Genome-wide comparative analysis of Oryza sativa (japonica) and Arabidopsis thaliana 5′-UTR sequences for translational regulatory signals

Untranslated regions of eukaryotic genes contain elements that in combination with proteins/RNAs modulate translation of individual messenger RNAs. Elements present in 5� -UTRs that influence translational efficiency include AUG sequence context, and presence of uAUGs/uORFs. To assess the level of 5� -UTR mediated translational regulation in rice, a genome-wide computational analysis of rice 5� -UTRs was carried out in comparison with 5� -UTRs of Arabidopsis. Rice 5� - UTRs were generally longer and more GC-rich than those of Arabidopsis. 30% of rice and 34% of Arabidopsis cDNAs contained upstream AUG triplets (uAUGs). For both organisms, a higher proportion of uAUG-less cDNAs possessed start codons which conformed to the consensus sequence context compared to uAUG-containing cDNAs. Although the GC composition of the start codon context varied between and within rice and Arabidopsis, the critical positions, � 4 and � 3, were conserved. 24% of rice and 30% of Arabidopsis cDNAs possessed upstream open reading frames (uORFs). Combinatorial analyses of start-codon context, uAUG context and context of uAUGs of upstream open reading frames of individual genes indicate that about 30-34% of genes in rice and Arabidopsis are likely to be influenced at translational level by signals present in 5� -UTR as they possess uAUG/uORFs with sequence context conforming to the consensus sequence There was very little conservation of uAUG positions or uORFs between rice and Arabidopsis. However, there was conservation of uAUG positions between rice, wheat and barley.