Genome-wide adenine N6-methylation map unveils epigenomic regulation of lipid accumulation in Nannochloropsis

Epigenetic marks on histones and DNA, such as DNA methylation at N6-adenine (6mA), play crucial roles in gene expression and genome maintenance, yet the mechanism in microalgae remains largely unknown. Here for the model industrial oleaginous microalga Nannochloropsis oceanica, we unveiled a genome-wide 6mA map via single-molecule real-time (SMRT) sequencing. Found in 0.1% of adenine, 6mA sites are mostly enriched at the AGGYV motif, elevated in transposons (TEs) and 3' untranslated regions (UTRs), and associated with active transcription. Moreover, 6mA gradually increases in abundance along the direction of gene transcription, and shows special positional enrichment neighboring splicing donor and transcription termination site (TTS). Highly expressed genes tend to show higher 6mA abundance in gene-body than poorly expressed genes, indicating positive interaction between 6mA and general transcription factors. Furthermore, knockout of a putative 6mA methylase NO08G00280 via genome editing leads to methylation pattern alterations, which are correlated with gene expression changes in molybdenum cofactor, sulfate transporter, glycosyl transferase and lipase genes that underlie reduction in biomass and oil productivity. In contrast, knockout of a candidate demethylase NO06G02500 results in 6mA-level elevation and growth reduction. The unraveling of epigenomic players and their roles in biomass productivity and lipid metabolism laid the foundation for epigenetic engineering of industrial microalgae.