An atlas of differential gene expression during early Xenopus embryogenesis

Abstract

We have carried out a large-scale, semi-automated whole-mount in situ hybridization screen of 8369 cDNA clones in Xenopus laevis embryos. We confirm that differential gene expression is prevalent during embryogenesis since 24% of the clones are expressed non-ubiquitously and 8% are organ or cell type specific marker genes. Sequence analysis and clustering yielded 723 unique genes displaying a differential expression pattern. Of these, 18% were already described in Xenopus, 47% have homologs and 35% are lacking significant sequence similarity in databases. Many of them encode known developmental regulators. We classified 363 of the 723 genes for which a Gene Ontology annotation for molecular function could be attributed and found 'DNA binding' and 'enzyme' the most represented terms. The most common protein domains encoded in these embryonic, differentially expressed genes are the homeobox and RNA Recognition Motif (RRM). Fifty-nine putative orthologs of human disease genes, and 254 organ or cell specific marker genes were identified. Markers were found for nasal placode and archenteron roof, organs for which a specific marker was previously unavailable. Markers were also found for novel subdomains of various other organs. The tissues for which most markers were found are muscle and epidermis. Expression of cell cycle regulators fell in two classes, containing proliferation-promoting and anti-proliferative genes, respectively. We identified 66 new members of the BMP4, chromatin, endoplasmic reticulum, and karyopherin synexpression groups, thus providing a first glimpse of their probable cellular roles. Cluster analysis of tissues to measure tissue relatedness yielded some unorthodox affinities besides expectable lineage relationships. In conclusion, this study represents an atlas of gene expression patterns, which reveals embryonic regionalization, provides novel marker genes, and makes predictions about the functional role of unknown genes.

ΔNp63 is regulated by BMP4 signaling and is required for early epidermal development in Xenopus

“…3B; 83%; n ¼ 78), and Rexp52 ( Fig. 3C; 56%; n ¼ 63), a marker of epidermis inner layer (Pollet et al, 2005). In addition, we observed an increase in the expression of the cement gland marker XAG ( Fig.…”

“…Grainger, personal communication), cytokeratin XK81a (Jonas et al, 1985), FoxD3 (Sasai et al, 2001), Dlx3 and Dlx5 (Luo et al, 2001), Six1 (Pandur and Moody, 2000), and Rexp52 (Pollet et al, 2005) by in vitro transcription. Specimens were prepared, hybridized and stained as previously described Tribulo et al, 2003).…”

Negative autoregulation of Oct3/4 through Cdx1 promotes the onset of gastrulation

“…The microarrays used were based on Xenopus laevis gastrula cDNA libraries and contained 3,500 genes. The array consists of unique genes identified by whole mount in situ hybridization (Pollet et al, 2005), and additional unique genes selected from Xenopus embryonic EST sequenced clones. Expression of the Xenopus Oct3/4 (Pou5f1) gene family, Oct25, Oct91, and Oct60 (Hinkley et al, 1992;Morrison and Brickman, 2006), was altered as a result of Cdx1 manipulation.…”

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

“…of times isolated Insert (kbp) Homology search method TABLE 4 eral studies using systematic analyses of ESTs and expression patterns successfully isolated candidate genes of developmental regulators (Gawantka et al, 1998, Lee et al, 1999, Kudoh et al, 2001, Satou et al, 2001, Shibata et al, 2001, Satou et al, 2002, Pollet et al, 2005.…”