N6-methyladenosine methylation analysis reveals transcriptome-wide expression response to salt stress in rice roots

The N6-methyladenosine (m6A) modifications play crucial regulatory roles in plant yield development, nutritional growth and stress adaption. Rice (Oryza sativa) is relatively sensitive to salt stress among cereal crops, while its regulatory mechanism conferring salt tolerance is still unclear. Here, we performed transcriptome-wide m6A analysis in roots of rice cultivar Nipponbare under salt conditions (0 and 75 mM NaCl). After salt treatments for 4 d, a total of 18,115 m6A peak callings of 12,516 genes and 22,052 peaks of 14,235 genes were identified under salt and control conditions, respectively. These m6A peaks were mostly enriched in CDS and 3′UTR regions. Totally, 346 m6A differentially peaks (DPs) and 1522 differentially expressed genes (DEGs) were identified in response to salt stress, which were mainly enriched in "MAPK signaling module" and "metal ion binding". Among them, the m6A related genes including 2 writers (MTB and TRM4A), 1 reader (CPSF30) and 1 eraser (ALKBH9A). The m6A modified salt-responding genes including HAK4, CIPK06, RBOHH, Myb10, ERF067 and other transcription factors might participate in transcriptional regulation or multiple Ca2+, ABA and ROS signal pathways. The m6A level and gene expression of these genes were further confirmed by m6A-IP-qPCR and qRT-PCR, respectively, which showed a high consistency with the m6A-seq and transcriptome data. This study provides epigenetic responses of molecular regulatory mechanisms of salt tolerance in rice.