor Gcn4, differently modulated by suppressor genes. rpc128-1007 mutation, regardless of the presence of suppressors, also resulted in a weak increase in the expression of ribosome biogenesis genes. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. In summary, our results provide the regulatory links affected by Pol III assembly that contribute differently to cellular fitness.
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Project description:There are about 600 loci in the mammalian genome that are annotated as RNA polymerase III genes. These comprise tRNA genes, the genes encoding 5S RNA, the smallest ribosomal RNA, and genes encoding catalytic or structural RNAs involved in processes as diverse as RNA processing or transcription elongation. Most RNA polymerase III genes have similar promoter structures, yet they are transcribed with different efficiencies. Here we have explored how RNA polymerase III occupancy of these genomic loci varies in a normal tissue, the liver, during the transition from a resting state to a proliferating state. We find that after partial hepatectomy, which causes synchronous entry of remaining liver cells into the cell division cycle, there is a tremendous increase in RNA polymerase III occupancy. This increase is, however, not uniform and concerns mostly loci that were lowly occupied by RNA polymerase III in resting liver. The changes in RNA polymerase III occupancy cannot be correlated with changes in RNA polymerase II occupancy around the RNA polymerase III loci nor at nearby RNA polymerase II promoters. RNA polymerase III loci with the largest fold change tend to be located in clusters, with the cluster displaying the largest changes located on chromosome 13. This suggests that increases in RNA polymerase III occupancy during the transition from resting to proliferating state affect mostly genes whose basal rate of transcription is relatively low and which are located in clusters.
2018-12-12 | GSE114650 | GEO
Project description:ChIP-seq of FLAG-tagged RPA190 (subunit of RNA Polymerase I) or FLAG-tagged RPO31 (subunit of RNA Polymerase III) was performed on WT and isw2∆ nhp10∆ cells. Sample naming convention: <ChIP target>_<growth condition>_<genotype>_<strain name>
2018-10-30 | GSE112425 | GEO
Project description:Many regulatory proteins and complexes have been identified which influence transcription by RNA polymerase (pol) II with a fine precision. In comparison, only a few regulatory proteins are known for pol III, which transcribes mostly house-keeping and non-coding RNAs. Yet, pol III transcription is precisely regulated under various stress conditions like starvation. We used proteomic approaches and pol III transcription complex components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits to find identify the potential interactors through mass spectrometry-based proteomics. A large number of proteins were found in the interactome, which includes known chromatin modifiers, factors and regulators of transcription by pol I and pol II.
2019-01-02 | PXD003748 | Pride
Project description:Genome wide mapping of RNA polymearase III binding sites in Saccharomyces cerevisiae under normal growth and nutrient starved condition using ChIP-seq. Chromatin Immuno-precipitation (ChIP) was performed for FLAG tagged version of pol III subunit RPC128 after crosslinking the log-phase cells with formaldehyde. MOCK and IP DNA was sequenced and coverage of pol III was calculated at each base of the genome.
2013-06-21 | GSE39566 | GEO
Project description:RNA polymerase III regulation during mammalian tissue regeneration
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Project description:POLR3G and POLR3GL-RNA polymerase III target genes
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Project description:Posttranslational modification by the small ubiquitin-like modifier Sumo regulates many cellular processes including the adaptive response to various types of stress, which has been referred to as Sumo Stress Response (SSR). However, it remains unclear whether the SSR involves a common set of core proteins regardless of the type of stress, or whether each particular type of stress induces a stress-specific SSR that targets a unique, largely non-overlapping set of Sumo substrates. In this study we used mass spectrometry to identify differentially sumoylated proteins during heat shock, hyperosmotic stress, oxidative stress, nitrogen starvation and DNA alkylation in Saccharomyces cerevisiae. Our results show that each stress triggers a specific SSR signature centered on proteins involved in transcription, translation, and chromatin regulation. Strikingly, while the various stress-specific SSRs were largely non-overlapping, all types of stresses tested here resulted in desumoylation of subunits of RNA polymerase III, which correlated with a decrease in tRNA synthesis. We conclude that desumoylation and subsequent inhibition of RNA polymerase III constitutes the core of all stress-specific SSRs.
2019-11-01 | PXD013884 | Pride
Project description:The mechanism of assembly of RNA polymerase III (Pol III), the 17-subunit enzyme that synthesizes tRNAs, 5S rRNA, and other small-nuclear (sn) RNAs in eukaryotes, is not clearly understood. The recent discovery of the HSP90 co-chaperone PAQosome (Particle for Arrangement of Quaternary structure) revealed a function for this machinery in the biogenesis of nuclear RNA polymerases. However, the connection between Pol III subunits and the PAQosome during the assembly process remains unexplored. Here, we report the development of a mass spectrometry-based assay that allows the characterization of Pol III assembly. This assay was used to dissect the stages of Pol III assembly, to start defining the function of the PAQosome in this process, to dissect the assembly defects driven by the leukodystrophy-causative R103H substitution in POLR3B, and to discover that riluzole, an FDA-approved drug for alleviation of ALS symptoms, partly corrects these assembly defects. Together, these results shed new light on the mechanism and regulation of human nuclear Pol III biogenesis.
2023-03-10 | PXD034961 | Pride