Collaborative Research: Multimodal RNA structural motifs in alphavirus genomes: discovery and validations

研究最充分的RNA分子结构，特别是tRNA和rRNA，以单一的优势构象存在。然而，已知越来越多的小的非编码RNA序列通过在多个稳定构型之间切换来发挥作用。预计这样的多模式结构主题点缀着 像基孔肯雅这样的RNA病毒基因组的低能结构，调节病毒的生命周期。表征这些嵌入在具有高度结构多样性的长序列中的小的重叠的稳定碱基对集合，对于理解关键结构信号如何编码这些重要病原体的功能是至关重要的。 这一合作利用了以前结果的互补优势-从结构集合(剖析)和下一代化学足迹(SHAPE-MAP)中挖掘相互竞争的信号-以解决在三个甲型病毒基因组测试集中发现多模式基序的挑战。这第一个目标将通过制定必要的地貌轮廓特征和形状地图特征来实现，以确定具有多种原生构象的目标区域。这些独立的结果将在当前预测方法得到实验确认后，通过组合SHAPE定向剖析在单独的序列中得到验证。第二个目标将展示对这些新主题的进化支持，首先跨越三个主题 测试序列，然后是整个字母病毒家族，通过计算代数拓扑的新应用。持久同源性和单纯复合体将被用来分析生物信息在RNA病毒基因组中编码的不同尺度上的进化，从基因组序列到脊椎动物宿主。随后将对另外三个甲型病毒序列进行化学探测确认。该项目将通过将基于组合学和代数拓扑学的新数学模型和分析与化学足迹生物化学的最新进展相结合，扩展RNA折叠的前沿，以识别长RNA病毒基因组中具有多峰结构的重要基序。这一研究结果是甲病毒基因组中一组新的二级结构基序，是作为重要功能元件进行进一步研究的理想候选者，将成为RNA病毒学家的关键资源。此外， 拟议的理论和算法发展一般适用于所有RNA病毒，因此对科学界具有重要的实用价值和兴趣。

The most well-studied RNA molecular structures, notably tRNA and rRNA, exist as a single dominant conformation. However, a growing number of small non-coding RNA sequences are known to function by switching between multiple stable configurations. It is expected that such multi modal structural motifs punctuate the ensemble of low-energy structures for an RNA viral genome like Chikungunya, regulating the viral lifecycle. Characterizing these small overlapping sets of stable base pairs, embedded in lengthy sequences with high structural diversity, is essential to understanding how critical structural signals encode the functionality of these important pathogens. This collaboration leverages complementary strengths of previous results --- mining competing signals from the structural ensemble (profiling) and next generation chemical footprinting (SHAPE-MaP) --- to tackle the challenge of multi modal motif discovery in a test set of three alphavirus genomes. This first aim will be achieved by developing the necessary characterizations of profiling landscapes and of SHAPE-MaP signatures to identify target regions with multiple native conformations. These separate results will be validated in individual sequences by the combination of SHAPE-directed profiling, following experimental confirmation of the current prediction methodology. The second aim will demonstrate evolutionary support for these new motifs, first across the three test sequences and then the entire alphaviral family, through a new application of computational algebraic topology. Persistent homology and simplicial complexes will be used to analyze evolution across the different scales at which biological information is encoded in RNA viral genomes, ranging from genomic sequence to vertebrate host. This will be followed by chemical probing confirmation for three additional alphavirus sequences. This project will extend the frontiers of RNA folding by integrating new mathematical models and analyses based on combinatorics and algebraic topology with recent advances in the biochemistry of chemical footprinting for the purposes of identifying significant motifs with multimodal structure in lengthy RNA viral genomes. The results of this study, a set of novel secondary structure motifs in alphavirus genomes which are ideal candidates for further investigation as important functional elements, will be a key resource for RNA virologists. Furthermore, the proposed theoretical and algorithmic developments are generally applicable to all RNA viruses, and hence of significant utility and interest to the scientific community.