Initiators counteract Polycomb repression and stimulate long-range contacts between enhancers and the Abdominal-B promoter in Drosophila

The specification of abdominal segments A5 to A9 depends on the expression of Abdominal-B (Abd-B), which is regulated by four infraabdominal domains: iab-5 through iab-8,9. Each iab domain contains an initiation element that determines its active state, along with enhancers responsible for tissue-specific activation of Abd-B. These iab domains function autonomously due to their flanking boundaries, Fab-6, Fab-7 and Fab-8, which both block crosstalk between adjacent iab domains (insulator function) and facilitate long-range interactions with the Abd-B promoter (bypass function). In inactive iab domains, enhancers are repressed by Polycomb group (PcG) proteins. Activation of the iab domains is driven by initiators, which are stimulated in a segment-specific manner by products of the gap and pair-rule genes during early embryogenesis. By creating truncations of the Fab-6 boundary, we identified that the bypass module is adjacent to CTCF binding sites and overlaps with sequences responsible for recruiting PcG proteins. Using genome editing, we demonstrated that the iab-5 and iab-6 initiators enhance the activity of the Fab-6 bypass module. Therefore, initiators represent a novel class of regulatory elements that control long-distance interactions between iab enhancers and Abd-B promoters.