highlights
Most Archaeplastida microalgae contain histone H3 lysine 27 methyltransferase genes.
Pervasive DNA cytosine methylation seems to rely on diverged DNA methyltransferases.
RNA interference mechanisms, when present, may suppress transposons and viruses.
The role of epigenetic silencing mechanisms in gene regulation remains uncharacterized.
RNA interference is a useful tool for functional analyses and genetic engineering.