Acetylation-specific interference by anti histone H3K9ac intrabody results in precise modulation of gene expression

The goal of this study is to compared the global gene expression changes driven by the histone PTM-selective interference with those induced by the inhibition of the corresponding modifying enzymes. We chose site-specific histone H3 acetylation as a target for this comparison, and we investigated the transcriptomic response in yeast cells, either expressing the intrabody anti-H3K9ac scFv-58F or treated with HATs inhibitors (Curcumin and CPTH2) Overall design: Three yeast strains were used: the pL200-58F-HA strain, stably expressing the scFv-58F-HA, the pL200-645-HA strain expressing an unrelated intrabody scFv-645-HA (an anti neuroligin-2 intrabody) and a pL220-HA strain, carrying the empty vector pL220. Inhibition of histone H3 acetylation was obtained by treating the control yeast strain pL220-HA with either Curcumin (200 µM) or CPTH2 (400 µM) in SD-L media for 1 hour (see Fig. S1). The baseline control was represented by pL220-HA cells treated with the same concentration of DMSO (0.4%) used to dissolve the drugs. Total RNA was extracted from pL220-HA grown either in presence of Curcumin or CPTH2, as well as from pL200-HA, pL200-58F-HA or pL220-645-HA (the two intrabody-expressing strains), and RNA samples underwent RNA-sequencing (RNA-seq) analysis. Differential gene expression (DEG) analysis was performed, comparing either the two HATi-treated or the two intrabody-expressing conditions against the DMSO-treated baseline control condition.