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

该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，90-300bp)的转录、翻译和功能提供实验证据。全基因组表达谱研究的进展导致发现，在几个真核基因组中，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未得到解决，因为它们主要是通过转录证据来验证，而不是翻译。小的蛋白质编码基因尤其难以发现，因为它们的表达水平较低，而且缺乏预测它们的统计能力。这是不幸的，因为已经发现小蛋白编码基因在真核生物中发挥重要功能。为了在全球范围内评估这些sORF和其他潜在的新编码基因的转录和翻译，将对多聚体相关的转录本进行测序，以确定注定要翻译的转录本的身份。为了揭示sORF的潜在作用，将使用平铺阵列数据研究应力条件下的差异调节。此外，具有翻译证据的sORF基因将被用于确定组织特定的表达模式和功能获得和丧失的表型。为了克服目前编码序列预测方法的局限性，将识别新的sORF基因的序列属性并用于改进编码潜力的措施。尽管科学界已经对基因组中的功能元件有了很多了解，但我们仍然将基因组的相当大一部分称为“暗物质”，因为许多基因组显示出各种类型的功能签名，但没有被识别为基因。从广义上讲，这项计划将为基因组“暗物质”的研究提供重要的见解。鉴于从农业和经济上具有重要意义的植物中获得了大量的序列，该项目将大大有助于更好地了解基因组中的部分列表，并最终帮助改进作物的努力。该项目还为各级学生提供了独特的培训环境。此外，计划的外展活动向高中生介绍基因组的概念，这将提高学生的科学素养，并加强大学前的生物教育。

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