Non-coding RNA structure change in Chronic Obstructive Pulmonary Disease

慢性阻塞性肺疾病中非编码RNA结构的变化

• 批准号: 10159303
• 负责人: Alain T Laederach
• 金额: $ 52.02万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-01-01 至 2023-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10159303
• 关键词: 5' Untranslated Regions; Affect; Alternative Splicing; American; Area; Chronic Obstructive Airway Disease; Complex; Computer Models; Data; Development; Disease; Down-Regulation; Elements; Exons; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genome; Genomic approach; Genomics; Goals; Human; Human Genome; Laboratories; Lead; Liver; Location; Lung; Maps; Measures; Mediating; Messenger RNA; Modeling; Molecular; Mutate; Nucleotides; Open Reading Frames; Outcome; Participant; Protein Biosynthesis; Protein Isoforms; Proteins; RNA; RNA Splicing; Regulation; Resolution; Resources; Ribosomes; Risk Factors; Scanning; Severity of illness; Site; Smoking; Structural Models; Structure; Testing; Tissues; Transcript; Translating; Translations; Untranslated RNA; Untranslated Regions; Up-Regulation; Variant; Work; base; causal variant; computer framework; design; differential expression; experimental study; genetic association; genetic variant; mRNA Expression; mortality; novel; precision medicine; programs

SUMMARY Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality in the developed world. Smoking is an important risk factor for the disease, but genetics determine outcome and disease severity. A significant and broad challenge in establishing the causal molecular mechanism from genetic association data is the fact that a majority of COPD-associated variants map to non-coding regions of the human genome. One of the genes strongly associated with COPD is SERPINA1, which encodes the a-1 antitrypsin protein. The SERPINA1 gene is remarkably complex: It has eleven splice variants, all of which change the 5'-untranslated region (5'-UTR) without altering the sequence of the encoded protein. We found that translation efficiencies of the mRNAs varied by orders of magnitude due to the strengths of upstream RNA structure and of open reading frames (uORFs). uORFs are found in roughly 50% of human genes and tend to function to reduce translation of the downstream gene but, other than this observation, are poorly understood mechanistically. We have developed and parameterized a structure-based leaky scanning model of translation that considers alternative splicing, uORF Kozak sequence strength, the RNA structure at the initiation site of uORFs, and the efficiency of translation of the primary open reading frame. We propose in our first aim to define how RNA structure and alternative splicing control expression of a-1 antitrypsin and extend this approach to two other COPD-associated genes. In our second aim we will comprehensively characterize the RNA structural elements in the SERPINA1 mRNA 5'-UTRs and in two other COPD-related mRNAs that control translation efficiency, without and with uORFs. These experiments will establish accurate and broadly impactful frameworks to define the RNA structural features that modulate translation efficiency in 5'-UTRs and will refine ribosomal leaky scanning models to better predict tissue-specific expression of COPD-associated proteins.

摘要 在发达国家，慢性阻塞性肺疾病(COPD)是导致死亡的主要原因。吸烟 是疾病的重要风险因素，但遗传决定了结果和疾病的严重程度。一个重要的 而从遗传关联数据建立因果分子机制的广泛挑战是这样一个事实 大多数与COPD相关的变异都映射到人类基因组的非编码区。其中一个基因 与COPD密切相关的是SERPINA1，它编码a-1抗胰蛋白酶蛋白。SERPINA1基因 非常复杂：它有11个剪接变体，所有这些都改变了5‘-非翻译区(5’-UTR) 而不改变编码蛋白质的序列。我们发现，mRNAs的翻译效率各不相同 由于上游RNA结构和开放阅读框架(UORF)的优势，这一点可达数量级。 在大约50%的人类基因中发现了uORF，它们的功能往往是减少下游的翻译 但是，除了这一观察之外，人们对这一现象的机械理解很少。我们已经开发出了 考虑可选剪接的基于结构的翻译泄漏扫描模型uORF的参数化 Kozak序列强度、uORFs起始点的RNA结构和翻译效率 主要的开放阅读框架。在我们的第一个目标中，我们建议定义RNA的结构和选择性剪接 控制α-1抗胰蛋白酶的表达，并将这一方法扩展到其他两个COPD相关基因。在我们的 第二个目的，我们将全面表征SERPINA1基因5‘-UTRs中的RNA结构元素 以及另外两个控制翻译效率的COPD相关mRNAs，没有uORF和有uORF。这些 实验将建立准确和广泛影响的框架来定义RNA结构特征 调整5‘-UTRs的翻译效率，并将改进核糖体泄漏扫描模型以更好地预测 COPD相关蛋白的组织特异性表达。