Abstract
N(6)-adenine methylation (m(6)A) as an epitranscriptomic mark is the most abundant modification in eukaryotic RNA and plays a dynamically regulated role. However, m(6)A dynamics, deposition and engineering in microalgae remain largely unknown. Here, in Nannochloropsis oceanica, the dynamic alterations and reprogramming in m(6)A RNA modifications after the shift from high to low CO(2) conditions were first investigated using methylated RNA immunoprecipitation sequencing. The m(6)A peaks in N. oceanica were mainly enriched in 3'UTR. A positive association between m(6)A abundance and mRNA transcription of CO(2)-responsive genes was observed; moreover, N. oceanica cells adopted versatile strategies in a dynamic reprogramming of m(6)A in response to low CO(2) stress. Secondly, knockout of two putative m(6)A methylases including NoMTA (NO04G02990) and NoMTB (NO07G02450) by genome editing induced methylation reprogramming, which was associated with expression changes of low-CO(2) responsive genes such as carbon/nitrogen metabolism, and photorespiration genes that underlie reductions in growth and biomass. Lastly, m(6)A modification reprogramming was first engineered to increase low-CO(2) stress tolerance and biomass productivity by the CRISPR/dCas13 system combined with MTA and NoMTB under low CO(2) in N. oceanica. Therefore, these strides would pave the way for microalgal epigenetics and future industrial applications.