Nitric Oxide is an Epigenetic Regulator of Transcription via Alteration of Histone Modification Profiles

Nitric oxide (•NO) production has long been associated with aggressive cancers and is considered a negative prognostic indicator; however, its role in disease etiology has remained promiscuous. The aim of this project was to identify significant molecular mechanisms of •NO-signaling that drive cancer progression. Methylation and acetylation of histone lysine residues are important epigenetic regulators of cellular transcription. Aberrant histone methylation or acetylation patterns are often detected in high-grade tumors. Therefore, we tested the ability of •NO to mediate oncogenic phenotypes by acting as an epigenetic regulator. We generated a comprehensive map of histone modification changes at 15 different lysine residues in response to •NO via high-resolution mass spectrometry. Our data revealed that lysine K9 on histone H3 was extensively modified by •NO. Specifically, we saw an increase in dimethylation (H3K9me2), attributable to inhibition of demethylase activity at this site. •NO also significantly lowered acetylation at H3K9 (H3K9ac), potentially precluded due to increased methylation at the same residue. Next, we examined the ability of •NO to regulate gene expression downstream of histone modification changes. Genes differentially expressed due to association with •NO-altered H3K9me2/ac were identified by combined bioinformatic analysis of microarray and ChIP-seq data across the genome. Almost 6500 genes were differentially expressed in response to •NO and a significant proportion of transcription was regulated via epigenetic mechanisms. Our data revealed that differential enrichment of H3K9me2/ac at specific genes correlated with corresponding changes in their expression levels. These data demonstrate a unique mechanism of •NO signaling via regulation of multiple posttranslational histone modifications, which ultimately dictate gene expression changes leading to an oncogenic phenotype.