Biochemical predictions of regulatory elements and XenMINE for Xenopus

非洲爪蟾调控元件和 XenMINE 的生化预测

基本信息

批准号：
9050693
负责人：
Julie C Baker
金额：
$ 44.36万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
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/9050693
关键词：
3&apos Untranslated Regions 5&apos Untranslated Regions Adult Biochemical Biochemistry Biological Biological Models ChIP-seq Chromosome Mapping Communities Data Data Set Databases Development Elements Embryonic Development Enhancers European France Gene Expression Gene Expression Regulation Gene Structure Genes Genome Genomics Goals Grant Health 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 RNA Untranslated Regions Variant Xenopus abstracting cost genome annotation genome database genome-wide genomic data genomic tools human disease interactive tool meetings model organisms databases open source promoter tool transcriptome sequencing

项目摘要

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获取至关重要。目前，我们和其他人估计，在热带 X. 中，只有 36% 的转录本具有伴随转录起始位点的 5' UTR，只有 37% 的转录本具有与多聚 A 尾相关的 3' UTR。 X. laevis 中可能也存在类似的情况。此外，人们对这两个物种中的启动子、增强子和其他调控元件知之甚少，尤其是考虑到它们广泛的时间和空间用途时。 2012 年 9 月广泛发表的大量 ENCODE 发现最近清楚地说明了绘制完整基因体和定义全基因组元素的巨大效用。由于非洲爪蟾群体刚刚开始观察并管理基因组，我们可以利用这些其他基因组工作驱动的技术。与 ENCODE 的情况不同——必须调动大型实验室和资源——成本的降低和技术的进步使得非洲爪蟾的类似努力可以通过小型实验室以大大降低的速度实现。非洲爪蟾社区了解严格的基因组注释的迫切需要。这在法国国际爪蟾会议资源会议（2012 年 9 月）上得到了明确的回应，会议确认基因组注释是欧洲爪蟾种群中心更新后的最高优先事项。在这笔赠款中，我们建议对非洲爪蟾的整个发育过程中的基因组元件进行分类，并将建立一个交互式数据库来访问基因组元件。具体来说，我们的目标是通过生化手段阐明 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有效地管理热带 X.tropicis 和 X.laevis 的基因模型和调控元件。值得注意的是，我们还将建立 XenMine - 一种基因组交互工具，允许研究人员直接与来自这些工作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相互作用组的一个分支，其总体目标是编译、注释并传播来自非洲角线虫和热带角线虫的基因组数据。虽然我们将直接参与多项工作，但我们的重点是利用生物化学来“填补非洲爪蟾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。