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XB-ART-51980
Dev Biol. June 15, 2017; 426 (2): 176-187.

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 .


Abstract
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: Howard Hughes Medical Institute , HHMI_DE ROBERTIS_E Howard Hughes Medical Institute , R25 GM055052 NIGMS NIH HHSHoward Hughes Medical Institute , R25 GM055052 NIGMS NIH HHSHoward Hughes Medical Institute , R25 GM055052 NIGMS NIH HHS , T34 GM008563 NIGMS NIH HHS , HHMI_DE ROBERTIS_E Howard Hughes Medical Institute , R25 GM055052 NIGMS NIH HHS , T34 GM008563 NIGMS NIH HHSHoward Hughes Medical Institute , R25 GM055052 NIGMS NIH HHS , T34 GM008563 NIGMS NIH HHSHoward Hughes Medical Institute , R25 GM055052 NIGMS NIH HHS , T34 GM008563 NIGMS NIH HHS

Genes referenced: admp ag1 anks6 anxa11 bambi cat2 cdx2 cer1 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 nodal1 nodal3.1 nodal3.2 nog nppb odc1 otx2 oxsr1 phyhd1 pkdcc.1 pkdcc.2 prok2 rax satb2 socs3 szl tbl1x tbx22 tbx3 tmem150b ventx1.1 ventx1.2 ventx3.2 wif1 wnt8a

Morpholinos referenced: ctnnb1 MO1

References:
Anders, 2011, Pubmed[+]


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