Computational and Experimental Tools to Monitor the Changes in Translation Efficiency of Plant mRNA on a Genome-Wide Scale: Advantages, Limitations, and Solutions

• Published in: International journal of molecular sciences Vol. 20; no. 1; p. 33
• Main Authors: Goldenkova-Pavlova, Irina V, Pavlenko, Olga S, Mustafaev, Orkhan N, Deyneko, Igor V, Kabardaeva, Ksenya V, Tyurin, Alexander A
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 21-12-2018; MDPI
• Subjects: Algorithms; computational algorithms; Computational Biology - methods; Computer applications; Efficiency; experimental approaches; features of plant mRNAs; Flowers & plants; Gene expression; Gene Expression Regulation, Plant; Genome, Plant; Genome-Wide Association Study; genome-wide scale; Genomes; Genomics - methods; Methods; Nucleotides; Peptides; Plants - genetics; Polyribosomes; Protein Biosynthesis; Proteins; Proteomes; Proteomics; regulation and efficiency of translation; Research methodology; Review; RNA Transport; RNA, Messenger - genetics; Software; Specimen preparation; Translation; experimental approaches; computational algorithms; genome-wide scale; regulation and efficiency of translation; features of plant mRNAs
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms20010033

The control of translation in the course of gene expression regulation plays a crucial role in plants' cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein products in eukaryotic cells, including plants, requires thorough investigation of the regulatory mechanisms of translation. A wide and amazingly complex network of mechanisms decoding the plant genome into proteome challenges researchers to design new methods for genome-wide analysis of translational control, develop computational algorithms detecting regulatory mRNA contexts, and to establish rules underlying differential translation. The aims of this review are to (i) describe the experimental approaches for investigation of differential translation in plants on a genome-wide scale; (ii) summarize the current data on computational algorithms for detection of specific structure⁻function features and key determinants in plant mRNAs and their correlation with translation efficiency; (iii) highlight the methods for experimental verification of existed and theoretically predicted features within plant mRNAs important for their differential translation; and finally (iv) to discuss the perspectives of discovering the specific structural features of plant mRNA that mediate differential translation control by the combination of computational and experimental approaches.