Global Identification of transcribed elements in the C. elegans genome

描述（由申请人提供）：解码基因组中存储的信息的基本挑战是描述从中读取的转录本及其结构。线虫C.秀丽隐杆线虫为真核生物提供了实现这一目标的绝佳机会。小而紧凑的基因组被完全测序。简单的解剖结构，固定的细胞谱系和整个生命周期的透明体，使每个细胞都可以随时观察和分析。 已经有超过1,300种非编码RNA和大约21,000种蛋白质编码基因中的17,000种，连同沿着的2,500种可变剪接形式，已经完全或至少部分地被实验确定。本研究的目的是完成C.优雅我们将通过组装所有可用的实验数据与各种基因模型来准确定义已知转录基因组的范围。从这个基础上，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，包括对microRNA的靶向分析，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沿着来自社区的任何其他新数据与基因模型和开发的任何新模型集成在一起。我们将尝试通过RT-PCR和定制阵列直接确认未经确认的基因模型，从最初的基因模型集开始，并在可用时添加新数据。我们还将使用质谱法区分蛋白质编码转录本和非编码转录本的小的潜在开放阅读框架。结果将是一组转录本，其将接近蛋白质编码基因及其UTR和可变剪接形式以及非编码RNA的完成。从这个不起眼的基因组中获得的经验应该对解释更复杂的基因组（如人类）有价值。

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.