Skip to main content

Math 1 target genes are enriched with evolutionarily conserved clustered e-box binding sites

Abstract

The basic helix-loop-helix (bHLH) transcription factor Math1 and its orthologs are fundamental for proper development of various neuronal subpopulations, such as cerebellar granule cells, D1 interneurons in the spinal cord, and inner ear hair cells. Although crucial for neurogenesis, the mechanisms by which Math1 specifically recognizes its direct targets are not fully understood. To search for direct and indirect target genes and signaling pathways controlled by Math1, we analyzed the effect of Math1 knockout on the expression profile of multiple genes in the embryonic cerebellum. Eighteen differentially expressed transcripts were identified and found to belong to a few developmentally-related functional groups, such as transcriptional regulation, proliferation, organogenesis, signal transduction, and apoptosis. Importantly, genomic analysis of E-box motifs has identifieda significant enrichment and clustering of MATH1-binding E-boxes only in a subset of differentially expressed genes (Nr2f6, Hras1, and Hes5) in both mouse and man. Moreover, Math1 was shown by chromatin immuno-precipitation (ChIP) to bind, and by a luciferase reporter assay to activate transcription, of an upstream genomic fragment of Nr2f6. Taken together, we propose that when putative direct targets of Math1 are being selected for detailed studies on DNA microarray hybridization, the enrichment and clustering of binding E-boxes in multiple species may be helpful criteria. Our findings may be useful to the study of other bHLH transcription factors, many of which control the development of the nervous system.

This is a preview of subscription content, access via your institution.

References

  1. Akazawa C., Ishibashi M., Shimizu C., Nakanishi S., and Kageyama R. (1995) Amammalian helix-loop-helix factor structurally related to the product of Drosophila proneural gene atonal is a positive transcriptional regulator expressed in the developing nervous system. J. Biol. Chem. 270, 8730–8738.

    PubMed  Article  CAS  Google Scholar 

  2. Alder J., Cho N., and Hatten M. (1996) Embryonic precursor cells from the rhombic lip are specified to a cerebellar granule neuron identity. Neuron 17, 389–399.

    PubMed  Article  CAS  Google Scholar 

  3. Ashburner M., Ball C. A., Blake J. A., et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29.

    PubMed  Article  CAS  Google Scholar 

  4. Atchley W. R., and Fitch W. M. (1997) Anatural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. U. S. A. 94, 5172–5176.

    PubMed  Article  CAS  Google Scholar 

  5. Avram D., Ishmael J. E., Nevrivy D. J. et al. (1999) Heterodimeric interactions between chicken ovalbumin upstream promoter-transcription factor family members ARP1 and ear2. J. Biol. Chem. 274, 14,331–14,336.

    Article  CAS  Google Scholar 

  6. Ben Arie N., Bellen H. J., Armstrong D. L., et al. (1997) Math1 is essential for genesis of cerebellar granule neurons. Nature 390, 169–172.

    PubMed  Article  CAS  Google Scholar 

  7. Ben-Arie N., Hassan B. A., Bermingham N. A., et al. (2000) Functional conservation of atonal and Math1 in the CNS and PNS. Development 127, 1039–1048.

    PubMed  CAS  Google Scholar 

  8. Ben-Arie N., McCall A. E., Berkman S., Eichele G., Bellen H. J., and Zoghbi H. Y. (1996) Evolutionary conservation of sequence and expression of the bHLH protein Atonal suggests a conserved role in neurogenesis. Hum. Mol. Genet. 5, 1207–1216.

    PubMed  Article  CAS  Google Scholar 

  9. Benowitz L. I. and Routtenberg A. (1997) GAP-43: an intrinsic determinant of neuronal development and plasticity. Trends Neurosci. 20, 84–91.

    PubMed  Article  CAS  Google Scholar 

  10. Bergstrom D. A., Penn B. H., Strand A., Perry R. L., Rudnicki M. A., and Tapscott S. J. (2002) Promoter-specific regulation of MyoD binding and signal transduction cooperate to pattern gene expression. Mol. Cell. 9, 587–600.

    PubMed  Article  CAS  Google Scholar 

  11. Bermingham N. A., Hassan B. A., Price S. D., et al. (1999) Math1: an essential gene for the generation of inner ear hair cells. Science 284, 1837–1841.

    PubMed  Article  CAS  Google Scholar 

  12. Bermingham N. A., Hassan B. A., Wang V. Y., et al. (2001) Proprioceptor pathway development is dependent on Math1. Neuron 30, 411–422.

    PubMed  Article  CAS  Google Scholar 

  13. Bertrand N., Castro D. S., and Guillemot F. (2002) Proneural genes and the specification of neural cell types. Nat. Rev. Neurosci. 3, 517–530.

    PubMed  Article  CAS  Google Scholar 

  14. Brandon E. P., Zhuo M., Huang, Y. Y., et al. (1995) Hippocampallong-term depression and depotentiation are defective in mice carrying a targeted disruption of the gene encoding the RI beta subunit of cAMP-dependent protein kinase. Proc. Natl. Acad. Sci. U.S.A. 92, 8851–8855.

    PubMed  Article  CAS  Google Scholar 

  15. Bruhn L., Munnerlyn A., and Grosschedl R. (1997) ALY, a context-dependent coactivator of LEF-1 and AML-1, is required for TCRalpha enhancer function. Genes Dev. 11, 640–653.

    PubMed  Article  CAS  Google Scholar 

  16. Cachon-Gonzalez M. B., San-Jose I., Cano A., et al. (1999) The hairless gene of the mouse: relationship of phenotypic effects with expression profile and genotype. Dev. Dyn. 216, 113–126.

    PubMed  Article  CAS  Google Scholar 

  17. Cawley S., Bekiranov S., Ng H. H., et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499–509.

    PubMed  Article  CAS  Google Scholar 

  18. Chen P., Johnson J. E., Zoghbi H. Y., and Segil N. (2002) The role of Math1 in inner ear development: Uncoupling the establishment of the sensory primordium from hair cell fate determination. Development 129, 2495–2505.

    PubMed  Article  CAS  Google Scholar 

  19. Chiaramello A., Neuman T., Peavy D. R., and Zuber M. X. (1996) The GAP-43 gene is a direct downstream target of the basic Helix-Loop-Helix transcription factors. J. Biol. Chem. 271, 22,035–22,043.

    CAS  Google Scholar 

  20. Crackower M. A., Scherer S. W., Rommens J. M., et al. (1996) Characterization of the split hand/split foot malformation locus SHFM1 at 7q21.3-q22.1 and analysis of a candidate gene for its expression during limb development. Hum. Mol. Genet. 5, 571–579.

    PubMed  Article  CAS  Google Scholar 

  21. Dibner C., Elias S., and Frank D. (2001) XMeis 3 protein activity is required for proper hindbrain patterning in Xenopus laevis embryos. Development 128, 3415–3426.

    PubMed  CAS  Google Scholar 

  22. Dionne M. S., Skarnes W. C., and Harland R. M. (2001) Mutation and analysis of Dan, the founding member of the Dan family of transforming growth factor beta antagonists. Mol. Cell Biol. 21, 636–643.

    PubMed  Article  CAS  Google Scholar 

  23. Feng L., Hatten M. E., and Heintz N. (1994) Brain lipid-binding protein (BLBP): a novel signaling system in the developing mammalian CNS. Neuron 12, 895–908.

    PubMed  Article  CAS  Google Scholar 

  24. Ferguson K. L., Callaghan S. M., O'Hare M. J., Park D. S., and Slack R. S. (2000) The Rb-CDK4/6 signaling pathway is critical in neural precursor cell cycle regulation. J. Biol. Chem. 275, 33,593–33,600.

    CAS  Google Scholar 

  25. Gazit R., Krizhanovsky V., and Ben-Arie N. (2004) Math1 controls cerebellar granule cell differentiation by regulating multiple components of the Notch signaling pathway. Development 131, 903–913.

    PubMed  Article  CAS  Google Scholar 

  26. Gibert J. M. and Simpson P. (2003) Evolution of cis-regulation of the proneural genes. Int. J. Dev. Biol. 47, 643–651.

    PubMed  CAS  Google Scholar 

  27. Haggerty T. J., Zeller K. I., Osthus R. C., Wonsey D. R., and Dang C. V. (2003) A strategy for identifying transcription factor binding sites reveals two classes of genomic c-Myc target sites. Proc. Natl. Acad. Sci. USA 100, 5313–5318.

    PubMed  Article  CAS  Google Scholar 

  28. Hartigan J. A. and Wong M. A. (1979) A K-Means Clustering Algorithm. Applied Statistics 28, 100–108.

    Article  Google Scholar 

  29. Hatten M. E. and Heintz N. (1995) Mechanisms of neural patterning and specification in the developing cerebellum. Ann. Rev. Neurosci. 18, 385–408.

    PubMed  CAS  Google Scholar 

  30. Helms A. W., Abney A. L., Ben-Arie N., Zoghbi H. Y., and Johnson J. E. (2000) Autoregulation and multiple enhancers control Math1 expression in the developing nervous system. Development 127, 1185–1196.

    PubMed  CAS  Google Scholar 

  31. Helms A. W. and Johnson J. E. (1998) Progenitors of dorsal commissural interneurons are defined by MATH1 expression. Development 125, 919–928.

    PubMed  CAS  Google Scholar 

  32. Holley S. J., Hall S. B., and Mellon P. L. (2002) Complementary expression of IGF-II and IGBP-5 during anterior pituitary development. Dev. Biol. 244, 319–328.

    PubMed  Article  CAS  Google Scholar 

  33. Hong N. A., Flannery M., Hsieh S. N., Cado D., Pedersen R., and Winoto A. (2000) Mice lacking Dad1, the defender against apoptotic death-1, express abnormal N-linked glycoproteins and undergo increased embryonic apoptosis. Dev. Biol. 220, 76–84.

    PubMed  Article  CAS  Google Scholar 

  34. Hu Y., Wang T., Stormo G. D., and Gordon J. I. (2004) RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites. Proc. Natl. Acad. Sci. USA 101, 5559–5564.

    PubMed  Article  CAS  Google Scholar 

  35. Izumikawa M., Minoda R., Kawamoto K., et al. (2005) Auditory hair cell replacement and hearing improvement by Atoh1 gene therapy in deaf mammals. Nat. Med. 11, 271–276.

    PubMed  Article  CAS  Google Scholar 

  36. Jensen P., Smeyne R., and Goldowitz D. (2004) Analysis of cerebellar development in math1 null embryos and chimeras. J. Neurosci. 24, 2202–2211.

    PubMed  Article  CAS  Google Scholar 

  37. Jones S. (2004) An overview of the basic helix-loop-helix proteins. Genome biol. 5, 226.

    PubMed  Article  Google Scholar 

  38. Kagami Y. and Furuichi T. (2001) Investigation of differentially expressed genes during the development of mouse cerebellum. Gene Expression Patterns 1, 39–59.

    PubMed  Article  CAS  Google Scholar 

  39. Kageyama R., Ohtsuka T., Hatakeyama J., and Ohsawa R. (2005) Roles of bHLH genes in neural stem cell differentiation. Exp. Cell Res. 306, 343–348.

    PubMed  Article  CAS  Google Scholar 

  40. Kawamoto K., Ishimoto S., Minoda R., Brough D. E., and Raphael Y. (2003) Math1 gene transfer generates new cochlear hair cells in mature guinea pigs in vivo. J. Neurosci. 23, 4395–4400.

    PubMed  CAS  Google Scholar 

  41. Koera K., Nakamura K., Nakao K., et al. (1997) K-ras is essential for the development of the mouse embryo. Oncogene 15, 1151–1159.

    PubMed  Article  CAS  Google Scholar 

  42. Krizhanovsky V., Golenser E., and Ben-Arie N. (2004) Genotype identification of Math1/LacZknockoutmice based on real-time PCR with SYBR Green I dye. J. Neurosci. Methods 136, 187–192.

    PubMed  Article  CAS  Google Scholar 

  43. Lanford P. J., Shailam R., Norton C. R., Gridley T., and Kelley M. W. (2000) Expression of Math1 and HES5 in the cochleae of wildtype and Jag2 mutant mice. J. Assoc. Res. Otolaryngol. 1, 161–171.

    PubMed  Article  CAS  Google Scholar 

  44. Lee K. J. and Jessell T. M. (1999) The specification of dorsal cell fates in the vertebrate central nervous system. Ann. Rev. Neurosci. 22, 261–294.

    PubMed  Article  CAS  Google Scholar 

  45. Lee Y., Miller H. L., Jensen P., et al. (2003) A molecular fingerprint for medulloblastoma. Cancer Res. 63, 5428–5437.

    PubMed  CAS  Google Scholar 

  46. Leonard J. H., Cook A. L., Van Gele M., et al. (2002) Proneural and proneuroendocrine transcription factor expression in cutaneous mechanoreceptor (Merkel) cells and Merkel cell carcinoma. Int. J. Cancer 101, 103–110.

    PubMed  Article  CAS  Google Scholar 

  47. Leow C. C. Romero M. S., Ross S., Polakis P., and Gao W. Q. (2004) Hath1, down-regulated in colon adenocarcinomas, inhibits proliferation and tumorigenesis of colon cancer cells. Cancer Res. 64, 6050–6057.

    PubMed  Article  CAS  Google Scholar 

  48. Lin C. H., Stoeck J., Ravanpay A. C., Guillemot F., Tapscott S. J., and Olson J. M. (2004) Regulation of neuroD2 expression in mouse brain. Dev. Biol. 265, 234–245.

    PubMed  Article  CAS  Google Scholar 

  49. Ma Q., Kintner C., and Anderson D. J. (1996) Identification of neurogenin, a vertebrate neuronal determination gene. Cell 87, 43–52.

    PubMed  Article  CAS  Google Scholar 

  50. Manohar C. F., Bray J. A., Salwen H. R. et al. (2004) MYCN-mediated regulation of the MRP1 promoter in human neuroblastoma. Oncogene 23, 753–762.

    PubMed  Article  CAS  Google Scholar 

  51. Maskos U. and McKay R. D. (2003) Neural cells without functional N-Methyl-D-Aspartate (NMDA) receptors contribute extensively to normal postnatal brain development in efficiently generated chimaeric NMDA R1-/-<->+/+ mice. Dev. Biol. 262, 119–136.

    PubMed  Article  CAS  Google Scholar 

  52. Massari M. E. and Murre C. (2000) Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell Biol. 20, 429–440.

    PubMed  Article  CAS  Google Scholar 

  53. McWhirter J. R., Goulding M., Weiner J. A., Chun J., and Murre C. (1997) A novel fibroblast growth factor gene expressed in the developing nervous system is a down-stream target of the chimeric homeodomain oncoprotein E2A-Pbx1. Development 124, 3221–3232.

    PubMed  CAS  Google Scholar 

  54. Muroyama Y., Fujihara M., Ikeya M., Kondoh H., and Takada S. (2002) Wnt signaling plays an essential role in neuronal specification of the dorsal spinal cord. Genes Dev. 16, 548–553.

    PubMed  Article  CAS  Google Scholar 

  55. Murre C., Bain G., van Dijk M. A., et al. (1994) Structure and function of helix-loop-helix proteins. Biochem. Biophys. Acta 1218, 129–135.

    PubMed  CAS  Google Scholar 

  56. Nakada Y., Hunsaker T. L., Henke R. M., and Johnson J. E. (2004) Distinct domains within Mash1 and Math1 are required for function in neuronal differentiation versus neuronal cell-type specification. Development 131, 1319–1330.

    PubMed  Article  CAS  Google Scholar 

  57. Ohtsuka T., Ishibashi M., Gradwohl G., Nakanishi S., Guillemot F., and Kageyama R. (1999) Hes1 and Hes5 as notch effectors in mammalian neuronal differentiation. EMBO J. 18, 2196–2207.

    PubMed  Article  CAS  Google Scholar 

  58. Potter G. B., Beaudoin G. M., 3rd, DeRenzo C. L., Zarach J. M., Chen S. H., and Thompson C. C. (2001) The hairless gene mutated in congenital hair loss disorders encodes a novel nuclear receptor corepressor. Genes Dev. 15, 2687–2701.

    PubMed  Article  CAS  Google Scholar 

  59. Rankin C. T., Bunton T., Lawler A. M., and Lee S. J. (2000) Regulation of left-right patterning in mice by growth/differentiation factor-1. Nat. Genet. 24, 262–265.

    PubMed  Article  CAS  Google Scholar 

  60. Roztocil T., Matter-Sadzinski L., Gomez M., Ballivet M., and Matter J. M. (1998) Functional properties of the neuronal nicotinic acetylcholine receptor beta 3 promoter in the developing central nervous system. J. Biol. Chem. 273, 15,131–15,137.

    Article  CAS  Google Scholar 

  61. Salsano E., Pollo B., Eoli M., Giordana M. T., and Finocchiaro G. (2004) Expression of MATH1, a marker of cerebellar granule cell progenitors, identifies different medulloblastoma sub-types. Neurosci. Lett. 370, 180–185.

    PubMed  Article  CAS  Google Scholar 

  62. Satoh J. and Kuroda Y. (2000) Differential gene expression between human neurons and neuronal progenitor cells in culture: an analysis of arrayed cDNA clones in NTera2 human embryonal carcinoma cell line as a model system. J. Neurosci. Methods 94, 155–164.

    PubMed  Article  CAS  Google Scholar 

  63. Schroder N. and Gossler A. (2002) Expression of Notch pathway components in fetal and adult mouse small intestine. Gene Expr. Patterns 2, 247–250.

    PubMed  Article  CAS  Google Scholar 

  64. Seki K., Fujimori T., Savagner P., et al. (2003) Mouse Snail family transcription repressors regulate chondrocyte, extracellular matrix, type II collagen, and aggrecan. J. Biol. Chem. 278, 41,862–41,870.

    Article  CAS  Google Scholar 

  65. Shou J., Zheng J. L., and Gao W. Q. (2003) Robust generation of new hair cells in the mature mammalian inner ear by adenoviral expression of Hath1. Mol. Cell Neurosci. 23, 169–179.

    PubMed  Article  CAS  Google Scholar 

  66. Theodosiou N. A. and Tabin C. J. (2003) Wnt signaling during development of the gastrointestinal tract. Dev. Biol. 259, 258–271.

    PubMed  Article  CAS  Google Scholar 

  67. Tong W.-M., Ohgaki H., Huang H., Granier C., Kleihues P., and Wang Z.Q. (2003) Null Mutation of DNA Strand Break-Binding Molecule Poly (ADP-ribose) Polymerase Causes Medulloblastomas in p53-/-Mice. Am. J. Pathol. 162, 343–352.

    PubMed  CAS  Google Scholar 

  68. Tsang M., Lijam N., Yang Y., Beier D. R., Wynshaw-Boris A., and Sussman D. J. (1996) Isolation and characterization of mouse dishevelled-3. Dev. Dyn. 207, 253–262.

    PubMed  Article  CAS  Google Scholar 

  69. Uittenbogaard M., Martinka D. L., and Chiaramello A. (2003) The basic helix-loop-helix differentiation factor Nex1/MATH-2 functions as a key activator of the GAP-43 gene. J. Neurochem. 84, 678–688.

    PubMed  Article  CAS  Google Scholar 

  70. Visel A., Thaller C., and Eichele G. (2004) Gene Paint. org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 32, D552–556.

    PubMed  Article  CAS  Google Scholar 

  71. Wang V.Y. and Zoghbi H. Y. (2001) Genetic regulation of cerebellar development. Nat. Rev. Neurosci. 2, 484–491.

    PubMed  Article  CAS  Google Scholar 

  72. Warnecke M., Oster H., Revelli J. P., Alvarez-Bolado G., and Eichele G. (2005) Abnormal development of the locus coeruleus in Ear2 (Nr2f6)-deficient mice impairs the functionality of the forebrain clock and affects nociception. Genes Dev. 19, 614–625.

    PubMed  Article  CAS  Google Scholar 

  73. Yang Q., Bermingham N. A., Finegold M. J. and Zoghbi H. Y. (2001) Requirement of Math1 for secretory cell lineage commitment in the mouse intestine. Science 294, 2155–2158.

    PubMed  Article  CAS  Google Scholar 

  74. Yoh S. M. and Privalsky M. L. (2001) Transcriptional repression by thyroid hormone receptors. A role for receptor homodimers in the recruitment of SMRT corepressor. J. Biol. Chem. 276, 16,857–16,867.

    Article  CAS  Google Scholar 

  75. Zheng J. L. and Gao W. Q. (2000) Overexpression of Math1 induces robust production of extra hair cells in postnatal rat inner ears. Nat Neurosci 3, 580–586.

    PubMed  Article  CAS  Google Scholar 

  76. Zhu Y., Yu T., and Rao Y. (2004) Temporal regulation of cerebellar EGL migration through a switch in cellular responsiveness to the meninges. Dev. Biol. 267, 153–164.

    PubMed  Article  CAS  Google Scholar 

  77. Zine A. and de Ribaupierre F. (2002) Notch/Notch ligands and Math1 expression patterns in the organ of Corti of wild-type and Hes1 and Hes5 mutant mice. Hear. Res. 170, 22–31.

    PubMed  Article  CAS  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to Nissim Ben-Arie.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Krizhanovsky, V., Soreq, L., Kliminski, V. et al. Math 1 target genes are enriched with evolutionarily conserved clustered e-box binding sites. J Mol Neurosci 28, 211–229 (2006). https://doi.org/10.1385/JMN:28:2:211

Download citation

Index Entries

  • bHLH transcription factor
  • Math1
  • E-box, cerebellum
  • cerebellar granule cells
  • target gene
  • Nr2f6