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Xenopus社区进入后基因组时代，它是关键的完整基因模型，并且监管元素是迅速，准确的定义，然后使社区容易访问。目前，我们和其他人估计 - 在X. tropicalis中 - 只有36％的成绩单具有5'UTR，并随附的转录起始位点，只有37％的成绩单与多个尾巴相关的3'UTR。 X. laevis可能是类似的情况。此外，对于任何两种物种的启动子，增强子和其他调节元素，尤其是在考虑其广泛的时间和空间使用时，知之甚少。最近，在2012年9月广泛发布的大规模编码发现中清​​楚地说明了绘制完整基因体和定义元素的巨大效用。由于Xenopus社区刚刚开始观察，然后策划基因组，我们可以利用这些其他基因组努力驱动的技术进步。与编码的情况不同 - 大型实验室和资源必须动员 - 成本下降和前进的技术允许小型实验室在Xenopus中进行类似的努力，并以降低的速度降低。 Xenopus社区了解严格的基因组注释的直接需求。在法国国际Xenopus会议上的资源会议上，这显然是回应的（2012年9月），在该会议上，基因组注释被确认为欧洲Xenopus Stock Center续签后的最高优先事项。 在这笔赠款中，我们建议在整个开发过程中对Xenopus中的基因组元素进行分类，并将建立一个访问基因组元素的交互式数据库。具体而言，我们的目标是生化阐明5'UTR，3'UTR，启动子，增强子和长期非编码RNA。这些数据集将允许在X. Tropicalis和X. Laevis中快速有效地策划基因模型和调节元素。值得注意的是，我们还将建立Xenmine - 一种基因组相互作用工具，可让研究人员与这些努力和社区中的基因组数据集直接接触。总体而言，这项工作是较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. laevis和X. tropicalis的基因组数据。尽管我们将直接与多种努力接触，但我们的OLE是利用生物化学在Xenopus的基因组曲目中“填补大空白”，以实现基因模型和基因调节元件的准确映射。