Genomic code for Sox2 binding uncovers its regulatory role in Six3 activation in the forebrain

The SRY-related HMG box transcription factor Sox2 plays critical roles throughout embryogenesis. Haploinsufficiency for SOX2 results in human developmental defects including anophthalmia, microphthalmia and septo-optic dysplasia, a congenital forebrain defect. To understand how Sox2 plays a role in neurogenesis, we combined genomic and in vivo transgenic approaches to characterize genomic regions occupied by Sox2 in the developing forebrain. Six3, a homeobox gene associated with holoprosencephaly, a forebrain midline defect, was identified as a Sox2 transcriptional target. This study shows that Sox2 directly regulates a previously unidentified long-range forebrain enhancer to activate Six3 expression in the rostral diencephalon. Further biochemical and genetic evidences indicated a direct regulatory link between Sox2 and Six3 during forebrain development, providing a better understanding of a common molecular mechanism underlying these forebrain defects. •We characterize genomic regions occupied by Sox2 in the developing forebrain.•Six3 is identified as a Sox2 transcriptional target.•Sox2 binds and activates a Six3 forebrain enhancer.•SoxB1 mutants fail to activate Six3 transcription in the ventral forebrain.