Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA content of yeast nuclear mRNPs

ABSTRACT: RNA content of yeast nuclear mRNPs

PROVIDER: PRJNA941889 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23725274_1.fastq.gz	Fastqsanger.gz
	SRR23725274_2.fastq.gz	Fastqsanger.gz
	SRR23725275_1.fastq.gz	Fastqsanger.gz
	SRR23725275_2.fastq.gz	Fastqsanger.gz
	SRR23725276_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

RNA content of yeast nuclear mRNPs

Project description:We isolated nuclear mRNPs from yeast using an endogenous bi-molecular tagging approach on Sub2 and Hpr1. To validate the nature of these isolated particles, extracted RNA was sequenced and differential enrichment, as well as metagene coverage analysis were performed.

2023-07-24 | GSE226854 | GEO

Protein content and proximity map of yeast nuclear mRNPs

Project description:We isolated nuclear mRNPs from yeast using an endogenous bi-molecular tagging approach on Sub2 and Hpr1.

2023-07-25 | PXD040736 | Pride

Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition

Project description:Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3’-processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the newly synthesized yeast transcriptome, providing ~10^5-10^6 high-confidence RNA interaction sites per factor.

2014-07-23 | GSE59676 | GEO

RNA-seq of Yra1 associated mRNAs

Project description:Gene expression results from mRNA - RNA-binding protein (RBP) interactions within messenger ribonucleoprotein (mRNP) particles. We identified heterogeniety of nuclear mRNP composition involved in mRNA biogenesis and export with different occupancy and stoichiometry of RNA-binding proteins. Especially, mRNA export adopter protein Yra1 showed large variation of its stoichiometry on single mRNPs. We identified stoichiometry of Yra1 in the nuclear cap binding complex (Cbp80) bound mRNPs and it can be dissected into two categories (one and multiple Yra1 bound mRNPs). Multiple Yra1 containing mRNPs specifically co-occupied with THO complex (Hpr1). To investigate gene dependency to form different Yra1 stoichiometry mRNPs, we performed RNA-IP experiment for Yra1 with two step purification by Cbp80/Yra1 and Hpr1/Yra1.

2024-02-14 | GSE226972 | GEO

Mediator is essential for small nuclear and nucleolar RNA transcription in yeast

Project description:Mediator is essential for small nuclear and nucleolar RNA transcription in yeast

| PRJNA448794 | ENA

RNA content of transcription factories

Project description:RNA content of transcription factories

| PRJEB7531 | ENA

Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition

Project description:Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3M-bM-^@M-^Y-processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the newly synthesized yeast transcriptome, providing ~10^5-10^6 high-confidence RNA interaction sites per factor. PAR-CLIP data of 23 mRNP biogenesis factors in Saccharomyces cerevisiae

2014-07-23 | E-GEOD-59676 | biostudies-arrayexpress

Photo-cross-linking mass spectrometry for single amino acid assignment of RNA-binding sites in RNA-binding proteins

Project description:Mass spectrometry data of peptide–RNA cross-links derived from complex biological systems. Yeast (pre-)mRNPs were isolated by TAP tag purification of Cbp20; human protein–RNA complexes were assembled on an aptamer tagged pre-mRNA. Isolated complexes were UV irradiated. For each of the aforementioned experiments, a non-irradiated control was prepared. Yeast RBPs cross-linked in vivo after labeling with 4-thio-uridine (4SU) were isolated with oligo d(T). All samples were enriched for cross-linked heteroconjugates prior to LC-MS analysis.

2014-08-07 | PXD000513 | Pride

Mediator is essential for small nuclear and nucleolar RNA transcription in yeast

Project description:Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein coding RNAs (ncRNAs) including small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA promoters use the same factors as mRNA promoters, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear. Here, we investigated a potential role for the Mediator complex, essential for mRNA gene transcription, in the transcription of sn/snoRNA genes. We found that the Mediator maps to most sn/snoRNA gene regulatory regions and that rapid depletion of the essential structural subunit Med14 strongly reduces RNAPII and TFIIB occupancy as well as nascent transcription of sn/snoRNA genes. Deletion of Med3 and Med15, subunits of the activator-interacting Mediator tail module, does not affect Mediator recruitment to or RNAPII and TFIIB occupancy of sn/snoRNA genes. Our analyses suggest that Mediator promotes PIC formation and transcription at sn/snoRNA genes, expanding the role of this critical regulator beyond its known functions in mRNA gene transcription and demonstrating further mechanistic similarity between the transcription of mRNA and sn/snoRNA genes.

2018-10-08 | GSE112721 | GEO

Nuclear RNA decay pathways aid rapid remodeling of gene expression in yeast

Project description:In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprograming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II (Pol II) and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV-crosslinking immediately following glucose withdrawal (0, 4, and 8 minutes). In glucose, mRNA binding by Nab3 and Mtr4 was mainly restricted to promoter-proximal sites, reflecting early transcription termination. Following glucose withdrawal, many mRNAs showed reduced transcription but increased Nab3 binding, accompanied by downstream recruitment of Mtr4, and oligo(A) tailing. This indicates transcription termination followed by TRAMP-mediated RNA decay. Upregulated transcripts generally showed low or strongly reduced binding of Nab3 and Mtr4. We conclude that nuclear surveillance pathways regulate both positive and negative responses to glucose availability.

2017-01-01 | GSE86483 | 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