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

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

PROVIDER: PRJNA258164 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1548720_1.fastq.gz	Fastqsanger.gz
	SRR1548720_2.fastq.gz	Fastqsanger.gz
	SRR1548664.fastq.gz	Fastqsanger.gz
	SRR1548665.fastq.gz	Fastqsanger.gz
	SRR1548715_1.fastq.gz	Fastqsanger.gz

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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 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.

2015-07-15 | GSE60392 | GEO

Neuronal activity regulates alternative exon usage

Project description:Neuronal activity regulates alternative exon usage

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KIS counteracts PTBP2 and regulates alternative exon usage in neurons

Project description:Alternative RNA splicing is an essential and dynamic process in neuronal differentiation and synapse maturation, and dysregulation of this process has been associated with neurodegenerative diseases. Recent studies have revealed the importance of RNA-binding proteins in the regulation of neuronal splicing programs. However, the molecular mechanisms involved in the control of these splicing regulators are still unclear. Here we show that KIS, a kinase upregulated in the developmental brain, imposes a genome-wide alteration in exon usage during neuronal differentiation. KIS contains a protein-recognition domain common to spliceosomal components and phosphorylates PTBP2, counteracting the role of this splicing factor in exon exclusion. At the molecular level, phosphorylation of unstructured domains within PTBP2 causes its dissociation from two co-regulators, Matrin3 and hnRNPM, and hinders the RNA-binding capability of the complex. Furthermore, KIS and PTBP2 display strong and opposing functional interactions in synaptic spine emergence and maturation. Taken together, our data uncover a post-translational control of splicing regulators that link transcriptional and alternative exon usage programs in neuronal development.

2024-04-25 | PXD050320 | Pride

DSCAM-AS1-driven proliferation of breast cancer cells involves regulation of alternative exon splicing and 3’-end usage

Project description:DSCAM-AS1-driven proliferation of breast cancer cells involves regulation of alternative exon splicing and 3’-end usage

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KIS counteracts PTBP2 and regulates alternative exon usage in neurons

Project description:KIS counteracts PTBP2 and regulates alternative exon usage in neurons

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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

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