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。
基本信息
- 批准号:2023310
- 负责人:
- 金额:$ 202.2万
- 依托单位:
- 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:
- 关键词:
项目摘要
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
期刊论文数量(12)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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:
- 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:
- 影响因子:9.4
- 作者:Alamdari, Kamran;Fisher, Karen E.;Woodson, Jesse D.
- 通讯作者:Woodson, Jesse D.
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Andrew Nelson其他文献
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
解决 SARS-CoV-2 系统发育中大流行范围内的系统错误
- DOI:
10.1101/2024.04.29.591666 - 发表时间:
2024 - 期刊:
- 影响因子:0
- 作者:
Martin Hunt;Angie Hinrichs;Daniel Anderson;Lily Karim;Bethany L Dearlove;Jeff Knaggs;B. Constantinides;Philip W. Fowler;G. Rodger;Teresa Street;S. Lumley;Hermione Webster;T. Sanderson;Christopher Ruis;N. de Maio;L. Amenga;D. Amuzu;M. Avaro;G. Awandare;Reuben Ayivor;M. Bashton;Elizabeth M Batty;Yaw Bediako;Denise De Belder;Estefania Benedetti;A. Bergthaler;Stefan A. Boers;Josefina Campos;Rosina Afua Ampomah Carr;Facundo Cuba;M. E. Dattero;W. Dejnirattisai;A. Dilthey;K. Duedu;L. Endler;Ilka Engelmann;Ngiambudulu M Francisco;Jonas Fuchs;Etienne Z. Gnimpieba;S. Groc;Jones Gyamfi;Dennis Heemskerk;Torsten Houwaart;N. Hsiao;Matthew Huska;Martin Hölzer;A. Iranzadeh;Hanna Jarva;C. Jeewandara;B. Jolly;R. Joseph;Ravi Kant;Karrie Ko Kwan Ki;S. Kurkela;Maija Lappalainen;Marie Lataretu;Chang Liu;G. Malavige;T. Mashe;J. Mongkolsapaya;Brigitte Montes;Jose Arturo Molina Mora;C. Morang’a;Bernard Mvula;Niranjan Nagarajan;Andrew Nelson;Joyce M. Ngoi;Joana Paula da Paixão;M. Panning;Tomás Poklépovich;Peter K. Quashie;D. Ranasinghe;Mara L Russo;J. E. San;Nicholas D Sanderson;V. Scaria;Gavin R. Screaton;T. Sironen;Abay Sisay;Darren Smith;T. Smura;P. Supasa;Chayaporn Suphavilai;J. Swann;H. Tegally;Bryan Tegomoh;Olli Vapalahti;Andreas Walker;Robert J Wilkinson;Carolyn Williamson;Tulio de Oliveira;Timothy E. A. Peto;Derrick Crook;Russell Corbett;Zam Iqbal - 通讯作者:
Zam Iqbal
On the Efficacy of Post-Build Thermomechanical Treatments to Improve Properties of Zirconium Fabricated using Ultrasonic Additive Manufacturing
构建后热机械处理对改善超声波增材制造制造的锆性能的功效
- DOI:
- 发表时间:
2022 - 期刊:
- 影响因子:11
- 作者:
C. Massey;M. Gussev;Cody Havrilak;R. Seibert;E. Cakmak;Andrew Nelson - 通讯作者:
Andrew Nelson
From Romance to Tragedy: House Ownership and Relocation in the Resettlement Narratives of Nepali Bhutanese Refugees
从浪漫到悲剧:尼泊尔不丹难民安置叙事中的房屋所有权和搬迁
- DOI:
10.1093/jrs/feaa079 - 发表时间:
2020 - 期刊:
- 影响因子:1.7
- 作者:
Andrew Nelson - 通讯作者:
Andrew Nelson
Empirical assessments of small-scale ecosystem service flows in rural mosaic landscapes in the Ethiopian highlands
埃塞俄比亚高地乡村马赛克景观小规模生态系统服务流的实证评估
- DOI:
- 发表时间:
2024 - 期刊:
- 影响因子:7.6
- 作者:
Tegegne Molla Sitotaw;L. Willemen;Derege Tsegaye Meshesha;Andrew Nelson - 通讯作者:
Andrew Nelson
978 CTNNB1 Mutation and L1CAM Expression are Not Mutually Exclusive in Endometrial Cancer
978 CTNNB1 突变与 L1CAM 表达在子宫内膜癌中并非相互排斥
- DOI:
10.1016/j.labinv.2024.103212 - 发表时间:
2025-03-01 - 期刊:
- 影响因子:4.200
- 作者:
Dina El-Rayes;Lynn Messersmith;Liberty Bonestroo;Sandhyarani Dasaraju;Elizabeth Ferreira;Andrew Nelson;Mahmoud Khalifa - 通讯作者:
Mahmoud Khalifa
Andrew Nelson的其他文献
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{{ truncateString('Andrew Nelson', 18)}}的其他基金
Collaborative Research: Mechanisms of differentiation and morphogenesis of the ligule/auricle hinge
合作研究:叶舌/耳廓铰链的分化和形态发生机制
- 批准号:
2120131 - 财政年份:2021
- 资助金额:
$ 202.2万 - 项目类别:
Standard Grant
Regulation of trophoblast differentiation by BAF complex chromatin remodelling factors
BAF 复合染色质重塑因子对滋养层分化的调节
- 批准号:
MR/S021531/1 - 财政年份:2019
- 资助金额:
$ 202.2万 - 项目类别:
Research Grant
MINE-PGR: Mining public RNA-seq data to identify and annotate long non-coding RNAs in fifteen diverse angiosperms
MINE-PGR:挖掘公共 RNA-seq 数据以识别和注释 15 种不同被子植物中的长非编码 RNA
- 批准号:
2021753 - 财政年份:2019
- 资助金额:
$ 202.2万 - 项目类别:
Standard Grant
Phase III IUCRC at University of Idaho: Center for Advanced Forestry Systems
爱达荷大学 IUCRC 第三阶段:先进林业系统中心
- 批准号:
1916699 - 财政年份:2019
- 资助金额:
$ 202.2万 - 项目类别:
Continuing Grant
MINE-PGR: Mining public RNA-seq data to identify and annotate long non-coding RNAs in fifteen diverse angiosperms
MINE-PGR:挖掘公共 RNA-seq 数据以识别和注释 15 种不同被子植物中的长非编码 RNA
- 批准号:
1758532 - 财政年份:2018
- 资助金额:
$ 202.2万 - 项目类别:
Continuing Grant
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KLF12通过调控PGR和GDF10的表达抑制孕激素诱导子宫内膜癌细胞分化的机制研究
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HBP1调节PGR转录活性在胚胎植入及妊娠维持中的作用机制
- 批准号:82160296
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- 批准年份:2015
- 资助金额:20.0 万元
- 项目类别:青年科学基金项目
相似海外基金
Collaborative Research: RESEARCH-PGR: Development of epigenetic editing for crop improvement
合作研究:RESEARCH-PGR:用于作物改良的表观遗传编辑的开发
- 批准号:
2331437 - 财政年份:2024
- 资助金额:
$ 202.2万 - 项目类别:
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Collaborative Research: TRTech-PGR TRACK: Discovery and characterization of small CRISPR systems for virus-based delivery of heritable editing in plants.
合作研究:TRTech-PGR TRACK:小型 CRISPR 系统的发现和表征,用于基于病毒的植物遗传编辑传递。
- 批准号:
2334028 - 财政年份:2024
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$ 202.2万 - 项目类别:
Standard Grant
RESEARCH-PGR: Cycling to low-temperature tolerance
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- 批准号:
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$ 202.2万 - 项目类别:
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TRTech-PGR: PlantTransform: Boosting Agrobacterium-mediated transformation efficiency in the orphan crop tef (Eragrostis tef) for trait improvement
TRTech-PGR:PlantTransform:提高孤儿作物 tef(画眉草 tef)中农杆菌介导的转化效率,以改善性状
- 批准号:
2327906 - 财政年份:2024
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2331438 - 财政年份:2024
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Collaborative Research: TRTech-PGR TRACK: Discovery and characterization of small CRISPR systems for virus-based delivery of heritable editing in plants.
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2334027 - 财政年份:2024
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RESEARCH-PGR: Unlocking the Genetic and Epigenetic Basis of Cereal Crop Adaptation to Acidic Soil Regions
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Collaborative Research: RUI: RESEARCH-PGR Meeting Future Food Demands: Phosphoproteomics to Unravel Signaling Pathways in Soybean's Response to Phosphate and Iron Deficiency
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TRTech-PGR: Unlocking Bread Wheat Genome Diversity: Foundational Genome Sequences and Resources to Advance Breeding and Biotechnological Improvement of a Global Food Security Crop
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