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Background  The habenula and the thalamus are two critical nodes in the forebrain circuitry and they connect the midbrain and the cerebral cortex in vertebrates. The habenula is derived from the epithalamus and rests dorsally to the thalamus. Both epithalamus and thalamus arise from a single diencephalon segment called prosomere (p)2. Shh is expressed in the ventral midline of the neural tube and in the mid-diencephalic organizer (MDO) at the zona limitans intrathalamica between thalamus and prethalamus. Acting as a morphogen, Shh plays an important role in regulating cell proliferation and survival in the diencephalon and thalamic patterning. The molecular regulation of the MDO  Shh  expression and the potential role of Shh in development of the habenula remain largely unclear.    Results  We show that deleting paired-box and homeobox-containing gene  Pax6  results in precocious and expanded expression of  Shh  in the prospective MDO in fish and mice, whereas gain-of-function of  pax6  inhibits MDO  shh  expression in fish. Using gene expression and genetic fate mapping, we have characterized the expression of molecular markers that demarcate the progenitors and precursors of habenular neurons. We show that the thalamic domain is shifted dorsally and the epithalamus is missing in the alar plate of p2 in the  Pax6  mutant mouse. Conversely, the epithalamus is expanded ventrally at the expense of the thalamus in mouse embryos with reduced Shh activity. Significantly, attenuating Shh signaling largely rescues the patterning of p2 and restores the epithalamus in  Pax6  mouse mutants, suggesting that  Shh  acts downstream of  Pax6  in controlling the formation of the habenula. Similar to that found in the mouse, we show that  pax6  controls the formation of the epithalamus mostly via the regulation of MDO  shh  expression in zebrafish.    Conclusions  Our findings demonstrate that Pax6 has an evolutionarily conserved function in establishing the temporospatial expression of  Shh  in the MDO in vertebrates. Furthermore, Shh mediates Pax6 function in regulating the partition of the p2 domain into the epithalamus and thalamus.

Pax6 regulates the formation of the habenular nuclei by controlling the temporospatial expression of Shhin the diencephalon in vertebrates