Nuclease Profiling as an Integrative Resource for Maize Epigenomics

PI：亨利W.巴斯（佛罗里达州立大学塔拉哈西分校）CoPI：乔纳森H。Dennis，Jinfeng Zhang，and丹尼尔L.维拉（佛罗里达州立大学塔拉哈西分校），奥格内科梅大学。Onokpise和Violeta Tsolova（佛罗里达A M大学）真核染色体由称为染色质的DNA-蛋白质复合物组成。 目前对染色质结构和基因组行为之间关系的理解仍然相对不发达。 该项目的目标是使用先前NSF资助开发的新方法来识别和绘制玉米五种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中以前未检测到的生物化学功能区域，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，这些信息可以加速作物改良战略，以应对当前和未来的粮食和生物燃料生产挑战。 在外联和培训方面，该项目将为博士后助理、研究生和本科生，特别是代表性不足群体的研究生和本科生提供研究培训。 该项目将组织公共领域的展示，并为高中生举办科学夏令营，让不同群体的人参与与农业、基因组学和生物信息学相关的科学、技术、工程和数学（STEM）学科。一种使用微球菌核酸酶（MNase）进行全基因组核酸酶谱分析的新方法将用于开发玉米五种核心组织染色质的参考核酸酶谱：来自根和茎尖、未成熟的穗、发育中的营养种子组织（胚乳）和花粉精核的干细胞。 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偶联的定位位点。 这种方法独特地映射了基因组的专门和功能重要的区域，同时大大增强了核小体位置数据的信息内容，为跨不同项目连接表观基因组数据提供了新的机会。 所有数据都将通过各种长期储存库和门户网站向公众开放。 这些包括NCBI的GEO和SRA以及UCSC Genomaize（http：//genomaize.org/）、EPIC-CoGe（https：//www.plant-epigenome.org/）和iPlant Collaborative（数据存储、发现环境、Powered-by-iPlant基因组浏览器）。

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).