C. elegans transcriptional regulatory elements

描述（由申请人提供）：顺式作用调控元件控制基因表达，并参与发育、行为和生理的所有方面;但对于任何后生动物基因组，还不存在顺式调控元件图谱。因此，我们建议确定基因组范围内的顺式调控元件在C。优雅在现有的模式生物中，C.线虫提供了生物学特性、转基因技术、与四个兄弟物种的基因组的比较以及关键的计算和生物信息学基础设施的强大组合。我们打算在基因中找到基因组调控元件，这些基因具有广泛不同的表达模式、基因功能和顺式元件含量，这些元件在不同的发育阶段、细胞类型和生理条件下驱动表达。一个基因组预测的管道，然后是高效的转基因报告基因分析，将使我们能够每周生成和分析10个DNA构建体。在第一年，我们计划确定数百个调控元件，随着我们更好地预测功能元件，在接下来的几年中会有更多的调控元件。预测元素将根据其支持计算和实验数据的质量分配统计评分。我们还将使用染色质免疫沉淀通过强测序（ChIP-seq）分析来寻找调控模块，并将其在寻找功能序列方面的准确性与基于比较基因组学的预测进行比较。我们对预测元素和ChIP-seq的直接测试的第一轮结果将与modENCODE的外部数据相结合，以改进我们的预测算法，用于全基因组元素预测的后期周期。我们的数据将立即发布到WormBase，我们所有的计算工具都可以免费获得完整的源代码。 公共卫生相关性：控制转录的时间、地点和水平的调控DNA序列对正常发育、行为和生理以及疾病至关重要;然而，对于任何动物基因组，都没有它们的全基因组图谱，研究人员目前也无法从它们的DNA序列预测它们的功能输出。我们将尝试通过在简单的动物基因组中对计算预测进行广泛的、反复的实验测试来解决这个问题。

DESCRIPTION (provided by applicant): Cis-acting regulatory elements control gene expression and are involved in all aspects of development, behavior and physiology; but no cis-regulatory element map yet exists for any metazoan genome. We therefore propose to identify genome-wide cis-regulatory elements in C. elegans. Among existing model organisms, C. elegans offers a strong combination of biological properties, transgenic technology, comparisons to genomes in four sibling species, and critical computational and bioinformatic infrastructure. We intend to find genomic regulatory elements in genes with widely varying expression patterns, gene functions, and cis-element content that drive expression in diverse developmental stages, cell types and physiological conditions. A pipeline of genomic predictions followed by efficient transgenic reporter assays will allow us to generate and analyze 10 DNA constructs each week. In year 1 we plan to identify hundreds of regulatory elements, with higher numbers in following years as we become better at predicting functional elements. Predicted elements will be assigned statistical scores based on the quality of their supporting computational and experimental data. We will also use chromatin immunoprecipitation analyzed by intense sequencing (ChIP-seq) to find regulatory modules, and compare its accuracy in finding functional sequences to that of predictions based on comparative genomics. The first round of our results from direct tests of predicted elements and ChIP-seq will be combined with external data from modENCODE to improve our predictive algorithms for later cycles of genome-wide element prediction. Our data will be released promptly to WormBase, and all our computational tools are freely available with full source code. PUBLIC HEALTH RELEVANCE: Regulatory DNA sequences that control the time, place, and level of transcription are crucial for normal development, behavior and physiology as well as disease; yet there is no genome-wide map of them for any animal genome, nor are researchers currently able to predict their functional output from their DNA sequences. We will attempt to solve this problem by extensive, reiterated experimental tests of computational predictions in a simple animal genome.