Exploring N6-methyladenosine (m6A) modification in tree species: opportunities and challenges

Abstract

N ⁶-methyladenosine (m⁶A) in eukaryotes is the most common and widespread internal modification in mRNA. The modification regulates mRNA stability, translation efficiency, and splicing, thereby fine-tuning gene regulation. In plants, m⁶A is dynamic and critical for various growth stages, embryonic development, morphogenesis, flowering, stress response, crop yield, and biomass. Although recent high-throughput sequencing approaches have enabled the rapid identification of m⁶A modification sites, the site-specific mechanism of this modification remains unclear in trees. In this review, we discuss the functional significance of m⁶A in trees under different stress conditions and discuss recent advancements in the quantification of m⁶A. Quantitative and functional insights into the dynamic aspect of m⁶A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.

Figure 1

Schematic overview of the m⁶A writers, erasers, and readers so far identified and their known biological functions in trees. Created with BioRender.com.

Figure 2

Different methods for m⁶A detection and profiling. Created with BioRender.com.

Figure 3

Detection and visualization of rRNA modification in plants. A Distribution of pseudouridine (Ψ) and 2′-O-methylation (Nm) in the tomato ribosome. The cryo-EM model and map are presented for the entire ribosome. B Cryo-EM density map of selected rRNA modification in plant ribosomes. The cryo-EM data ware derived from Cottilli et al. [114], deposited in PDB (PDB ID-7QIZ and EMD-14004).

Figure 4

Deamination of unmethylated adenosines to inosines for a transcriptome-wide absolute quantification of m⁶A using GLORI (glyoxal- and nitrite-mediated deamination of unmethylated adenosines). This method consists of three steps: guanosine protection, adenosine deamination, and guanosine deprotection, followed by sequencing and absolute quantification of m⁶A. The schematic representation is based on Liu et al. [117] and Jones et al. [118]. Created with BioRender.com.