The invention provides a system of enhancing the expression of transgenes in algae. Transgenes are engineered to have a binding site for certain proteins in proximity to their promoter, for example a LexA binding site. The algae is also engineered to express a nucleosome alteration protein fused to a protein with affinity to the DNA binding site acting in coordination. An example is a LexA-p300 fusion protein, where the p300 is derived from Chlamydomonas. The LexA binding domain guides the p300 to the binding site and the p300 loosens the nucleosome structure by acetylating histones within proximity of the transgene, thus remodeling the local chromatin structure to allow for high-level expression.