Epigenomic Transcriptome Regulation of Growth and Development and Stress Response in Cucurbitaceae Plants: The Role of RNA Methylation

TL;DR

This paper reviews how RNA methylation affects growth, development, and stress responses in cucurbit plants, highlighting current knowledge gaps and future research directions.

Contribution

The paper systematically summarizes recent advances in RNA methylation research in cucurbit crops and identifies key challenges for future studies.

Findings

High-throughput technologies have revealed RNA methylation's role in fruit development and stress responses in cucurbits.

Current research lacks detailed understanding of RNA methylation's core protein families and their functions in cucurbits.

Limited genetic resources and tools hinder functional studies of RNA methylation in cucurbit crops.

Abstract

RNA methylation, particularly N6-methyladenosine (m6A) and 5-methylcytosine (m5C), functions as a pivotal post-transcriptional regulatory mechanism and plays a central role in plant growth, development, and stress responses. This review provides a systematic summary of recent advances in RNA methylation research in cucurbit crops. To date, high-throughput technologies such as MeRIP-seq and nanopore direct RNA sequencing have enabled the preliminary construction of RNA methylation landscapes in cucurbit species, revealing their potential regulatory roles in key agronomic traits, including fruit development, responses to biotic and abiotic stresses, and disease resistance. Nevertheless, this field remains in its early stages for cucurbit crops and faces several major challenges: First, mechanistic understanding is still limited, with insufficient knowledge regarding the composition and biological functions of the core protein families involved in methylation dynamics—namely, “writers,” “erasers,” and “readers.” Second, functional validation remains inadequate, as direct evidence linking specific RNA methylation events to downstream gene regulation and phenotypic outcomes is largely lacking. Third, resources are scarce; compared to model species such as Arabidopsis thaliana and rice, cucurbit crops possess limited species-specific genetic data and genetic engineering tools (e.g., CRISPR/Cas9-based gene editing systems), which significantly hampers comprehensive functional studies. To overcome these limitations, future research should prioritize the development and application of more sensitive detection methods, integrate multi-omics datasets—including transcriptomic and methylomic profiles—to reconstruct regulatory networks, and conduct rigorous functional assays to establish causal relationships between RNA methylation modifications and phenotypic variation. The ultimate objective is to fully elucidate the biological significance of RNA methylation in cucurbit plants and harness its potential for crop improvement through genetic and biotechnological approaches.

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