Ontology highlight
ABSTRACT:
PROVIDER: PRJNA660570 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12560248_1.fastq.gz | Fastqsanger.gz | |||
| SRR12560248_2.fastq.gz | Fastqsanger.gz | |||
| SRR12560249_1.fastq.gz | Fastqsanger.gz | |||
| SRR12560249_2.fastq.gz | Fastqsanger.gz |
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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
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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.
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