High-throughput m(6)A-seq reveals RNA m(6)A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana

This study is the first to comprehensively characterize m(6)A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m(6)A in the two organelles. Over 550 and 350 m(6)A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m(6)A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m(6)A methylation extent in the two organelles was greatly higher than that in the nucleus. The m(6)A motif sequences in the transcriptome of two organelles were similar to the nuclear motifs, suggesting that selection of the m(6)A motifs for RNA methylation was conserved between the nucleus and organelle transcriptomes. The m(6)A patterns of rRNAs and tRNAs in the organelle were similar to those in the nucleus. However, the m(6)A patterns in coding RNAs were distinct between the nucleus and the organelle, suggesting that that regulation of the m(6)A methylation patterns may be different between the nuclei and the organelles. The extensively methylated transcripts in the two organelles were mainly associated with rRNA, ribosomal proteins, photosystem reaction proteins, tRNA, NADH dehydrogenase and redox. On average, 64% and 79% of the transcripts in the two organelles showed differential m(6)A methylation across three organs of the leaves, flowers and roots. The m(6)A methylation extent in the chloroplast was higher than that in the mitochondria. This study provides deep insights into the m(6)A methylation topology and differentiation in the plant organelle transcriptomes.