title: Genome-wide network of regulatory genes for construction of a chordate embryo.
abstract: Animal development is controlled by gene regulation networks that are composed of sequence-specific transcription factors (TF) and cell signaling molecules (ST). Although housekeeping genes have been reported to show clustering in the animal genomes, whether the genes comprising a given regulatory network are physically clustered on a chromosome is uncertain. We examined this question in the present study. Ascidians are the closest living relatives of vertebrates, and their tadpole-type larva represents the basic body plan of chordates. The Ciona intestinalis genome contains 390 core TF genes and 119 major ST genes. Previous gene disruption assays led to the formulation of a basic chordate embryonic blueprint, based on over 3000 genetic interactions among 79 zygotic regulatory genes. Here, we mapped the regulatory genes, including all 79 regulatory genes, on the 14 pairs of Ciona chromosomes by fluorescent in situ hybridization (FISH). Chromosomal localization of upstream and downstream regulatory genes demonstrates that the components of coherent developmental gene networks are evenly distributed over the 14 chromosomes. Thus, this study provides the first comprehensive evidence that the physical clustering of regulatory genes, or their target genes, is not relevant for the genome-wide control of gene expression during development.
authors.affiliation: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan. eiichi@ascidian.zool.kyoto-u.ac.jp
authors.forename: Eiichi
authors.initials: E
authors.lastname: Shoguchi
authors.forename: Makoto
authors.initials: M
authors.lastname: Hamaguchi
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002938:Ciona intestinalis / Q000196:embryology / Q000235:genetics*; D003001:Cloning, Molecular; D019295:Computational Biology; D004625:Embryo, Nonmammalian / Q000502:physiology*; D005809:Genes, Regulator; D016678:Genome; D017404:In Situ Hybridization, Fluorescence; D008677:Metaphase; D015053:Zygote / Q000502:physiology