Global gene expression profiling and cluster analysis in Xenopus laevis

Abstract

We have undertaken a large-scale microarray gene expression analysis using cDNAs corresponding to 21,000 Xenopus laevis ESTs. mRNAs from 37 samples, including embryos and adult organs, were profiled. Cluster analysis of embryos of different stages was carried out and revealed expected affinities between gastrulae and neurulae, as well as between advanced neurulae and tadpoles, while egg and feeding larvae were clearly separated. Cluster analysis of adult organs showed some unexpected tissue-relatedness, e.g. kidney is more related to endodermal than to mesodermal tissues and the brain is separated from other neuroectodermal derivatives. Cluster analysis of genes revealed major phases of co-ordinate gene expression between egg and adult stages. During the maternal-early embryonic phase, genes maintaining a rapidly dividing cell state are predominantly expressed (cell cycle regulators, chromatin proteins). Genes involved in protein biosynthesis are progressively induced from mid-embryogenesis onwards. The larval-adult phase is characterised by expression of genes involved in metabolism and terminal differentiation. Thirteen potential synexpression groups were identified, which encompass components of diverse molecular processes or supra-molecular structures, including chromatin, RNA processing and nucleolar function, cell cycle, respiratory chain/Krebs cycle, protein biosynthesis, endoplasmic reticulum, vesicle transport, synaptic vesicle, microtubule, intermediate filament, epithelial proteins and collagen. Data filtering identified genes with potential stage-, region- and organ-specific expression. The dataset was assembled in the iChip microarray database, , which allows user-defined queries. The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes.

Systematic screening for genes specifically expressed in the anterior neuroectoderm during early Xenopus development

“…The structures of predicted proteins and their developmental expression patterns will facilitate functional analysis of novel genes during the development of various tissues and organs, including the brain. All Xenopus transcripts will be identified in the future by repeated systematic screening and expression pattern analysis including our studies (this paper and the previous one (Shibata et al, 2001)) as well as studies by other groups (Gawantka et al, 1998, Baldessari et al, 2005, Pollet et al, 2005, Voigt et al, 2005 and substantial accumulation of ESTs and expression patterns will facilitate advances in functional genomics.…”

Chicken skeletal muscle-associated macroarray for gene discovery

“…However, mesoderm-derived tissues ('skeletal muscle' and 'heart') and endoderm ('liver') did not show expression consistent with this hypothesis. Inconsistent dendrograms generated from tissue profiling and embryonic origin were previously observed in Xenopus laevis (Baldessari et al, 2005). Dendrograms generated from hierarchical clustering analysis.…”

Cis-regulatory properties of medaka synexpression groups

“…'cardiovascular system'), whereas others were also found in Xenopus, suggesting evolutionary conservation [e.g. 'cell cycle' (Baldessari et al, 2005), 'muscle and epidermis' (Pollet et al, 2005), 'ribosome biogenesis' (Wischnewski et al, 2000)]. …”

“…The whole-genome study of SGs is mainly constrained by technical limitations in the simultaneous recording of precise spatiotemporal expression patterns during development. DNA microarray assays, for instance, have been successfully applied for studying genome-wide transcriptional regulation (Furlong et al, 2001;Baldessari et al, 2005) as they allow quantitative and temporal monitoring of expression during embryonic development, but lack the threedimensional information concerning tissue connectivity within the embryo. Large-scale ISH on whole-mount embryos is an approach that can provide spatial information at high resolution for gene expression on an entire organism level (Lynch et al, 1995;Gawantka et al, 1998;Kawashima et al, 2000;Neidhardt et al, 2000;Kudoh et al, 2001;Pollet et al, 2005;Lecuyer et al, 2007).…”

“…In Xenopus, microarray analysis not only confirmed SGs identified by ISH, but also allowed the discovery of novel SGs. Nevertheless, because they provide a low-resolution analysis of gene expression patterns compared with ISH, the risk of including false positives will increase (Baldessari et al, 2005). Studies combining both techniques would be ideal, as demonstrated in invertebrate models (Tomancak et al, 2002).…”