Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans

ABSTRACT: Chemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans

PROVIDER: PRJNA276134 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1814040.fastq.gz	Fastqsanger.gz
	SRR1814041.fastq.gz	Fastqsanger.gz
	SRR1814042.fastq.gz	Fastqsanger.gz
	SRR1814043.fastq.gz	Fastqsanger.gz
	SRR1814044.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Chemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans

Project description:Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our High-throughput Annotation of Modified Ribonucleotides (HAMR) pipeline to identify and classify modifications that affect Watson-Crick base-pairing at three different levels of the human and Arabidopsis thaliana transcriptomes (polyadenylated, small, and degrading RNAs). We find modifications primarily within actively degrading mRNAs and lncRNAs, suggesting they can act as a potent signal for RNA turnover. Additionally, modifications within stable mRNAs mark alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis of RNA modification across multiple RNA classes yields new functional insights into these covalent RNA additions. polyA-selected RNA-seq, smRNA-seq, and polyA-selected global mapping of uncapped transcripts (GMUCT) in Arabidopsis thaliana; smRNA-seq in HEK293T and HeLa human cell lines.

2015-10-31 | E-GEOD-66224 | biostudies-arrayexpress

Chemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans

2015-10-31 | GSE66224 | GEO

Glycine max Alternatively Spliced Transcript Detecting Microarray (GmASDM).

Project description:Glycine max Alternatively Spliced Transcript Detecting Microarray (GmASDM).

| PRJNA643563 | ENA

An alternatively spliced p62 isoform promotes breast cancer chemoresistance

Project description:An alternatively spliced p62 isoform promotes breast cancer chemoresistance

| PRJNA812680 | ENA

Mutations primarily alter the inclusion of alternatively spliced exons

Project description:Mutations primarily alter the inclusion of alternatively spliced exons

| PRJNA637776 | ENA

Affinity Purification Mass Spectrometry of protein protein interactors with alternatively-spliced Uromodulin

Project description:We identified an alternatively spliced UMOD which is uniquely localized intracellularly. This intracellular isoform enhanced mitochondrial function. To understand its molecular mechanism, we performed affinity-purification coupled to mass spectrometry using MDCK cell lysate expressing UMOD variant. We prepared MDCK cells which express mock (negative control), wild-type human UMOD or alternatively spliced human UMOD. UMOD was isolated by Immunoprecipitation and interacting proteins were identified by mass spectrometry proteomics analysis.

2024-03-15 | MSV000094329 | MassIVE

Mutations primarily alter the inclusion of alternatively spliced exons

Project description:Systematic mutagenesis has revealed that synonymous, non-synonymous and intronic mutations frequently alter the inclusion levels of alternatively spliced exons, suggesting that altered splicing might be a common mechanism by which mutations cause disease. However, most exons expressed in any cell are highly-included in mature mRNAs. Here, by performing deep mutagenesis of highly-included exons and by analysing the association between sequence variation and exon inclusion across the genome, we report that mutations only very rarely alter the inclusion of highly-included exons. This is true for both exonic and intronic mutations as well as for perturbations in trans. Therefore, mutations that affect splicing are not evenly distributed across the genome but are focussed in and around alternatively spliced exons with intermediate inclusion levels. These results provide a resource for prioritising synonymous and other variants as disease-causing mutations.

2020-06-29 | GSE151942 | GEO

Gene expression profiling of Capan-1 and Pt45P1 cells treated or not with alternatively spliced tissue factor (asTF)

Project description:The effects of alternatively spliced tissue factor (asTF) were measured by gene expression profiling of Capan-1 and Pt45P1 cells.

2013-04-10 | GSE45928 | GEO

Heterogeneous Expression of Alternatively Spliced lncRNA mediates Vascular Smooth Cell Plasticity

Project description:Heterogeneous Expression of Alternatively Spliced lncRNA mediates Vascular Smooth Cell Plasticity

| PRJNA869091 | ENA

An alternatively spliced variant of METTL3 mediates tumor suppression in hepatocellular carcinoma

Project description:An alternatively spliced variant of METTL3 mediates tumor suppression in hepatocellular carcinoma

| PRJNA782673 | ENA