Multi-dimensional epigenomic dynamics converge on H3K4-mediated regulation of low-CO2 adaptation in Nannochloropsis oceanica

Despite their ecological and biotechnological importance, the extent to which microalgae are regulated by epigenetic mechanisms has remained poorly understood. In the model industrial microalga Nannochloropsis oceanica, by comprehensive, multi-dimensional epigenomic analyses, this study uncovers an epigenetic regulatory network responsive to CO₂ levels. This network involves intricate interactions among DNA methylation, histone modifications, dynamic nucleosome positioning, and three-dimensional chromatin organization during adaptation to low-CO₂ conditions. Although DNA methylation is minimal, histone modifications-such as lysine acetylation, crotonylation, and methylation-are associated with active chromatin states and linked to 43.1% of differentially expressed genes. Notably, histone H3K4 di-methylation (H3K4me2) displays a distinct dual-peak profile around the transcription start site and is correlated with chromatin compartment dynamics. Knockout of NO24G02310, a putative H3K4 methyltransferase gene, caused genome-wide shifts in H3K4me2 peaks and decreased H3K4me1 levels, accompanied by direct or indirect downregulation of NoHINT and NoPMA2 expression, slower algal growth, and reduced photosynthetic efficiency (indicated by Fv/Fm), specifically under low-CO₂ conditions. Deletion and overexpression of genes encoding the histidine triad nucleotide-binding protein NoHINT and the plasma membrane H⁺-ATPase NoPMA2 confirmed their roles in growth and photosynthetic efficiency under low CO₂; NoHINT influences growth and NoPMA2 affects photosynthesis. As a previously unrecognized low-CO₂ adaptation mechanism, NO24G02310 likely coordinates the regulation of NoHINT and NoPMA2 through H3K4 modifications. These findings provide a foundation for enhancing microalgal productivity through targeted epigenetic engineering.