Characterization of Regulated Intron Retention in T Cell Activation

项目概述/摘要T细胞活化是免疫反应的重要步骤，异常会导致致病性疾病，包括免疫缺陷、感染性休克和自身免疫性疾病。激活过程包括在转录和转录后水平上协调的基因表达调控程序。我们在人类CD4+ T细胞中的初步研究表明，受调控的内含子保留与mRNA降解可能是T细胞激活的一种新的转录后调节机制。内含子保留是真核生物选择性剪接的关键形式之一。然而，其在基因调控中的功能参与尚未得到很好的探讨。我们建议通过实现以下具体目标来弥合差距。目的1：描述内含子保留的定义特征。我们的初步结果表明，内含子保留具有基因特异性和内含子特异性。内含子保留基因与一种独特的表观遗传状态有关。序列和染色质特征将有助于为IR的未来机制研究铺平道路。我们还建议研究跨细胞类型和物种的调节内含子保留的保护。为了了解其保守程度，我们建议收集人类CD8+ T细胞和小鼠CD4+ T细胞的转录组学特征（RNA- seq）、RNA聚合酶II全基因组占用（ChIP-Seq）以及其他表观基因组数据。综合计算分析将用于评估内含子保留的普遍性及其在免疫系统激活中的功能作用。总的来说，来自这些系统的数据将为内含子保留的核心特征及其在序列、表观遗传和网络水平上的调控提供新的见解。目的2：了解受调控的内含子保留与其他基因调控模式的联系。为了全面了解激活过程的调节，研究它们是如何协同工作的是很重要的。我们将确定转录调控、受调控的内含子保留和3‘非翻译区缩短之间的分工，3’非翻译区缩短是T细胞活化过程中突出的另一种转录后调控模式。这项工作有望为内含子保留及其调控的分子机制提供线索，并为我们对适应性免疫反应调控的理解开辟一个新的维度。此外，我们期望在这个项目中开发的综合计算框架对研究其他系统中的内含子保留有用。

DESCRIPTION (provided by applicant): Project Summary/Abstract T cell activation is an essential step in immune response and abnormalities result in pathogenic conditions, including immunodeficiency, septic shock and auto-immune diseases. The activation process involves a coordinated program of gene expression regulations at both transcriptional and post-transcriptional levels. Our preliminary work in human CD4+ T cells demonstrated that regulated intron retention coupled with mRNA degradation may serve as a novel post- transcriptional regulatory mechanism underlying T cell activation. Intron retention is one of the key forms of alternative splicing in eukaryotes. However, its functional involvement in gene regulation has not been well explored. We propose to bridge the gap by accomplishing the following specific aims. Aim 1: Characterize the defining features of intron retention. Our preliminary results showed that intron retention is gene- and intron- specific. Intron-retained genes are associated with a unique epigenetic state. The sequence and chromatin signatures will help pave the path for future mechanistic studies of IR. We also propose to examine the conservation of regulated intron retention across cell-types and species. To understand the extent of its conservation, we propose to collect transcriptomic profile (RNA-Seq), genome-wide occupancy of RNA Polymerase II (ChIP-Seq), as well as other epigenomic data for human CD8+ T cells and mouse CD4+ T cells. An Integrated computational analysis will be used to assess the prevalence of intron retention and its functional role in immune system activation. Collectively, data from these systems will provide novel insights into the core features of intron retention and its regulation at the sequence, epigenetic and network level. Aim 2: Understand the connection of regulated intron retention with other modes of gene regulation. To gain a comprehensive understanding of the regulation of the activation process, it is important to examine how they work in concert. We will determine the division of labor between transcriptional regulation, regulated intron retention, and shortening of 3' untranslated region, another mode of post-transcriptional regulation prominent in the T cell activation process. The proposed work promises to yielding clues to the molecular mechanism of intron retention and its regulation, and opening up a new dimension in our understanding of the regulation of adaptive immune response. In addition, we anticipate the integrative computational frameworks developed in this project to be useful for studying intron retention in other systems.