Nuclease Profiling as an Integrative Resource for Maize Epigenomics

核酸酶分析作为玉米表观基因组学的综合资源

• 批准号: 1444532
• 负责人: Henry Bass
• 金额: $ 213.38万
• 依托单位: Florida State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1444532&HistoricalAwards=false
• 关键词: Nuclease; Profiling; Integrative; Resource; Maize

PI: Henry W. Bass (Florida State University-Tallahassee)CoPIs: Jonathan H. Dennis, Jinfeng Zhang, and Daniel L. Vera (Florida State University-Tallahassee), Oghenekome U. Onokpise and Violeta Tsolova (Florida A & M University)Eukaryotic chromosomes consist of DNA-protein complexes referred to as chromatin. The current understanding of the relationship between chromatin structure and genome behavior is still relatively underdeveloped. The goal of this project is to identify and map genome-wide changes in chromatin structure in five diverse tissues of maize using a novel method developed with previous NSF funding. It is expected that chromatin mapping will reveal previously undetected and biochemically functional regions of the maize genome, while integrating genetic information from maize and other plant genome research projects. Together these efforts will provide basic information about chromatin structure that could accelerate crop improvement strategies to address current and future challenges in food and biofuel production. With regard to outreach and training, the project will provide research training for postdoctoral associates, graduate and undergraduate students, particularly from underrepresented groups. The project will organize public field displays and hold summer science camps for high school students to engage a diverse group of people in several Science, Technology, Engineering, and Mathematics (STEM) disciplines related to agriculture, genomics, and bioinformatics.A novel assay for genome-wide nuclease profiling using micrococcal nuclease (MNase) will be used to develop reference nuclease profiles for chromatin from five core tissues of maize: stem cells from root and shoot tips, the immature ear, developing nutritive seed tissue (endosperm), and pollen sperm nuclei. Measuring the differential nuclease sensitivity (DNS-seq) across the entire maize genome will uncover localized sites coupled to evolutionarily conserved sequences, transcription factor binding sites, and gene expression levels. This method uniquely maps specialized and functionally important regions of the genome while greatly enhancing the information content of nucleosome position data, providing new opportunities to connect epigenomic data across disparate projects. All data will be made accessible to the public through various long-term repositories and portals. These include the NCBI's GEO and SRA as well as the UCSC Genomaize (http://genomaize.org/), EPIC-CoGe (https://www.plant-epigenome.org/), and the iPlant Collaborative (Data Store, Discovery Environment, Powered-by-iPlant genome browsers).

PI：Henry W.Bass(佛罗里达州立大学-塔拉哈西)Copis：Jonathan H.Dennis，Jengeng Zhang和Daniel L.Vera(佛罗里达州立大学-塔拉哈西)，Oghenekome U.Onokpise和Violeta Tsolova(佛罗里达农工大学)真核染色体由DNA-蛋白质复合体组成，称为染色质。目前对染色质结构和基因组行为之间的关系的了解还相对较不发达。该项目的目标是利用之前NSF资助开发的一种新方法，识别和定位玉米五个不同组织中染色质结构的全基因组变化。预计染色质图谱将揭示玉米基因组以前未被检测到的生化功能区域，同时整合来自玉米和其他植物基因组研究项目的遗传信息。这些努力将共同提供有关染色质结构的基本信息，这些信息可以加快作物改良战略，以应对粮食和生物燃料生产中当前和未来的挑战。关于外联和培训，该项目将为博士后助理、研究生和本科生，特别是来自任职人数不足的群体的学生提供研究培训。该项目将为高中生组织公开的田野展示和夏季科学夏令营，以吸引与农业、基因组学和生物信息学相关的几个科学、技术、工程和数学(STEM)学科的不同群体。一种使用微球菌核酸酶(MNase)的全基因组核酸酶图谱的新方法将用于开发玉米五种核心组织的染色质的参考核酸酶图谱：来自根和茎尖的干细胞、未成熟的穗、发育中的营养种子组织(胚乳)和花粉核。测量整个玉米基因组的差异核酸酶敏感性(dns-seq)将揭示与进化上保守的序列、转录因子结合位点和基因表达水平相耦合的定位位点。这种方法独特地绘制了基因组的特殊和功能重要的区域，同时极大地增强了核小体位置数据的信息含量，为连接不同项目的表观基因组数据提供了新的机会。所有数据将通过各种长期储存库和门户网站向公众开放。其中包括国家地球物理研究所的地球观测组织和国家地球物理研究所以及加州大学洛杉矶分校的基因组数据库(http://genomaize.org/)，EPIC-COGE(https://www.plant-epigenome.org/)，)和iPLANT协作组(数据存储、发现环境、由iPLANT提供支持的基因组浏览器)。