title: Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing.
abstract: During early vertebrate embryogenesis, cell fate specification is often coupled with cell acquisition of specific adhesive, polar and/or motile behaviors. In Xenopus gastrulae, tissues fated to form different axial structures display distinct motility. The cells in the early organizer move collectively and directionally toward the animal pole and contribute to anterior mesendoderm, whereas the dorsal and the ventral-posterior trunk tissues surrounding the blastopore of mid-gastrula embryos undergo convergent extension and convergent thickening movements, respectively. While factors regulating cell lineage specification have been described in some detail, the molecular machinery that controls cell motility is not understood in depth. To gain insight into the gene battery that regulates both cell fates and motility in particular embryonic tissues, we performed RNA sequencing (RNA-seq) to investigate differentially expressed genes in the early organizer, the dorsal and the ventral marginal zone of Xenopus gastrulae. We uncovered many known signaling and transcription factors that have been reported to play roles in embryonic patterning during gastrulation. We also identified many uncharacterized genes as well as genes that encoded extracellular matrix (ECM) proteins or potential regulators of actin cytoskeleton. Co-expression of a selected subset of the differentially expressed genes with activin in animal caps revealed that they had distinct ability to block activin-induced animal cap elongation. Most of these factors did not interfere with mesodermal induction by activin, but an ECM protein, EFEMP2, inhibited activin signaling and acted downstream of the activated type I receptor. By focusing on a secreted protein kinase PKDCC1, we showed with overexpression and knockdown experiments that PKDCC1 regulated gastrulation movements as well as anterior neural patterning during early Xenopus development. Overall, our studies identify many differentially expressed signaling and cytoskeleton regulators in different embryonic regions of Xenopus gastrulae and imply their functions in regulating cell fates and/or behaviors during gastrulation.
authors.affiliation: Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
authors.forename: Ivan K
authors.initials: IK
authors.lastname: Popov
authors.affiliation: Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Republic of Korea.
authors.forename: Taejoon
authors.initials: T
authors.lastname: Kwon
authors.affiliation: Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
authors.forename: David K
authors.initials: DK
authors.lastname: Crossman
authors.affiliation: Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Crowley
authors.affiliation: Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States.
authors.forename: John B
authors.initials: JB
authors.lastname: Wallingford
authors.affiliation: Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, United States. Electronic address: cchang@uab.edu.
authors.forename: Chenbei
authors.initials: C
authors.lastname: Chang
mesh_terms: D028341:Activins / Q000502:physiology; D000818:Animals; D019521:Body Patterning / Q000235:genetics*; D004625:Embryo, Nonmammalian / Q000378:metabolism / Q000648:ultrastructure; D016326:Extracellular Matrix Proteins / Q000502:physiology; D005775:Gastrula / Q000378:metabolism* / Q000648:ultrastructure; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D005855:Germ Layers / Q000378:metabolism; D009024:Morphogenesis / Q000235:genetics; D020897:Organizers, Embryonic; D011505:Protein-Tyrosine Kinases / Q000502:physiology; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D017423:Sequence Analysis, RNA; D014981:Xenopus / Q000196:embryology / Q000235:genetics*; D029867:Xenopus Proteins / Q000502:physiology
chemical_list: D016326:Extracellular Matrix Proteins; D012333:RNA, Messenger; D029867:Xenopus Proteins; D028341:Activins; C000607563:Pkdcc.1 protein, Xenopus; D011505:Protein-Tyrosine Kinases
keywords: Convergent extension; Dorsal and ventral marginal zone; Organizer; PKDCC1; RNA-seq