Decoding the occupancy of RNA polymerase I on rDNA
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1013095 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25915323.fastq.gz | Fastqsanger.gz | |||
| SRR25915324.fastq.gz | Fastqsanger.gz | |||
| SRR25915325.fastq.gz | Fastqsanger.gz | |||
| SRR25915326.fastq.gz | Fastqsanger.gz |
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Project description:BMH-21 inhibits RNA polymerase I transcription cycle and rDNA occupancy
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Project description:The objective of this study was to determine the effect of a small-molecule Pol I inhibitor, BMH-21, on rRNA synthesis in vivo. NET-seq was performed to determine the Pol I occupancy after BMH-21 treatment, as compared to vehicle-treatment (phosphate buffer control). Our findings suggest that BMH-21 treatment reduces Pol I occupancy on the rDNA template. Additionally, BMH-21 induces repositioning of Pol I in AT-rich rDNA regions that are directly upstream from GC-rich regions. This study suggests that BMH-21 is a powerful inhibitor of transcription by Pol I, and gives a potential mechanism of action for this inhibitor in vivo.
2021-05-26 | GSE175553 | GEO
Project description:To sustain growth, budding yeast actively transcribes its ribosomal gene array (rDNA) in the nucoleolus to produce ribosomes and proteins. However, intense transcription during rDNA replication may provoke collisions between RNA polymerase I (Pol I) and the replisome, may cause replication fork instability, double-strand breaks, local recombinations and rDNA instability. The latter is manifested by rDNA array expansion or reduction and the formation of extrachromosomal rDNA circles, anomalies that accelerate aging in yeast. Transcription also interferes with the resolution, condensation and segregation of the sister chromatid rDNA arrays. As a consequence, rDNA segregation lags behind the rest of the yeast genome and occurs in late anaphase when rDNA transcription is temporarily shut off. How yeast promotes the stability and transmission of its rDNA array while satisfying a constant need for ribosomes remains unclear. Here we show that the downregulation of Pol I by the conserved cell cycle kinase Rio1 spatiotemporally coordinates rDNA transcription, replication and segregation. More specifically, Rio1 activity promotes copy-number stability of the replicating rDNA array by curtailing Pol I activity and by localising the histone deacetylase Sir2, which establishes a heterochromatic state that silences rDNA transcription. At anaphase entry, Rio1 and the Cdc14 phosphatase target Pol I subunit Rpa43 to dissociate Pol I from the 35S rDNA promoter. The rDNA locus then condensates and segregates, thereby concluding the genome transmission process. Rio1 is involved in ribosome maturation in the cytoplasm of budding yeast and human cells. Additional engagements in the cytoplasm or roles in the nucleus are unknown. Our study describes its first nuclear engagement as a Pol I silencing kinase. This activity may prove highly relevant as dysregulated RNA polymerase I activity has been associated with cancer initiation and proliferation.
2017-02-10 | GSE54930 | GEO
Project description:The central goal of this project was to determine the role of the RNA polymerase I (Pol I) subunits RPA34 and RPA49 in rRNA synthesis. Previous studies by various groups have demonstrated that these two subunits may play a role in transcription initiation and elongation by on Pol I occupancy in vivo, but this is still not clearly defined. Here, we deployed a high-resolution technique, native elongating transcript sequencing (NET-seq), to test the effects of RPA34 and RPA49 on Pol I occupancy in vivo. We found that when RPA34 was deleted, there was a significant reduction in Pol I occupancy across the rDNA template. Additionally, when RPA49 was deleted, Pol I occupancy was even further reduced across the template. Collectively, our findings suggest that perhaps RPA34 acts to stabilize RPA49 and these subunits may act primarily as transcription initiation factors for Pol I.
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Project description:Ribosome is the most abundant RNA-protein complex in a cell and many copies of the ribosomal RNA gene (rDNA) have to be maintained. However, arrays of tandemly repeated rDNA genes can lose the copies by intra-repeat recombination. Loss of the rDNA copies of Saccharomyces cerevisiae is counteracted by gene amplification whereby the number of rDNA repeats stabilizes around 150 copies, suggesting the presence of a monitoring mechanism that counts and adjusts the number. Here, we report that in response to rDNA copy loss, the upstream activating factor (UAF) for RNA polymerase I which transcribes the rDNA is released and directly bind to a RNA polymerase II transcribed gene, SIR2 to repress, whose gene products silence rDNA recombination. We show that the amount of UAF determines rDNA copies number that is stably maintained. UAF ensures rDNA production not only by rDNA transcription activation but also by its copy number maintenance.
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Project description:Transcription of tRNA genes by RNA Polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and for tuning the physiological response to changing metabolic demands.
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Project description:The relative amount of RNA polymerase II (Pol II) associated with a given ORF provides an estimate for transcriptional efficiency. We therefore established a systematic approach to measure Pol II occupancy using chromatin immunoprecipitation followed by analysis on microarrays
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Project description:hnRNP UL1 plays an important function in cell nuclei, where it is recruited to DNA damage sites and is involved in the repair of DNA double strand breaks. Furthermore, this protein is known as a transcriptional repressor of RNA polymerase II genes. In the present study, we have shown that hnRNP UL1 is also localized in the nucleoli. Revealing its function, we figured out that hnRNP UL1 stimulates rDNA gene transcription and may be involved in the transport of the proteins between the nucleolus and the nucleoplasm. Moreover, we observed that cells with hnRNP UL1 silencing are more sensitive to DNA damage, suggesting its role in rDNA repair pathways and nucleolar genome integrity. Indeed, we confirmed that hnRNP UL1 interacts with yH2A.X, RPA32, XRCC1, and Chk1 in cell nucleoli, suggesting its involvement in repairing of DNA damages.
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