Global Identification of transcribed elements in the C. elegans genome

描述(申请人提供)：对存储在基因组中的信息进行解码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。线虫在真核生物中提供了一个非同寻常的机会来实现这一目标。小而紧凑的基因组被完全测序。简单的解剖结构、固定的细胞谱系和贯穿整个生命周期的透明身体，使每一个细胞都可以随时进行观察和分析。 在估计的21,000个蛋白质编码基因中，已有1,300多个非编码RNA和17,000个基因，以及2,500个可选剪接形式，已经完全或至少部分通过实验确定。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组合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不同阶段和细胞中系统地应用基因组拼接阵列，包括有针对性的分析microRNAs，来扩展我们对转录基因组的知识。反过来，我们将把这些新数据与来自社区的任何其他新数据与基因模型和任何开发出的新模型整合在一起。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，从最初的一组基因模型开始，并在可用时添加新的数据。我们还将使用质谱学来区分蛋白质编码转录本和小潜在开放阅读框的非编码转录本。结果将是一组转录本，这些转录本将接近完成蛋白质编码基因及其UTRs和替代剪接形式以及非编码RNA的工作。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应该是有价值的，比如人类。

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.