C. elegans transcriptional regulatory elements

描述(申请人提供)：顺式作用调控元件控制基因表达，参与发育、行为和生理的各个方面；但目前还没有任何后生动物基因组的顺式调节元件图谱。因此，我们建议在线虫中鉴定全基因组的顺式调控元件。在现有的模式生物中，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比较以及关键的计算和生物信息基础设施的强大组合。我们打算在具有广泛不同的表达模式、基因功能和顺式元件含量的基因中寻找基因组调控元件，这些元件驱动不同发育阶段、细胞类型和生理条件下的表达。在高效的转基因报告分析之后，一系列基因组预测将允许我们每周生成和分析10个DNA结构。在第一年，我们计划确定数百个监管要素，随着我们在预测功能要素方面变得更好，在接下来的几年中，我们的数量会更多。预测元素将根据其支持的计算和实验数据的质量被分配统计分数。我们还将使用高强度测序分析的染色质免疫沉淀(CHIP-SEQ)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。我们对预测元素和芯片序列直接测试的第一轮结果将与modENCODE的外部数据相结合，以改进我们对基因组范围元素预测的后续周期的预测算法。我们的数据将迅速发布到WormBase，我们所有的计算工具都可以免费获得，并提供完整的源代码。 与公共健康相关：控制时间、地点和转录水平的调控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根据它们的DNA序列预测它们的功能输出。我们将尝试通过对简单动物基因组中的计算预测进行广泛、重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.