TRTech-PGR: Comprehensive identification and functional characterization of cis-regulatory elements in legumes

TRTech-PGR：豆类顺式调控元件的综合鉴定和功能表征

• 批准号: 1856627
• 负责人: Robert Schmitz
• 金额: $ 358.48万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-15 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1856627&HistoricalAwards=false
• 关键词: TRTech; PGR; Comprehensive; identification; functional

This project will produce a large, high-quality and uniform dataset that includes several, complementary types of data to address a number of outstanding questions in the economically important legume family of plants, which includes soybean, common bean and peanut. These data are highly valuable for studying diverse developmental pathways such as leaf, root and seed development, as well as the formation and function of root nodules, specialized plant structures that fix atmospheric nitrogen. The datasets will also lead to the identification of critical DNA sequences that control gene expression and will allow their more accurate characterization as well as lead to engineering of these sequences for crop improvement. The datasets and genomic resources generated here will be released publicly and immediately following quality control through an interactive website and federal data repositories. In addition to the scientific and agricultural impact, the project continues a partnership with primarily Hispanic and Native American tribal colleges in the Southwest. A workshop that presents modern-day computational biology approaches to explore DNA sequences will be hosted at Santa Fe Community College. This event serves as a conduit to engage the public and interested undergraduates in research activities and also serves as a means to recruit interns and their faculty mentors for summer training at our research institutions annually. Significant progress has been made in recent years in plant genome assembly and gene annotation. However, the systematic identification and functional characterization of plant cis-regulatory DNA elements remain a challenge, as methods that are highly effective in animals have not translated to plants. A comprehensive and well-curated data set of plant cis-regulatory DNA elements is instrumental to understanding transcriptional regulation during development and/or in response to external stimuli. In addition, cis-regulatory DNA elements are hotspots for genetic variations underlying agronomically and evolutionarily important traits. The research team has recently optimized several high-throughput methods to identify cis-regulatory elements by chromatin signatures, their bound transcription factors, their target genes by direct physical chromatin interactions, and their regulatory activities in high-throughput reporter assays. The goal of this project is to use these methods to systematically identify, analyze and functionally validate cis-regulatory elements in important legume species including Glycine max (soybean), Phaseolus vulgaris (common bean), Phaseolus coccineus (runner bean), Arachis ipaensis, Arachis duranensis and Arachis hypogea (peanut). The results will be used to address a number of mechanistic, developmental and evolutionary questions.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.

该项目将产生一个大型、高质量和统一的数据集，其中包括几种互补类型的数据，以解决具有重要经济意义的豆类植物家族（包括大豆、菜豆和花生）中的一些悬而未决的问题。这些数据对于研究叶、根和种子发育等多种发育途径以及根瘤的形成和功能、固定大气氮的专门植物结构具有非常重要的价值。这些数据集还将导致控制基因表达的关键DNA序列的鉴定，并将允许它们更准确的表征，以及导致这些序列的工程改造以用于作物改良。这里生成的数据集和基因组资源将在质量控制后立即通过交互式网站和联邦数据库公开发布。除了科学和农业的影响，该项目继续与主要是西班牙裔和美国土著部落学院在西南部的伙伴关系。圣达菲社区学院将举办一个研讨会，介绍现代计算生物学方法来探索DNA序列。这项活动是一个渠道，让公众和感兴趣的本科生参与研究活动，也是一种手段，每年在我们的研究机构招募实习生和他们的教师导师进行暑期培训。近年来，植物基因组组装和基因注释研究取得了重大进展。然而，植物顺式调控DNA元件的系统鉴定和功能表征仍然是一个挑战，因为在动物中高度有效的方法还没有翻译到植物中。一个全面的和精心策划的数据集的植物顺式调控DNA元件是有助于了解转录调控过程中的发展和/或响应外部刺激。此外，顺式调控DNA元件是农艺学和进化上重要性状遗传变异的热点。该研究小组最近优化了几种高通量方法，通过染色质签名识别顺式调控元件，它们的结合转录因子，通过直接物理染色质相互作用识别靶基因，以及它们在高通量报告分析中的调控活性。本项目的目标是利用这些方法系统地鉴定、分析和功能验证重要豆科植物中的顺式调控元件，包括大豆（Glycine max）、菜豆（Phaseolus vulgaris）、红花菜豆（Phaseolus coccineus）、花生（Arachis ipaensis）、杜兰花生（Arachis duranensis）和花生（Arachis hypogea）。该奖项反映了NSF的法定使命，并被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing

• DOI: 10.1186/s13059-024-03235-5
• 发表时间: 2024-04-08
• 期刊: GENOME BIOLOGY
• 影响因子: 12.3
• 作者: Zhang，Xuan;Marand，Alexandre P.;Schmitz，Robert J.
• 通讯作者: Schmitz，Robert J.

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

• DOI: 10.1073/pnas.2010250117
• 发表时间: 2020-09-22
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Crisp, Peter A.;Marand, Alexandre P.;Springer, Nathan M.
• 通讯作者: Springer, Nathan M.

The prevalence, evolution and chromatin signatures of plant regulatory elements

• DOI: 10.1038/s41477-019-0548-z
• 发表时间: 2019-12-01
• 期刊: NATURE PLANTS
• 影响因子: 18
• 作者: Lu, Zefu;Marand, Alexandre P.;Schmitz, Robert J.
• 通讯作者: Schmitz, Robert J.

Editorial overview: COPB issue 2022 on “epigenetics and gene regulation”

编辑概述：COPB 2022 年关于“表观遗传学和基因调控”的问题

• DOI: 10.1016/j.pbi.2022.102305
• 发表时间: 2022
• 期刊: Current Opinion in Plant Biology
• 影响因子: 9.5
• 作者: Schmitz, Robert J.;Mittelsten Scheid, Ortrun
• 通讯作者: Mittelsten Scheid, Ortrun

Smar2C2: A Simple and Efficient Protocol for the Identification of Transcription Start Sites

Smar2C2：一种简单有效的转录起始位点识别方案

• DOI: 10.1002/cpz1.705
• 发表时间: 2023
• 期刊: Current Protocols
• 作者: Murray, Andrew;Vollmers, Christopher;Schmitz, Robert J.
• 通讯作者: Schmitz, Robert J.