The Drosophila speciation factor HMR localizes to genomic insulator sites. Drosophila melanogaster

Hybrid incompatibility between Drosophila melanogaster and D. simulans is caused by a lethal interaction of the proteins encoded by the Hmr and Lhr genes. In D. melanogaster the loss of HMR results in mitotic defects, an increase in transcription of transposable elements and a deregulation of heterochromatic genes. To investigate the molecular mechanisms that mediate HMRs function, we measured genome-wide localization of HMR in D. melanogaster by chromatin immunoprecipitation. Interestingly, we find HMR localizing to genomic insulator sites that can be classified into two groups. One group that belongs to the gypsy class of insulators and another one that separates HP1a binding regions from active promoters. The activity of these promoters is strongly affected in Hmr mutant flies. Our data provide a novel link between HMR and insulator proteins and suggest a key role for genome organization in the formation of species. Overall design: Examination of HMR binding in Drosophila S2 cells. Experiments were verified with replicates, unrelated antibody (IgG control) and HMR RNAi knock-down. CP190 RNAi knock-down experiments in combination with HMR ChIP and H3 ChIP were further used to dissect HMR binding dependencies.