Arabidopsis 2010: Establishing Regulatory Networks in Arabidopsis: Integrating AGRIS with the Identification of Direct Targets for Transcription Factors

转录因子（TFs）的层次排列（网络）提供了以特定空间和时间模式部署基因所需的信息。这方面的信息固定在由结合特定tf的顺式调控元件形成的启动子区域中。在启动子序列微阵列分析（ChIP-CHIP）的基础上，研究人员将利用染色质免疫沉淀技术确定31个与花发育和表皮功能相关的调节网络相关的tf的直接靶基因。确定的直接靶基因将通过体外dna结合实验进行验证，TF结合位点将通过体外足迹确定。获得的信息将被整合到已建立的AGRIS数据库中，从而形成整合tf、其结合位点和相应调控基序的公共资源。该项目的结果将在http://arabidopsis.med.ohio-state.edu/NSF2010Project上提供。在这项研究中开发的材料将通过ABRC随时提供。实验数据和强大的计算工具的结合将为建立负责所有拟南芥基因表达的调控网络提供第一步，这是2010年项目的中心目标之一。更广泛的影响——建立控制所有植物基因表达的调控网络为拟南芥基因组的阐明提供了一个自然的后续，并将对拟南芥和其他植物的研究产生重大影响。该项目集实验生物学、生物信息学、统计学和数学于一体，为跨学科研究培训提供了独特的机会。将继续开发通过万维网提供的若干数据库，以确保从这项工作中得出的结论得到尽可能广泛的传播。从这些研究中获得的工具和资源将在加州州立大学、圣马科斯大学和俄亥俄州立大学的课程中用于教育目的。

Hierarchical arrangements (networks) of transcription factors (TFs) provide the information necessary to deploy genes with particular spatial and temporal patterns. The information for this is hardwired in the promoter regions formed by cis-regulatory elements that bind specific TFs. Direct target genes for a group of 31 selected TFs involved in regulatory networks associated with flower development and epidermal functions will be identified using chromatin immunoprecipitation followed by analysis of microarrays of promoter sequences (ChIP-CHIP). Identified direct target genes will be validated by in vitro DNA-binding experiments, and the TF binding sites will be determined using in vitro footprinting. The information obtained will be integrated into the established AGRIS databases, resulting in public resources that integrate TFs, their binding sites and the corresponding regulatory motifs. Results derived from this project will be made available at http://arabidopsis.med.ohio-state.edu/NSF2010Project. Materials developed in this research will be made readily available through the ABRC. The combination of experimental data and powerful computational tools will provide the first steps towards establishing the regulatory networks responsible for the expression of all Arabidopsis genes, one of the central objectives of the 2010 project.Broader Impact - Establishing the regulatory networks that control the expression of all plant genes provides a natural follow-up to the elucidation of the Arabidopsis genome and will significantly impact the research in Arabidopsis and other plants. This project integrates experimental biology, bioinformatics, statistics and mathematics, offering unique opportunities for interdisciplinary research training. The development of several databases available through the Web will continue to ensure that findings derived from this work will have the broadest possible dissemination. Tools and resources obtained from these studies will be applied for educational purposes in courses at California State University, San Marcos and Ohio State University.