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Open Access Research

Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult

Rachel A Heimeier12*, Biswajit Das1, Daniel R Buchholz3, Maria Fiorentino14 and Yun-Bo Shi1*

Author Affiliations

1 Section on Molecular Morphogenesis, Laboratory of Gene Regulation and Development, Program in Cellular Regulation and Metabolism (PCRM), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 18 Library Dr., Bethesda, MD 20892, USA

2 Institute of Environmental Medicine (IMM), Karolinska Institutet (KI), Nobels väg 13, S-171 77, Stockholm, Sweden

3 Department of Biological Sciences, University of Cincinnati, 832 Rieveschl Hall, Cincinnati, OH 45221-0006, USA

4 Current address: Mucosal Biology Research Centre, University of Maryland School of Medicine, 20 Penn Street, HSFII, Rm S303, Baltimore, MD 2120-1192, USA

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Genome Biology 2010, 11:R55  doi:10.1186/gb-2010-11-5-r55

Published: 19 May 2010

Abstract

Background

To adapt to its changing dietary environment, the digestive tract is extensively remodeled from the embryo to the adult during vertebrate development. Xenopus laevis metamorphosis is an excellent model system for studying mammalian gastrointestinal development and is used to determine the genes and signaling programs essential for intestinal development and maturation.

Results

The metamorphosing intestine can be divided into four distinct developmental time points and these were analyzed with X. laevis microarrays. Due to the high level of conservation in developmental signaling programs and homology to mammalian genes, annotations and bioinformatics analysis were based on human orthologs. Clustering of the expression patterns revealed co-expressed genes involved in essential cell processes such as apoptosis and proliferation. The two largest clusters of genes have expression peaks and troughs at the climax of metamorphosis, respectively. Novel conserved gene ontology categories regulated during this period include transcriptional activity, signal transduction, and metabolic processes. Additionally, we identified larval/embryo- and adult-specific genes. Detailed analysis revealed 17 larval specific genes that may represent molecular markers for human colonic cancers, while many adult specific genes are associated with dietary enzymes.

Conclusions

This global developmental expression study provides the first detailed molecular description of intestinal remodeling and maturation during postembryonic development, which should help improve our understanding of intestinal organogenesis and human diseases. This study significantly contributes towards our understanding of the dynamics of molecular regulation during development and tissue renewal, which is important for future basic and clinical research and for medicinal applications.