Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA327415 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3734550.fastq.gz | Fastqsanger.gz | |||
| SRR3734560.fastq.gz | Fastqsanger.gz | |||
| SRR3734551.fastq.gz | Fastqsanger.gz | |||
| SRR3734561.fastq.gz | Fastqsanger.gz | |||
| SRR3734552.fastq.gz | Fastqsanger.gz |
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Project description:Alternative splicing drives transcriptome and proteome diversification. While splicing regulatory proteins govern this process, their global mechanisms remain enigmatic. We generated high resolution transcriptome-wide protein-RNA interaction maps to determine how the splicing repressor hnRNPA1 influences the global association of spliceosome assembly factor U2AF2 and SRSF1 with pre-mRNA. We observed changes in the distribution of U2AF2 crosslinking sites relative to the 3’ splice sites of cassette exons but not constitutive exons upon hnRNPA1 overexpression. By contrast, SRSF1 crosslinking patterns relative to splice sites are independent of hnRNPA1 expression levels. We also observed an hnRNPA1-dependent increase in U2AF2 but not SRSF1 crosslinking to exon proximal antisense Alu elements. Thus Alu elements can serve as splicing factor-responsive sinks for U2AF2. These results not only demonstrate a novel mechanism for alternative splicing regulation but also implicate retrotransposon-derived sequences in the evolution of species-specific alternative splicing.
2017-06-01 | GSE83923 | GEO
Project description:Splicing factor U2AF2 is known to play a pivotal role for 3' splice site recognition at an early step of spliceosome assembly. Here using proximity labeling and biochemical confirmations, we extend the repertoire of putative functional partners of U2AF2 mainly for splicing, chromatin modification, transcription, 3' end processing and RNA methylation. Removal of its RS domain alters numerous of these interactions, reduces its localisation in speckles and impacts splicing genome wide in a manner that depends both on splicing signals and on introns length. Indeed cassette exon flanked by short introns in genes or transcripts located closed to speckles are the most affected by U2AF2 knockdown or RS domain removal. Interestingly, our bioinformatic analyses further reveal that alternative splicing in general mainly occurs near speckles. Finally, we show that multiple phosphorylation sites within the U2AF2 RS domain are required for normal splicing, suggesting that its RS domain mediates U2AF2 regulations. Altogether our data indicate that U2AF2 is in limiting amount to ensure cassette exon inclusion near speckles and give a novel insight on the mechanism of alternative splicing.
2026-03-09 | PXD065448 | Pride
Project description:T cell activation leads to dramatic changes in cellular phenotype. We used CD3/CD28-activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show at the global level that U2AF2 binds the majority of transcripts that are differentially expressed and/or alternatively spliced during CD4 T cell activation. A unique protein interactome centered on U2AF2 is assembled in response to activation. Knocking down specific U2AF2 interacting partners (U2AF1, SYNCRIP, SRRM2, ILF2) selectively affects cytokine secretion and expression of activation markers. Furthermore, the expression and/or alternative splicing of transcripts important for immune cell function are also affected by knocking down these U2AF2 interacting proteins. U2AF1 and SYNCRIP knockdowns affect the proteins and transcripts bound to U2AF2, altering the transcriptome. Our work highlights the importance of RNA binding protein complexes in regulating the differential expression and alternative splicing that defines T cell activation. U2AF2 RIPseq on a primary CD4 T cell culture at rest and 48 hours after anti-CD3/CD28 bead activation
2015-11-04 | E-GEOD-62919 | biostudies-arrayexpress
Project description:T cell activation leads to dramatic changes in cellular phenotype. We used CD3/CD28-activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show at the global level that U2AF2 binds the majority of transcripts that are differentially expressed and/or alternatively spliced during CD4 T cell activation. A unique protein interactome centered on U2AF2 is assembled in response to activation. Knocking down specific U2AF2 interacting partners (U2AF1, SYNCRIP, SRRM2, ILF2) selectively affects cytokine secretion and expression of activation markers. Furthermore, the expression and/or alternative splicing of transcripts important for immune cell function are also affected by knocking down these U2AF2 interacting proteins. U2AF1 and SYNCRIP knockdowns affect the proteins and transcripts bound to U2AF2, altering the transcriptome. Our work highlights the importance of RNA binding protein complexes in regulating the differential expression and alternative splicing that defines T cell activation. RNAseq of total RNA from a primary CD4 T cell culture at rest and 48 hours after anti-CD3/CD28 bead activation
2015-11-04 | E-GEOD-62920 | biostudies-arrayexpress
Project description:Alternative splicing patterns have diverged rapidly during vertebrate evolution, yet the mechanisms and functional consequences of species-dependent splice isoform differences are not well understood. Through an integrative analysis of genome-wide predictions of highly stable RNA duplexes, alternative splicing profiles, and proximity ligation-detection of RNA-RNA interactions in vivo, we observe evidence that the majority of long-range intronic RNA duplexes are mediated by inverted Alu-repeat elements, and that these structures are associated with widespread exon skipping in primates. Our results further reveal evidence that Alu-derived RNA duplexes have contributed to divergence in alternative splicing patterns during mammalian evolution.
2026-03-04 | GSE296727 | GEO
Project description:Reversible pre-mRNA splicing factor phosphorylation is a well-documented feature of spliceosome assembly, activation, and disassembly, yet its functional and mechanistic roles are still emerging. SF3B1, a core spliceosome subunit, is extensively phosphorylated before the first catalytic step of pre-mRNA splicing. Intriguingly, most SF3B1 phosphorylation sites surround its binding sites for U2AF2, an early-stage pre-mRNA splicing factor. Here, we discovered that SF3B1 phosphorylation significantly decreases its association with U2AF2. We determined three crystal structures revealing electrostatic repulsion between an acidic U2AF2 alpha helix and the negatively charged phosphoryl group of SF3B1. Variants with amino acid substitutions that prevent or mimic SF3B1 phosphorylation perturbed thousands of splice sites, primarily those marked by uridine-rich splice site signals recognized by U2AF2. Collectively, our findings demonstrate a widespread but previously unrecognized role for SF3B1 phosphorylation as a gateway for U2AF2 dissociation so that pre-mRNA splicing can proceed.
2026-03-06 | GSE304018 | GEO
Project description:T cell activation leads to dramatic changes in cellular phenotype. We used CD3/CD28-activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show at the global level that U2AF2 binds the majority of transcripts that are differentially expressed and/or alternatively spliced during CD4 T cell activation. A unique protein interactome centered on U2AF2 is assembled in response to activation. Knocking down specific U2AF2 interacting partners (U2AF1, SYNCRIP, SRRM2, ILF2) selectively affects cytokine secretion and expression of activation markers. Furthermore, the expression and/or alternative splicing of transcripts important for immune cell function are also affected by knocking down these U2AF2 interacting proteins. U2AF1 and SYNCRIP knockdowns affect the proteins and transcripts bound to U2AF2, altering the transcriptome. Our work highlights the importance of RNA binding protein complexes in regulating the differential expression and alternative splicing that defines T cell activation. HTA 2.0 microarray results of U2AF2 RIP RNA from a primary CD4 T cell culture after treatment with siRNAs (Control, U2AF1, and SYNCRIP) and 24 hours after anti-CD3/CD28 bead activation Please note that the Series supplementary 'U2AF2RIP_HTA2_all_siRNA_100414.xlsx' file includes multiple worksheets containing: 1) Differentially expressed genes in ctrl siRNA vs. U2AF1 siRNA; 2) Differntially spliced genes in ctrl siRNA vs. U2AF1 siRNA; 3) Differentially spliced exons in ctrl siRNA vs. U2AF1 siRNA; 4) Differentially expressed genes in ctrl siRNA vs. SYNCRIP siRNA; 5) Differntially spliced genes in ctrl siRNA vs. SYNCRIP siRNA; 6) Differentially spliced exons in ctrl siRNA vs. SYNCRIP siRNA
2015-11-04 | E-GEOD-62922 | biostudies-arrayexpress
Project description:Alternative pre-messenger RNA (pre-mRNA) splicing is a post-transcriptional mechanism for controlling gene expression. Splicing patterns are determined by both RNA binding proteins and nuclear pre-mRNA structure. Here, we analyze pre-mRNA splicing patterns, RNA binding sites and RNA structures near these binding sites coordinately controlled by two splicing factors, the heterogeneous nuclear ribonucleoprotein hnRNPA1 and the RNA helicase DDX5. We identified thousands of alternative pre-mRNA splicing events controlled by these factors by RNA-seq following RNA interference. Enhanced CLIP (eCLIP) on nuclear extracts was used to identify protein-RNA binding sites for both proteins in the nuclear transcriptome. We found a significant overlap between hnRNPA1 and DDX5 splicing targets and that they share many closely linked binding sites as determined by eCLIP analysis. In vivo SHAPE chemical RNA structure probing data was used to model RNA structures near several exons controlled and bound by both proteins. Both sequence motifs and in vivo UV crosslinking sites for hnRNPA1 and DDX5 were used to map binding sites in their RNA targets and often these sites flanked regions of higher chemical reactivity suggesting an organized nature to nuclear pre-mRNPs. This work provides a first glimpse into the possible RNA structures surrounding pre-mRNA splicing factor binding sites.
2018-06-08 | GSE115442 | GEO
Project description:T cell activation leads to dramatic changes in cellular phenotype. We used activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show that U2AF2 binds the majority of transcripts that are differentially expressed and/or alternatively spliced during activation. Using RIP mass spectrometry, a unique protein interactome centered on U2AF2 is assembled by activation and comprised of both directly bound central members (RNAse-resistant) and indirectly bound peripheral members (RNAse-sensitive). Knocking down specific U2AF2 interactome members (U2AF1, SYNCRIP, SRRM2, ILF2) selectively affects cytokine secretion and activation markers. The expression and/or alternative splicing of transcripts important for immune cell function are also affected by knocking down these interactome members, both peripheral and central. Furthermore, we show that knockdown of interactome members can affect the proteins and transcripts bound to U2AF2, altering the transcriptome of activated T cells. Our work highlights the importance of understanding the assembly of RNA binding protein complexes as regulators of T cell activation and function.
2016-04-27 | PXD001846 | Pride
Project description:T cell activation leads to dramatic changes in cellular phenotype. We used activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show that U2AF2 binds the majority of transcripts that are differentially expressed and/or alternatively spliced during activation. Using RIP mass spectrometry, a unique protein interactome centered on U2AF2 is assembled by activation and comprised of both directly bound central members (RNAse-resistant) and indirectly bound peripheral members (RNAse-sensitive). Knocking down specific U2AF2 interactome members (U2AF1, SYNCRIP, SRRM2, ILF2) selectively affects cytokine secretion and activation markers. The expression and/or alternative splicing of transcripts important for immune cell function are also affected by knocking down these interactome members, both peripheral and central. Furthermore, we show that knockdown of interactome members can affect the proteins and transcripts bound to U2AF2, altering the transcriptome of activated T cells. Our work highlights the importance of understanding the assembly of RNA binding protein complexes as regulators of T cell activation and function.
2016-04-27 | PXD001843 | Pride