Recent Advances of Ribosome Profiling in Plants

doi:10.11983/CBB22028

Abstract

Abstract: With the great development and progress of high-throughput sequencing (HTS) technologies, many newborn techniques have provided solutions to unresolved biological puzzles. Ribosome profiling has emerged as an HTS-based technique that facilitates the genome-wide investigation of translation at single-nucleotide resolution, and it resolves the missing link between transcriptome and translatome. Ribosome profiling not only identifies the mRNAs in translation, but also provides precise positions of the ribosomes on mRNA to help identify the coding regions of the mRNAs. In addition, combined with the parallel RNA sequencing, ribosome profiling can determine the translation efficiency for each mRNA by comparing the rates of protein synthesis and the abundance of mRNAs. Based on its extraordinary advances, ribosome profiling has been successfully applied in animals, plants and microbes, and has thoroughly enhanced our understanding of translational regulation. However, due to the restrictions caused by the physical characteristics of plant cells and tissues, there are still considerable limitations in the application of ribosome profiling in plants. Here, we introduce the experimental principle of ribosome profiling and review the recent progresses made in botanical researches.

Key words: ribosome profiling, translational regulation, upstream open reading frame

Wang Yuying, Wang Weihao. Recent Advances of Ribosome Profiling in Plants[J]. Chinese Bulletin of Botany, 2022, 57(5): 673-683.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22028

https://www.chinbullbotany.com/EN/Y2022/V57/I5/673

Figures/Tables 1

Figure 1 A schematic diagram of ribosome profiling (A) In the experimental procedure of ribosome profiling (Ribo-seq), polysomes are degraded into monosomes by RNase, resulting in the preservation of the ~30 nucleotides of the ribosome-protected fragments (RPFs) owing to the resistance of the ribosome to the digestion. After isolation and purification from the monosomes, the RPFs are further used for high-throughput sequencing. The ribosome footprints typically show precise positioning within the coding sequence of a mRNA; (B) Ribosome profiling is usually accompanied by a parallel RNA sequencing (RNA-seq) to calculate the translation efficiency of the transcripts. RNA-seq captures mRNA fragments covering the entire transcripts. 5′UTR: 5′ untranslated region; 3′UTR: 3′ untranslated region; ORF: Open reading frame

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