TRTech-PGR: Identification and characterization of stress-responsive and evolutionary conserved epitranscriptomic modification sites in plant transcriptomes.

TRTech-PGR：植物转录组中胁迫响应和进化保守的表观转录组修饰位点的鉴定和表征。

• 批准号: 2023310
• 负责人: Andrew Nelson
• 金额: $ 202.2万
• 依托单位: Boyce Thompson Institute Plant Research
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-15 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2023310&HistoricalAwards=false
• 关键词: TRTech; PGR; Identification; characterization; stress

RNA is an essential molecule for life, serving many roles in the functioning of cells. Chemical modifications to RNA can affect its rate of turnover. In plants, little is known about the chemical diversity of these modifications and the biological contexts in which they occur, due to the difficulties in biochemically identifying them at the cellular level. This project aims to use computational approaches to systematically identify RNA modifications by reanalyzing ~1 petabyte of publicly available data from a broad diversity of model and agriculturally important plant species. This project will identify and classify RNA modifications based on where they are applied, the biological conditions (e.g., during the development of the plant, when the plant experiences stress, etc.), and the degree to which each modification is conserved between plant species. This project is devoted to training the next generation of plant scientists at the interface between computers and biology. Undergraduate students will play an integral role in the identification and biological validation of RNA modifications. Altogether, this project will provide insight into the biological significance of RNA modifications using novel applications of data in public repositories. RNA chemical modifications are diverse, occur on all classes of RNA molecules, and are physiologically relevant. However, RNA modifications have not yet been studied in depth in plants. This gap in knowledge is in large part due to the cost and technical difficulties of the biochemical assays used to measure abundance of specific RNA modifications. In light of these difficulties, in silico methods have been developed that facilitate high-throughput identification and prediction of these chemical additions. This proposal aims to address challenges in identifying modifications and placing them into a biological context by: 1) developing an exhaustive, annotated plant epitranscriptomic resource of over 47 unique modifications using approximately 1 petabase of publicly available RNA-seq data, and 2) provide a biological and evolutionary context for each of these modifications and the RNAs they are found to modify. To process the wealth of publicly available RNA-seq data and present the resulting information in a manner that will drive hypothesis generation, this project will develop novel computational workflows and data visualization tools.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.

RNA是生命所必需的分子，在细胞功能中起着许多作用。 对RNA的化学修饰可以影响其周转率。在植物中，由于在细胞水平上进行生物化学鉴定的困难，人们对这些修饰的化学多样性以及它们发生的生物背景知之甚少。该项目旨在使用计算方法，通过重新分析来自广泛多样的模型和农业重要植物物种的约1 PB的公开数据，系统地识别RNA修饰。该项目将根据RNA修饰的应用位置、生物条件（例如，在植物的发育过程中，当植物经历胁迫等时），以及每种修饰在植物物种之间的保守程度。该项目致力于培养下一代植物科学家在计算机和生物学之间的接口。本科生将在RNA修饰的鉴定和生物学验证中发挥不可或缺的作用。总之，该项目将提供深入了解RNA修饰的生物学意义，使用公共存储库中数据的新应用。RNA化学修饰是多样的，发生在所有类别的RNA分子上，并且是生理相关的。然而，RNA修饰尚未在植物中深入研究。这种知识上的差距在很大程度上是由于用于测量特异性RNA修饰丰度的生物化学测定的成本和技术困难。鉴于这些困难，已经开发了计算机模拟方法，以促进这些化学添加物的高通量鉴定和预测。该提案旨在通过以下方式解决识别修饰并将其置于生物学背景中的挑战：1）使用大约100%的公开可用的RNA-seq数据开发超过47种独特修饰的详尽的、注释的植物epitranscriptomic资源，以及2）为这些修饰中的每一种以及发现它们修饰的RNA提供生物学和进化背景。为了处理大量公开的RNA-seq数据，并以一种能够推动假设生成的方式呈现所产生的信息，该项目将开发新的计算工作流程和数据可视化工具。该奖项反映了NSF的法定使命，并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

Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization

植物 LORELEI 基因家族的进化分析揭示了调控亚功能化

• DOI: 10.1093/plphys/kiac444
• 发表时间: 2022
• 期刊: Plant Physiology
• 影响因子: 7.4
• 作者: Noble, Jennifer A.;Bielski, Nicholas V.;Liu, Ming-Che James;DeFalco, Thomas A.;Stegmann, Martin;Nelson, Andrew D. L.;McNamara, Kara;Sullivan, Brooke;Dinh, Khanhlinh K.;Khuu, Nicholas
• 通讯作者: Khuu, Nicholas

Chloroplast quality control pathways are dependent on plastid DNA synthesis and nucleotides provided by cytidine triphosphate synthase two

• DOI: 10.1111/nph.17467
• 发表时间: 2021-06-21
• 期刊: NEW PHYTOLOGIST
• 影响因子: 9.4
• 作者: Alamdari, Kamran;Fisher, Karen E.;Woodson, Jesse D.
• 通讯作者: Woodson, Jesse D.