TRTech-PGR: MAPPING AND FUNCTIONAL CHARACTERIZATION OF CIS-REGULATORY MODULE VARIATION IN PLANTS

TRTech-PGR：植物中 CIS 调节模块变异的绘图和功能表征

• 批准号: 1916804
• 负责人: Andrea Gallavotti
• 金额: $ 243.26万
• 依托单位: Rutgers University New Brunswick
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2025-07-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1916804&HistoricalAwards=false
• 关键词: TRTech; PGR; MAPPING; FUNCTIONAL; CHARACTERIZATION

Transcription factors are proteins that bind to short DNA sequence motifs in regulatory regions of their target genes and thus control the gene expression changes responsible for plant developmental programs and environmental responses. In crop species, variation in transcription factors and the regulatory regions they bind have been frequent drivers of productivity gains during domestication and modern breeding, and continue to offer great potential for further trait engineering. Yet, in plant genomes, the vast majority of transcription factor-DNA binding events and the gene expression changes they elicit remain largely uncharacterized, restricting the development of new varieties that meet the challenges of modern agriculture. In this project, detailed regulatory information maps and new methodologies will be generated to identify relationships between transcription factor binding and variability in gene expression, providing new tools for the rational design of crops with improved traits. These methods have the potential to fundamentally transform crop improvement strategies to adequately feed the expanding global population. To extend the reach of the project, scientists working under this award will provide specialized training in genomics and bioinformatics to students with diverse backgrounds. A large portion of plant genetic variation is regulatory and resides in non-coding regions, spaces that are often vast in genomes such as maize. Mining functional elements from these spaces represents a major challenge, in part because while potential transcription factor (TF) binding sites are naturally abundant within a genome, only a small fraction is actually bound and able to affect expression. Empirically cataloging plant TF binding events and their contribution to transcriptional outputs is therefore a priority for understanding transcriptional networks and trait variation. This project will develop TF-DNA interaction methods that enable comparative analysis of multiple genetic backgrounds, resulting in the generation of high-resolution maps of conserved regulatory regions and accession-specific variants that can be linked to transcriptional programs. This approach will be applied in two species with different genomic properties: maize, a major monocot crop with a large genome; and Arabidopsis, a model eudicot with a compact genome. Because many TFs do not function in isolation but instead interact with other proteins that can alter their DNA binding activity, this project will also develop techniques to better understand the contribution of TF pairs to transcriptional regulation. To directly link TF binding events to phenotypic outcomes, specific regulatory elements in key genes controlling plant architecture and reproductive development will be functionally characterized through precise genome editing. Such experiments will demonstrate how modulation of regulatory regions can be used to create subtle changes in gene expression levels or spatial expression patterns that may result in advantageous phenotypes.This award is supported jointly by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

转录因子是与靶基因调控区的短DNA序列基序结合的蛋白质，从而控制负责植物发育程序和环境响应的基因表达变化。在作物物种中，转录因子及其结合的调控区域的变化一直是驯化和现代育种期间生产力提高的常见驱动因素，并继续为进一步的性状工程提供巨大潜力。然而，在植物基因组中，绝大多数转录因子-DNA结合事件和它们引起的基因表达变化在很大程度上仍然是未知的，限制了新品种的开发，以满足现代农业的挑战。在该项目中，将生成详细的调控信息图和新方法，以确定转录因子结合和基因表达变异之间的关系，为合理设计具有改良性状的作物提供新工具。这些方法有可能从根本上改变作物改良战略，以充分养活不断扩大的全球人口。为了扩大该项目的范围，在该奖项下工作的科学家将为具有不同背景的学生提供基因组学和生物信息学方面的专业培训。 植物遗传变异的很大一部分是调节性的，并且存在于非编码区，非编码区在玉米等基因组中通常是巨大的空间。从这些空间中挖掘功能元件是一个重大挑战，部分原因是虽然潜在的转录因子（TF）结合位点在基因组中天然丰富，但只有一小部分实际上被结合并能够影响表达。因此，经验编目植物TF结合事件及其对转录输出的贡献是理解转录网络和性状变异的优先事项。该项目将开发TF-DNA相互作用方法，使多种遗传背景的比较分析，从而产生高分辨率的保守调控区和登录特异性变异，可以连接到转录程序的地图。这种方法将应用于两个具有不同基因组特性的物种：玉米，一种主要的单子叶作物，具有大的基因组;和拟南芥，一种模式真双子叶植物，具有紧凑的基因组。由于许多TF不能单独发挥作用，而是与其他蛋白质相互作用，从而改变其DNA结合活性，因此该项目还将开发技术，以更好地了解TF对转录调控的贡献。为了将TF结合事件与表型结果直接联系起来，控制植物结构和生殖发育的关键基因中的特定调控元件将通过精确的基因组编辑进行功能表征。这类实验将证明调控区域如何被用来产生基因表达水平或空间表达模式的微妙变化，从而可能导致有利的表型。该奖项由整合有机体系统部的植物基因组研究计划和分子和细胞生物科学部的遗传机制计划共同支持。该奖项反映了NSF的法定使命，通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Vision, challenges and opportunities for a Plant Cell Atlas.

• DOI: 10.7554/elife.66877
• 发表时间: 2021-09-07
• 期刊: eLife
• 影响因子: 7.7
• 作者: Plant Cell Atlas Consortium;Jha SG;Borowsky AT;Cole BJ;Fahlgren N;Farmer A;Huang SC;Karia P;Libault M;Provart NJ;Rice SL;Saura-Sanchez M;Agarwal P;Ahkami AH;Anderton CR;Briggs SP;Brophy JA;Denolf P;Di Costanzo LF;Exposito-Alonso M;Giacomello S;Gomez-Cano F;Kaufmann K;Ko DK;Kumar S;Malkovskiy AV;Nakayama N;Obata T;Otegui MS;Palfalvi G;Quezada-Rodríguez EH;Singh R;Uhrig RG;Waese J;Van Wijk K;Wright RC;Ehrhardt DW;Birnbaum KD;Rhee SY
• 通讯作者: Rhee SY

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors.

• DOI: 10.1038/s41467-023-38096-2
• 发表时间: 2023-05-05
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Li, Miaomiao;Yao, Tao;Lin, Wanru;Hinckley, Will E. E.;Galli, Mary;Muchero, Wellington;Gallavotti, Andrea;Chen, Jin-Gui;Huang, Shao-shan Carol
• 通讯作者: Huang, Shao-shan Carol

Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements.

阐明转录因子-DNA相互作用的生物学，以准确鉴定顺式调节元件。

• DOI: 10.1016/j.pbi.2022.102232
• 发表时间: 2022-08
• 期刊: CURRENT OPINION IN PLANT BIOLOGY
• 影响因子: 9.5
• 作者: Hajheidari, Mohsen;Huang, Shao-shan Carol
• 通讯作者: Huang, Shao-shan Carol

Potentials of single-cell genomics in deciphering cellular phenotypes.

• DOI: 10.1016/j.pbi.2021.102059
• 发表时间: 2021-10
• 期刊: Current opinion in plant biology
• 影响因子: 9.5
• 作者: Shojaee A;Saavedra M;Huang SC
• 通讯作者: Huang SC

Necrotic upper tips1 mimics heat and drought stress and encodes a protoxylem-specific transcription factor in maize

• DOI: 10.1073/pnas.2005014117
• 发表时间: 2020-08-25
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Dong, Zhaobin;Xu, Zhennan;Chuck, George
• 通讯作者: Chuck, George