Functional analysis of the zebrafish genome through RNA-seq and ribosome profile

描述（由申请人提供）：斑马鱼基因的功能表征需要准确的基因结构和基因表达知识。我们建议将高通量测序技术（核糖体谱和RNA-seq）和生物信息学结合起来，通过确定每个编码基因的翻译起始和停止位点（Aim 2），定义转录起始位点，5‘和3’ utr (Aim 1)，注释斑马鱼基因中可能的选择性剪接外显子（Aim 1），来改进当前编码和非编码基因的注释。本提案中概述的实验的最终目标是改善斑马鱼的功能基因组学，并将为社区提供两个基本工具：i)改进斑马鱼基因的注释，包括编码势，翻译起始位点和转录本结构；ii)社区定义的，开放获取的斑马鱼胚胎/幼虫阶段和器官发生的表达图谱。在未来，该项目的结果将有助于斑马鱼基因的功能表征，并将建立一个框架来了解脊椎动物基因的结构和功能。

DESCRIPTION (provided by applicant): Functional characterization of the zebrafish genes requires accurate knowledge of the gene structure and gene expression. In proposal we combine high-throughput sequencing techniques (Ribosome profile and RNA-seq) and bioinformatics to improve the current annotation of coding and non-coding genes, by determining the translation start and stop sites in each coding gene (Aim 2), define the transcription start site, 5' and 3'UTRs (Aim 1), annotate putative alternatively spliced exons in the zebrafish genes (Aim 1), and develop a gene expression atlas during embryogenesis and organogenesis (Aim 1) The experiments outlined in this proposal have the ultimate goal of improving functional genomics in zebrafish and will provide two fundamental tools to the community: i) improved annotation of the zebrafish genes including coding potential, translation start site and transcript structure and ii) community defined, open access zebrafish expression atlas across embryonic/ larval stages and organogenesis. In the future, the results derived from this project will facilitate the functional characterization of the zebrafish genes and will establsh a frame work to understand the structure and the function of vertebrate genes.