Functional Portraits of tRNA-derived Small Non-coding RNAs

tRNA 衍生的小非编码 RNA 的功能肖像

• 批准号: 8968710
• 负责人: Xiaoyong Bao
• 金额: $ 23.25万
• 依托单位: UNIVERSITY OF TEXAS MED BR GALVESTON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-15 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8968710
• 关键词: Algorithms; Animals; Bioinformatics; Biological; Biological Assay; Biological Markers; Biological Process; Biological Response Modifiers; Code; Collaborations; Communities; Consensus; Core Facility; Cytoplasm; Data; Databases; Development; Disease; Elements; Eukaryota; Event; Exhibits; Family; Funding; Future; Gene Expression; Gene Expression Regulation; Gene Silencing; Genes; Genetic Transcription; Genetic Translation; Genomics; Goals; Home environment; Human; Human Genetics; Learning; Length; Mediating; Messenger RNA; Methods; MicroRNAs; Molecular; Molecular Biology; Mutagenesis; National Heart, Lung, and Blood Institute; Nuclear; Nucleotides; Organism; Plants; Play; Portraits; Prevention; Prokaryotic Cells; Proteins; Proteomics; RNA; Regulation; Regulator Genes; Research; Resources; Respiratory syncytial virus; Role; Solid; System; Testing; The Sun; Transcriptional Regulation; Transfer RNA; Translations; Untranslated RNA; Viral; Viral Genes; Virus Diseases; Virus Replication; Western Blotting; Work; base; chemokine; cytokine; experience; genome-wide; human DICER1 protein; improved; mRNA Stability; mRNA Transcript Degradation; novel; novel therapeutics; public health relevance; response

 DESCRIPTION (provided by applicant): Recent discoveries about small non-coding RNAs (sncRNAs) have significantly advanced human genetics and molecular biology, largely due to the identification of a fundamental role of microRNAs (miRNAs), the best- characterized sncRNA family, as gene regulators. tRNA-derived RNA Fragments (tRFs) are a recently discovered sncRNA family that is ubiquitously expressed in organisms ranging from prokaryotes to humans, yet their biological functions and the mechanism(s) underlying those functions are largely unknown. Studies by our group have shown that the sncRNAs most highly induced by respiratory syncytial virus (RSV) belong to the tRF family, while the change in miRNA expression is minimal. These induced tRFs are functional and involved in the regulation of RSV replication. Notably, at least three tested tRFs have a gene trans- silencing function that is mechanistically distinct from that of miRNAs. However, more experimental evidence is needed to determine whether there is a widespread impact of mammalian tRFs on the regulation of gene expression, and more importantly, what mechanism(s) tRFs use for their gene regulatory function. In this project we propose the novel hypothesis that functional tRFs induced by RSV have a common gene trans-silencing function. Since RSV-induced tRFs are localized in the cytoplasm (and so are unlikely to play a role in regulating gene transcription, usually a nuclear event), we also hypothesize that the gene-suppression effect of tRFs occurs at post-transcriptional steps, e.g., mRNA stability or translation. In this exploratory project, these hypotheses will be tested in two Specific Aims. In Aim 1, tRFs important for RSV replication, viral gene expression and associated chemokine/cytokine induction will be identified. We will then determine whether these functional tRFs have gene trans-silencing activity. Aim 2 will test our second hypothesis that the gene- suppression effect of tRFs occurs at post-transcriptional steps. High-throughput methods, including microarray or proteomics analyses, will then be used to identify target candidates for a representative tRF. Target candidates will be experimentally confirmed by qRT-PCR and Western blot analysis. A mutagenesis study will also be performed to confirm that the effect of the tRF on its target(s) is direct and specific. This project may hav important translational implications by suggesting new therapeutic opportunities to modulate viral replication, providing experimental evidence to build a database of functional tRFs, and of more importance to identify the consensus features of tRF*target interaction for the development of a tRF target- prediction algorithm, which will undoubtedly facilitate the discovery of new gene regulatory networks and so will broadly benefit the research community. These goals will be explored in a future R01 application based on the results of this exploratory project.

 描述（由适用提供）：有关小型非编码RNA（SNCRNA）的最新发现具有显着晚期的人类遗传学和分子生物学，这在很大程度上是由于鉴定了MicroRNA（miRNA）（miRNA）的基本作用，是最典型的SNCRNA家族，作为基因调节剂。 tRNA衍生的RNA片段（TRF）是一个最近发现的SNCRNA家族，在从原核生物到人类的生物体中无处不在，但是它们的生物学功能和这些功能的基本机制在很大程度上尚不清楚。我们小组的研究表明，由呼吸道合胞病毒（RSV）诱导的SNCRNA属于TRF家族，而miRNA表达的变化很小。这些诱导的TRF具有功能性，并参与了RSV复制的调节。值得注意的是，至少三个测试的TRF具有机械上与miRNA的基因转移函数。但是，需要更多的实验证据来确定哺乳动物TRF对基因表达的调节是否存在宽度的影响，更重要的是，TRF用于其基因调节功能。在这个项目中，我们提出了一个新的假设，即由RSV诱导的功能性TRF具有共同的基因跨分解函数。由于RSV诱导的TRF位于细胞质中（因此，通常不太可能在调节基因转录中起作用，通常是核事件），因此我们还假设TRF的基因抑制作用发生在转录后步骤，例如，例如，MRNA稳定性或翻译。在这个探索性项目中，这些假设将以两个具体的目的进行检验。在AIM 1中，将确定TRF对于RSV复制，病毒基因表达和相关的趋化因子/细胞因子诱导很重要。然后，我们将确定这些功能性TRF是否具有基因反溶液活性。 AIM 2将检验我们的第二个假设，即TRF的基因抑制作用发生在转录后步骤。然后将使用高通量方法，包括微阵列或蛋白质组学分析，以识别代表性TRF的目标候选者。目标候选者将通过QRT-PCR和Western印迹分析实验确认。还将进行一项诱变研究，以确认TRF对其目标的影响是直接且具有特异性的。该项目通过提出新的治疗机会来调节病毒复制，提供实验证据来构建功能性TRF的数据库，并且更重要的是确定TRF*目标交互的共识特征，以开发TRF目标预测算法，这将无需支持新的基因的网络，因此将具有更为重要的研究，因此该项目可能具有重要的转化含义，并提供了实验性证据，并且更重要的是确定TRF*目标相互作用的共识特征。这些目标将根据该探索项目的结果在未来的R01应用程序中进行探讨。