Transcriptome-wide analysis of N6-methyladenosine uncovers its regulatory role in gene expression in the lepidopteran Bombyx mori

N6-methyladenosine (m6A) methylation is the most common form of RNA modification in eukaryotes and has been shown to act as an important epitranscriptomic marker, which can regulate gene expression, messenger RNA stability, alternative splicing and translation efficiency. Recent progress on determining insect m6A function has been limited to the dipteran Drosophila melanogaster, in which m6A is involved in neuronal functions and sex determination. Methylation and function of m6A in other insects, however, remain unknown. Here, we investigated a transcriptome-wide profile of m6A in the lepidopteran Bombyx mori and identified the methyltransferase subunits B. mori methyltransferase-like 3 (BmMETTL3) and BmMETTL14 in the m6A methylation pathway. Strikingly, loss of BmMETTL3 and BmMETTL14 in cultured B. mori cells led to arrest of cell cycle progression and caused deficiency of chromosome alignment and segregation. Specifically, we identified 2853 m6A peaks representing transcripts of 2043 genes, and the target genes with m6A methylation were shown to be involved in gene expression and translation. It was interesting that we found that the highly expressed genes tended to be methylated by m6A, and comparative analysis of RNA m6A and DNA N6-methyladenine (6mA) revealed two distinct regulatory mechanisms for gene expression. Overall, our work suggests RNA m6A and DNA 6mA play important roles in RNA and DNA epigenetic regulation in B. mori.