Genome-wide analysis of polyadenylation and translation in Xenopus

非洲爪蟾多聚腺苷酸化和翻译的全基因组分析

• 批准号: 8742224
• 负责人: Michael Demian Blower
• 金额: $ 47.8万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-15 至 2018-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8742224
• 关键词: Amphibia; Animal Model; Biochemical; Biological Assay; Biological Models; Biology; Cataloging; Catalogs; Cell Cycle Regulation; Cellular biology; Communities; DNA Sequence; Development; Developmental Biology; Ensure; Exhibits; Fertilization; Future; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Germ Cells; Goals; Growth; Guanosine; High-Throughput RNA Sequencing; Knowledge; Length; Link; Maps; Maternal Messenger RNA; Measurement; Measures; Meiosis; Messenger RNA; Methods; Modeling; Nature; Oogenesis; Organism; Output; Pattern; Poly(A) Tail; Polyadenylation; Process; Proteins; RNA; RNA Sequences; Rana; Regulation; Resources; Ribosomes; Site; Study models; Time; Transcript; Translations; Untranslated RNA; Up-Regulation; Xenopus; Xenopus laevis; base; comparative; design; genome sequencing; genome wide association study; genome-wide; genome-wide analysis; human disease; insight; novel; oligo (dT); programs; protein expression; public health relevance; tool; xenopus genome

DESCRIPTION (provided by applicant): Xenopus laevis and Xenopus tropicalis are major model organisms useful for the study of vertebrate development, germ cell biology, and various aspects of cell cycle control. Historically, X. laevis has been the preferred model frog due to ease of culture, large size, and availability of material for biochemical purifications. However, partly due to the allotetraploid nature of X. laevis it has lacked a sequenced and annotated genome until recently. The recent release of a draft of the Xenopus laevis genome sequence facilitates application of genome-wide approaches to study gene expression in this important model organism. Genome-wide approaches that assay gene expression by measuring the levels of transcripts at particular time points have been very successful at identification of nove factors important for many processes. However, knowledge of the steady state level of a particular transcript does not equate to precise knowledge of the timing of protein expression from that transcript. In organisms such as Xenopus where early development is programmed by translation of maternal mRNAs in the absence of transcription it is especially important to couple measurement of RNA abundance to measurement of translational output. In this proposal we describe the use of a novel mRNA-sequencing strategy that identifies mRNAs that show patterns of regulated expression during late oogenesis and early development when transcription is silent. In addition, we will use a recently developed method to measure RNA association with ribosomes to measure protein expression and provide a list of noncoding transcripts. Finally, we will use the information gained to identify novel proteins and RNAs that are important for the completion of meiosis. This proposal will use novel methods and the recent genome sequence of Xenopus laeivs to gain a deeper understanding of posttranscriptional regulation of gene expression and use this information to identify factors important for a key developmental time point. Finally, this proposal will generate many resources for the entire Xenopus community and ensure that Xenopus is a key model organism in the future.

描述（由申请人提供）：Xenopus laevis和xenopus tropicalis是主要模型生物，可用于研究脊椎动物发育，生殖细胞生物学和细胞周期控制的各个方面。从历史上看，X. laevis一直是首选模型青蛙，这是由于培养，大尺寸和生化净化材料的可用性。然而，部分原因是X. laevis的同种四倍体性质，直到最近才缺乏测序的注释基因组。最近发布的爪蟾Laevis基因组序列草稿促进了全基因组方法在这种重要模型生物中研究基因表达的应用。通过测量特定时间点的转录水平来测定基因表达的全基因组方法在识别对许多过程很重要的Nove因素方面非常成功。但是，对特定成绩单的稳态水平的了解并不等于从该转录本中蛋白质表达的时间的精确知识。在诸如Xenopus之类的生物中，在没有转录的情况下，通过对母体mRNA进行翻译来编程，将RNA丰度测量以测量转化产量的测量尤为重要。在此提案中，我们描述了一种新颖的mRNA测序策略的使用，该策略识别出在转录沉默时在卵子发生和早期发育过程中表现出调节表达模式的mRNA。此外，我们将使用最近开发的方法测量与核糖体的RNA关联来测量蛋白质表达并提供非编码转录本的列表。最后，我们将使用获得的信息来识别对减数分裂很重要的新型蛋白质和RNA。该提案将使用新颖的方法和最近的爪蟾laeivs的基因组序列，以更深入地了解基因表达后的转录后调节，并使用此信息来确定对关键发育时间点重要的因素。最后，该提案将为整个Xenopus社区创造许多资源，并确保Xenopus是将来的关键模型生物体。