Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene-Specific Control of tRNA expression by RNA Polymerase II (nascent RNA-seq)

ABSTRACT: Gene-Specific Control of tRNA expression by RNA Polymerase II (nascent RNA-seq)

PROVIDER: PRJNA541584 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9025770_1.fastq.gz	Fastqsanger.gz
	SRR9025770_2.fastq.gz	Fastqsanger.gz
	SRR9025771_1.fastq.gz	Fastqsanger.gz
	SRR9025771_2.fastq.gz	Fastqsanger.gz
	SRR9025768_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Gene-Specific Control of tRNA expression by RNA Polymerase II (nascent RNA-seq)

Project description:Increasing evidence suggests that tRNA levels are dynamically and specifically regulated in response to internal and external cues to modulate the cellular translational program. However, the molecular players and the mechanisms regulating the gene-specific expression of tRNAs are still unknown. Using an inducible auxin-degron system to rapidly deplete RPB1 (the largest subunit of RNA Pol II) in living cells, we identified Pol II as a direct gene-specific regulator of tRNA transcription. Our data suggest that Pol II transcription robustly interferes with Pol III function at specific tRNA genes. This activity was further found to be essential for MAF1-mediated repression of a large set of tRNA genes during serum starvation, indicating that repression of tRNA genes by Pol II is dynamically regulated. Hence, Pol II plays a direct and central role in the gene-specific regulation of tRNA expression.

2020-04-15 | GSE130853 | GEO

Gene-Specific Control of tRNA expression by RNA Polymerase II

Project description:Gene-Specific Control of tRNA expression by RNA Polymerase II

| PRJNA541871 | ENA

Splicing of nascent RNA coincides with intron exit from RNA polymerase II

Project description:Splicing of nascent RNA coincides with intron exit from RNA polymerase II

| PRJNA289900 | ENA

KINETIC AND COMPOSITIONAL ANALYSIS OF RNA POLYMERASE II IN TRYPANOSOMA BRUCEI

Project description:Genome-wide analysis of nascent RNA synthesis gives kinetic information on the transcriptional status of RNA polymerase II (Pol II). In parallel, immunoprecipitation of the largest subunit of Pol II (RPB1) provides the protein composition of the enzyme complex in the presence or absence of the transcriptional inhibitor Actinomycin D.

2023-05-23 | PXD039878 | Pride

Gene-Specific Control of tRNA expression by RNA Polymerase II (arrays)

Project description:Gene-Specific Control of tRNA expression by RNA Polymerase II (arrays)

| PRJNA541877 | ENA

Gene-Specific Control of tRNA expression by RNA Polymerase II (arrays)

2020-04-15 | GSE130877 | GEO

Gene-Specific Control of tRNA expression by RNA Polymerase II (ChIP-seq)

Project description:Gene-Specific Control of tRNA expression by RNA Polymerase II (ChIP-seq)

| PRJNA541564 | ENA

Gene-Specific Control of tRNA expression by RNA Polymerase II (ChIP-seq)

2020-04-15 | GSE130847 | GEO

Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts

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 5Â´ 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, 3Â´-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 3Â´-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 5Â´-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

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

Project description:Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly due to technical limitations in purifying authentic nascent transcripts. We present a new approach to purify and profile nascent RNA, called Polymerase Intact Nascent Transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5’ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano) and profiles whole transcription units (POINT-seq). In particular, we show by depletion of the nuclear exonuclease Xrn2 that this activity acts selectively on cleaved 5’P-RNA at polyadenylation sites. Furthermore, POINT-nano reveals that splicing occurs either immediately after splice site transcription or is delayed until Pol II transcribes downstream sequences. Finally, we connect RNA cleavage and splicing with either premature or full-length transcript termination. We anticipate that POINT technology will afford full dissection of the complexity of co-transcriptional RNA processing.

2021-03-19 | GSE159326 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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