ABI Sustaining: The REDfly database of transcriptional regulatory elements

ABI Sustaining：转录调控元件的 REDfly 数据库

• 批准号: 1758252
• 负责人: Marc Halfon
• 金额: $ 44.65万
• 依托单位: SUNY at Buffalo
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2021-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1758252&HistoricalAwards=false
• 关键词: ABI; Sustaining; REDfly; database; transcriptional

Transcriptional cis - regulatory modules (CRMs) are DNA sequences required for regulating gene expression - determining when and where genes are turned "on" and "off". CRMs play critical roles with respect to normal variation between individuals, birth defects, chronic diseases, and evolution. Despite the clear importance for many areas of biology, these sequences are not well-documented. The REDfly (Regulatory Element Database for Fly) database helps fill this gap in CRM annotation by curating known CRMs and transcription factor binding sites (TFBS) for the important research organism Drosophila melanogaster (fruit fly). REDfly is the most detailed existing platform for regulatory element annotation for any animal. It's records include over 16,000 experimentally verified CRMs and 2000 TFBSs along with their DNA sequence, their associated genes, and the gene expression patterns they direct. REDfly is a well-used and valuable resource for the genomics, bioinformatics, and Drosophila communities and is an important platform for supporting hypothesis-driven empirical and computational research. It has contributed to numerous studies in multiple areas relating to non-Drosophila as well as Drosophila systems including CRM biology, CRM discovery, construction of regulatory network models, interpretation of genomic datasets, and CRM evolution. The current project will focus on continued curation and maintenance of the database so that it remains up to date and functions with maximum utility for its users. This will ensure that REDfly continues to be available as an important source of raw data for analysis, hypothesis generation, assessment and validation, and empirical research in molecular and developmental biology, genetics, genomics, bioinformatics, and evolution. The current project also has a valuable undergraduate education component. It will continue to be the focus of a University at Buffalo course "Genome Annotation", in which the students participate in annotating regulatory elements for entry into REDfly, thus making genuine contributions to the research community while learning the techniques of genome annotation and biocuration and the science of gene regulation. In a new effort, a REDfly unit will be introduced into a Developmental Biology course at Baruch College-CUNY, one of the nation's most diverse campuses. Students who excel in the class will be invited to Buffalo to participate in the Summer Undergraduate Research Experience (SURE) program and serve as REDfly curators.The specific objectives of this Sustaining Award are to keep REDfly up to date with the rapidly increasing numbers of CRMs and TFBSs being discovered and reported in the literature, and to maintain the REDfly site in a manner that will maximize its utility to the research community. The focus is on: (1) Curation. REDfly will be kept up - to - date as new studies are published. Emphasis will remain on in vivo assays, but in vitro studies will be included where encountered and appropriate. (2) Education. The PI will continue to use REDfly as the basis for his "Genome Annotation" course. A REDfly unit will be introduced in an undergraduate course at Baruch College-CUNY, and bring up to two course alumni to Buffalo each summer to work on REDfly curation as a part of the University at Buffalo Medical School's Summer Research Experiences for Undergraduates (SURE) program. (3) Service. REDfly will continue to serve its user community with a high degree of responsiveness, including rapid response to queries, custom searches and downloads on request, error correction, and support for undergraduate courses. (4) General maintenance. REDfly will be maintained in peak operating condition through identification and correction of programming bugs, regular updates to genome annotations imported from FlyBase and other sources, active maintenance of links to outside resources, software and/or hardware updates, etc. These activities will ensure that REDfly data continue to be available as an important resource for the scientific community. The REDfly database can be found at http://redfly.ccr.buffalo.edu.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.

转录顺式调节模块 (CRM) 是调节基因表达所需的 DNA 序列，决定基因何时何地“打开”和“关闭”。 CRM 在个体之间的正常变异、出生缺陷、慢性疾病和进化方面发挥着关键作用。尽管这些序列对于生物学的许多领域具有明显的重要性，但并没有得到充分的记录。 REDfly（果蝇调控元件数据库）数据库通过为重要的研究生物果蝇（果蝇）整理已知的 CRM 和转录因子结合位点 (TFBS)，有助于填补 CRM 注释中的这一空白。 REDfly 是用于任何动物调控元件注释的最详细的现有平台。它的记录包括超过 16,000 个经过实验验证的 CRM 和 2000 个 TFBS 以及它们的 DNA 序列、相关基因以及它们指导的基因表达模式。 REDfly 是基因组学、生物信息学和果蝇社区的常用且有价值的资源，也是支持假设驱动的实证和计算研究的重要平台。它为与非果蝇和果蝇系统相关的多个领域的大量研究做出了贡献，包括 CRM 生物学、CRM 发现、监管网络模型的构建、基因组数据集的解释和 CRM 进化。当前的项目将侧重于数据库的持续管理和维护，以使其保持最新状态并为用户提供最大的实用性。这将确保 REDfly 继续作为原始数据的重要来源，用于分析、假设生成、评估和验证，以及分子和发育生物学、遗传学、基因组学、生物信息学和进化方面的实证研究。当前的项目还有一个有价值的本科教育部分。这将继续成为布法罗大学“基因组注释”课程的重点，在该课程中，学生参与注释调控元件以进入REDfly，从而在学习基因组注释和生物管理技术以及基因调控科学的同时为研究界做出真正的贡献。在一项新的努力中，REDfly 单元将被引入纽约市立大学巴鲁克学院（全美最多元化的校园之一）的发育生物学课程中。在课程中表现优异的学生将被邀请到布法罗参加暑期本科生研究体验 (SURE) 计划并担任 REDfly 策展人。该持续奖的具体目标是让 REDfly 及时了解文献中发现和报告的 CRM 和 TFBS 数量迅速增加的情况，并以最大限度地提高其对研究界的效用的方式维护 REDfly 网站。重点是：（1）策展。随着新研究的发表，REDfly 将保持最新状态。重点仍然是体内测定，但在遇到和适当的情况下也将包括体外研究。 (2)教育。 PI 将继续使用 REDfly 作为他的“基因组注释”课程的基础。纽约市立大学巴鲁克学院的本科课程中将引入 REDfly 单元，每年夏天将最多两名课程校友带到布法罗进行 REDfly 管理工作，作为布法罗大学医学院本科生暑期研究体验 (SURE) 计划的一部分。 (3)服务。 REDfly 将继续以高度响应能力为其用户社区提供服务，包括快速响应查询、根据请求进行自定义搜索和下载、纠错以及对本科课程的支持。 (4)一般维护。通过识别和纠正编程错误、定期更新从 FlyBase 和其他来源导入的基因组注释、积极维护与外部资源的链接、软件和/或硬件更新等，REDfly 将保持在峰值运行状态。这些活动将确保 REDfly 数据继续作为科学界的重要资源可用。 REDfly 数据库可在 http://redfly.ccr.buffalo.edu 上找到。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。