High-throughput m6A-seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana

Abstract

This study is the first to comprehensively characterize m6A 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 m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus. The m6A motif sequences in the transcriptome of two organelles were similar to the nuclear motifs, suggesting that selection of the m6A motifs for RNA methylation was conserved between the nucleus and organelle transcriptomes. The m6A patterns of rRNAs and tRNAs in the organelle were similar to those in the nucleus. However, the m6A patterns in coding RNAs were distinct between the nucleus and the organelle, suggesting that that regulation of the m6A 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 m6A methylation across three organs of the leaves, flowers and roots. The m6A methylation extent in the chloroplast was higher than that in the mitochondria. This study provides deep insights into the m6A methylation topology and differentiation in the plant organelle transcriptomes.

Topologies of N6‐adenosine methylation (m6A) in land plant mitochondria and their putative effects on organellar gene expression

“…Analyses of the relative m 6 A levels using calorimetric measurements have been previously shown to be well correlated with those of liquid MS/MS analyses (Slobodin et al , ; Engel et al , ). The data were also in agreement with previous reports by Luo et al () and Wang et al (), which suggested that the extent of m 6 A modifications in Arabidopsis organelles (i.e. chloroplasts and mitochondria) may be greater than that of nuclear‐encoded mRNAs (Shen et al , ).…”

“…These analyses further suggested that the organellar (i.e. chloroplasts and mitochondrial) transcripts may also undergo N 6 ‐methylations within various adenosine residues (Bodi et al , ; Chen and Liu, ; Luo et al , ; Shen et al , ; Wang et al , ). However, the topologies and significance of m 6 A modifications in plant organelles need to be further investigated.…”

“…RNAs (UGCC m6 AG) (Deng et al, 2015). The putative sequence elements in Arabidopsis and cauliflower mitochondria differ from the RRm 6 ACH motif previously suggested for Arabidopsis organellar RNAs (Wang et al, 2017). The differences between the analyses may relate to the use of m 6 A-RNA-seq with total RNA preparations in Wang et al (2017) that are only partially represented by mitochondrial reads.…”

“…These data may indicate an important regulatory role for m 6 A in controlling the OXPHOS capacity. Global transcriptome analyses suggested the presence of m 6 A in mitochondrial (and plastidial) transcripts in the model plant A. thaliana (Bodi et al , ; Chen and Liu, ; Luo et al , ; Shen et al , ; Wang et al , ). However, as these RNA‐seq driven analyses involved global RNA‐seq analyses, the occurrence and significance of N 6 ‐methyladenosine within organelles in plants (and maybe in animals, as well) need to be further investigated.…”

N6‐methyladenosine regulatory machinery in plants: composition, function and evolution

“…For example, there is tissue specificity for the m6A sites in rice callus compared with leaves (Li et al ., ). Over 86% of transcripts in the Arabidopsis chloroplast and mitochondria are m6A methylated, with 64% and 79% of m6A methylated transcription showing differential tissue expression across leaves, flowers and roots (Wang et al ., ). To understand the functional role of site‐specific m6A in mRNAs, it is necessary to determine m6A modifications in various species, cells and under external stresses.…”