RESEARCH-PGR: Determinants of Polycomb Recruitment in Monocot and Eudicot Crop Species

研究-PGR：单子叶植物和真双子叶作物中多梳子补充的决定因素

• 批准号: 1953279
• 负责人: Doris Wagner
• 金额: $ 80万
• 依托单位: University of Pennsylvania
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-15 至 2024-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1953279&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Determinants; Polycomb; Recruitment

The genomic era has provided a wealth of information about the composition of the genetic material in different organisms. How multicellular eukaryotes such as plants utilize the information content of their genomes to adjust their form and cellular function to a given environment is less well understood. Due to chromatin compaction, only certain portions of the genome are accessible for transcriptional activation; precisely which portions are accessible depends on the developmental stage, tissue type, or condition (biotic or abiotic stress, for example). Polycomb repression is a major epigenetic silencing and chromatin compaction mechanism for shutting off unnecessary or detrimental gene expression programs, and thus it is important for organismal form and function. A key question is how Polycomb Repressive Complexes, which lack inherent capability to bind specific DNA sequences, find their target loci in the genome. In Drosophila and mammals, different modes of Polycomb recruitment are employed – recruitment by sequence specific binding proteins to cis motifs in the former and genome scanning for dinucleotide repeats by Polycomb accessory proteins in the latter. Polycomb recruitment in Arabidopsis is very similar to that in Drosophila, yet, it is not known how Polycomb complexes are directed to the correct genomic locations in other plant species. The researchers hypothesize that the scanning mode of Polycomb recruitment may be better suited for organisms with a larger genome size and therefore aim to elucidate the mechanism for Polycomb Repressive Complex 2 recruitment in a plant crop species with a large genome size. This will test the hypothesis whether different modes of Polycomb recruitment also exist in the plant kingdom. New high school laboratory teaching modules focusing on plant epigenetics will be used to extend the impact of the research.The activity will develop and implement tools to test Polycomb repressive complex 2 (PRC2) recruitment by ChIPseq in several crops. Subsequent in-depth analysis will be conducted in a single crop species, which based on preliminary analysis, holds most promise for ability to test whether different modes of Polycomb recruitment also exist in the plant kingdom. These analyses will include PRC2, H3K27me3 and H3 ChIPseq as well as RNAseq to identify candidate Polycomb-recruiting DNA fragments linked to Polycomb regulated genes. Second, key features specifically enriched in the candidate Polycomb-recruiting DNA fragments, such as cis motifs or nucleotides, will be identified by computational approaches. The combined investigations will reveal commonalities or differences in the mode PRC2 recruitment in plants with different genome sizes. It will uncover critical regulatory DNA elements for genome annotation in crop species and set the groundwork for future epigenetic manipulation of crop genomes.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.

基因组时代提供了大量关于不同生物体中遗传物质组成的信息。多细胞真核生物如植物如何利用其基因组的信息内容来调整其形式和细胞功能以适应给定的环境还不太清楚。由于染色质致密化，只有基因组的某些部分可用于转录激活;确切地说，哪些部分可用于转录激活取决于发育阶段，组织类型或条件（例如生物或非生物胁迫）。多梳抑制是一种主要的表观遗传沉默和染色质压缩机制，用于关闭不必要或有害的基因表达程序，因此它对生物体的形式和功能非常重要。一个关键的问题是，缺乏结合特定DNA序列的固有能力的多梳抑制复合物如何在基因组中找到它们的靶位点。在果蝇和哺乳动物中，采用不同的Polycomb募集模式-在前者中通过序列特异性结合蛋白募集到顺式基序，在后者中通过Polycomb辅助蛋白基因组扫描二核苷酸重复。拟南芥中的Polycomb募集与果蝇中的Polycomb募集非常相似，然而，尚不清楚Polycomb复合物如何定向到其他植物物种中的正确基因组位置。研究人员假设，Polycomb募集的扫描模式可能更适合基因组大小较大的生物，因此旨在阐明基因组大小较大的植物作物物种中Polycomb抑制复合物2募集的机制。这将测试的假设是否不同模式的Polycomb招聘也存在于植物王国。新的高中实验室教学模块侧重于植物表观遗传学将用于扩大研究的影响。该活动将开发和实施工具，以测试ChIPseq在几种作物中的Polycomb抑制复合物2（PRC 2）招募。随后的深入分析将在单一作物物种中进行，基于初步分析，该物种最有希望测试植物王国中是否也存在不同的Polycomb招募模式。这些分析将包括PRC 2、H3 K27 me 3和H3 ChIPseq以及RNAseq，以鉴定与Polycomb调控基因相关的候选Polycomb募集DNA片段。其次，将通过计算方法鉴定在候选Polycomb募集DNA片段中特异性富集的关键特征，例如顺式基序或核苷酸。联合调查将揭示具有不同基因组大小的植物中PRC 2募集模式的共性或差异。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

Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data

• DOI: 10.1093/plcell/koac282
• 发表时间: 2022-09-19
• 期刊: PLANT CELL
• 影响因子: 11.6
• 作者: Klasfeld, Samantha;Roule, Thomas;Wagner, Doris
• 通讯作者: Wagner, Doris