**5. Conclusions**

Translation plays a key role in the overall implementation of genetic information and the new knowledge about the intricate and multilevel information encoded in the mRNA sequence are of a paramount importance. The research into translation has revealed many new and interesting facts about the structural and functional role of the mRNA regulatory sequences that mediate differential translation. In particular, this success has been determined by the use of state-of-the-art technologies for assessing the translational statuses of individual mRNA species on a genome-wide scale in combination with computational algorithms and the methods for experimental verification, summarized here (Figure 8).

The knowledge on roles of regulatory contexts in mRNA for translation efficiency as well as the combinations of these contexts will require improvement of both experimental approaches and theoretical algorithms. The researchers must have the opportunity not only to precisely determine the correlation between the observed fluctuations in expression of a transcript and the actual content of the corresponding protein in plants, but also to precisely define and estimate the contributions of individual regulatory contexts and their combinations within mRNAs. Correspondingly, the need for development of an integrated information resource for this purpose looks very reasonable. This resource would comprise the information about (i) the experimental methods for assessing the changes in translation on a genome-wide scale, including their modifications and applicability to different plant species; (ii) the resources for analyzing, interpreting, and visualizing the polysome and ribosome profiling data; (iii) the resources for constructing the target sequences of plant transcripts and predicting their characteristics; (iv) the methods for experimental verification of the regulatory codes of the plant transcripts involved in translation modulation; and so on. This will form the background

for coordination of the numerous studies and the insight into the fine mechanisms underlying the control of biological processes at the point of translation in plants. Also it will expand the capabilities for future studies and the potential of applications of the mRNA regulatory contexts, including their use in engineering novel plant genotypes carrying the best combinations of the corresponding alleles and the generation of new of transgenes, including the use of genome editing technologies. *Int. J. Mol. Sci.* **2018**, *19*, x 22 of 26 combinations of the corresponding alleles and the generation of new of transgenes, including the use of genome editing technologies.

**Figure 8.** General strategy for identification, prediction, and experimental verification of the functional elements within transcripts that mediate their efficient translation. (**a**) Primary data on the transcripts differing in their translation efficiencies are obtained by sequencing the pools of the transcripts generated by polysome profiling, TRAP, or ribosome profiling. (**b**) In silico analysis of the transcript sequences identified the functional elements of transcripts. (**c**) Experimental verification of the predicted functional elements within transcripts (case study of reporter systems). **Figure 8.** General strategy for identification, prediction, and experimental verification of the functional elements within transcripts that mediate their efficient translation. (**a**) Primary data on the transcriptsdiffering in their translation efficiencies are obtained by sequencing the pools of the transcripts generated by polysome profiling, TRAP, or ribosome profiling. (**b**) In silico analysis of the transcript sequences identified the functional elements of transcripts. (**c**) Experimental verification of the predictedfunctional elements within transcripts (case study of reporter systems).

**Supplementary Materials:** Supplementary materials can be found at www.mdpi.com/xxx/s1. **Author Contributions:** I.V.G-P., O.S.P., and A.A.T. literature review and preparation of material for the second **Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/1/ 33/s1.

section of the review; I.V.G-P., O.N.M., I.V.D., and A.A.T. literature review and preparation of material for the third section of the review; I.V.G-P., O.S.P., K.V.K., and A.A.T. literature review and preparation of material for the fourth section of the review; A.A.T. preparation of original figures; and I.V.G-P. wrote the manuscript. All authors were fully involved in preparing and revising the manuscript critically at its current state. All authors approved the final version for publishing. **Author Contributions:** I.V.G.-P., O.S.P., and A.A.T. literature review and preparation of material for the second section of the review; I.V.G.-P., O.N.M., I.V.D., and A.A.T. literature review and preparation of material for the third section of the review; I.V.G.-P., O.S.P., K.V.K., and A.A.T. literature review and preparation of material for the fourth section of the review; A.A.T. preparation of original figures; and I.V.G.-P. wrote the manuscript. All authors were fully involved in preparing and revising the manuscript critically at its current state. All authors approved the final version for publishing.

**Funding:** The authors thank the Russian Science Foundation (grant no. 18-14-00026) for supporting this project. **Funding:** The authors thank the Russian Science Foundation (grant no. 18-14-00026) for supporting this project.

**Conflicts of Interest:** The authors declare no conflicts of interest. **Conflicts of Interest:** The authors declare no conflicts of interest.

Profiling. *J. Vis. Exp.* **2016**, 10.3791/54231, doi:10.3791/54231.

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