Comprehensive profiling of the epitranscriptome and translatome in rice seedlings under salt stress

Plants dynamically regulate gene expression at multiple levels, including transcription, splicing, polyadenylation, modification, and translation, to adapt to environmental changes. However, comprehensive studies exploring the epitranscriptome and translatome in response to salt stress in rice (Oryza sativa) remain limited. In this study, we performed nanopore direct RNA sequencing (DRS) and ribosome profiling to investigate the post-transcriptional and translational landscapes of rice seedlings (Nipponbare) under salt stress. Time-course transcriptome data revealed that differentially expressed genes uniquely identified 8 h post-salt treatment were significantly enriched in Gene Ontology terms related to RNA processing and translation. DRS analysis showed that the global N6-methyladenosine (m6A) ratio decreased, while the N5-methylcytosine (m5C) ratio increased during early salt stress. Genes with significant changes in transcript abundance and RNA modifications were both enriched in oxidation-reduction processes. Notably, we found that the transcript abundance of modified genes exhibited a significant positive correlation with m5C ratios and a negative correlation with m6A ratios, particularly in oxidoreductase activity-related genes. Ribosome profiling demonstrated that the translation efficiency of modified mRNAs was significantly increased under early salt stress. Furthermore, we identified 2,078 transcripts with differential poly(A) tail length (PAL), with an increased number of transcripts exhibiting increased PAL. Further analysis revealed that the PAL of modified transcripts increased after salt treatment. These results broaden our understanding of the intricate interplay among transcript abundance, RNA modification, PAL, and translation under early salt stress in rice.