Global Identification of transcribed elements in the C. elegans genome

线虫基因组中转录元件的整体鉴定

基本信息

批准号：
7923469
负责人：
ROBERT H WATERSTON
金额：
$ 63.81万
依托单位：
UNIVERSITY OF WASHINGTON
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-11 至 2013-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7923469
关键词：
Adult Age Alternative Splicing Anatomy Animals C. elegans genome Caenorhabditis elegans Cell Lineage Cells Characteristics Classification Code Communities Complex Computer Simulation Custom Data Data Set Databases Derivation procedure Elements Embryo Eukaryota Exons Expressed Sequence Tags Foundations Fractionation Functional RNA Gene Expression Regulation Genes Genetic Genome Goals Grant Human Immunoprecipitation Indium Introns Knowledge Length Life Cycle Stages Longevity Mass Spectrum Analysis Methods MicroRNAs Modeling Nematoda Neurons Open Reading Frames Peptides Population Proteins Pseudogenes RNA RNA Splicing Race Reading Recording of previous events Research Personnel Reverse Transcriptase Polymerase Chain Reaction Sampling Staging Structure Synapses Time Tissues Transcript Untranslated RNA Untranslated Regions Validation base blastomere structure comparative design experience genome sequencing improved programs research study sex telomere

项目摘要

DESCRIPTION (provided by applicant): A fundamental challenge in decoding the information stored in a genome is to describe the transcripts read from it and their structure. The nematode C. elegans offers an extraordinary opportunity among eukaryotes to accomplish this goal now. The small, compact genome is completely sequenced. The simple anatomy, fixed cell lineage and transparent body through the full life span make each and every cell available for observation and analysis at any time. Already more than 1,300 noncoding RNAs and 17,000 of the estimated 21,000 protein coding genes, along with 2,500 alternative splice forms, have been fully or at least partially defined experimentally. The present proposal seeks to complete the definition of the transcribed genome of C. elegans. We will do this by assembly of all the available experimental data with a variety of gene models to define accurately the extent of the known transcribed genome. From this base, we will extend our knowledge of the transcribed genome through systematic application of genome tiling arrays across various stages and cells of the life cycle, including targeted analysis of microRNAs. In turn we will integrate this new data along with any other new data from the community with the gene models and any new models that develop. We will attempt directed confirmation of unconfirmed gene models through RT-PCR and custom arrays, starting with the initial set of gene models and adding new data as it becomes available. We will also use mass spectrometry to distinguish protein coding transcripts from noncoding transcripts for small potential open reading frames. The result will be a set of transcripts that will approach completion for protein coding genes and their UTRs and alternative splice forms as well as non-coding RNAs. The experience gained with this modest genome should be of value in interpreting more complex genomes, such as human.

描述（由申请人提供）：解码基因组中存储的信息的一个基本挑战是描述从基因组中读取的转录本及其结构。线虫秀丽隐杆线虫为真核生物中实现这一目标提供了绝佳的机会。小而紧凑的基因组已完全测序。简单的解剖结构、固定的细胞谱系和全生命周期的透明体，使每一个细胞都可供随时观察和分析。已经有超过 1,300 个非编码 RNA 和大约 21,000 个蛋白质编码基因中的 17,000 个，以及 2,500 个替代剪接形式，已通过实验得到完全或至少部分定义。本提案旨在完成线虫转录基因组的定义。我们将通过将所有可用的实验数据与各种基因模型进行组装来准确定义已知转录基因组的范围来做到这一点。在此基础上，我们将通过在生命周期的各个阶段和细胞中系统地应用基因组平铺阵列（包括 microRNA 的靶向分析）来扩展我们对转录基因组的了解。反过来，我们将把这些新数据以及来自社区的任何其他新数据与基因模型和任何开发的新模型整合起来。我们将尝试通过 RT-PCR 和定制阵列直接确认未确认的基因模型，从初始的一组基因模型开始，并在可用时添加新数据。我们还将使用质谱法来区分蛋白质编码转录本和非编码转录本，以获得小的潜在开放阅读框。结果将是一组接近完整的蛋白质编码基因及其 UTR、选择性剪接形式以及非编码 RNA 的转录本。从这个简单的基因组中获得的经验对于解释更复杂的基因组（例如人类）应该具有价值。