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Type: Journal article
Title: Conserved upstream open reading frames in higher plants
Author: Tran, M.
Schultz, C.
Baumann, U.
Citation: BMC Genomics, 2008; 9(1):1-17
Publisher: BioMed Central Ltd.
Issue Date: 2008
ISSN: 1471-2164
Statement of
Michael K Tran, Carolyn J Schultz and Ute Baumann
Abstract: Background Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants. Results We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs. Conclusion This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.
Keywords: Plants
5' Untranslated Regions
RNA, Plant
Sequence Analysis
Conserved Sequence
Open Reading Frames
Expressed Sequence Tags
Rights: © 2008 Tran et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI: 10.1186/1471-2164-9-361
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