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）：非洲爪蟾和热带爪蟾是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的主要模式生物。从历史上看，由于易于培养、体型大以及可用于生化纯化的材料，非洲蟾蜍一直是首选的模型蛙。然而，部分由于 X. laevis 的异源四倍体性质，直到最近它还缺乏测序和注释的基因组。最近发布的非洲爪蟾基因组序列草案促进了全基因组方法的应用，以研究这种重要模式生物的基因表达。通过测量特定时间点转录物水平来分析基因表达的全基因组方法在识别对许多过程重要的新因子方面非常成功。然而，了解特定转录本的稳态水平并不等于精确了解该转录本的蛋白质表达时间。在非洲爪蟾等生物体中，早期发育是通过在没有转录的情况下翻译母体 mRNA 来编程的，因此将 RNA 丰度测量与翻译输出测量结合起来尤为重要。在本提案中，我们描述了一种新型 mRNA 测序策略的使用，该策略可识别在卵子发生晚期和转录沉默时早期发育期间显示受调节表达模式的 mRNA。此外，我们将使用最近开发的方法来测量 RNA 与核糖体的关联，以测量蛋白质表达并提供非编码转录本列表。最后，我们将利用获得的信息来识别对于完成减数分裂很重要的新蛋白质和 RNA。该提案将使用新颖的方法和非洲爪蟾的最新基因组序列来更深入地了解基因表达的转录后调控，并利用这些信息来识别对关键发育时间点重要的因素。最后，该提案将为整个非洲爪蟾社区产生许多资源，并确保非洲爪蟾成为未来的关键模式生物。