Modeling Alternative Translation Initiation Sites in Plants Reveals Evolutionarily Conserved -regulatory Codes in Eukaryotes

Overview

Journal Genome Res

Specialty Genetics

Date 2024 Mar 13

PMID 38479836

Authors

Ting-Ying Wu

Ya-Ru Li

Kai-Jyun Chang

Jhen-Cheng Fang

Daisuke Urano

Ming-Jung Liu

Affiliations

Soon will be listed here.

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 the tomato (). Distinct feature sets were predictive of AUG and nonAUG 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 humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby -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 -regulatory signatures across plant species, humans, and viruses suggests their broad and critical roles in reprogramming the translational landscape.

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