title: A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo.
abstract: Gene regulatory networks (GRNs) involve highly combinatorial interactions between transcription factors and short sequence motifs in cis-regulatory modules of target genes to control cellular phenotypes. The GRNs specifying most cell types are largely unknown and are the subject of wide interest. A catalog of transcription factors is a valuable tool toward obtaining a deeper understanding of the role of these critical effectors in any biological setting. Here we present a comprehensive catalog of the transcription factors for the diploid frog Xenopus tropicalis. We identify 1235 genes encoding DNA-binding transcription factors, comparable to the numbers found in typical mammalian species. In detail, the repertoire of X. tropicalis transcription factor genes is nearly identical to human and mouse, with the exception of zinc finger family members, and a small number of species/lineage-specific gene duplications and losses relative to the mammalian repertoires. We applied this resource to the identification of transcription factors differentially expressed in the early gastrula stage embryo. We find transcription factor enrichment in Spemann's organizer, the ventral mesoderm, ectoderm and endoderm, and report 218 TFs that show regionalized expression patterns at this stage. Many of these have not been previously reported as expressed in the early embryo, suggesting thus far unappreciated roles for many transcription factors in the GRNs regulating early development. We expect our transcription factor catalog will facilitate myriad studies using Xenopus as a model system to understand basic biology and human disease.
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States. Electronic address: ilblitz@uci.edu.
authors.forename: Ira L
authors.initials: IL
authors.lastname: Blitz
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
authors.forename: Kitt D
authors.initials: KD
authors.lastname: Paraiso
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
authors.forename: Ilya
authors.initials: I
authors.lastname: Patrushev
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
authors.forename: William T Y
authors.initials: WTY
authors.lastname: Chiu
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States. Electronic address: kwcho@uci.edu.
authors.forename: Ken W Y
authors.initials: KWY
authors.lastname: Cho
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK. Electronic address: mike.gilchrist@crick.ac.uk.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
mesh_terms: D000818:Animals; D001483:Base Sequence; D004625:Embryo, Nonmammalian / Q000378:metabolism; D005775:Gastrula / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D051379:Mice; D013045:Species Specificity; D014157:Transcription Factors / Q000096:biosynthesis* / Q000235:genetics; D014981:Xenopus / Q000196:embryology / Q000235:genetics / Q000378:metabolism*; D029867:Xenopus Proteins / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D014157:Transcription Factors; D029867:Xenopus Proteins
keywords: Ectoderm; Endoderm; Gastrulation; Gene regulatory networks; Mesoderm; Transcription factors