The Hedgehog (Hh) pathway has been well‐studied and implicated in neural crest cell (NCC) survival and facial patterning; however, the mechanism(s) by which the transcription factors (TFs) of the pathway, the Gli TFs, orchestrate Hh signal transduction remains elusive. For example, Gli ChIP‐seq data from NCCs in the developing mandibular prominence (MNP) reveal that the presence of a peak is not sufficient to predict a Gli “target.” In light of these data and previous studies suggesting Gli proteins interact with co‐factors, we performed genome‐wide analyses to identify motifs that frequently appear near Gli binding regions (GBRs). These analyses revealed that E‐box motifs (bHLH TF binding sites) were significantly enriched (p=0.001) within Gli ChIP‐seq peaks compared to random sequences. Additionally, ChIP‐seq peaks for Hand2, a bHLH TF known to be necessary for MNP development, were 111‐fold enriched within Gli peaks. A comparison of Hand2f/f;Wnt1‐Cre and Gli2f/f;Gli3f/f;Wnt1‐Cre MNP phenotypes shows striking similarities, which in conjunction with the significant overlap of Gli and Hand2 co‐occupied genomic regions suggests these two proteins may work in tandem to influence Gli target gene expression. Interrogation of DNA motifs within genomic locations occupied by Gli and Hand2 together versus those occupied by Gli alone revealed the existence of two distinct types of GBRs: a ‘canonical’ GBR defined by the presence of a medially located A (GACCACCC), and a ‘deviant’ GBR defined by a T in the medial position (GACCTCCC). Interestingly, the ‘canonical’ GBR is 19‐fold enriched (p<10−136) in Gli3 peaks without a Hand2 peak, whereas it is only 3‐fold enriched (p<10−47) in Gli3 peaks that contain a Hand2 peak. To test if these distinct GBRs convey biological relevance, we identified canonical and deviant GBRs within Gli and Hand2 ChIP‐seq peaks of Gli targets important for mandibular development and linked them to reporter constructs transfected into 09–1 cells. We found that Hand2 and Gli utilize a deviant GBR to synergistically activate Gli targets including Foxd1 and Foxd2. In sum, our work establishes insight into the existence of a sequence‐dependent mechanism for Gli target gene regulation in which molecular accomplices may be necessary for optimal transcription of Gli targets in NCCs of the developing MNP.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
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