ATAC-seq and ChIP-seq targeting PBX1 and PBX3 in the chick FEZ at stage 22

This genome-wide sequencing data set displays open accessible chromatin regions and binding sites for PBX1 and PBX3 in the embryonic chick frontonasal ectodermal tissue by ATAC-seq and ChIP-seq. SHH is a key regulator of the upper jaw morphogenesis, and its expression pattern in the frontonasal process defines a signaling center, the frontonasal ectodermal zone (FEZ), by Hamburger and Hamilton stage 22 (HH22). Expression of SHH is regulated by homeodomain transcription factors, PBX1 and PBX3, in a complementary manner. To evaluate their direct interaction with chromatin in the chick FEZ at HH22, we generated these ATAC-seq data and ChIP-seq data targeting PBX1 and PBX3 (n=2). With this data set, we identified a 400 bp-long open chromatin region within Intron 1 of SHH where both PBX1 and PBX3 bind. This intronic element modulates transcription through complementary mechanisms by PBX transcription factors; transcription is activated when bound by PBX1 while transcription is repressed when bound by PBX3. We named this regulatory element SHH FEZ Enhancer 1 (SFE1).