title: Asymmetrically reduced expression of hand1 homeologs involving a single nucleotide substitution in a cis-regulatory element.
abstract: During vertebrate evolution, whole genome duplications resulted in a number of duplicated genes, some of which eventually changed their expression patterns and/or levels via alteration of cis-regulatory sequences. However, the initial process involved in such cis-regulatory changes remains unclear. Therefore, we investigated this process by analyzing the duplicated hand1 genes of Xenopus laevis (hand1.L and hand1.S), which were generated by allotetraploidization 17-18 million years ago, and compared these with their single ortholog in the ancestral-type diploid species X. tropicalis. A dN/dS analysis indicated that hand1.L and hand1.S are still under purifying selection, and thus, their products appear to retain ancestral functional properties. RNA-seq and in situ hybridization analyses revealed that hand1.L and hand1.S have similar expression patterns to each other and to X. tropicalis hand1, but the hand1.S expression level was much lower than the hand1.L expression level in the primordial heart. A comparative sequence analysis, luciferase reporter analysis, ChIP-PCR analysis, and transgenic reporter analysis showed that a single nucleotide substitution in the hand1.S promoter was responsible for the reduced expression in the heart. These findings demonstrated that a small change in the promoter sequence can trigger diversification of duplicated gene expression prior to diversification of their encoded protein functions in a young duplicated genome.
authors.affiliation: Institute for Promotion of Medical Science Research, Yamagata University, Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan. Electronic address: harukiochi@med.id.yamagata-u.ac.jp.
authors.forename: Haruki
authors.initials: H
authors.lastname: Ochi
authors.affiliation: Institute for Promotion of Medical Science Research, Yamagata University, Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan. Electronic address: nanoka.s@med.id.yamagata-u.ac.jp.
authors.forename: Nanoka
authors.initials: N
authors.lastname: Suzuki
authors.affiliation: Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan. Electronic address: akane.kawaguchi@imp.ac.at.
authors.forename: Akane
authors.initials: A
authors.lastname: Kawaguchi
authors.affiliation: Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan; Amphibian Research Center, Hiroshima University, 1-3-1 Kagami-yama, Higashi-hiroshima, Hiroshima 739-8526, Japan. Electronic address: oginohaj@hiroshima-u.ac.jp.
authors.forename: Hajime
authors.initials: H
authors.lastname: Ogino
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030801:Animals, Genetically Modified; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000737:chemistry / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D004625:Embryo, Nonmammalian / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D017930:Genes, Reporter; D006801:Humans; D017403:In Situ Hybridization; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D026801:Synteny / Q000235:genetics; D014981:Xenopus / Q000196:embryology / Q000235:genetics*
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; C097341:helix-loop-helix protein, eHAND
keywords: Cis-regulatory element; Hand; Tetraploidization; Whole genome duplication; Xenopus laevis (X. laevis); Xenopus tropicalis (X. tropicalis)