Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4+ T cell activation

Abstract

CD4 T cell activation is a central component of the mammalian adaptive immune response and is underscored by a dramatic change in the gene expression profile in these cells. The changes in gene expression that occur during T cell activation are regulated in multiple ways including post-transcriptionally by complexes of RNA-binding proteins. Recently, our study explored the role of the RNA-binding protein U2AF2 and its interacting proteins in mediating posttranscriptional changes in constitutive and alternative splicing during T cell activation. First, we used RNA-seq to identify the global changes in gene expression and splicing that occur with T cell activation. Next, we used RIP-seq to identify the specific genes bound to U2AF2 during T cell activation. After identification of the protein interacting partners of U2AF2, we used splicing sensitive microarrays to measure the effects on global gene expression of using siRNAs to knock down a sampling of these proteins. Finally, we used RIP-chip to measure the effects of the same siRNA knockdown on the transcripts specifically bound to U2AF2. Here we provide the experimental details and analysis of the gene expression data for each of these techniques, which have been deposited into Gene Expression Omnibus (GEO) with the Superseries ID: GSE62923.

Keywords

• RNA-seq
• RIP-seq
• RIP-chip
• T-cell activation