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The effects of the loss of EWSR1 on alternative splicing

ABSTRACT: EWSR1 belongs to the FET family of proteins and has the ability to bind RNA. However, the role of EWSR1 in alternative RNA splicing remains unclear. Here, we performed an RNA sequencing study in the EWSR1 knockout cells to identify genome-wide changes in alternative splicing following loss of EWSR1.

ORGANISM(S): Homo sapiens

PROVIDER: GSE270149 | GEO | 2026/06/26

REPOSITORIES: GEO

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EWSR1 influences alternative splicing through direct and indirect mechanisms

Project description:FET family RNA binding proteins are implicated in cancer and neurological disorders and yet their biological function is incompletely understood. We used cross-linking and immunoprecipitation followed by high-throughput sequencing (HITS-CLIP) as well as gene expression and alternative splicing analysis by RNAseq to characterize the molecular function of the FET family RNA binding protein EWSR1. In HeLA cells, EWSR1 binding is enriched at 3’UTRs and at both 5’ exon/intron and 3’ intron/exon boundaries. RNAs bound by EWSR1 are functionally enriched for RNA binding and RNA processing genes, suggesting a key role for EWSR1 in RNA regulation. While EWSR1 knock-down altered expression of hundreds of genes, only a subset of the transcripts for these genes were directly bound by EWSR1. By overlapping the HITS-CLIP data with the RNAseq splicing analysis we identified genes where EWSR1 binding is more likely to directly affect splicing. EWSR1 regulated splicing events were varied and included exon inclusion, alternative 3 exon usage and intron retention. These results indicate that EWSR1 has pleiotropic effects on splicing and that these effects are caused both by direct regulation of splicing and through effects on a large number of RNAs that themselves code for splicing effectors. Further understanding of this complex splicing regulation network may be important to disentangle the role of EWSR1 in multiple human diseases.

2018-05-01 | GSE98836 | GEO

The effects of the loss of EWSR1 on alternative splicing

Project description:The effects of the loss of EWSR1 on alternative splicing

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hnRNPDL extensively regulates transcription and alternative splicing

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Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets

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IGF2BP3 may contributes to lung tumorigenesis by regulating the alternative splicing of PKM [RIP-seq]

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Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

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