Comparative Transcriptomics to Identify RNA Writers and Erasers in Microalgae

Epitranscriptomics is considered as a new regulatory step in eukaryotes for developmental processes and stress responses. The aim of this study was, for the first time, to identify RNA methyltransferase (writers) and demethylase (erasers) in four investigated species, i.e., the dinoflagellates Alexandrium tamutum and Amphidinium carterae, the diatom Cylindrotheca closterium, and the green alga Tetraselmis suecica. As query sequences for the enzymatic classes of interest, we selected those ones that were previously detected in marine plants, evaluating their expression upon nutrient starvation stress exposure. The hypothesis was that upon stress exposure, the activation/deactivation of specific writers and erasers may occur. In microalgae, we found almost all plant writers and erasers (ALKBH9B, ALKBH10B, MTB, and FIP37), except for three writers (MTA, VIRILIZER, and HAKAI). A sequence similarity search by scanning the corresponding genomes confirmed their presence. Thus, we concluded that the three writer sequences were lacking from the studied transcriptomes probably because they were not expressed in those experimental conditions, rather than a real lack of these genes from their genomes. This study showed that some of them were expressed only in specific culturing conditions. We also investigated their expression in other culturing conditions (i.e., nitrogen depletion, phosphate depletion, and Zinc addition at two different concentrations) in A. carterae, giving new insights into their possible roles in regulating gene expression upon stress.