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

描述(由申请人提供)：斑马鱼基因的功能特征需要准确的基因结构和基因表达知识。在该方案中，我们结合高通量测序技术(核糖体图谱和RNA-SEQ)和生物信息学来改进编码和非编码基因的当前注释，通过确定每个编码基因中的翻译开始和结束位置(目标2)，定义转录起始点，5‘和3’UTRs(目标1)，注释斑马鱼基因中假定的可选择性剪接的外显子(目标1)，建立斑马鱼胚胎发生和器官发生过程中的基因表达图谱(目标1)本建议中概述的实验的最终目标是改善斑马鱼的功能基因组学，并将为该群体提供两个基本工具：i)改进斑马鱼基因的注释，包括编码潜力、翻译起始点和转录本结构；ii)群落定义的、开放访问的跨胚胎/幼体阶段和器官发生的斑马鱼基因表达图谱。在未来，该项目的结果将有助于斑马鱼基因的功能表征，并将为理解脊椎动物基因的结构和功能建立一个框架。

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.