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Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE60392 | GEO | 2015/07/15

SECONDARY ACCESSION(S): PRJNA258164

REPOSITORIES: GEO

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Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors.

Project description:The mechanisms that regulate alternative precursor mRNA (pre-mRNA) splicing are largely unknown. Here, we perform an RNAi screen to identify factors required for alternative splicing regulation by RBFOX2, an RNA-binding protein that promotes either exon inclusion or exclusion. Unexpectedly, we find that two mRNA 3' end formation factors, cleavage and polyadenylation specificity factor (CPSF) and SYMPK, are RBFOX2 cofactors for both inclusion and exclusion of internal exons. RBFOX2 interacts with CPSF/SYMPK and recruits it to the pre-mRNA. RBFOX2 and CPSF/SYMPK then function together to regulate binding of the early intron recognition factors U2AF and U1 small nuclear ribonucleoprotein particle (snRNP). Genome-wide analysis reveals that CPSF also mediates alternative splicing of many internal exons in the absence of RBFOX2. Accordingly, we show that CPSF/SYMPK is also a cofactor of NOVA2 and heterologous nuclear ribonucleoprotein A1 (HNRNPA1), RNA-binding proteins that also regulate alternative splicing. Collectively, our results reveal an unanticipated role for mRNA 3' end formation factors in global promotion of alternative splicing.

| S-EPMC4458236 | biostudies-literature

Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-07-15 | E-GEOD-60392 | biostudies-arrayexpress

Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [Affymetrix]

Project description:Transcriptome analysis of samples from Non-silencing, RBFOX2 and CPSF3 knockdown cells. Our analysis shows the role of CPSF-SYMPK in regulation of global alternative splicing.

2015-07-15 | GSE47465 | GEO

Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [iCLIP-Seq]

Project description:iCLIP was performed in duplicates using RBFOX2 and CPSF2 antibodies. iCLIP was performed in duplicates using RBFOX2 and CPSF2 antibodies.

2015-07-15 | E-GEOD-60385 | biostudies-arrayexpress

Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [RNA-Seq]

Project description:RNA-seq analysis of samples from Non-silencing, RBFOX2 and CPSF2 knockdown cells We analyzed 6 samples using the Illumina HiSeq 2000. Sequence data was processed by DexSeq. Two biological replicates were performed for Non-silencing, RBFOX2 and CPSF2 knockdown cells

2015-07-15 | E-GEOD-60391 | biostudies-arrayexpress

Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [iCLIP-Seq]

Project description:iCLIP was performed in duplicates using RBFOX2 and CPSF2 antibodies.

2015-07-15 | GSE60385 | GEO

Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [RNA-Seq]

Project description:RNA-seq analysis of samples from Non-silencing, RBFOX2 and CPSF2 knockdown cells

2015-07-15 | GSE60391 | GEO

Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors

Project description:Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors

| PRJNA258164 | ENA

Computational detection of alternative exon usage.

Project description:BACKGROUND:With the advent of the GeneChip Exon Arrays, it is now possible to extract "exon-level" expression estimates, allowing for detection of alternative splicing events, one of the primary mechanisms of transcript diversity. In the context of (1) a complex trait use case and (2) a human cerebellum vs. heart comparison on previously validated data, we present a transcript-based statistical model and validation framework to allow detection of alternative exon usage (AEU) between different groups. To illustrate the approach, we detect and confirm differences in exon usage in the two of the most widely studied mouse genetic models (the C57BL/6J and DBA/2J inbred strains) and in a human dataset. RESULTS:We developed a computational framework that consists of probe level annotation mapping and statistical modeling to detect putative AEU events, as well as visualization and alignment with known splice events. We show a dramatic improvement (?25 fold) in the ability to detect these events using the appropriate annotation and statistical model which is actually specified at the transcript level, as compared with the transcript cluster/gene-level annotation used on the array. An additional component of this workflow is a probe index that allows ranking AEU candidates for validation and can aid in identification of false positives due to single nucleotide polymorphisms. DISCUSSION:Our work highlights the importance of concordance between the functional unit interrogated (e.g., gene, transcripts) and the entity (e.g., exon, probeset) within the statistical model. The framework we present is broadly applicable to other platforms (including RNAseq).

| S-EPMC3097375 | biostudies-literature

Neuronal activity regulates alternative exon usage.

Project description:Neuronal activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. A large number of genes regulated by different neuronal plasticity inducing pathways have been identified, but altered gene expression levels represent only part of the complexity of the activity-regulated transcriptional program. Alternative splicing, the differential inclusion and exclusion of exonic sequence in mRNA, is an additional mechanism that is thought to define the activity-dependent transcriptome. Here, we present a genome wide microarray-based survey to identify exons with increased expression levels at 1, 4 or 8 h following neuronal activity in the murine hippocampus provoked by generalized seizures. We used two different bioinformatics approaches to identify alternative activity-induced exon usage and to predict alternative splicing, ANOSVA (ANalysis Of Splicing VAriation) which we here adjusted to accommodate data from different time points and FIRMA (Finding Isoforms using Robust Multichip Analysis). RNA sequencing, in situ hybridization and reverse transcription PCR validate selected activity-dependent splicing events of previously described and so far undescribed activity-regulated transcripts, including Homer1a, Homer1d, Ania3, Errfi1, Inhba, Dclk1, Rcan1, Cda, Tpm1 and Krt75. Taken together, our survey significantly adds to the comprehensive understanding of the complex activity-dependent neuronal transcriptomic signature. In addition, we provide data sets that will serve as rich resources for future comparative expression analyses.

| S-EPMC7656758 | biostudies-literature

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