Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome maps of general eukaryotic RNA degradation factors

ABSTRACT: Transcriptome maps of general eukaryotic RNA degradation factors

PROVIDER: PRJNA527105 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8729590.fastq.gz	Fastqsanger.gz
	SRR8729600.fastq.gz	Fastqsanger.gz
	SRR8729610.fastq.gz	Fastqsanger.gz
	SRR8729620.fastq.gz	Fastqsanger.gz
	SRR8729630.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 75

Similar Datasets

Transcriptome maps of general eukaryotic RNA degradation factors

Project description:RNA degradation pathways underlie RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast S. cerevisiae. The profiles define the distribution of factors between RNA classes. They are also consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind already to intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3, TRAMP4, and the exosome, targets aberrant nuclear RNAs, pre-processes snoRNAs, and regulates attenuated genes. Finally, mRNA transcript optimality is the most predictive feature for binding of decapping factors and the Xrn1 exonuclease to mRNA, consistent with rapid 5´-degradation of inefficiently translated mRNAs.

2019-05-28 | GSE128312 | GEO

Transcriptome maps of general eukaryotic RNA degradation factors.

Project description:RNA degradation pathways enable RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. The profiles reveal the distribution of degradation factors between different RNA classes. They are consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Decapping factors preferentially bind mRNAs with non-optimal codons, consistent with rapid degradation of inefficiently translated mRNAs. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3 and TRAMP4, targets aberrant nuclear RNAs and processes snoRNAs.

| S-EPMC6570525 | biostudies-literature

A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance

Project description:The RNA exosome is an RNA degradation machine that is critical for eukaryotic transcriptome surveillance and mutations in exosome components cause numerous human diseases. The exosome is directed to specific RNAs by adaptor protein complexes. However, it remains unclear how these adaptors specifically recognize their target RNAs. The PAXT connection is an adaptor that recruits the exosome to polyadenylated RNAs in the nucleus, especially transcripts polyadenylated at intronic poly(A) sites. Here we show that PAXT-mediated degradation is induced by the combination of a 5′ splice site and a poly(A) junction, which includes the poly(A) signal and the poly(A) tail, but not by either sequence alone. These two sequences are bound by the splicing factor U1 snRNP and pre-mRNA 3′ processing factors, which in turn cooperatively recruit PAXT. As 5′ splice sites and poly(A) junctions are typically found on unspliced precursors and processed RNAs respectively, we propose that their presence on the same RNA molecule constitutes an “RNA degradation code”. Consistent with this model, disease-associated single nucleotide polymorphisms that create novel 5′ splice sites near poly(A) sites induce aberrant RNA degradation. Our results revealed the first nuclear RNA degradation code that plays important roles in transcriptome surveillance and may also influence gene evolution.

2024-07-29 | GSE267857 | GEO

Sumoylation regulates general transcription factors at promoters of highly transcribed genes

Project description:Sumoylation regulates general transcription factors at promoters of highly transcribed genes

| PRJNA704633 | ENA

Computer Assisted Early Detection of Liver Metastases From fMRI Maps

Project description:The purpose of this protocol is to develop a detailed MRI technique and haemodynamic maps enabling early detection of colorectal metastases in the liver.

| 2037102 | ecrin-mdr-crc

SHARP1 suppresses breast cancer metastasis by promoting degradation of hypoxia-inducible factors

Project description:Triple Negative Breast cancer accounts for some of the most aggressive types of breast cancer. By interrogating clinical datasets, we found that the activities of p63 and Hypoxia-Inducible-Factors (HIFs), two master regulators of the invasive and metastatic cancer cell phenotype are linked in TNBC through the p63-target Sharp1. Mechanistically, Sharp1 promotes HIF-1α/HIF-2α proteasomal degradation by serving as HIFs presenting factor to the proteasome independently from oxygen levels and prior ubiquitination. To investigate unbiasedly if Sharp1 is a general inhibitor of HIF induced transcriptional program, we compared the transcriptomic profile of cells either overexpressing Sharp1 or depleted of HIF1a and HIF2a.

2012-07-19 | GSE33950 | GEO

Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators

Project description:Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators

| PRJNA1196388 | 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

General fungi

Project description:General fungi Genome sequencing and assembly

| PRJNA800463 | ENA

Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals

Project description:Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that stability of the yeast transcriptome is regulated by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. WT, rnt1 delta and rrp6 delta strains where grown independently and analyzed by Affymetrix yeast tiling microarray analysis

2015-02-16 | E-GEOD-57390 | biostudies-arrayexpress

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