Characterization of Small Open Reading Frames (sORFs) that Encode for Proteins

编码蛋白质的小型开放阅读框 (sORF) 的表征

基本信息

批准号：
7965734
负责人：
Munira Basrai
金额：
$ 12.69万
依托单位：
DIVISION OF BASIC SCIENCES - NCI
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/7965734
关键词：
Antithymoglobulin Biochemical Biological Biological Process Biology Carbon Cell Cycle Progression Chelating Agents Classification Codon Nucleotides Collaborations Collection DNA Replication Damage Data Databases Defect Energy Metabolism Epitopes Eukaryota Exhibits Functional RNA Gene Deletion Gene Silencing Genes Genetic Screening Genome Genome Stability Genomics Growth Haploidy Heat shock proteins High temperature of physical object Human Investigation Ions Kinetochores Laboratories Mediating Metals Modeling Molecular Mutagenesis Open Reading Frames Organism Partner in relationship Pathway interactions Phenotype Pheromone Plague Plasmids Proteins Proteolipids Publications RNA Reporting Research Ribosomal Proteins Role Saccharomyces cerevisiae Source System Thioredoxin Transcript Transcriptional Regulation Translations Universities base chaperonin chromosome loss comparative functional genomics fungus genome sequencing genome wide association study member mutant nuclease nucleocytoplasmic transport overexpression serial analysis of gene expression stress protein

项目摘要

Utilizing data from independent experimental approaches and computational analyses we proposed the existence for 299 sORFs in the S. cerevisiae genome, representing about 5% of annotated ORFs. We determined that a similar percentage of sORFs are annotated in other eukaryotes, including humans, and 184 of the S. cerevisiae sORFs exhibit similarity with ORFs in other organisms. In collaboration with the laboratories of Jef Boeke (The Johns Hopkins University), Ron Davis (Stanford University), and Michael Snyder (Yale University), we constructed a collection of gene-deletion mutants of 140 newly identified sORFs and integrated them into the existing deletion collection. Our laboratory undertook a comprehensive analysis of the sORF deletion strains and identified 22 sORFs required for haploid growth, growth at high temperature, growth in the presence of a non-fermentable carbon source, or growth in the presence of DNA damage and replication arrest agents. Our limited analysis of the sORFs was based on a narrow range of experimental conditions and comparison to sequences currently available in the databases. We propose that additional sORFs will be identified as the databases expand. In continuation with our ongoing research objective we found that three of the newly identified sORFs have been identified as kinetochore components in global mass spectrometric studies. This result indicates that these sORFs likely have a role in kinetochore function and suggests the potential for the role of additional sORFs in kinetochore function and genome stability. We will analyze the sORF deletion strains for chromosome loss and defects in checkpoint function, and perform secondary genetic screens to further define the molecular role of the sORFs. In efforts to define other roles for sORFs, we have several ongoing collaborations to examine if the sORF deletion strains have phenotypes related to defects in cell cycle progression, nuclear transport, gene silencing and transcriptional regulation. We have also generated epitope tagged sORF strains and plasmids overexpressing the sORFs for public use. Our studies with sORFs will identify and establish the role of sORFs in diverse biological pathways. We propose that additional sORFs will be identified as the databases expand.. We will utilize computational, biochemical, and genomic approaches to validate the presence of sORFs and understand their biological function.

利用来自独立的实验方法和计算分析的数据，我们提出了在 s中的299 sorfs的存在。酿酒酵母基因组，约占注释的ORF的5％。我们确定在包括人类在内的其他真核生物和 s的184个真核生物中有类似百分比的SORF。酿酒酵母 sorfs与其他生物体中的ORF表现出相似性。与Jef Boeke（约翰·霍普金斯大学），罗恩·戴维斯（Ron Davis）（斯坦福大学）和迈克尔·斯奈德（Michael Snyder）（耶鲁大学）的实验室合作，我们构建了140个新鉴定的Sorfs的基因脱落突变体的集合，并将它们整合到现有的DELETION收集中。我们的实验室对SORF缺失菌株进行了全面分析，并确定了22种单倍体生长，高温生长，在存在不可发酵碳源的生长或在存在DNA损伤和复制阻止剂的情况下生长所需的SORF。我们对SORF的有限分析是基于狭窄的实验条件范围，并与数据库中当前可用的序列进行了比较。我们建议将其他SORF确定为数据库扩展。在持续的研究目标中，我们发现三个新鉴定的SORF在全球质谱研究中被鉴定为动力学成分。该结果表明这些SORF可能在动力学功能中起作用，并提出了其他SORF在动力学功能和基因组稳定性中的作用的潜力。我们将分析SORF缺失菌株的染色体损失和检查点功能中的缺陷，并执行次级遗传筛选以进一步定义SORF的分子作用。为了定义SORF的其他角色，我们进行了几项持续的合作，以检查SORF缺失菌株是否具有与细胞周期进展，核转运，基因沉默和转录调控的缺陷有关的表型。我们还产生了表位标记的SORF菌株和质粒过表达SORF以供公众使用。我们对SORF的研究将识别并确定SORF在不同生物学途径中的作用。我们建议将其他SORF确定为数据库扩展。我们将利用计算，生化和基因组方法来验证SORF的存在并了解其生物学功能。