Variant induced RNA structure change in human genetic disease

总结 我的研究项目主要集中在定量表征RNA结构在转录后的作用， 监管程序。在基因组规模上比较蛋白质和信使RNA（mRNA）丰度， 在大多数人体组织和其他生物体中，两种基因表达水平之间的相关性较低。这个可怜 相关性表明，大量的基因调控发生在转录后。发现 基因中控制其活动的元件，我们测量人类疾病相关结构的影响， 映射到转录组的非编码区的变体。具体来说，我们整合计算结构 用体内高通量等位基因特异性化学结构探测进行预测，以评估功能性 RNA结构改变的后果。我们还建立了这些变量的因果关系，通过使用定量 报告基因测定以测量翻译效率、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 运用计算和实验方法来研究细胞中的RNA结构。我们提出的 研究计划将进一步发展两项重要的技术创新。第一种是混合动力 实验/计算方法，用于在体内同时研究前体和成熟mRNA结构; 该方法整合了SHAPE-MaP数据（通过引物的选择性2 ′-羟基酰化）的突变谱 扩展-突变分析）与二级结构集合的玻尔兹曼次优采样。的 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 一种逆转录酶，它可以“跳跃”穿过化学交联，探测空间三维接触 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合作研究， 正链RNA病毒分子间和分子内相互作用。总之，该计划将识别新的RNA 调节前体和成熟mRNA以及病毒基因组功能的结构基序。

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.