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Cited by 96Developmental Biology and Gene RegulationGene Regulatory Network AnalysisGenomics and Chromatin Dynamics

Xenopus as a model system to study transcriptional regulatory networks

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Koide, Tetsuya, Hayata, Tadayoshi, Cho, Ken W. Y.·2005·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0408125102PMC PMC555977
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Abstract

Development is controlled by a complex series of events requiring sequential gene activation. Understanding the logic of gene networks during development is necessary for a complete understanding of how genes contribute to phenotype. Pioneering work initiated in the sea urchin and Drosophila has demonstrated that reasonable transcriptional regulatory network diagrams representing early development in multicellular animals can be generated through use of appropriate genomic, genetic, and biochemical tools. Establishment of similar regulatory network diagrams for vertebrate development is a necessary step. The amphibian Xenopus has long been used as a model for vertebrate early development and has contributed greatly to the elucidation of gene regulation. Because the best and most extensively studied transcriptional regulatory network in Xenopus is that underlying the formation and function of Spemann's organizer, we describe the current status of our understanding of this gene regulatory network and its relationship to mesodermal patterning. Seventy-four transcription factors currently known to be expressed in the mesoendoderm of Xenopus gastrula were characterized according to their modes of action, DNA binding consensus sequences, and target genes. Among them, nineteen transcription factors were characterized sufficiently in detail, allowing us to generate a gene regulatory network diagram. Additionally, we discuss recent amphibian work using a combined DNA microarray and bioinformatics approach that promises to accelerate regulatory network studies.

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  • Xenopus mesoderm, C. elegans gut/mesoderm, and zebrafish endoderm and mesoderm GRNs also display deep hierarchical organization.

    “GRNs for specification of mesoderm in Xenopus embryos10, for specification of the gut and mesoderm cell lineages in Caenorhabditis elegans embryos11, and for specification of endoderm and dorsal, anterior and ventral gene expression domains12, and of mesoderm13 in zebrafish, also display deep, hierarchical organizations.”

    From Emerging properties of animal gene regulatory networks (2010) · cites this paper as [10]

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Authors
Koide, T., Hayata, T., & Cho, K. W. Y.
Affiliations
University of California, Irvine (US)
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2005-03-28
Volume
102
Issue
14
Pages
4943-4948
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0408125102
PMC
PMC555977
OpenAlex
W2095008230
Cited by
96
References
71
Citations by year
2025: 1 · 2024: 2 · 2023: 2 · 2022: 2 · 2021: 5 · 2020: 1 · 2019: 1 · 2018: 1 · 2017: 4 · 2016: 5 · 2015: 2 · 2014: 6 · 2013: 3 · 2012: 5
FWCI
4.16
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD-29507, R01HD029507)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
Xenopus, transcriptional regulatory networks, Spemann's organizer, transcription factors, target genes, DNA microarrays, bioinformatics
MeSH terms
Animals, Base Sequence, DNA, Endoderm, Genes, Regulator, Mesoderm, Models, Genetic, Phylogeny, Promoter Regions, Genetic, Proteins, Transcription, Genetic, Xenopus, Signal Transduction, Transcriptional Activation, Gene Expression Regulation, Developmental, Oligonucleotide Array Sequence Analysis, Genomics, Xenopus Proteins, Intercellular Signaling Peptides and Proteins

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