Chromosome conformation capture and ecdysone signaling: insights into the regulation of early genes. Travis J. Bernardo, Xie Xie, Edward Dubrovsky. Fordham University, 441 East Fordham Road, Bronx, NY 10458.

   The early genes are a key group of ecdysone targets that function at the top of the ecdysone signaling hierarchy. They are transcriptionally complex, encoding multiple isoforms that are activated in different tissue- and stage- specific patterns in vivo and exhibiting distinct temporal patterns in response to ecdysone. While the general mechanism of ecdysone-dependent transcription is well characterized, it is not understood how a pulse of ecdysone is transmitted into complicated patterns of early gene expression. We previously found that one of the early genes - E75 - harbors multiple enhancers with functional ecdysone response elements, but it was unclear how these enhancers were involved in regulating the expression of different E75 isoforms. To address this question we employed the chromosome conformation capture (3C) method in S2 cells to identify interactions between the enhancers and three of the E75 promoters. We found that the E75A, E75B, and E75C promoters possess pre-existing, ecdysone-responsive interactions with different enhancers and, correspondingly, each promoter exhibits distinct temporal patterns of activation by ecdysone. These observations were extended to E74 in S2 cells and also to individual larval tissues. Our findings suggest that the distinct spatial and temporal responses to ecdysone by early genes are determined in part by local enhancers which act on different promoters in a tissue- or stage-specific manner.