UCSF

Haploinsufficiency of the Single Minded homology 1 (SIM1) gene in humans and mice leads to severe obesity, suggesting that altered expression of SIM1, by way of regulatory elements such as enhancers, could predispose individuals to obesity. To identify enhancers that could regulate SIM1, we used comparative genomics coupled with zebrafish and mouse transgenic enhancer assays. Due to the dual role of Sim1 in hypothalamic development and in adult energy homeostasis, the enhancer activity of these sequences was annotated from embryonic to adult age. Of the seventeen tested sequences, two (SCE2 and SCE8) were found to have midbrain enhancer activity in zebrafish. Both SCE2 and SCE8 also exhibited embryonic hypothalamus enhancer expression in mice, and time course analysis of SCE2 activity showed overlapping expression to Sim1 from embryonic to adult age. Using a deletion series, we identified the critical region in SCE2 that is needed for hypothalamus enhancer activity. Sequencing this region in obese and lean cohorts revealed a higher prevalence of SNPs that were unique to obese individuals, with one variant reducing developmental enhancer activity in zebrafish. In summary, we have characterized two hypothalamus enhancers in the SIM1 locus and identified a set of obesity-specific SNPs within one of them, which may predispose individuals to obesity.