Transcriptome-Wide Profiling of mRNA N6-Methyladenosine Modification in Rice Panicles and Flag Leaves

N6-methyladenosine (m6A) modification is essential for plant growth and development. However, the spatiotemporal dynamics of m6A methylation in rice organ differentiation and development remain largely unknown. We profiled transcriptome-wide m6A landscapes from panicle at booting stage (PB) and flowering stage (PF), and flag leaf at flowering stage (LF), the global m6A level significantly differed among three tissues, which was closely associated with the expression of writer and eraser genes. The methylated gene ratio was higher in flag leaf than in panicle. Compared with common methylated genes, tissue-specific methylated genes showed both lower m6A modification and expression level, and the preference of m6A deposition in CDS region. The m6A profiles varied more between different organs than the same organ at different stages. Negative correlation between m6A level and gene expression was observed in PF vs. PB, but not in PF vs. LF, indicting the complicated regulation of m6A on gene expression. The distinct expression pattern of m6A reader genes imply they may affect gene stability through binding. Overall, our findings demonstrate the crucial roles of m6A in panicle development and photosynthesis feature of the flag leaf, and provide new insights into molecular mechanism of organ differentiation and development in rice. Overall design: Examination of m6A modification patterns in rice panicles and flag leaves at two different stages.