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Mutations primarily alter the inclusion of alternatively spliced exons

ABSTRACT: Mutations primarily alter the inclusion of alternatively spliced exons

PROVIDER: PRJNA637776 | ENA |

REPOSITORIES: ENA

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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

Mutations primarily alter the inclusion of alternatively spliced exons.

Project description: Not available

| S-EPMC7673789 | biostudies-literature

Validation of alternatively spliced protein isoforms in human mesenchymal stem cells

Project description:Alternative splicing of mRNA diversifies the function of human proteins, with tissue- and cell-specific protein isoforms being the most difficult to validate. While transcriptomic experiments enable the detection of many alternatively spliced transcripts, it is not known if these transcripts have protein-coding potential. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and exon-exon junctions of spliced transcripts by integrating transcriptomics and proteomics data. Using the PG Nexus, we analyzed undifferentiated human mesenchymal stem cells and compared the number of protein isoforms validated using different protein sequence database, including public online databases and RNA-seq derived databases. With significant overlaps with other databases, we identified 8,011 exons and 3,824 splice junctions with the Ensembl database. Both exonic and junction peptides were important for protein isoform validation. The Ensembl database consistently outperformed the other data sources, but predicted open reading frames from RNA-seq derived transcripts were comparable, with only 6 less splice junctions validated. Using proteotypic and isoform-specific peptides, we validated 462 protein isoforms. This number increases to 1,083 if multiple proteotypic peptides per protein are included. Multiplexing proteotypic peptides in SRM assays or similar experiments will increase the confidence and coverage of protein isoform validation experiments.

2015-05-20 | PXD001449 | Pride

Alternatively Spliced Variants of Interleukin-4 Promote Inflammation Differentially

Project description:IL-4d2 is a natural splice variant of IL-4 which lacks the region encoded by the second exon. Numerous recent reports suggested that the expression levels of IL-4d2 change in various diseases, especially those with pulmonary involvement, but the effects of IL-4d2 on the lungs in vivo have never been studied. Replication-deficient adenovirus-mediated gene delivery of mouse IL-4d2 to mouse lungs in vivo was used, and the effects compared with similar adenoviral delivery of mouse IL-4 or with infection with a NULL viral construct. The objective was to determine whether full-length wild-type Interleukin-4 encoded by exons 1-4 (IL-4) and alternatively spliced variant econded by exons 1,3, and 4 (IL-4d2) differentially affect gene expression in the lungs in vivo. The results show that IL-4d2 and IL-4 affected global gene expression differentially. Keywords: Comparative analysis of gene delivery of alternative splice variants in vivo

2011-03-07 | GSE23016 | GEO

Glycine max Alternatively Spliced Transcript Detecting Microarray (GmASDM).

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

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Alternatively Spliced Variants of Interleukin-4 Promote Inflammation Differentially

2011-03-07 | E-GEOD-23016 | biostudies-arrayexpress

RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons

Project description:The goal of this study was to determine the role of RBM25 in pre-mRNA splicing and examine whether lysine 77 contributes to this function.

2016-10-26 | GSE89140 | GEO

An alternatively spliced p62 isoform promotes breast cancer chemoresistance

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

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Alu-containing exons are alternatively spliced.

Project description: Not available

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Homo sapiens

Project description:RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons

| PRJNA350387 | ENA