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Dev Biol 2017 Jun 15;4262:176-187. doi: 10.1016/j.ydbio.2016.02.032.
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Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula.

Ding Y , Colozza G , Zhang K , Moriyama Y , Ploper D , Sosa EA , Benitez MDJ , De Robertis EM .

RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the X. laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.

PubMed ID: 27016259
PMC ID: PMC5033668
Article link: Dev Biol
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: admp ag1 anks6 anxa11 bambi cat2 cdx2 cer1 chrd cpe ctnnb1 dkk1 dkk2 dlx3 dmbx1 egr1 evx1 fgf16 fos foxd3 foxg1 fst fzd8 gabbr1 gsc hepacam hoxb6 hsf3 junb lif lnx2 msx1 msx2 myc ncr3 nkx6-1 nkx6-2 nodal nodal3.1 nodal3.2 nog nppb odc1 otx2 oxsr1 phyhd1 pkdcc.1 pkdcc.2 prok2 rax satb2 sia1 smc1a socs3 szl tbl1x tbx22 tbx3 tmem150b ventx1 ventx1.2 ventx3.2 wif1 wnt8a
Morpholinos: ctnnb1 MO1

GEO Series: GSE75278: Xenbase,  NCBI
Phenotypes: Xla Wt + pkdcc.1 (fig.6.b) [+]

Article Images: [+] show captions
References [+] :
Anders, Differential expression analysis for sequence count data. 2010, Pubmed