Direct transcriptional regulation of Six6 is controlled by SoxB1 binding to a remote forebrain enhancer

► We identify regulatory elements to control Six6 expression in the ventral forebrain and eye. ► The forebrain Six6 enhancer is dependent on homeodomain and SoxB1 binding sites. ► SoxB1 binds and activates the Six6 forebrain enhancer. ► SoxB1 mutants fail to activate Six6 transcription in the ventral forebrain.