Function and evolution of microRNAs

描述（由申请人提供）：最近的实验表明，蠕虫、苍蝇、人类和小鼠等生物体的基因组编码了数百种新的microRNA基因。许多这些小的非编码基因被认为通过结合到目标信使rna的部分互补位点来调节其他基因的翻译表达。初始表型和表达分析表明，microrna在基本细胞过程中发挥重要作用，如发育、病毒反应和细胞凋亡。此外，许多microrna在大的进化距离上是保守的。然而，大多数microrna的生物学功能尚不清楚。尽管最近的计算方法在鉴定microRNA靶点方面取得了进展，但没有实验高通量的方法来解剖microRNA功能。我们的长期目标是创建一个将生物信息学和实验方法相结合的系统，以实现对microRNA功能的高通量组合分析。在这里，我们建议建立这个系统。具体来说，我们将(a)采用二氧化硅方法预测五种不同线虫物种中的microRNA靶点，(b)使用抑制剂寡核苷酸在体内敲低几种线虫物种中的20个microRNA的功能，并在整个发育过程中记录它们的功能缺失表型，(c)开发一个系统来验证体内预测的microRNA靶点，并测试25个计算预测的靶点。这些数据将对microrna的生物学功能及其在塑造生物多样性方面的潜在作用产生新的见解。该项目是生物信息学实验室（专注于基因调控过程）和实验实验室（线虫的RNAi功能基因组学）之间的紧密合作。

DESCRIPTION (provided by applicant): Recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of novel microRNA genes. Many of these small non-coding genes are thought to regulate the translational expression of other genes by binding to partially complementary sites in target messenger RNAs. Initial phenotypic and expression analyses suggest an important role for microRNAs in basic cellular processes such as development, viral response, and apoptosis. Furthermore, many microRNAs are conserved over large evolutionary distances. However, the biological function of most microRNAs is unknown. Although recent computational methods have made progress towards the identification of microRNA targets, no experimental high-throughput method for dissecting microRNA function exists. Our long-term goal is to create a system where bioinformatic and experimental methods are integrated to make possible the high-throughput combinatorial analysis of microRNA function. Here, we propose to setup this system. Specifically, we will (a) employ in silica methods to predict microRNA targets in five different nematode species, (b) use inhibitor oligonucleotides to knock down the function of 20 microRNAs across several nematode species in vivo, and register their loss-of-function phenotypes throughout development, (c) develop a system to validate predicted microRNA targets in vivo and test 25 computationally predicted targets. These data will generate novel insights into the biological function of microRNAs and their potential role in shaping biological diversity. This project is an intensive collaboration between a bioinformatics lab (focused on gene regulatory processes), and an experimental lab (RNAi functional genomics in nematodes)