Arabidopsis 2010: High-resolution Mapping of Regulatory DNA

生物体的基因组不仅对基因及其RNA和蛋白质产物进行编码，而且还对决定不同基因何时、何地以及在何种程度上被激活或沉默的综合程序进行编码。在DNA水平上，基因调控信号是由调控元件编码的，这些调控元件包括DNA结合蛋白的集群识别位点。然而，绝大多数拟南芥调控序列的位置和功能目前尚不清楚。在这个项目中，新的高通量表观基因组技术——数字DNA图谱和数字基因组足迹——将被应用于在核苷酸分辨率下绘制和表征整个拟南芥基因组的调控DNA。这些技术能够绘制出调控DNA序列的位置，并描绘出这些区域内调控因子结合的特定位点。由于基因调控程序在不同细胞类型之间和分化过程中在同一细胞类型内差异很大，因此该项目将涵盖参考菌株的多个发育阶段和组织。作为无根生物，植物将许多信号整合到适当的发育和胁迫反应中，其中大多数依赖于主要的重编程基因调控反应。因此，参与这些反应的调控DNA将通过标准应激条件的研究来绘制。在群体水平上，大多数表型变异可能来源于非编码遗传变异。通过系统地扩展不同拟南芥和相关物种的调控DNA图谱，该项目将在全基因组范围内揭示基因型变异和基因调控程序之间的关系。由此产生的数据将为内源和环境响应性植物调控程序提供前所未有的见解，并将显著加快识别相关表型变异背后的功能性非编码变异。更广泛的影响。该项目有可能从根本上改变拟南芥和一般植物基因调控研究的格局，因为它既适用于基本机制，也适用于解决各种定量变化表型的应用。全面的、高分辨率的拟南芥发育阶段、组织、处理、加入和进化相关物种的调控DNA图谱的可用性将立即将拟南芥带到调控基因组学的前沿，并将为该领域带来强大的吸引力。该项目对拟南芥调控区域和转录因子结合位点的综合注释将对整个植物生物学社区有用，并将开发重要的数据资源，这将增强确定基因功能的实验方法。该项目将通过基因组数据库和相关分析工具将数据快速传播到公共领域，以协助不同研究人员利用这些数据，从而促进植物调控基因组学的发展。该项目还将包括一个重要的教育组成部分，旨在培养下一代植物调控基因组学的领导者，招募和培训来自不同背景的有才华的本科生和研究生科学家。

The genome of an organism encodes not only genes and their RNA and protein products, but also the integrated programs that define when, where, and to what extent different genes are activated or silenced. At the DNA level, gene regulatory signals are encoded by regulatory elements that comprise clustered recognition sites for DNA binding proteins. However, the location and function of the vast majority of Arabidopsis regulatory sequences is currently obscure. In this project, novel high-throughput epigenomic technologies--Digital DNaseI Mapping and Digital Genomic Footprinting--will be applied to map and characterize regulatory DNA across the A. thaliana genome at nucleotide resolution. These technologies are capable of mapping the locations of regulatory DNA sequences, and delineating the specific sites of regulatory factor binding within such regions. Because gene regulatory programs vary widely both between different cell types and within a cell type during differentiation, the project will encompass multiple developmental stages and tissues of a reference strain. As sessile organisms, plants integrate many cues into appropriate developmental and stress responses, most of which rely on major re-programming gene regulatory responses. Regulatory DNA involved in such responses will therefore be mapped through study of standard stress conditions. At the population level, most phenotypic variation is likely to derive from non-coding genetic variation. By systematically extending maps of regulatory DNA across both diverse A. thaliana accessions and related species, the project will expose relationships between genotypic variation and gene regulatory programs on a genome-wide scale. The resulting data will provide unprecedented insight into endogenous and environmentally-responsive plant regulatory programs, and will significantly accelerate the identification of functional non-coding variation underlying relevant phenotypic variation. Broader impacts. This project has the potential to change fundamentally the landscape of gene regulation research in A. thaliana and in plants generally, both as it applies to basic mechanisms and in its application to solve diverse quantitatively varying phenotypes. The availability of comprehensive, high-resolution regulatory DNA maps for A. thaliana stages, tissues, treatments, accessions, and evolutionarily related species will immediately bring A. thaliana to the forefront of regulatory genomics, and will provide a powerful attraction for bringing dynamic new investigators to the field. The comprehensive annotation of A. thaliana regulatory regions and transcription factor binding sites targeted under this project will be of use to the entire plant biology community, and will develop significant data resources that will potentiate experimental approaches to determining gene function. The project will foster the advancement of plant regulatory genomics through rapid dissemination of data to the public domain via genomic databases as well as relevant analytical tools to assist in its utilization by diverse investigators. The project will also encompass a significant educational component aimed at training next-generation leaders in plant regulatory genomics, and recruitment and training of talented undergraduate and graduate scientists from diverse backgrounds.