"Ribonomics" of Gene Regulation to predict Innate Immune Responses

基因调控的“核糖组学”预测先天免疫反应

• 批准号: 8991718
• 负责人: Douglas L Black
• 金额: $ 193.96万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-01-05 至 2017-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8991718
• 关键词: 3' Splice Site; Accounting; Affect; Biological Models; Biological Phenomena; Biology; Cells; Chromatin; Chromatin Modeling; Clip; Complement; Computer Simulation; Cytoplasm; DNA Methylation; DNA Polymerase II; Data; Data Set; Degradation Pathway; Endotoxins; Enhancers; Environment; Event; Exons; Experimental Models; Gene Expression; Gene Expression Regulation; Gene Structure; Genes; Genetic Transcription; Genomic approach; Genomics; Half-Life; Health; Immune; Immune Response Genes; Immune response; Inflammatory; Introns; Kinetics; Machine Learning; Measures; Mediating; Messenger RNA; MicroRNAs; Modeling; Nucleic Acids; Nucleoplasm; Pattern; Phase; Process; Production; Protein Isoforms; Proteins; RNA; RNA Splicing; RNA-Binding Proteins; Recording of previous events; Regulation; Regulator Genes; Research Personnel; Resolution; Role; Stimulus; Systems Biology; Testing; Time; Transcription Initiation; Translations; Up-Regulation; Yeasts; analytical tool; base; cell type; chromatin modification; epigenome; exon skipping; experimental analysis; gene product; genome browser; histone modification; mRNA Decay; mRNA Transcript Degradation; macrophage; mutant; network models; next generation sequencing; novel; pathogen; predictive modeling; programs; promoter; response; tool; transcription factor; transcriptomics

DESCRIPTION (provided by applicant): The expression of genes involves a sequence of enzymatic events, such as transcription, mRNA processing, mRNA decay, and translation, that are subject to gene regulatory networks (GRNs) of protein-nucleic acid interactions. It is well appreciated that the control of transcription via regulatory networks that regulate enhancer and promoter activities are not the sole determinant of what gene products result, but that exon skipping is pervasive and post-transcriptional mechanisms such as mRNA splicing and decay determine the kinetics of mRNA induction and abundance. Indeed, in our preliminary studies of the macrophage response to pathogens, we find that a majority of induced gene expression events result in mRNAs that deviate substantially from those predicted by the genome-browser, and that mRNA decay is controlled by both protein- nucleic acid and miRNA regulatory networks. The proposed Center for the "Ribonomics" of Gene Regulation leverages and pioneers Next Gen Sequencing and computational modeling approaches to develop a predictive model for which mRNA isoforms are expressed and at what level given a given promoter activity and transcription initiation rate. We will develop generally applicable tools in conjunction with or in depth and quantitative experimental analysis of the macrophage response to pathogen-associated endotoxin, which results in the dramatic up regulation of more than 1000 genes. Strikingly, our preliminary data identified more than 900 exon skipping events in addition to numerous cases of alternative 5' or 3' splice site use, emphasizing the essential contribution of post-initiation events. Further, these splice patterns are dependent on the macrophage subtype-specific chromatin landscape and are altered by inducible splice factors in primed or tolerated states. Thus we will leverage the well-described macrophage biology and associated experimental model systems, to examine the role of gene structure and sequence (Aim 1), the role of chromatin modifications (Aim 2), and of trans-acting splicing factors (Aim 3) in determining the identity of mature mRNAs and their associated synthesis rates, before adding the stimulus-responsive regulatory networks that confer mRNA half-life control and thus determine the abundance of each mRNA isoform (Aim 4).

描述（由申请人提供）：基因的表达涉及一系列酶促事件，如转录、mRNA加工、mRNA降解和翻译，这些事件受到蛋白质-核酸相互作用的基因调控网络（GRNs）的影响。很好地理解，通过调节增强子和启动子活性的调节网络对转录的控制不是产生什么基因产物的唯一决定因素，但是外显子跳跃是普遍的，并且转录后机制如mRNA剪接和衰变决定mRNA诱导和丰度的动力学。事实上，在我们对巨噬细胞对病原体的反应的初步研究中，我们发现大多数诱导的基因表达事件导致的mRNA与基因组浏览器预测的mRNA基本上偏离，并且mRNA衰减受蛋白质-核酸和miRNA调控网络的控制。拟议中的基因调控“核糖体组学”中心利用并开拓了下一代测序和计算建模方法，以开发一种预测模型，用于表达mRNA亚型以及给定启动子活性和转录起始速率的水平。我们将开发普遍适用的工具，结合或深入和定量的实验分析巨噬细胞对病原体相关内毒素的反应，这导致超过1000个基因的急剧上调。引人注目的是，我们的初步数据确定了超过900个外显子跳跃事件，除了许多情况下的选择性5'或3'剪接位点的使用，强调了重要的贡献后启动事件。此外，这些剪接模式依赖于巨噬细胞亚型特异性染色质景观，并在引发或耐受状态下被诱导型剪接因子改变。因此，我们将利用已充分描述的巨噬细胞生物学和相关实验模型系统，来研究基因结构和序列（Aim 1）、染色质修饰（Aim 2）和反式作用剪接因子（Aim 3）在确定成熟mRNA及其相关合成速率中的作用，在加入刺激响应调节网络之前，该网络赋予mRNA半衰期控制，从而确定每种mRNA同种型的丰度（目的4）。