Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA311752 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:For a typical RNA polymerase (pol) II transcribed budding yeast gene, the 5' -end is characterized by a nucleosome-free region (NFR) immediate upstream of the transcription start site (TSS), flanked by two well-positioned nucleosomes (-1 and +1) containing H2A.Z. A similar arrangement of nucleosomes containing H2A.Z is found on the genes transcribed by pol III, which reside in the NFR actively maintained by the chromatin remodeling complexes. We did genome-wide MNase-seq and ChIP-seq experiments to study the nucleosome arrangement near pol III transcribed genes. We also measured the levels of different tRNAs in the tRNA pool of the wild type and Spt16 mutant (*spt16-197*) cells using tRNA-HySeq method. Although, it is difficult to measure the primary transcripts of tRNA due to their quick processing and the sequence degeneracy of the tRNA isogenes; a comparison of the wild type and Spt16 mutant showed both increase or decrease of tRNA transcripts. The result suggest that Spt16 may not be necessary for the transcription per se of tRNA genes.
2023-12-31 | GSE109527 | GEO
Project description:tRNA genes (tDNAs) are widely studied sites of replication-fork arrest and genome instability in the budding yeast Saccharomyces cerevisiae. tDNAs are extremely highly transcribed, and serve as constitutive condensin binding sites. Although tRNA transcription by RNA polymerase III (RNAPIII) has previously been identified as stimulating replication-fork arrest at these loci, the nature of the block to replication has not been incontrovertibly demonstrated. Here, we describe a systematic, genome-wide analysis of the contributions of transcription factor binding, transcription, topoisomerase activity, and condensin-mediated clustering to replication-fork arrest at tDNAs in yeast. We show that a polar block to replication is maintained at tDNAs even when tRNA transcription is abolished by depletion of one or more subunits of RNAPIII. By contrast, analogous depletion of the essential transcription factor TFIIIB removes the obstacle to replication in the same background. Therefore, our data suggest that the RNA polymerase III transcription complex itself represents an asymmetric obstacle to replication even in the absence of RNA synthesis. We additionally demonstrate that replication-fork mobility past tDNAs is unaffected by the global depletion of condensin from the nucleus, but can be stimulated by the removal of topoisomerases or Rad18-dependent DNA repair pathways.
2019-11-02 | GSE139860 | GEO
Project description:RNA polymerase III (RNAPIII) synthesizes a range of highly abundant small stable RNAs, principally pre-tRNAs. Here we report the genome-wide analysis of nascent transcripts attached to RNAPIII under permissive and restrictive growth conditions. This revealed strikingly uneven polymerase distributions across transcription units, generally with a predominant 5´ peak. This peak was higher for more heavily transcribed genes, suggesting that initiation site clearance is rate limiting during RNAPIII transcription. Down-regulation of RNAPIII transcription under stress conditions was found to be uneven; a subset of tRNA genes showed low response to nutrient shift or loss of the major transcription regulator Maf1, suggesting potential âhousekeepingâ roles. Many tRNA genes were found to generate long, 3´-extended forms due to read-through of the canonical poly(U) terminators. The degree of read-through was anti-correlated with the density of T-residues in the coding strand, and multiple, functional terminators can be located far downstream. The steady-state levels of 3´-extended pre-tRNA transcripts are low, apparently due to targeting by the nuclear surveillance machinery; especially the RNA-binding protein Nab2, cofactors for the nuclear exosome and the 5´-exonuclease Rat1. CRAC protocol performed on samples containing HTP-tagged proteins: Rpc160(Rpo31), Nab2, Rrp44(Dis3), Rrp6 and Mtr4. Rpc-160-bound RNAs were analyzed in wildtype and maf1 mutant cells and after a shift to medium containing glycerol.
2016-05-18 | E-GEOD-77863 | biostudies-arrayexpress
Project description:Mediator is a co-regulator of RNA polymerase II (Pol II), transducing signals from regulatory elements and transcription factors to the general transcription machinery at the promoter. We here demonstrate that Med20 influences ribosomal protein expression in fission yeast. In addition, loss of Med20 leads to an accumulation of aberrant readthrough tRNA transcripts. The aberrant transcripts are polyadenylated and targeted for degradation by the exosome. Similarly, other specialized RNA molecules, such as snRNA, snoRNA and rRNA are also accumulated in the absence of Med20. We suggest that fission yeast Mediator takes part in a regulatory pathway of Pol III transcripts.
2016-01-01 | GSE73792 | GEO
Project description:Mapping transcriptionally engaged RNA polymerase II in C2C12 myoblasts
| PRJNA308190 | ENA
Project description:RNA polymerase III (RNAPIII) synthesizes a range of highly abundant small stable RNAs, principally pre-tRNAs. Here we report the genome-wide analysis of nascent transcripts attached to RNAPIII under permissive and restrictive growth conditions. This revealed strikingly uneven polymerase distributions across transcription units, generally with a predominant 5´ peak. This peak was higher for more heavily transcribed genes, suggesting that initiation site clearance is rate limiting during RNAPIII transcription. Down-regulation of RNAPIII transcription under stress conditions was found to be uneven; a subset of tRNA genes showed low response to nutrient shift or loss of the major transcription regulator Maf1, suggesting potential “housekeeping” roles. Many tRNA genes were found to generate long, 3´-extended forms due to read-through of the canonical poly(U) terminators. The degree of read-through was anti-correlated with the density of T-residues in the coding strand, and multiple, functional terminators can be located far downstream. The steady-state levels of 3´-extended pre-tRNA transcripts are low, apparently due to targeting by the nuclear surveillance machinery; especially the RNA-binding protein Nab2, cofactors for the nuclear exosome and the 5´-exonuclease Rat1.
2016-05-18 | GSE77863 | GEO
Project description:Pathogenic variants in subunits of RNA polymerase (Pol) III cause a spectrum of neurodegenerative diseases including 4H leukodystrophy. We developed a postnatal whole-body mouse model expressing pathogenic mutations in Polr3a to examine the molecular mechanisms by which reduced Pol III activity results primarily in central nervous system phenotypes. Polr3a mutant mice exhibit behavioral deficits, exocrine pancreatic atrophy and cerebral pathology. Transcriptome and immunohistochemistry analyses of cerebra show a reduction in most Pol III transcripts, induction of innate immune and integrated stress responses and cell type-specific gene expression changes reflecting neuron and oligodendrocyte loss and microglial activation. A global decrease in mature tRNA levels and an altered tRNA profile preceded cerebral neurodegeneration suggesting a causal role in disease initiation. In cerebella, heart and kidney, Pol III transcripts other than tRNAs were generally unaffected. The results suggest tissue-specific thresholds of sensitivity to defects in Pol III transcription.
2024-01-10 | GSE246161 | GEO
Project description:Pathogenic variants in subunits of RNA polymerase (Pol) III cause a spectrum of neurodegenerative diseases including 4H leukodystrophy. We developed a postnatal whole-body mouse model expressing pathogenic mutations in Polr3a to examine the molecular mechanisms by which reduced Pol III activity results primarily in central nervous system phenotypes. Polr3a mutant mice exhibit behavioral deficits, exocrine pancreatic atrophy and cerebral pathology. Transcriptome and immunohistochemistry analyses of cerebra show a reduction in most Pol III transcripts, induction of innate immune and integrated stress responses and cell type-specific gene expression changes reflecting neuron and oligodendrocyte loss and microglial activation. A global decrease in mature tRNA levels and an altered tRNA profile preceded cerebral neurodegeneration suggesting a causal role in disease initiation. In cerebella, heart and kidney, Pol III transcripts other than tRNAs were generally unaffected. The results suggest tissue-specific thresholds of sensitivity to defects in Pol III transcription.
2024-01-10 | GSE246160 | GEO
Project description:Nuclear pores associate with active protein-coding genes in yeast and have been implicated in transcriptional regulation. Here, we show that in addition to transcriptional regulation, key components of C. elegans nuclear pores are required for processing of a subset of small nucleolar RNAs (snoRNAs) and tRNAs transcribed by RNA Polymerase (Pol) III. Chromatin immunoprecipitation of NPP-13 and NPP-3, two integral nuclear pore components, and importin-ß IMB-1, provides strong evidence that this requirement is direct. All three proteins associate specifically with tRNA and snoRNA genes undergoing Pol III transcription. These pore components bind immediately downstream of the Pol III pre-initiation complex, but are not required for Pol III recruitment. Instead, NPP-13 is required for cleavage of tRNA and snoRNA precursors into mature RNAs, whereas Pol II transcript processing occurs normally. Our data suggest that integral nuclear pore proteins act to coordinate transcription and processing of Pol III transcripts in C. elegans.
2013-09-05 | GSE42714 | GEO
Project description:Nuclear pores associate with active protein-coding genes in yeast and have been implicated in transcriptional regulation. Here, we show that in addition to transcriptional regulation, key components of C. elegans nuclear pores are required for processing of a subset of small nucleolar RNAs (snoRNAs) and tRNAs transcribed by RNA Polymerase (Pol) III. Chromatin immunoprecipitation of NPP-13 and NPP-3, two integral nuclear pore components, and importin-ß IMB-1, provides strong evidence that this requirement is direct. All three proteins associate specifically with tRNA and snoRNA genes undergoing Pol III transcription. These pore components bind immediately downstream of the Pol III pre-initiation complex, but are not required for Pol III recruitment. Instead, NPP-13 is required for cleavage of tRNA and snoRNA precursors into mature RNAs, whereas Pol II transcript processing occurs normally. Our data suggest that integral nuclear pore proteins act to coordinate transcription and processing of Pol III transcripts in C. elegans.
2013-09-05 | GSE42651 | GEO