Defining the Xenopus translatome

非洲爪蟾翻译组的定义

基本信息

批准号：
8697085
负责人：
Michael D Sheets
金额：
$ 17.74万
依托单位：
UNIVERSITY OF WISCONSIN-MADISON
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 2017-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8697085
关键词：
Address Animals Bioinformatics Biometry Cell Cycle Cell Differentiation process Cells Complex Data Development Embryo Embryonic Development Event Exhibits Fertilization Freezing Gene Expression Gene Expression Profile Genetic Transcription Genetic Translation Genomics Harringtonine Individual Initiator Codon Interdisciplinary Study Life Maps Maternal Messenger RNA Measures Mediating Meiosis Messenger RNA Methodology Methods MicroRNAs Molecular Molecular Machines Oogenesis Open Reading Frames Pattern Polyribosomes Population Positioning Attribute Post-Transcriptional Regulation Proteins Proteome RNA RNA Sequences RNA-Binding Proteins Rana Regulation Regulatory Element Research Research Personnel Ribosomes Sampling Site Staging Transcript Translating Translation Initiation Translational Regulation Translations Untranslated Regions Xenopus Xenopus laevis Xenopus oocyte deep sequencing egg gastrulation inhibitor/antagonist loss of function nuclease oocyte maturation prospective public health relevance research study xenopus development

项目摘要

DESCRIPTION (provided by applicant): ABSTRACT This application describes a multidisciplinary collaboration between Dr. Michael Sheets, a developmental biologist who focuses on post-transcriptional regulation of early Xenopus embryogenesis and Dr. Colin Dewey, an expert in biostatistics and bioinformatics who focuses on analyzing gene expression using deep sequencing methodologies. While progress has been achieved in understanding Xenopus laevis development from a transcriptional point of view, significantly less is known about the translation of mRNA transcripts into proteins. We propose to use ribosome profiling to globally measure the translational activity of Xenopus mRNAs across the window of development that extends from oogenesis to gastrulation. Results from the proposed experiments will provide an unprecedented view of the dynamic translational landscape that exists during Xenopus development and this data has numerous applications. First, our experiments will identify biologically relevant Xenopus mRNAs. Transcriptome analysis only identifies the mRNAs present in cells, but it cannot define which mRNAs are translated into protein and therefore biologically relevant. We will use ribosome profiling to identify the actively translated and biologically relevant Xenopus mRNAs. This subset of the mRNA population and especially those that exhibit regulation represent ideal candidates for loss of function studies. Second, our results will identify groups of mRNAs that exhibit similar patterns of translational regulation. These co-regulated mRNAs will provide important starting points for molecular studies that seek to identify common sequence motifs for RNA binding proteins or miRNAs that mediate regulation. Third, ribosome profiling in the presence of the inhibitor harringtonine will allow us to identify the translational initiation site(s) for each Xenpus mRNA in our samples. The position of initiation defines the amino termini of the protein product encoded by an mRNA and therefore globally identifying the initiation sites of all mRNAs defines the N-terminus of the proteome. In addition, identifying the sites of initiation for specific mRNAs can reveal the presence of 5' RNA sequences, called uORFs that often function to regulate translational initiation. Results from the proposed experiments will provide an unprecedented genomic scale analysis of mRNA translation in Xenopus and how the translation of each mRNA changes during development. Our results and the associated methods will be useful for Xenopus researchers and researchers addressing the same questions in other vertebrate embryos.

描述（由申请人提供）：摘要该应用程序描述了发展后生物学家Michael Sheets博士之间的跨学科合作，他重点介绍了早期Xenopus Embryogenation的转录后调节和生物信息学专家Colin Dewey博士，他们专注于使用深层测序方法分析基因表达的生物信息学专家。尽管从转录的角度理解爪蟾发育方面已经取得了进步，但对mRNA转录物转化为蛋白质的翻译知之甚少。我们建议使用核糖体分析，以全球范围内测量爪蟾mRNA的翻译活性，从卵子发生到胃肠道。拟议的实验的结果将提供对Xenopus开发过程中存在的动态翻译局势的前所未有的观点，并且该数据具有许多应用。首先，我们的实验将确定与生物学相关的爪蟾mRNA。转录组分析仅识别细胞中存在的mRNA，但无法定义哪些mRNA被转化为蛋白质，因此在生物学上相关。我们将使用核糖体分析来识别主动翻译和生物学相关的Xenopus mRNA。 mRNA种群的这一子集，尤其是表现出调节的子集，代表了丧失功能研究的理想候选者。其次，我们的结果将确定表现出相似的翻译调节模式的mRNA组。这些共同调节的mRNA将为分子研究提供重要的起点，该研究试图鉴定介导调节的RNA结合蛋白或miRNA的共同序列基序。第三，在抑制剂哈灵顿的存在下进行核糖体分析将使我们能够识别样品中每个Xenpus mRNA的翻译起始位点。起始位置定义了由mRNA编码的蛋白质产物的氨基末端，因此在全球范围内识别所有mRNA的起始位点定义了蛋白质组的N末端。此外，识别特定mRNA的启动位点可以揭示5'RNA序列的存在，称为UORF，通常可以调节翻译起始。提出的实验的结果将提供对爪蟾中mRNA翻译的前所未有的基因组量表分析，以及在发育过程中每个mRNA的翻译如何变化。我们的结果和相关方法将对Xenopus的研究人员和研究人员有用，这些研究人员和研究人员在其他脊椎动物胚胎中解决了相同的问题。