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Mech Dev 2005 Mar 01;1223:365-439. doi: 10.1016/j.mod.2004.11.009.
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An atlas of differential gene expression during early Xenopus embryogenesis.

Pollet N , Muncke N , Verbeek B , Li Y , Fenger U , Delius H , Niehrs C .

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.

PubMed ID: 15763213
Article link: Mech Dev

Species referenced: Xenopus laevis
Genes referenced: abr acsl1 ahnak akap13 aldh16a1 angpt4.2 apob arpp19 astl2e.2 atp2a1 basp1 bin1 bmp4 c5 c5.2 c8h19orf47 capn8.1 carhsp1 carns1 cbfa2t3 ckmt1b copg1 cpeb4 ddx21 dhcr7 dlst dnajc30 efnb1 efr3a elk3 elovl7 eno1 epn2 epn3 esrp1 f2 fen1 ferry3 fndc3a foxc2 ftmt fxr1 gata4 gjb2 glud1 gnao1 gnb3 gsto1 gstp1 hap1 has-rs has1 hmgcs1 hspb1 itm2a lgals3 mespa myh4 myh8 myl11 myod1 nedd9 net1 nt5c2 otud6b p4hb pacsin3 pde3a perp pfkp pi4k2a plekhg4 ppib ppif ppp1r3c ppp1r3c.2 prkd1 prkg1 rab5b rbfox2 rbm12b.5 rbm24 rhoc rreb1 rsph6a samd4b sash3 sat1 sdha sgk1 slc16a3 slc25a1 smarcc1 sox17a spam1 speg spmip8 sra1 srl stxbp6 synm tbl1x tent2 thbs4 tpbg tpm3 trim29 tuba1cl.3 tubb4b upk3a vgll4l wbp11 XB22062450 XB22062458 XB22063322 XB22064002 XB22164556 zdhhc9

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