Reversal of methylation-mediated repression with short-chain fatty acids: evidence for an additional mechanism to histone deacetylation

We have constructed a stable cell line, human embryonal kidney 293M(+), con taining a lacZ reporter gene controlled by an in vitro methylated hormone-r esponsive enhancer. Methylation of the enhancer-promoter abolishes lacZ exp ression controlled by ponasterone A (an analogue of ecdysone). Ponasterone A-induced expression is restored by the short-chain fatty acids valeric > b utyric > proplonic > acetic acid, but not by the histone deacetylase inhibi tors trichostatin A and suberoylanilide hydroxamic acid (SAHA). lacZ expres sion is restored to levels approaching that from an unmethylated counterpar t. Incubation with short-chain fatty acids alone does not promote demethyla tion of the lacZ promoter, however, some demethylation (30%) is observed wh en transcription is triggered by addition of ponasterone A. Similar levels of hyperacetylated histones H3 and H4 were observed in cells treated with s hort-chain fatty acids, trichostatin A or SAHA. In vivo DNase I footprintin g indicates a more open chromatin structure at the promoter region for buty ric acid-treated cells. A synergistic effect in reversing the methylation-m ediated repression of the lacZ gene is obtained by combined treatments with the normally ineffective compounds trichostatin A and the short-chain fatt y acid caproic acid. Our results suggest the existence of an alternative si lencing mechanism to histone deacetylation in executing methylation-directe d gene silencing.