The Diversity and Functions of Plant RNA Modifications: What We Know and Where We Go from Here

Abstract

Since the discovery of the first ribonucleic acid (RNA) modifications in transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), scientists have been on a quest to decipher the identities and functions of RNA modifications in biological systems. The last decade has seen monumental growth in the number of studies that have characterized and assessed the functionalities of RNA modifications in the field of plant biology. Owing to these studies, we now categorize RNA modifications based on their chemical nature and the RNA on which they are found, as well as the array of proteins that are involved in the processes that add, read, and remove them from an RNA molecule. Beyond their identity, another key piece of the puzzle is the functional significance of the various types of RNA modifications. Here, we shed light on recent studies that help establish our current understanding of the diversity of RNA modifications found in plant transcriptomes and the functions they play at both the molecular (e.g., RNA stability, translation, and transport) and organismal (e.g., stress response and development) levels. Finally, we consider the key research questions related to plant gene expression and biology in general and highlight developments in various technologies that are driving our insights forward in this research area. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit

“…Methylation of 2′-OH ribose (2′-O-Me, Nm) and pseudouridylation (Ψ) are the most abundant post-transcriptional modifications (PTM) of rRNA in eukaryotes [16,17].…”

Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce

“…In addition to DNA methylation, epigenetic modifications also occur in RNAs. RNA methylation at the N-6 position of adenosine found in many eukaryotes, known as N 6 -methyladenosine (m 6 A), represents the most prevalent internal modification in messenger RNAs (mRNAs) and has emerged as an indispensable posttranscriptional regulatory mechanism affecting various mRNA metabolism processes, such as splicing, stability, and translation [ 25–27 ]. m 6 A modifications exhibit dynamic changes in different tissues and upon stress stimulation in plants, and they modulate multiple aspects of plant development and stress responses [ 28–30 ].…”

The m6A Reader ECT1 Mediates Seed Germination via the DAG2-ECT1-PHYB Regulatory Cascade inArabidopsis

“…Currently, m 6 A has been revealed to play functional roles in modulating various aspects of mRNA metabolism including pre-mRNA splicing, mRNA stability, translation efficiency, alternative polyadenylation, alternative splicing, nuclear-to-cytoplasmic mRNA export, and microRNA processing (Wang et al, 2014;Huang et al, 2018;Wang et al, 2015;Roundtree et al, 2017;Zhou et al, 2022). The importance of m 6 A modifications in gene regulation and biological functions has become increasingly evident (Sharma et al, 2023;Shen et al, 2023). m 6 A modification has been found to modulate shoot stem cell proliferation, trichome branching, floral transition, abscisic acid (ABA) response, chilling tolerance, drought and salt tolerance, photosynthesis, and nitrate signaling in Arabidopsis (Wang et al, 2021;Wang et al, 2022a;Jiang et al, 2023;Wei et al, 2018;Shen et al, 2016;Wang et al, 2022b;Zhou et al, 2022;Zhang et al, 2022b;Hou et al, 2021).…”