Our most recent paper, published in PLOS Genetics, showing that low affinity binding sites for the Hox protein Ubx and its cofactors Exd/Hth are used to reduce the levels of Ubx transcription in the proximal compartment of the haltere. In transgenes, if these binding sites are killed, down regulation of Ubx does not occur, and if the affinity of these binding sites is increased, Ubx down regulation is even stronger. Thus, the affinity of TF binding sites is tuned in this case to result in the correct amount of negative autoregulation. Things are more complicated in the endogenous locus, where many binding sites are likely contributing to negative autoregulation.
Congratulations to Rebecca Delker and Vikram Ranade!