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Global analysis of uORF evolution and function

uORF进化和功能的全局分析

基本信息

批准号：
10093996
负责人：
Charles Joel McManus
金额：
$ 32.56万
依托单位：
CARNEGIE-MELLON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-02-01 至 2023-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10093996
关键词：
Address Affect Aspergillus fumigatus Binding Proteins Biology Candida albicans Catalogs DNA Data Development Disease Elements Eukaryota Evolution Fluorescence Fostering Gene Expression Genes Genetic Diseases Genetic Transcription Genetic Variation Genome Genomics Genotype Glean Goals Histoplasma capsulatum Human Human Genetics Individual Initiator Codon Knowledge Left Link Location Mediating Messenger RNA Mission Modeling Molecular Biology Mus Mutation Noise Open Reading Frames Organism Outcome Phenotype Play Post-Transcriptional Regulation Production Property Proteins Public Health RNA RNA-Binding Proteins Regulation Regulator Genes Regulatory Element Reporter Research Role Saccharomyces Students System Systems Biology Testing Transcript Transcription Process Translations United States National Institutes of Health Untranslated RNA Variant Work Yeasts base biological adaptation to stress cis acting element experimental study genome-wide high throughput screening human disease improved innovation novel pathogenic fungus predictive modeling tool

项目摘要

While variation in gene expression clearly affects the phenotypes of organisms, there is a fundamental gap in understanding the role of post-transcriptional processes. Because post-transcriptional processes are critical for the regulation of protein production, addressing this knowledge gap will facilitate better models of the relationship between genotype and phenotype. upstream Open Reading Frames (uORFs) are regulatory elements found in most human genes, and some disease-linked mutations appear to alter the presence of uORFs. Recently, hundreds of uORFs initiating with non-AUG start codons have been identified in many organisms. Despite the vast number of these elements, the functions and evolution of AUG and non-AUG uORFs remain elusive. The long-term goal of this project is to determine the functions and impact of genetic variation in post-transcriptional cis-regulatory elements. The objective of this proposal is to determine how new uORFs evolve and regulate translation. Our central hypothesis is that AUG and non-AUG uORFs have different regulatory roles, leading to different evolutionary trajectories. This hypothesis is based on our preliminary data, as we have identified hundreds of AUG and non-AUG uORFs with different genomic properties in Saccharomyces yeasts. We will test our central hypothesis by pursuing the following specific aims: 1) Investigate the evolution of AUG and non-AUG uORFs; 2) Determine the functions of AUG and non- AUG uORFs; and 3) Identify the roles of RNA binding proteins in uORF-mediated regulation. In the first aim, we will identify active uORFs in diverse strains and species of yeasts grown under four conditions to test the hypothesis that AUG and non-AUG uORFs have different evolutionary tempo and mode. The second aim will determine the gene-regulatory functions of hundreds of uORFs using FACS-uORF, a novel dual-fluorescence reporter system we developed. We will use these data to generate predictive models of uORF function. Aim 3 will identify genome-wide roles of RNA Binding Proteins in regulating uORFs, and integrate this knowledge in our predictive models. This approach is innovative, in that it combines exquisite systems biology tools with an excellent model genus to investigate the evolution of post-transcriptional gene regulation. The proposed research is significant because it is expected to fundamentally advance the fields of genomics, evolutionary, and systems biology by deciphering the evolutionary and functional properties of uORFs. Because translation mechanisms are highly conserved, the knowledge generated by the proposed work is expected to improve models of the relationship between non-coding genetic variation and phenotype in other eukaryotes, including humans.

虽然基因表达的变化明显影响生物体的表型，但有一个基本的在理解转录后过程的作用的差距。因为转录后过程对于调节蛋白质生产至关重要，解决这一知识缺口将有助于更好地基因型和表型之间关系的模型。上游开放阅读帧（uORF）是在大多数人类基因中发现的调控元件，并且一些疾病相关的突变似乎改变了uORF的存在最近，数百个以非AUG起始的uORF开始于密码子在许多生物体中已被鉴定。尽管这些元素数量众多， AUG和非AUG uORF的功能和进化仍然难以捉摸。这个项目的长期目标是是为了确定基因变异在转录后顺式调控中的功能和影响，元素该提案的目的是确定新的uORF如何进化和调节翻译.我们的中心假设是AUG和非AUG uORF具有不同的调节作用，导致不同的进化轨迹。这一假设是基于我们的初步数据，因为我们已经鉴定了数百个具有不同基因组特性的AUG和非AUG uORF，酵母属酵母。我们将通过追求以下具体目标来检验我们的中心假设：1）研究AUG和非AUG uORF的进化; 2）确定AUG和非AUG uORF的功能， AUG uORF;和3）鉴定RNA结合蛋白在uORF介导的调节中的作用。上目的是，我们将鉴定在四种条件下生长的不同菌株和酵母物种中的活性uORF 以检验AUG和非AUG uORF具有不同进化克里思和模式的假设。的第二个目标是使用FACS-uORF确定数百个uORF的基因调控功能，我们开发的新型双荧光报告系统。我们将利用这些数据来预测 uORF功能模型。目的3将确定RNA结合蛋白在调节细胞凋亡中的全基因组作用。 uORF，并将这些知识整合到我们的预测模型中。这种方法是创新的，因为它结合了精致的系统生物学工具和一个优秀的模型属来研究转录后基因调控这项研究意义重大，因为它有望从根本上推进基因组学，进化和系统生物学领域的破译， uORF的进化和功能特性。因为翻译机制是高度保存，所提出的工作产生的知识，预计将改善模型的非编码遗传变异与其他真核生物表型之间的关系，包括人类