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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：
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
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/8692995
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 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

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）：