Microarray-based analysis of early development in Xenopus laevis

Altmann CR, Bell E, Sczyrba A, Pun J, Bekiranov S, Gaasterland T, Brivanlou AH (2001)
DEVELOPMENTAL BIOLOGY 236(1): 64-75.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Author
; ; ; ; ; ;
Abstract
In order to examine transcriptional regulation globally, during early vertebrate embryonic development, we have prepared Xenopus laevis cDNA microarrays. These prototype embryonic arrays contain 864 sequenced gastrula cDNA. In order to analyze and store array data, a microarray analysis pipeline was developed and integrated with sequence analysis and annotation tools. In three independent experimental settings, we demonstrate the power of these global approaches and provide optimized protocols for their application to molecular embryology. in the first set, by comparing maternal versus zygotic transcription, we document groups of genes that are temporally regulated. This analytical approach resulted in the discovery of novel temporally regulated genes. In the second, we examine changes in gene expression spatially during development by comparing dorsal and ventral mesoderm dissected from early gastrula embryos. We have discovered novel genes with spatial enrichment from these experiments. Finally, we use the prototype microarray to examine transcriptional responses from embryonic explants treated with activin. We selected genes (two of which are novel) regulated by activin for further characterization. All results obtained by the arrays were independently tested by RT-PCR or by in situ hybridization to provide a direct assessment of the accuracy and reproducibility of these approaches in the context of molecular embryology. (C) 2001 Academic Press.
Publishing Year
ISSN
PUB-ID

Cite this

Altmann CR, Bell E, Sczyrba A, et al. Microarray-based analysis of early development in Xenopus laevis. DEVELOPMENTAL BIOLOGY. 2001;236(1):64-75.
Altmann, C. R., Bell, E., Sczyrba, A., Pun, J., Bekiranov, S., Gaasterland, T., & Brivanlou, A. H. (2001). Microarray-based analysis of early development in Xenopus laevis. DEVELOPMENTAL BIOLOGY, 236(1), 64-75. doi:10.1006/dbio.2001.0298
Altmann, C. R., Bell, E., Sczyrba, A., Pun, J., Bekiranov, S., Gaasterland, T., and Brivanlou, A. H. (2001). Microarray-based analysis of early development in Xenopus laevis. DEVELOPMENTAL BIOLOGY 236, 64-75.
Altmann, C.R., et al., 2001. Microarray-based analysis of early development in Xenopus laevis. DEVELOPMENTAL BIOLOGY, 236(1), p 64-75.
C.R. Altmann, et al., “Microarray-based analysis of early development in Xenopus laevis”, DEVELOPMENTAL BIOLOGY, vol. 236, 2001, pp. 64-75.
Altmann, C.R., Bell, E., Sczyrba, A., Pun, J., Bekiranov, S., Gaasterland, T., Brivanlou, A.H.: Microarray-based analysis of early development in Xenopus laevis. DEVELOPMENTAL BIOLOGY. 236, 64-75 (2001).
Altmann, CR, Bell, E, Sczyrba, Alexander, Pun, J, Bekiranov, S, Gaasterland, T, and Brivanlou, AH. “Microarray-based analysis of early development in Xenopus laevis”. DEVELOPMENTAL BIOLOGY 236.1 (2001): 64-75.
This data publication is cited in the following publications:
This publication cites the following data publications:

45 Citations in Europe PMC

Data provided by Europe PubMed Central.

A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis.
Chalmers AD, Goldstone K, Smith JC, Gilchrist M, Amaya E, Papalopulu N., Mech Dev 122(3), 2005
PMID: 15763212
An atlas of differential gene expression during early Xenopus embryogenesis.
Pollet N, Muncke N, Verbeek B, Li Y, Fenger U, Delius H, Niehrs C., Mech Dev 122(3), 2005
PMID: 15763213
Global analysis of RAR-responsive genes in the Xenopus neurula using cDNA microarrays.
Arima K, Shiotsugu J, Niu R, Khandpur R, Martinez M, Shin Y, Koide T, Cho KW, Kitayama A, Ueno N, Chandraratna RA, Blumberg B., Dev Dyn 232(2), 2005
PMID: 15614783
Global gene expression profiling and cluster analysis in Xenopus laevis.
Baldessari D, Shin Y, Krebs O, König R, Koide T, Vinayagam A, Fenger U, Mochii M, Terasaka C, Kitayama A, Peiffer D, Ueno N, Eils R, Cho KW, Niehrs C., Mech Dev 122(3), 2005
PMID: 15763214
Macroarray-based analysis of tail regeneration in Xenopus laevis larvae.
Tazaki A, Kitayama A, Terasaka C, Watanabe K, Ueno N, Mochii M., Dev Dyn 233(4), 2005
PMID: 15977180
Identification of a Hoxd10-regulated transcriptional network and combinatorial interactions with Hoxa10 during spinal cord development.
Hedlund E, Karsten SL, Kudo L, Geschwind DH, Carpenter EM., J Neurosci Res 75(3), 2004
PMID: 14743444
Defining a large set of full-length clones from a Xenopus tropicalis EST project.
Gilchrist MJ, Zorn AM, Voigt J, Smith JC, Papalopulu N, Amaya E., Dev Biol 271(2), 2004
PMID: 15223350
Microarray gene expression profiling during the segmentation phase of zebrafish development.
Linney E, Dobbs-McAuliffe B, Sajadi H, Malek RL., Comp Biochem Physiol C Toxicol Pharmacol 138(3), 2004
PMID: 15533793
Screening of FGF target genes in Xenopus by microarray: temporal dissection of the signalling pathway using a chemical inhibitor.
Chung HA, Hyodo-Miura J, Kitayama A, Terasaka C, Nagamune T, Ueno N., Genes Cells 9(8), 2004
PMID: 15298682
Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization.
King MW, Nguyen T, Calley J, Harty MW, Muzinich MC, Mescher AL, Chalfant C, N'Cho M, McLeaster K, McEntire J, Stocum D, Smith RC, Neff AW., Dev Dyn 226(2), 2003
PMID: 12557218
Identification of transcription coactivator OCA-B-dependent genes involved in antigen-dependent B cell differentiation by cDNA array analyses.
Kim U, Siegel R, Ren X, Gunther CS, Gaasterland T, Roeder RG., Proc Natl Acad Sci U S A 100(15), 2003
PMID: 12857960
Neural crest specification: migrating into genomics.
Gammill LS, Bronner-Fraser M., Nat Rev Neurosci 4(10), 2003
PMID: 14523379
Applying genomics technologies to neural development.
Blackshaw S, Livesey R., Curr Opin Neurobiol 12(1), 2002
PMID: 11861173
The latent-TGFbeta-binding-protein-1 (LTBP-1) is expressed in the organizer and regulates nodal and activin signaling.
Altmann CR, Chang C, Muñoz-Sanjuán I, Bell E, Heke M, Rifkin DB, Brivanlou AH., Dev Biol 248(1), 2002
PMID: 12142025
Gene expression profiling of osteoclast differentiation by combined suppression subtractive hybridization (SSH) and cDNA microarray analysis.
Rho J, Altmann CR, Socci ND, Merkov L, Kim N, So H, Lee O, Takami M, Brivanlou AH, Choi Y., DNA Cell Biol 21(8), 2002
PMID: 12215257
Developmental biology: an array of new possibilities.
Ali A, Crawford MJ., Biotechnol Adv 20(5-6), 2002
PMID: 14550022
DNA microarrays and toxicogenomics: applications for ecotoxicology?
Neumann NF, Galvez F., Biotechnol Adv 20(5-6), 2002
PMID: 14550024
An amphibian with ambition: a new role for Xenopus in the 21st century.
Beck CW, Slack JM., Genome Biol 2(10), 2001
PMID: 11597339

43 References

Data provided by Europe PubMed Central.


Nieuwkoop, 1956
Transcriptional regulation of the Xlim-1 gene by activin is mediated by an element in intron I.
Rebbert ML, Dawid IB., Proc. Natl. Acad. Sci. U.S.A. 94(18), 1997
PMID: 9275190
Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.
Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW., Proc. Natl. Acad. Sci. U.S.A. 93(20), 1996
PMID: 8855227
Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.
Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW., Proc. Natl. Acad. Sci. U.S.A. 93(20), 1996
PMID: 8855227
Characterization of a subfamily of related winged helix genes, XFD-12/12'/12" (XFLIP), during Xenopus embryogenesis.
Solter M, Koster M, Hollemann T, Brey A, Pieler T, Knochel W., Mech. Dev. 89(1-2), 1999
PMID: 10559492
Pfam: a comprehensive database of protein domain families based on seed alignments.
Sonnhammer EL, Eddy SR, Durbin R., Proteins 28(3), 1997
PMID: 9223186
Leptin-specific patterns of gene expression in white adipose tissue.
Soukas A, Cohen P, Socci ND, Friedman JM., Genes Dev. 14(8), 2000
PMID: 10783168
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B., Mol. Biol. Cell 9(12), 1998
PMID: 9843569
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B., Mol. Biol. Cell 9(12), 1998
PMID: 9843569
Über Induktion von Embryonanlagen dürch Implantation artfremder Organisatoren
Spemann, Arch. Mikrosk. Anat. Entwicklungsmech. 100(), 1924
Activins are expressed early in Xenopus embryogenesis and can induce axial mesoderm and anterior structures.
Thomsen G, Woolf T, Whitman M, Sokol S, Vaughan J, Vale W, Melton DA., Cell 63(3), 1990
PMID: 2225062
Developmental and differential regulations in gene expression of Xenopus pleiotrophic factors-alpha and -beta.
Tsujimura A, Yasojima K, Kuboki Y, Suzuki A, Ueno N, Shiokawa K, Hashimoto-Gotoh T., Biochem. Biophys. Res. Commun. 214(2), 1995
PMID: 7677748
Epidermal induction and inhibition of neural fate by translation initiation factor 4AIII.
Weinstein DC, Honore E, Hemmati-Brivanlou A., Development 124(21), 1997
PMID: 9334272
FGF-mediated mesoderm induction involves the Src-family kinase Laloo.
Weinstein DC, Marden J, Carnevali F, Hemmati-Brivanlou A., Nature 394(6696), 1998
PMID: 9732875
Induction of epidermis and inhibition of neural fate by Bmp-4.
Wilson PA, Hemmati-Brivanlou A., Nature 376(6538), 1995
PMID: 7630398

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 11456444
PubMed | Europe PMC

Search this title in

Google Scholar