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Background  The transcription factor Pax6 is essential for the development of the central nervous system and it exerts its multiple functions by regulating the expression of downstream target molecules. To screen for genes downstream of Pax6, we performed comprehensive transcriptome profiling analyses in the early hindbrain of  Pax6  homozygous mutant and wild-type rats using microarrays.    Results  Comparison of quadruplicate microarray experiments using two computational methods allowed us to identify differentially expressed genes that have relatively small fold changes or low expression levels. Gene ontology analyses of the differentially expressed molecules demonstrated that Pax6 is involved in various signal transduction pathways where it regulates the expression of many receptors, signaling molecules, transporters and transcription factors. The up- or down-regulation of these genes was further confirmed by quantitative RT-PCR.  In situ  staining of  Fabp7 ,  Dbx1, Unc5h1  and  Cyp26b1  mRNAs showed that expression of these transcripts not only overlapped with that of  Pax6  in the hindbrain of wild-type and  Pax6  heterozygous mutants, but also was clearly reduced in the hindbrain of the  Pax6  homozygous mutant. In addition, the  Pax6  homozygous mutant hindbrain showed that  Cyp26b1  expression was lacked in the dorsal and ventrolateral regions of rhombomeres 5 and 6, and that the size of rhombomere 5 expanded rostrocaudally.    Conclusions  These results indicate that  Unc5h1  and  Cyp26b1  are novel candidates for target genes transactivated by Pax6. Furthermore, our results suggest the interesting possibility that Pax6 regulates anterior-posterior patterning of the hindbrain via activation of Cyp26b1, an enzyme that metabolizes retinoic acid.

Downstream genes of Pax6 revealed by comprehensive transcriptome profiling in the developing rat hindbrain