Table 1.

Some examples of metabolites, their synthases, and effectors involved in chromatin-dependent gene regulation.

Metabolite	Synthase	Effector	Outcome
Acetyl-CoA	Acetyl-CoA Synthetase ATP-Citrate Lyase	Acetyltransferases Acetyltransferases	Histone acetylation Histone acetylation
ATP	ATP Synthase	Kinases Chromatin remodeling complexes	Phosphorylation Chromatin remodeling
FAD+	FMN adenylyltransferase	LSD family demethylases	Histone demethylation
α-Ketoglutarate	Isocitrate dehydrogenase	Jmj family demethylases	Histone demethylation
NAD+ (and related cofactors)	NMNAT-1* (and NAD+ cofactor kinases and reductases)	Sirtuins (NAD+) PARPs (NAD+) CtBP (NAD+/NADH) Clock:BMAL1 [NAD(P)+/NAD(P)H] NPAS2:BMAL1 [NAD(P)+/NAD(P)H]	Histone deacetylation ADP-ribosylation Transcriptional corepression Modulation of DNA binding Modulation of DNA binding
O-Acetyl-ADP-ribose	Sirtuins	Sir2/3/4 MacroH2A1.1	Regulation of enzyme activity Regulation of protein-protein interactions
S-adenosylmethionine	MatIIα*	Protein Methyltransferases DNA Methyltransferases	Histone methylation DNA methylation

^*Of the metabolite producers (“synthases”) listed here, only MATIIα (Katoh et al., 2011) and NMNAT-1 (Zhang et al., 2009) have been shown to be recruited to chromatin. The extent to which other metabolite-producing enzymes are recruited to target gene promoters has yet to be determined.