Patterns & Phenotypes
A Xenopus DNA microarray approach to identify novel direct BMP target genes involved in early embryonic development
Article first published online: 21 DEC 2004
Copyright © 2004 Wiley-Liss, Inc.
Volume 232, Issue 2, pages 445–456, February 2005
How to Cite
Peiffer, D. A., Von Bubnoff, A., Shin, Y., Kitayama, A., Mochii, M., Ueno, N. and Cho, K. W.Y. (2005), A Xenopus DNA microarray approach to identify novel direct BMP target genes involved in early embryonic development. Dev. Dyn., 232: 445–456. doi: 10.1002/dvdy.20230
- Issue published online: 13 JAN 2005
- Article first published online: 21 DEC 2004
- Manuscript Accepted: 8 SEP 2004
- Manuscript Revised: 31 AUG 2004
- Manuscript Received: 5 JUL 2004
- National Institutes of Health. Grant Numbers: HD38761, HD29507, GM07311
- 1999. The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb Symp Quant Biol 64: 71–78. , , , , , , , , , , , , , , , , , , , .
- 2002. Signalling via type IA and type IB bone morphogenetic protein receptors (BMPR) regulates intramembranous bone formation, chondrogenesis and feather formation in the chicken embryo. Int J Dev Biol 46: 243–253. , , .
- 2001. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509–519. , .
- 1995. Anterior neurectoderm is progressively induced during gastrulation: the role of the Xenopus homeobox gene orthodenticle. Development 121: 993–1004. , .
- 2003. Twisted gastrulation loss-of-function analyses support its role as a BMP inhibitor during early Xenopus embryogenesis. Development 130: 4975–4988. , , .
- 2002. Angiomotin belongs to a novel protein family with conserved coiled-coil and PDZ binding domains. Gene 298: 69–77. , , , , , , .
- 1994. Structure-function studies of FGF-1: dissociation and partial reconstitution of certain of its biological activities. Mol Reprod Dev 39: 56–60; discussion 60–61. , , .
- 1997. Cellular interpretation of multiple TGF-beta signals: intracellular antagonism between activin/BVg1 and BMP-2/4 signaling mediated by Smads. Development 124: 4467–4480. , , , , , , , .
- 1994. The ubiquitin-mediated proteolytic pathway: mechanisms of action and cellular physiology. Biol Chem Hoppe Seyler 375: 565–581. .
- 2000. The ubiquitin-mediated proteolytic pathway: mode of action and clinical implications. J Cell Biochem 77: 40–51. , , .
- 1995. Bone morphogenetic protein 2 in the early development of Xenopus laevis. Mech Dev 52: 357–370. , , , , .
- 1992. Bone morphogenetic protein 4: a ventralizing factor in early Xenopus development. Development 115: 573–585. , , , .
- 1999. BMP signalling in early Xenopus development. Bioessays 21: 751–760. , .
- 1999. DNA arrays for analysis of gene expression. Methods Enzymol 303: 179–205. , .
- 2000. Endogenous patterns of TGFbeta superfamily signaling during early Xenopus development. Development 127: 2917–2931. , , , , .
- 2002. Cooperative interaction of Xvent-2 and GATA-2 in the activation of the ventral homeobox gene Xvent-1B. J Biol Chem 277: 23872–23881. , .
- 1992. Spatially restricted expression of fibroblast growth factor receptor-2 during Xenopus development. Development 116: 1051–1058. , .
- 2003. Caenorhabditis elegans nucleoporins Nup93 and Nup205 determine the limit of nuclear pore complex size exclusion in vivo. Mol Biol Cell 14: 5104–5115. , , .
- 1991. Chromosome tangling and breakage at anaphase result from mutations in lodestar, a Drosophila gene encoding a putative nucleoside triphosphate-binding protein. Genes Dev 5: 1786–1799. , .
- 2002. Seven BMPs and all their receptors are simultaneously expressed in osteosarcoma cells. Int J Oncol 20: 143–147. , , , , , , , , , , , , , , .
- 1991. In situ hybridization: an improved whole-mount method for Xenopus embryos. Methods Cell Biol 36: 685–695. .
- 2000. OAZ uses distinct DNA- and protein-binding zinc fingers in separate BMP-Smad and Olf signaling pathways. Cell 100: 229–240. , , , , , .
- 1995. Ventral mesodermal patterning in Xenopus embryos: expression patterns and activities of BMP-2 and BMP-4. Dev Genet 17: 78–89. , .
- 1996. Bone morphogenetic proteins in development. Curr Opin Genet Dev 6: 432–438. .
- 1999. Id genes are direct targets of bone morphogenetic protein induction in embryonic stem cells. J Biol Chem 274: 19838–19845. , , , , .
- 1998. Transcriptional regulation of blood formation during Xenopus development. Semin Immunol 10: 103–109. , .
- 2003. Smad4 and beta-catenin co-activators functionally interact with lymphoid-enhancing factor to regulate graded expression of Msx2. J Biol Chem 278: 48805–48814. , , .
- 2000. Involvement of BMP-4/msx-1 and FGF pathways in neural induction in the Xenopus embryo. Dev Growth Differ 42: 307–316. , , , , , .
- 1998. Propionyl-CoA carboxylase of Myxococcus xanthus: catalytic properties and function in developing cells. Arch Microbiol 170: 179–184. , , , .
- 2003. Gene array analysis of bone morphogenetic protein type I receptor-induced osteoblast differentiation. J Bone Miner Res 18: 1177–1185. , , , , .
- 2002. Identification and functional characterization of distinct critically important bone morphogenetic protein-specific response elements in the Id1 promoter. J Biol Chem 277: 4883–4891. , .
- 2001. Expression of the Xenopus homologue of the receptor for activated c-kinase 1 (RACK1) in the Xenopus embryo. Dev Genes Evol 211: 195–197. , , , .
- 1996. Xom: a Xenopus homeobox gene that mediates the early effects of BMP-4. Development 122: 2385–2394. , , , .
- 2003. Cloning and characterization of Xenopus Id4 reveals differing roles for Id genes. Dev Biol 264: 339–351. , .
- 2001. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276: 19937–19944. , , , , , .
- 1999. A BMP-inducible gene, dlx5, regulates osteoblast differentiation and mesoderm induction. Dev Biol 208: 123–133. , , , , , , , .
- 1992. Genes for bone morphogenetic proteins are differentially transcribed in early amphibian embryos. Biochem Biophys Res Commun 186: 1487–1495. , , , , .
- 1995. BMP-4 regulates the dorsal-ventral differences in FGF/MAPKK-mediated mesoderm induction in Xenopus. Dev Biol 172: 242–252. , , , , , , .
- 1998. Id helix-loop-helix proteins in cell growth and differentiation. Trends Cell Biol 8: 58–65. , , , .
- 1996. The Xvent-2 homeobox gene is part of the BMP-4 signalling pathway controlling [correction of controling] dorsoventral patterning of Xenopus mesoderm. Development 122: 3045–3053. , , , , , , .
- 2000. Oracle, a novel PDZ-LIM domain protein expressed in heart and skeletal muscle. Mech Dev 92: 277–284. , , .
- 2003. Xenopus DNA Microarrays. Curr Genom 4: 665–672. , , .
- 1999. Transcriptional regulation of Xvent homeobox genes. Mech Dev 81: 139–149. , , , .
- 1995. Competition between noggin and bone morphogenetic protein 4 activities may regulate dorsalization during Xenopus development. Proc Natl Acad Sci U S A 92: 12141–12145. , , .
- 2002. Notch signaling is involved in the regulation of Id3 gene transcription during Xenopus embryogenesis. Differentiation 69: 198–208. , , , , , , , , .
- 1991. Localized and inducible expression of Xenopus-posterior (Xpo), a novel gene active in early frog embryos, encoding a protein with a ‘CCHC’ finger domain. Development 112: 747–753. , .
- 1996. Regulation of dorsal-ventral patterning: the ventralizing effects of the novel Xenopus homeobox gene Vox. Development 122: 1711–1721. , , .
- 1998. Structural and functional architecture of the yeast cell-cycle transcription factor swi6. J Mol Biol 281: 763–775. , , , , , , , , , , .
- 1998. Characterization of the human NIPSNAP1 gene from 22q12: a member of a novel gene family. Gene 212: 13–20. , , , , .
- 2003. Mechanisms of TGF-beta signaling from cell membrane to the nucleus. Cell 113: 685–700. , .
- 2005. Identification of neural genes using Xenopus DNA microarrays. Dev Dyn 232: 000–000. , , , , , , , .
- 2002. XPOX2-peroxidase expression and the XLURP-1 promoter reveal the site of embryonic myeloid cell development in Xenopus. Mech Dev 117: 173–186. , , , , .
- 1991. Progressively restricted expression of a new homeobox-containing gene during Xenopus laevis embryogenesis. Development 111: 1179–1187. , , , .
- 1997. Xenopus msx1 mediates epidermal induction and neural inhibition by BMP4. Development 124: 3037–3044. , , .
- 2002. Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res 30: e54. , , , , , .
- 2001. Angiomotin: an angiostatin binding protein that regulates endothelial cell migration and tube formation. J Cell Biol 152: 1247–1254. , , , , .
- 2002. Comprehensive microarray analysis of bone morphogenetic protein 2-induced osteoblast differentiation resulting in the identification of novel markers for bone development. J Bone Miner Res 17: 2106–2118. , , , , , , , , .
- 2001. Intracellular BMP signaling regulation in vertebrates: pathway or network? Dev Biol 239: 1–14. , .
- 2002. Adult and embryonic blood and endothelium derive from distinct precursor populations which are differentially programmed by BMP in Xenopus. Development 129: 5683–5695. , , .
- 2003. The 26S proteasome system in the signaling pathways of TGF-beta superfamily. Front Biosci 8: d1109–d1127. .
- 1995. Induction of epidermis and inhibition of neural fate by Bmp-4. Nature 376: 331–333. , .
- 1995. XIdx, a dominant negative regulator of bHLH function in early Xenopus embryos. Mech Dev 49: 211–222. , .
- 1999. Opposite effects of FGF and BMP-4 on embryonic blood formation: roles of PV.1 and GATA-2. Dev Biol 208: 352–361. , , , , , , , .
- 1999. The RACK1 signaling scaffold protein selectively interacts with the cAMP-specific phosphodiesterase PDE4D5 isoform. J Biol Chem 274: 14909–14917. , , , , .
- 1998. Cloning of the Xenopus laevis aldolase C gene and analysis of its promoter function in developing Xenopus embryos and A6 cells. Biochim Biophys Acta 1442: 199–217. , , , , , .
- 2002. Role of Id family proteins in growth control. J Cell Physiol 190: 21–28. , .
- 2000. Negative Regulation of BMP/Smad Signaling by Tob in Osteoblasts. Cell 103: 1085–1097. , , , , , , , , , , , , , .
- 1995. Id gene activity during Xenopus embryogenesis. Mech Dev 50: 119–130. , , , , .
- 2002. Rescue of cleft palate in Msx1-deficient mice by transgenic Bmp4 reveals a network of BMP and Shh signaling in the regulation of mammalian palatogenesis. Development 129: 4135–4146. , , , , , .