Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4 + T cell activation.
Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4 + T cell activation.
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DOI：
10.1016/j.gdata.2016.12.006
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发表时间：
2017-03
期刊：
影响因子：
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通讯作者：
Whisenant, Thomas C
中科院分区：
文献类型：
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作者：
Whisenant, Thomas C
CD4 T细胞活化是哺乳动物适应性免疫反应的核心组成部分，并且这些细胞中基因表达谱的巨大变化强调了这一点。在T细胞活化过程中发生的基因表达变化受到多种方式的调节，包括转录后由rna结合蛋白复合物调节。最近，我们的研究探索了rna结合蛋白U2AF2及其相互作用蛋白在T细胞激活过程中介导组成剪接和选择性剪接转录后变化中的作用。首先，我们使用RNA-seq来鉴定基因表达和剪接在T细胞活化时发生的全局变化。接下来，我们使用RIP-seq鉴定T细胞活化过程中与U2AF2结合的特定基因。在确定了U2AF2的蛋白相互作用伙伴后，我们使用剪接敏感微阵列来测量使用sirna敲除这些蛋白样本对全局基因表达的影响。最后，我们使用rip芯片测量了相同的siRNA敲低对U2AF2特异性结合转录本的影响。在这里，我们提供了每种技术的实验细节和基因表达数据的分析，这些数据已存入基因表达综合数据库（GEO）， Superseries ID: GSE62923。
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.