Experimental Characterization of Novel Coding Small ORFs in the Arabidopsis thaliana Genome

本项目的主要目的是为拟南芥基因组中新的小开放阅读框架（sORFs，90-300 bp）的转录、翻译和功能提供实验依据。全基因组表达谱研究的进展已经发现，在几个真核生物基因组中，数千个基因没有注释。这些新基因是否编码蛋白质的问题在很大程度上仍然没有得到解决，因为它们主要通过转录而不是翻译的证据来验证。小的蛋白质编码基因特别难以发现，因为它们的表达水平较低，并且缺乏预测它们的统计能力。这是不幸的，因为已经发现小的蛋白质编码基因在真核生物中发挥重要功能。为了全面评估这些sORF和其他潜在的新型编码基因的转录和翻译，将对多核糖体相关转录物进行测序，以确定注定要翻译的转录物的身份。为了揭示sORF的潜在作用，将使用平铺阵列数据检查胁迫条件下的差异调节。此外，具有翻译证据的sORF基因将被靶向用于确定组织特异性表达模式以及功能获得和丧失表型。为了克服当前编码序列预测方法的局限性，将鉴定新型sORF基因的序列特性并用于改进编码潜力的测量。尽管科学界已经对基因组中的功能元件有了很多了解，但我们仍然把基因组的相当大的部分称为“暗物质”，因为事实上，基因组的大部分显示出各种类型的功能特征，但并没有被确定为基因。从广义上讲，该项目将为基因组“暗物质”提供重要见解。鉴于农业和经济上重要植物的大量序列的可用性，该项目将大大有助于更好地理解基因组中的部分列表，并最终帮助改善作物的努力。该项目还为各级学生提供了独特的培训环境。此外，计划中的外联活动向高中生介绍基因组概念，这将提高科学素养，加强大学预科生物学教育

The major goal of this project is to provide experimental evidence for the transcription, translation, and functions of novel small Open Reading Frames (sORFs, 90-300 bp) in the Arabidopsis thaliana genome. Advances in whole genome expression profiling have led to the discovery that thousands of genes are not annotated in several eukaryotic genomes. The question of whether these novel genes code for proteins remains largely unresolved because they are mainly verified by evidence of transcription but not translation. Small protein coding genes are particularly difficult to uncover due to their lower levels of expression and the lack of statistical power to predict them. This is unfortunate because small protein coding genes have been found to play important functions in eukaryotes. To globally assess the transcription and translation of these sORFs and other potential novel coding genes, polysome-associated transcripts will be sequenced to determine the identity of transcripts that are destined to be translated. To uncover potential roles of sORFs, differential regulation under stress conditions will be examined using tiling array data. In addition, sORF genes with evidence of translation will be targeted for determining tissue-specific expression patterns and gain- and loss-of-function phenotypes. To overcome current limitations in coding sequence prediction methods, the sequence properties of novel sORF genes will be identified and used for improving measures of coding potential. A revised coding potential measure will then be applied to the prediction of novel protein genes in plant sequences.Although the scientific community has gained much knowledge of the functional elements within genomes, we still refer to substantial parts of genomes as "dark matter" due to the fact that much of the genome displays various types of functional signatures but are not identified as genes. In a broad sense, this project will provide important insights into genome "dark matter". Given the availability of a large amount of sequences from agriculturally and economically important plants, this project will contribute significantly to a better understanding of the parts list in genomes and eventually aid efforts to improve crops. This project also provides a unique training environment for students of all levels. In addition, the planned outreach activities introduce concepts of genomes to high school students that will increase science literacy and enhance pre-college biology education