Transcriptome-wide analysis of m6A methylation reveals genetic responses to cadmium stress at germination stage in rice

Excess cadmium (Cd) seriously suppresses plant growth and development. Rice (Oryza sativa L.) is more susceptible to Cd toxicity than other crops. N6-methyladenosine (m6A) modifications play important regulatory roles in plant adaption to various stresses. However, the post-transcriptional RNA modification in response to Cd stress is still largely unclear in rice. In this study, seeds of the rice cultivar Nipponbare were treated with 0.5 μM CdCl2 for 10 days at germination stage, and then the roots were sampled for the transcriptome-m6A methylation profiling. Here, 1920 differential peaks (DPs) of m6A modifications and 1710 differentially expressed genes (DEGs) were identified in the roots after Cd treatment. Among them, root cell expansion suppressor OsRePRPs were remarkably up-regulated, while auxin/cytokinin-related genes were differentially modified by m6A under Cd stress including OsYUCCA1, OsCKX4, OsRR6, and OsEIL1. Besides, peroxidases (PRXs), metallothioneins (MTs), glutathione S-transferases (GSTs) and sulfate transporter SULTRs were modified by m6A and significantly up-regulated, which might be related to the Cd detoxification via the cell wall modifications and Cd chelate formation. Moreover, several m6A modified transcription factors and MAPK signaling genes showed obviously increased expression, consequently participating in the Cd-response regulatory network as the upstream components. The present study proposes a working model for the m6A modification and transcriptional regulation in rice during germination, and also provides new insights into how plants alleviate Cd toxicity.