Non-coding RNA structure change in Chronic Obstructive Pulmonary Disease

摘要 慢性阻塞性肺疾病(COPD)是一种与160多个基因相关的复杂遗传性疾病 再加上众多的环境因素。在大多数情况下，单核苷酸多态(SNPs)最 与COPD强烈相关的基因不会改变蛋白质编码序列，而是映射到非编码序列， 但通常是转录的，基因组的区域，包括UTRs和内含子。到目前为止，我们的协作工作已经 重点研究了SNPs对5‘和3’非编码区RNA结构的影响，并揭示了许多序列 改变调节RNA结构并改变COPD相关基因的翻译。对这一概念的理解 RNA结构和基因表达之间的相互关系还处于起步阶段，主要集中在 基于外显子配对的二级结构，并受到我们无法充分探索RNA的严重限制 细胞中的结构。我们已经开发了三种新的基于化学的RNA结构探测策略，允许 美国将(I)研究细胞中的前体mRNA结构，(Ii)确定UTRs中可能采用真高表达的区域。 有序的三级结构，以及(Iii)确定RNA中的穿越空间接触并开发三维 它们复杂结构的模型。这些技术打开了广泛和长期的研究领域，研究如何 复杂的RNA结构调节基因表达，以及SNPs如何改变RNA结构 疾病。另一个关键的联合发展是收集了广泛的全人群转录 (RNA-seq)通过我们参与的联合体获得COPD患者的肺和血液组织的数据。基于 这些转录数据及其分析，我们已经表征了剪接和 COPD相关基因的多聚腺苷酸化；这两个过程事件都对基因有重要影响 表情。我们的计划还利用了大量的探索性工作，表明编码中的RNA结构 与COPD相关的基因序列调节它们的翻译。对于这项提议，我们现在处于一个独特的 利用新技术和转录分析来询问RNA结构是如何调节的 COPD相关基因的信使核糖核酸翻译。我们希望确定包含强健靶标的RNA结构 用于RNA疗法，旨在改变蛋白质表达的转录后基因调控。这个项目 将最终揭示RNA结构如何调节蛋白质翻译和选择性剪接的新原理 并将确定与COPD相关的人类转录组中的RNA调节结构。

SUMMARY Chronic obstructive pulmonary disease (COPD) is a complex genetic disease associated with over 160 genes coupled with numerous environmental factors. In most cases, the single-nucleotide polymorphisms (SNPs) most strongly associated with COPD do not alter the protein coding sequence of genes but instead map to non-coding, but often transcribed, regions of the genome, including UTRs and introns. Our collaborative work to date has focused on how 5' and 3' UTR RNA structures are affected by SNPs and has revealed that many sequence changes modulate RNA structures and alter translation of COPD-associated genes. Understanding of the interrelationships between RNA structure and gene expression is in its infancy, has primarily focused on the based-paired secondary structure of exons, and has been severely limited by our inability to fully explore RNA structure in cells. We have developed three novel chemistry-based RNA structure probing strategies that allow us to (i) investigate precursor mRNA structure in cells, (ii) identify regions in UTRs that likely adopt true higher- order tertiary structure, and (iii) determine through-space contacts in RNAs and develop three-dimensional models of their complex structures. These technologies open broad and long-term research areas into how complex RNA structures modulate gene expression and how RNA structure is changed by SNPs associated with disease. Another critical, allied development has been collection of extensive population-wide transcriptomic (RNA-seq) data of COPD patient lung and blood tissues through consortia in which we participate. Based on these transcriptomic data and their analysis, we have characterized important changes in both splicing and polyadenylation of COPD associated genes; both processing events have important consequences on gene expression. Our program also leverages substantial exploratory work that shows that RNA structure in coding sequences of genes associated with COPD modulates their translation. For this proposal, we are now in a unique position to leverage novel technologies and transcriptomic analyses to interrogate how RNA structure regulates mRNA translation of COPD-associated genes. We expect to identify RNA structures that comprise robust targets for RNA therapeutics designed to alter post-transcriptional gene regulation of protein expression. This project will ultimately reveal new principles for how RNA structure regulates protein translation and alternative splicing and will identify RNA regulatory structures in the human transcriptome associated with COPD.