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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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High-resolution analysis of SRSF3 and SRSF4 binding sites by iCLIP

ABSTRACT: Endogenous SRSF3 and SRSF4 RNA binding sites were identified genome-wide by iCLIP in P19 BAC trangenic cell lines using GFP-epitope tag.

ORGANISM(S): Mus musculus

SUBMITTER: Minna-Liisa Anko

PROVIDER: E-MTAB-747 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes.

Änkö Minna-Liisa ML Müller-McNicoll Michaela M Brandl Holger H Curk Tomaz T Gorup Crtomir C Henry Ian I Ule Jernej J Neugebauer Karla M KM

Genome biology 20120101 3

<h4>Background</h4>The SR proteins comprise a family of essential, structurally related RNA binding proteins. The complexity of their RNA targets and specificity of RNA recognition in vivo is not well understood. Here we use iCLIP to globally analyze and compare the RNA binding properties of two SR proteins, SRSF3 and SRSF4, in murine cells.<h4>Results</h4>SRSF3 and SRSF4 binding sites mapped to largely non-overlapping target genes, and in vivo consensus binding motifs were distinct. Interaction ...[more]

PMID: 22436691

Similar Datasets

SRSF7 and SRSF3 affectSRSF7 and SRSF3 affect 3’UTR length in opposite directions by controlling proximal poly(A)-site usage and CFIm levels 3’UTR length in opposite directions by controlling proximal poly(A)-site usage and CFIm levels

Project description:Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which affects the length of their 3’ untranslated regions (3’UTRs). APA regulates stage- and tissue-specific gene expression by affecting the stability, subcellular localization or translation rate of transcripts. We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, link APA to mRNA export. However, the underlying mechanism for APA regulation by SRSF3 and SRSF7 remained unknown. Here, we combined iCLIP and 3’-end sequencing to find that both proteins bind upstream of proximal PAS (pPAS), but exert opposing effects on 3’UTR length. We show that SRSF7 enhances pPAS usage in a splicing-independent and concentration-dependent manner by recruiting the cleavage factor FIP1, thereby generating short 3’UTRs. SRSF7-specific domains that are absent in SRSF3 are necessary and sufficient for FIP1 recruitment. SRSF3 promotes long 3’UTRs by maintaining high levels of the cleavage factor Im (CFIm) via alternative splicing. Using iCLIP, we show that CFIm binds before and after the pPASs of SRSF3 targets, which masks them and inhibits polyadenylation. In the absence of SRSF3, CFIm levels are strongly reduced, which exposes the pPASs and leads to shorter 3’UTRs. Conversely, during cellular differentiation, 3’UTRs are massively extended, while the levels of SRSF7 and FIP1 strongly decline. Altogether, our data suggest that SRSF7 acts as a sequence-specific enhancer of pPASs, while SRSF3 inhibits pPAS usage by controlling CFIm levels. Our data shed light on a long-standing puzzle of how one factor (CFIm) can inhibit and enhance PAS usage.

2021-09-09 | PXD018090 | Pride

RNA-Seq analysis of SRSF3 KO hearts compared to controls and iCLIP analysis of SRSF3 binding profile in neonatal cardiomyocytes

Project description:The goal of this study is to analyse the transcriptome of control hearts vs hearts lacking SRSF3 expression and to analyse binding preferences of SRSF3 in cardiac myocytes.

2019-05-27 | GSE123002 | GEO

High-resolution analysis of SRSF3 and SRSF4 binding sites by iCLIP

Project description:High-resolution analysis of SRSF3 and SRSF4 binding sites by iCLIP

| PRJEB2638 | ENA

iCLIP mapping of coilin-RNA interactions in HeLa and P19 cells

Project description:Our ChIP resuls suggested that coilin association with U3, snRNA and histone genes might be dependent on coilin-RNA interaction. We used iCLIP of coilin-GFP expressed in HeLa and P19 cell lines at endogenous levels to identify coilin RNA targets and investigate RNA-binding specificity. P19 cells expressing GFP fused to a nuclear localization signal (GFP-NLS) was used as a negative control. iCLIP results revealed that coilin binds several classes of ncRNA including snRNAs, U3 snoRNA and scaRNAs. Interestlignly the majority of coilin targets were intronic snoRNAs, suggesting a novel role of CBs in snoRNA biogenesis.

2014-11-06 | GSE58448 | GEO

iCLIP mapping of coilin-RNA interactions in HeLa and P19 cells

2014-11-06 | E-GEOD-58448 | biostudies-arrayexpress

Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm

Project description:We report a new method which combines subcellular fractionation to advance sequencing technique iCLIP. In this way we identified the spectrum of interactions of two SR-proteins (SRSF3 and SRSF7) to their target RNAs in different subcellular compartments

2017-08-10 | GSE79792 | GEO

MACE-seq of P19 cells after knockdown of Srsf3 and Srsf7

Project description:Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3’ untranslated regions (3’UTRs). APA regulates stage- and tissue-specific gene expression by affecting the stability, subcellular localization and translation rate of transcripts. We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained, however, unknown. Here, we combined iCLIP, RNA-Seq and 3’-end sequencing to find that both proteins bind upstream of proximal PASs (pPASs), yet they exert opposite effects on 3’UTR length. We show that SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, thereby generating short 3’UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, and hypo-phosphorylation contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3’UTRs by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon reduced expression of SRSF3, CFIm levels strongly decrease and 3’UTRs are globally shortened. In SRSF3-regulated transcripts, CFIm and FIP1 bind upstream of dPASs and promote their usage. Surprisingly, both factors are also recruited to pPASs under conditions where their usage is blocked, suggesting the formation of inactive cleavage complexes. Thus, we identify SRSF3 as a novel regulator of CFIm activity, provide evidence that CFIm inhibits pPAS usage and show that small differences in the domain architecture of SR proteins confer opposite effects on PAS selection.

2021-01-28 | GSE151722 | GEO

RNA-Seq analysis of SRSF3 KO hearts compared to controls and iCLIP analysis of SRSF3 binding profile in neonatal cardiomyocytes

Project description:RNA-Seq analysis of SRSF3 KO hearts compared to controls and iCLIP analysis of SRSF3 binding profile in neonatal cardiomyocytes

| PRJNA507187 | ENA

Transcriptome-wide mapping of RNA:protein interactions of SRSF7 variants in P19 cells by iCLIP and piCLIP

Project description:We used P19 cells that overexpress GFP-tagged SRSF7 by 3.4-fold and expression-matched SRSF7 mutants that either lack a functional Zinc-knuckle domain or a part of their RS-domain and compared the extent and pattern of binding to mRNAs. For this we performed iCLIP using anti-GFP antibodies. We also performed iCLIP from monosomal and polysomal fractions. In addition we performed iCLIP using anti-SRSF7 antibodies to compare the binding patterns of SRSF7-GFP, endogenous SRSF7 protein and its truncated SRSF7_RRM variant.

2020-03-02 | GSE140721 | GEO

RNAi profiling by array of mouse P19 cells to investigate how SR proteins coordinate gene expression programs

Project description:Members of the SR protein family of RNA binding proteins play numerous roles in gene expression, including the regulation of pre-mRNA splicing, mRNA export, and translation. How SR proteins coordinate gene expression programs has been largely unexplored, and comprehensive knowledge of endogenous mRNA targets is lacking. Gene expression changes upon SRp20 or SRp75 RNAi in P19 parental, SRp75-BAC, and SRp20-BAC cells were measured with mouse whole genome microarrays. The knockdown of either SRp20 or SRp75 led to up- or downregulation of specific transcripts. Phenotypic rescue in the SRp75-BAC, and SRp20-BAC cells demonstrated functionality of the GFP-tagged SR proteins, and showed the specificity of the knockdowns.

2010-07-20 | E-MEXP-2640 | biostudies-arrayexpress

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