Integrated Approcahes to Find Hox-regulated DNA Elements

描述（由申请人提供）：该合作项目的目标是鉴定果蝇基因组中由同源结构域蛋白Hox家族直接调控的转录调控元件。为了实现这一目标，将进行三个实验步骤。首先，将使用最先进的基因表达谱方法来分析含有Hox基因突变的胚胎中的基因表达差异。用于基因谱分析的基因型包括冗余的疼痛/疼痛比较，以增加真正的hox调节基因被识别的可能性。第二步将使用两种方法中的一种——DamID或染色质免疫沉淀（ChIP）——来确定果蝇基因组中的哪些基因在体内直接与Hox蛋白结合。结合第一步，这些实验将允许在全基因组范围内直接识别Hox靶基因。该分析的第三步将是使用计算方法来识别在直接调控的Hox靶基因亚群之间共享的顺式调控元件。通过体外蛋白质- dna结合实验和体内报告基因分析，计算鉴定的调控元件将在实验中得到证实。一旦这些方法被制定出来，它们将适用于生物学中各种各样的问题。

DESCRIPTION (provided by applicant): The goal of this collaborative project is to identify transcriptional regulatory elements in the Drosophila melanogaster genome that are directly regulated by the Hox family of homeodomain proteins. To accomplish this goal, three experimental steps will be carried out. In the first, state-of-the art gene expression profiling methods will be used to analyze gene expression differences in embryos containing Hox gene mutations. The genotypes that will be used for gene profiling analysis incorporate redundant pain/vise comparisons to increase the probability that bona fide Hox-regulated genes will be identified. The second step will be to use one of two methods -- DamID or chromatin immunoprecipitation (ChIP) - to determine which genes in the Drosophila genome are directly bound by Hox proteins in vivo. Combined with the first step, these experiments will allow the identification of direct Hox target genes on a genome-wide scale. The third step in this analysis will be to use computational approaches to identify cis-regulatory elements that are shared between subsets of the directly regulated Hox target genes. Computationally-identified regulatory elements will be confirmed experimentally, both by in vitro protein-DNA binding experiments and by in vivo reporter gene analysis. Once these methods are worked out, they will be applicable to a wide variety of problems in biology.