During development of the central nervous system (CNS), proliferation, cell fate designation, and patterning decisions are tightly regulated by interdependent networks of key transcriptional regulators. We propose a novel aspect of how Pax6 not only utilizes its modular structure to perform distinct functions but also employs individual sub-domains, thus generating a new level of complexity for transcriptional regulation by one single transcription factor in dorso-ventral and rostro-caudal neural tube patterning.