Key result
Machine learning models using ribosome profiling identified distinct feature sets predictive of AUG and non-AUG translation initiation sites in plants, revealing a conserved cis-regulatory strategy.
Why the study?
Alternative translation initiation sites (TISs) are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear.
The study identifies a conserved eukaryotic cis-regulatory strategy involving a novel CU-rich sequence that helps ribosomes distinguish AUG and non-AUG triplets for protein synthesis.
Models for plant alternative TIS prediction are hypothesis-generating; experimental validation needed before broader use.
Abstract mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in Arabidopsis thaliana and tomato ( Solanum lycopersicum ). Distinct feature sets were predictive of AUG and non-AUG TISs in 5′ untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots and also in humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis -regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis -regulatory signatures across eukaryotes and viruses suggests their broad, critical roles in reprogramming the translational landscape in the plant–virus arms race. Teaser New insights into how plant ribosomes distinguish AUG and non-AUG triplets for protein synthesis via a conserved eukaryotic cis -regulatory strategy.
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Wu et al. (2023) studied this question. Machine learning models using ribosome profiling identified distinct feature sets predictive of AUG and non-AUG translation initiation sites in plants, revealing a conserved cis-regulatory strategy.
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