Synthetic Hunchback P2 Sequences for “Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity”

This file contains sequences of synthetic versions of the Hunchback P2 enhancer, computationally designed to contain only Bicoid binding sites and various amounts of flanking sequence. These synthetic enhancers drive expression in the anterior of the Drosophila blastoderm embryo.

To create SynHbP2, SiteOut was used to remove motifs of interest (Estrada et al., 2016a). First the sequence of WThbP2 was scrambled to remove known motifs of TFs (Bcd, Cad, dStat, D, Gt, Hb, Kni, Kr, Nub, Tll, Zld) involved in AP patterning of the blastoderm embryo. Then Bcd TFBS were restored to their native locations and the resultant sequence checked for any newly created motifs around the restored Bcd TFBS using PATSER (http://stormo.wustl.edu/software.html). The binding motifs are from FlyFactorSurvey (http://pgfe.umassmed.edu/ffs/; Noyes et al., 2008b), and a pseudocount of 0.1 and a GC (guanine and cytosine) content of 0.406 when generating position weight matrices from these count matrices was used.