Biochemical predictions of regulatory elements and XenMINE for Xenopus

非洲爪蟾调控元件和 XenMINE 的生化预测

• 批准号: 8692995
• 负责人: Julie C Baker
• 金额: $ 47.72万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-07-05 至 2018-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8692995
• 关键词: 3' Untranslated Regions; 5' Untranslated Regions; Adult; Biochemical; Biochemistry; Biological; Biological Models; ChIP-seq; Chromosome Mapping; Communities; Data; Data Set; Databases; Development; Elements; Embryonic Development; Enhancers; European; France; Functional RNA; Gene Expression; Gene Expression Regulation; Gene Structure; Genes; Genome; Genomics; Goals; Grant; Histones; Housing; Imagery; Indium; Intercistronic Region; International; Laboratories; Learning; Maps; Modeling; Nucleic Acid Regulatory Sequences; Poly A; Poly(A) Tail; Programming Languages; Publishing; Regulatory Element; Research Personnel; Resources; Role; Staging; Technology; Time; Tissues; Transcript; Transcription Initiation Site; Transcriptional Regulation; Untranslated Regions; Variant; Xenopus; abstracting; cost; genome annotation; genome database; genome-wide; human disease; meetings; model organisms databases; open source; promoter; public health relevance; tool; transcriptome sequencing

DESCRIPTION (provided by applicant): Abstract As the Xenopus community moves into the post-genomic era, it is critical complete gene models and regulatory elements are rapidly and accurately defined and then made readily accessible to the community. Currently, we and others have estimated that - in X. tropicalis - only 36% of transcripts have 5' UTRs with accompanying transcription start site and only 37% have 3' UTRs associated with the poly A tail. A similar situation is probably true in X. laevis. Additionally, very little is known about promoters, enhancers and other regulatory elements in either species especially when considering their broad temporal and spatial usage. The enormous utility in mapping complete gene bodies and defining elements genome-wide has recently been clearly illustrated by the massive ENCODE findings published widely in September 2012. As the Xenopus community is just beginning to observe and then curate genomes, we can harness the advances in technology driven by these other genome efforts. Unlike the situation in ENCODE - whereby large laboratories and resources had to be mobilized - the decreasing cost and advancing technologies allow similar efforts in Xenopus to be achieved by small labs and at a much reduced rate. The Xenopus community understands the immediate need for rigorous genome annotation. This was clearly echoed at the Resources Meeting at the International Xenopus Meeting in France (Sept. 2012), where genome annotation was confirmed as the highest priority after renewal of the European Xenopus Stock Center. In this grant, we propose to classify genomic elements in Xenopus throughout development and will establish an interactive database in which to access genomic elements. Specifically, our goal is to biochemically elucidate the 5' UTR, 3' UTR, promoters, enhancers and long non-coding RNAs. These datasets will allow rapid and efficient curation of gene models and regulatory elements in both X. tropicalis and X. laevis. Significantly, we will also establish XenMine - a genomic interaction tool that allows researchers to directly interface with genomic datasets from these efforts and from the community. Overall, this effort is one branch of a larger interactome - whose overall goal is to compile, annotate and then disseminate genomic data from both X. laevis and X. tropicalis. While we will directly interface with multiple efforts, our ole is to utilize biochemistry to 'fill a large gap' in the genomic repertoire of Xenopus to enable accurate mapping of gene models and gene regulatory elements.

描述(由申请人提供)： 摘要随着非洲爪哇群落进入后基因组时代，快速和准确地确定完整的基因模型和调控元件并使其易于为群落所访问是至关重要的。目前，我们和其他人估计，在热带X线虫中，只有36%的转录本具有伴随转录起点的5‘UTRs，只有37%的转录本具有与Poly A尾巴相关的3’UTRs。莱维斯的情况可能也是如此。此外，对启动子、增强子和其他调控元件在这两个物种中的作用知之甚少，特别是考虑到它们在时间和空间上的广泛用途。最近，2012年9月广泛发表的大量ENCODE发现清楚地说明了在绘制完整基因体和定义全基因组元素方面的巨大效用。由于非洲爪哇社区刚刚开始观察和管理基因组，我们可以利用这些其他基因组努力推动的技术进步。与ENCODE的情况不同--必须调动大型实验室和资源--成本的下降和技术的进步使非洲爪哇的类似努力能够由小型实验室以低得多的速度实现。非洲爪哇群体理解对严格的基因组注释的迫切需求。这一点在法国国际Xenopus会议的资源会议上得到了明显的呼应(9月1日)。2012年)，基因组注释被确认为欧洲非洲爪哇股票中心更新后的最高优先事项。在这笔赠款中，我们建议对非洲爪哇整个发育过程中的基因组成分进行分类，并将建立一个交互数据库，在其中访问基因组元素。具体地说，我们的目标是从生化上阐明5‘非编码区、3’非编码区、启动子、增强子和长的非编码RNA。这些数据集将允许对热带和莱维氏X.laevis的基因模型和调控元件进行快速和有效的管理。值得注意的是，我们还将建立Xenmine，这是一个基因组交互工具，允许研究人员直接与这些努力和社区的基因组数据集进行交互。总体而言，这项工作是一个更大的互动组的一个分支--其总体目标是汇编、注释并随后传播来自莱维氏X.laevis和热带X.tropicalis的基因组数据。虽然我们将直接与多种努力对接，但我们的OE是利用生物化学来填补非洲爪哇基因组库中的一个巨大空白，以实现基因模型和基因调控元件的准确定位。