Using a fly model of paternally induced obesity, Öst et al. show that acute changes in paternal diet — as short as 24 hours — reprogram offspring metabolism without affecting growth and development. Paternal intergenerational metabolic reprogramming altered chromatin states and gene expression in the F1 generation via mechanisms that are dependent on Polycomb proteins and the core heterochromatin machinery. Specifically, obesity susceptibility resulted from reduced stage-specific epigenetic regulation of histone H3 lysine 27 trimethylation (H3K27me3)- and H3K9me3-defined domains both in mature sperm and in offspring embryos. The authors propose a model whereby phenotype is evolutionarily encoded directly into the chromatin state of specific loci and suggest that this mechanism directionally controls phenotypic variation within a population. Analysing two murine and three human microarray data sets of adipose tissue samples from lean and obese individuals, the team identified conserved gene signatures for epigenetically defined phenotypic variation.