Detection, regulation, and functions of RNA N6-methyladenosine modification in plants

Abstract

N⁶-Methyladenosine (m⁶A) is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation, including transcriptional and post-transcriptional regulation. m⁶A is a reversible modification that is installed, removed, and recognized by methyltransferases (writers), demethylases (erasers), and m⁶A-binding proteins (readers), respectively. Recently, the breadth of research on m⁶A in plants has expanded, and the vital roles of m⁶A in plant development, biotic and abiotic stress responses, and crop trait improvement have been investigated. In this review, we discuss recent developments in research on m⁶A and highlight the detection methods, distribution, regulatory proteins, and molecular and biological functions of m⁶A in plants. We also offer some perspectives on future investigations, providing direction for subsequent research on m⁶A in plants.

Keywords: RNA modification; epitranscriptome; m(6)A; plants.

Figure 1

High-throughput m⁶A sequencing technologies. (A) Schematic diagram of antibody-based m⁶A sequencing methods: MeRIP-seq/m⁶A-seq, m⁶A-seq2, and m⁶A-CLIP/miCLIP. (B) Schematic diagram of antibody-independent m⁶A sequencing methods: m⁶A-SEAL-seq, m⁶A-SAC-seq, nanopore direct RNA-seq, and GLORI-seq.

Figure 2

Single-gene m⁶A detection methods. Schematic diagram of site-specific m⁶A detection methods: MeRIP-qRT-PCR, SELECT, and SCARLET.

Figure 3

Regulatory proteins and molecular functions of m⁶A in plants. Most mRNA m⁶A modification is catalyzed by a multiprotein complex containing MTA, MTB, FIP37, VIR, HAKAI, and HIZ2. FIONA1 is another m⁶A methyltransferase. m⁶A is removed by the m⁶A demethylases ALKBH10B, ALKBH9B, and SlALKBH2. YTH domain-containing proteins, such as ECT2, ECT3, ECT4, and CPSF30L, recognize m⁶A. To date, multiple molecular functions of m⁶A have been discovered in plants, including roles in chromatin state, miRNA maturation, alternative polyadenylation, RNA stability, and translational regulation.

Figure 4

Biological functions of m⁶A in plants. (A) Biological functions of m⁶A in plant development, including embryogenesis, floral transition, root development, stem cell fate determination, circadian rhythms, leaf morphology, trichome branching, nitrate signaling, tomato ripening, strawberry ripening, and rice meiosis. (B) Biological functions of m⁶A in stress responses, including responses to salt, drought, cadmium, virus infection, and fungal infection. The proteins involved are marked in light blue.