cross_species. cross_species

The binding patterns of some transcription factors have been shown to diverge substantially between closely related species. Here, we show that the binding pattern of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at developmental enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their cooperative binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. We predict that conservation, dynamic occupancy, and combinatorial regulation will be generally true for developmental enhancers.