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

Keiko Numayama-Tsuruta12, Yoko Arai13, Masanori Takahashi1, Makiko Sasaki-Hoshino12, Nobuo Funatsu4, Shun Nakamura5 and Noriko Osumi12*

Author Affiliations

1 Division of Developmental Neuroscience, Center for Translational and Advanced Animal Research (CTAAR), Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan

2 Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

3 Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden D-01307, Germany

4 Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Medical Sciences I, Irvine, CA 92697-4800, USA

5 Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan

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BMC Developmental Biology 2010, 10:6  doi:10.1186/1471-213X-10-6

Published: 18 January 2010



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.


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.


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.