Variant induced RNA structure change in human genetic disease

人类遗传病中变异诱导的RNA结构变化

• 批准号: 10620737
• 负责人: Alain T Laederach
• 金额: $ 41.64万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10620737
• 关键词: 3-Dimensional; Acylation; Alleles; Biological; Biological Assay; Cells; Chemical Structure; Chemicals; Data; Disease; Disease model; Elements; Etiology; Gene Expression; Gene Expression Regulation; Genetic Diseases; Goals; Human Genetics; Hybrids; Hydroxyl Radical; Maps; Measures; Messenger RNA; Modeling; Modification; Molecular; Mutation; Organism; Primer Extension; Process; Proteins; RNA; RNA Stability; RNA, Messenger, Splicing; RNA-Directed DNA Polymerase; Reagent; Reporter; Research; Role; Sampling; Structure; Technology; Translations; Untranslated RNA; Variant; Viral Genome; Virus; Work; crosslink; experimental study; genetic variant; genome-wide; human disease; human tissue; in vivo; innovation; novel; posttranscriptional; programs; technological innovation; transcriptome

SUMMARY My research program focuses on quantitatively characterizing the role of RNA structure in post-transcriptional regulatory processes. Comparisons of protein and messenger RNA (mRNA) abundance at genome scale reveal low correlation between the two gene expression levels in most human tissues and other organisms. This poor correlation suggests that a significant amount of gene regulation occurs post-transcriptionally. To discover elements in mRNAs that control their activities, we measure the effects of human disease-associated structure variants that map to non-coding regions of the transcriptome. Specifically, we integrate computational structure prediction with high-throughput allele-specific chemical structure probing in vivo to assess the functional consequences of RNA structure change. We also establish the causality of these variants by using quantitative reporter assays to measure translation efficiency, splicing, and mRNA stability. In total, these experiments provide molecular explanations of disease mechanisms. To support these goals, we develop, implement, and apply both computational and experimental approaches to study RNA structure in the cell. Our proposed research program will further develop two important technological innovations. The first is a hybrid experimental/computational approach for studying precursor and mature mRNA structure simultaneously in vivo; this approach integrates mutational profiling of SHAPE-MaP data (Selective 2’-Hydroxyl Acylation by Primer Extension – Mutational Profiling) with Boltzmann suboptimal sampling of the secondary structural ensemble. The second innovation is SHAPE-JuMP, which uses a bifunctional RNA modification reagent and a highly processive reverse transcriptase that “jumps” across chemical crosslinks to probe through-space three-dimensional contacts in RNA. We will use these technologies to establish the structures of both precursor and mature mRNAs. In addition, we will extend the biological scope of our work by using these technologies to collaboratively investigate inter- and intramolecular interactions in positive strand RNA viruses. In sum, this program will identify novel RNA structure motifs that regulate the functions of precursor and mature mRNAs and viral genomes.

概括 我的研究项目侧重于定量表征 RNA 结构在转录后的作用 监管流程。基因组规模上蛋白质和信使 RNA (mRNA) 丰度的比较揭示了 在大多数人体组织和其他生物体中，这两个基因表达水平之间的相关性较低。这个可怜的 相关性表明大量的基因调控发生在转录后。去发现 mRNA 中控制其活动的元件，我们测量人类疾病相关结构的影响 映射到转录组非编码区域的变体。具体来说，我们整合计算结构 通过体内高通量等位基因特异性化学结构探测进行预测，以评估功能 RNA结构改变的后果。我们还通过使用定量方法来确定这些变异的因果关系 报告基因检测可测量翻译效率、剪接和 mRNA 稳定性。总的来说，这些实验 提供疾病机制的分子解释。为了支持这些目标，我们制定、实施和 应用计算和实验方法来研究细胞中的 RNA 结构。我们提出的 研究计划将进一步开发两项重要的技术创新。第一个是混合体 在体内同时研究前体和成熟 mRNA 结构的实验/计算方法； 该方法集成了 SHAPE-MaP 数据的突变分析（通过 Primer 进行选择性 2’-羟基酰化 扩展 - 突变分析）与二级结构整体的玻尔兹曼次优采样。这 第二个创新是 SHAPE-JuMP，它使用双功能 RNA 修饰试剂和高度加工性的 “跳跃”化学交联以探测空间三维接触的逆转录酶 在RNA中。我们将使用这些技术来建立前体和成熟 mRNA 的结构。在 此外，我们将通过使用这些技术来协作研究来扩展我们工作的生物学范围 正链RNA病毒的分子间和分子内相互作用。总之，该程序将识别新的 RNA 调节前体和成熟 mRNA 以及病毒基因组功能的结构基序。

项目成果

Sequence and tissue targeting specificity of ZFP36L2 reveals Elavl2 as a novel target with co-regulation potential.

• DOI: 10.1093/nar/gkac209
• 发表时间: 2022-04-22
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Redmon, Ian C.;Ardizzone, Matthew;Hekimoglu, Hilal;Hatfield, Breanne M.;Waldern, Justin M.;Dey, Abhishek;Montgomery, Stephanie A.;Laederach, Alain;Ramos, Silvia B., V
• 通讯作者: Ramos, Silvia B., V