title: Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula.
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.
authors.affiliation: Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Ding
authors.affiliation: Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Colozza
authors.affiliation: Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA.
authors.forename: Kelvin
authors.initials: K
authors.lastname: Zhang
authors.affiliation: Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Moriyama
authors.affiliation: Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
authors.forename: Diego
authors.initials: D
authors.lastname: Ploper
authors.affiliation: Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Sosa
authors.affiliation: Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA.
authors.forename: Maria D J
authors.initials: MDJ
authors.lastname: Benitez
authors.affiliation: Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, CA 90095-1662, USA. Electronic address: ederobertis@mednet.ucla.edu.
authors.forename: Edward M
authors.initials: EM
authors.lastname: De Robertis
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000235:genetics*; D004625:Embryo, Nonmammalian / Q000378:metabolism; D020224:Expressed Sequence Tags; D005775:Gastrula / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D006257:Head / Q000196:embryology; D008845:Microinjections; D020897:Organizers, Embryonic / Q000378:metabolism; D011505:Protein-Tyrosine Kinases / Q000096:biosynthesis / Q000235:genetics; D012313:RNA / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D060449:Wnt Signaling Pathway; D029867:Xenopus Proteins / Q000096:biosynthesis / Q000235:genetics; D014982:Xenopus laevis / Q000196:embryology* / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D029867:Xenopus Proteins; D012313:RNA; C000607563:Pkdcc.1 protein, Xenopus; C000607564:Pkdcc.2 protein, Xenopus; D011505:Protein-Tyrosine Kinases
keywords: Dorsal–Ventral patterning; RNA-Seq; Secreted Tyrosine kinase; Spemann organizer; Vlk; Xenopus laevis