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

Michigan State University, East Lansing MI

Investigators

Abstract

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