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）： 摘要随着非洲爪蟾群落进入后基因组时代，快速准确地定义完整的基因模型和调控元件并使其易于为群落所用至关重要。目前，我们和其他人估计-在X。tropicalis -只有36%的转录物具有伴随转录起始位点的5'UTR，并且只有37%具有与poly A尾相关的3' UTR。类似的情况可能在X中也是如此。光滑。此外，很少有人知道的启动子，增强子和其他调控元件在这两个物种，特别是当考虑到他们广泛的时间和空间的用途。2012年9月广泛发表的大量ENCODE研究结果最近清楚地说明了绘制完整基因体和全基因组定义元件的巨大效用。由于非洲爪蟾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工作推动的技术进步。与ENCODE的情况不同--必须动员大型实验室和资源--成本的降低和技术的进步使非洲爪蟾的类似工作可以由小型实验室以更低的速度完成。Xenopus社区理解严格的基因组注释的迫切需要。这一点在法国国际爪蟾会议的资源会议上得到了明确的回应（9月10日）。2012年），其中基因组注释被确认为欧洲非洲爪蟾种群中心更新后的最高优先事项。 在这项资助中，我们建议对非洲爪蟾的基因组成分进行分类，并将建立一个交互式数据库，以获取基因组成分。具体而言，我们的目标是生物化学地阐明5' UTR，3' UTR，启动子，增强子和长非编码RNA。这些数据集将允许快速和有效地管理X。tropicalis和X.光滑。值得注意的是，我们还将建立XenMine -一个基因组交互工具，使研究人员能够直接与来自这些工作和社区的基因组数据集进行交互。总的来说，这项工作是更大的相互作用组的一个分支--其总体目标是编译、注释然后传播来自X的基因组数据。laevis和X.热带植物虽然我们将直接与多方面的努力，我们的OLE是利用生物化学，以“填补一个大的差距”在非洲爪蟾的基因组库，使基因模型和基因调控元件的准确定位。