1
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Ochi H, Kato T, Zorn A, Hayashi T, Inoue T, Kondo M, Taira M, Michiue T. Versatile utilities of amphibians (part 5). Dev Growth Differ 2023; 65:459-460. [PMID: 37881023 DOI: 10.1111/dgd.12889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 10/27/2023]
Affiliation(s)
- Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Takashi Kato
- Molecular Physiology, Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | - Aaron Zorn
- Center for Stem Cell and Organoid Medicine, Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Toshinori Hayashi
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takeshi Inoue
- Faculty of Medicine, Tottori University, Yonago, Japan
| | - Mariko Kondo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Tatsuo Michiue
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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2
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Ogino H, Kamei Y, Hayashi T, Sakamoto J, Suzuki M, Igawa T, Kondo M, Taira M. Invention sharing is the mother of developmental biology (part 4). Dev Growth Differ 2023; 65:286-287. [PMID: 37610050 DOI: 10.1111/dgd.12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2023] [Indexed: 08/24/2023]
Affiliation(s)
- Hajime Ogino
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yasuhiro Kamei
- Optics and Bioimaging Facility, Trans-Scale Biology Center, National Institute for Basic Biology, Okazaki, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Joe Sakamoto
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Mariko Kondo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masanori Taira
- Faculty of Science and Engineering, Chuo University, Tokyo, Japan
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3
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Takahashi-Kanemitsu A, Lu M, Knight CT, Yamamoto T, Hayashi T, Mii Y, Ooki T, Kikuchi I, Kikuchi A, Barker N, Susaki EA, Taira M, Hatakeyama M. The Helicobacter pylori CagA oncoprotein disrupts Wnt/PCP signaling and promotes hyperproliferation of pyloric gland base cells. Sci Signal 2023; 16:eabp9020. [PMID: 37463245 DOI: 10.1126/scisignal.abp9020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/24/2023] [Indexed: 07/20/2023]
Abstract
Helicobacter pylori strains that deliver the oncoprotein CagA into gastric epithelial cells are the major etiologic agents of upper gastric diseases including gastric cancer. CagA promotes gastric carcinogenesis through interactions with multiple host proteins. Here, we show that CagA also disrupts Wnt-dependent planar cell polarity (Wnt/PCP), which orients cells within the plane of an epithelium and coordinates collective cell behaviors such as convergent extension to enable epithelial elongation during development. Ectopic expression of CagA in Xenopus laevis embryos impaired gastrulation, neural tube formation, and axis elongation, processes driven by convergent extension movements that depend on the Wnt/PCP pathway. Mice specifically expressing CagA in the stomach epithelium had longer pyloric glands and mislocalization of the tetraspanin proteins VANGL1 and VANGL2 (VANGL1/2), which are critical components of Wnt/PCP signaling. The increased pyloric gland length was due to hyperproliferation of cells at the gland base, where Lgr5+ stem and progenitor cells reside, and was associated with fewer differentiated enteroendocrine cells. In cultured human gastric epithelial cells, the N terminus of CagA interacted with the C-terminal cytoplasmic tails of VANGL1/2, which impaired Wnt/PCP signaling by inducing the mislocalization of VANGL1/2 from the plasma membrane to the cytoplasm. Thus, CagA may contribute to the development of gastric cancer by subverting a Wnt/PCP-dependent mechanism that restrains pyloric gland stem cell proliferation and promotes enteroendocrine differentiation.
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Affiliation(s)
- Atsushi Takahashi-Kanemitsu
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Mengxue Lu
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Christopher Takaya Knight
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Yamamoto
- Department of Biological Sciences, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yusuke Mii
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Takuya Ooki
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Ippei Kikuchi
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
| | - Nick Barker
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Division of Epithelial Stem Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa 924-1192, Japan
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Masanori Hatakeyama
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo 141-0021, Japan
- Research Center of Microbial Carcinogenesis, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan
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4
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Ochi H, Michiue T, Kato T, Zorn A, Hayashi T, Inoue T, Kondo M, Taira M. Versatile utilities of amphibians (part 4). Dev Growth Differ 2023; 65:4-5. [PMID: 36740732 DOI: 10.1111/dgd.12838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2023] [Indexed: 02/07/2023]
Affiliation(s)
- Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Tatsuo Michiue
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kato
- Molecular Physiology, Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | - Aaron Zorn
- Center for Stem Cell and Organoid Medicine, Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Toshinori Hayashi
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takeshi Inoue
- Faculty of Medicine, Tottori University, Yonago, Japan
| | - Mariko Kondo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
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5
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Michiue T, Kato T, Ochi H, Zorn A, Hayashi T, Inoue T, Kondo M, Taira M. Versatile utilities of amphibians (Part 3). Dev Growth Differ 2022; 64:472-473. [PMID: 36579413 DOI: 10.1111/dgd.12829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Tatsuo Michiue
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kato
- Molecular Physiology, Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Aaron Zorn
- Center for Stem Cell and Organoid Medicine, Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Toshinori Hayashi
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takeshi Inoue
- Faculty of Medicine, Tottori University, Yonago, Japan
| | - Mariko Kondo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
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6
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Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Rep 2022; 38:110364. [PMID: 35172134 PMCID: PMC8917868 DOI: 10.1016/j.celrep.2022.110364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 10/30/2021] [Accepted: 01/19/2022] [Indexed: 01/01/2023] Open
Abstract
Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data composed of more than two data types is challenging. Here, we use linked self-organizing maps to combine chromatin immunoprecipitation sequencing (ChIP-seq)/ATAC-seq with temporal, spatial, and perturbation RNA sequencing (RNA-seq) data from Xenopus tropicalis mesendoderm development to build a high-resolution genome scale mechanistic GRN. We recover both known and previously unsuspected TF-DNA/TF-TF interactions validated through reporter assays. Our analysis provides insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly dimensional multi-omic datasets.
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Affiliation(s)
- Camden Jansen
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Jeff J Zhou
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Margaret B Fish
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Rebekah M Charney
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jin Sun Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Norihiro Sudou
- Department of Anatomy, School of Medicine, Toho University, Tokyo, Japan
| | - Ann Rose Bright
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, the Netherlands
| | - Marcin Wlizla
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, the Netherlands
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Aaron M Zorn
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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7
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Matsuda S, Schaefer JV, Mii Y, Hori Y, Bieli D, Taira M, Plückthun A, Affolter M. Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nat Commun 2021; 12:6435. [PMID: 34750371 PMCID: PMC8576045 DOI: 10.1038/s41467-021-26726-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
How morphogen gradients control patterning and growth in developing tissues remains largely unknown due to lack of tools manipulating morphogen gradients. Here, we generate two membrane-tethered protein binders that manipulate different aspects of Decapentaplegic (Dpp), a morphogen required for overall patterning and growth of the Drosophila wing. One is "HA trap" based on a single-chain variable fragment (scFv) against the HA tag that traps HA-Dpp to mainly block its dispersal, the other is "Dpp trap" based on a Designed Ankyrin Repeat Protein (DARPin) against Dpp that traps Dpp to block both its dispersal and signaling. Using these tools, we found that, while posterior patterning and growth require Dpp dispersal, anterior patterning and growth largely proceed without Dpp dispersal. We show that dpp transcriptional refinement from an initially uniform to a localized expression and persistent signaling in transient dpp source cells render the anterior compartment robust against the absence of Dpp dispersal. Furthermore, despite a critical requirement of dpp for the overall wing growth, neither Dpp dispersal nor direct signaling is critical for lateral wing growth after wing pouch specification. These results challenge the long-standing dogma that Dpp dispersal is strictly required to control and coordinate overall wing patterning and growth.
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Affiliation(s)
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Yusuke Mii
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- JST PRESTO, Kawaguchi, Saitama, Japan
| | - Yutaro Hori
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | | | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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8
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Kuretani A, Yamamoto T, Taira M, Michiue T. Evolution of hes gene family in vertebrates: the hes5 cluster genes have specifically increased in frogs. BMC Ecol Evol 2021; 21:147. [PMID: 34325655 PMCID: PMC8320183 DOI: 10.1186/s12862-021-01879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/08/2021] [Indexed: 11/29/2022] Open
Abstract
Background hes genes are chordate homologs of Drosophila genes, hairy and enhancer of split, which encode a basic helix-loop-helix (bHLH) transcriptional repressor with a WRPW motif. Various developmental functions of hes genes, including early embryogenesis and neurogenesis, have been elucidated in vertebrates. However, their orthologous relationships remain unclear partly because of less conservation of relatively short amino acid sequences, the fact that the genome was not analyzed as it is today, and species-specific genome duplication. This results in complicated gene names in vertebrates, which are not consistent in orthologs. We previously revealed that Xenopus frogs have two clusters of hes5, named “the hes5.1 cluster” and “the hes5.3 cluster”, but the origin and the conservation have not yet been revealed. Results Here, we elucidated the orthologous and paralogous relationships of all hes genes of human, mouse, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark and three species of frogs, Xenopus tropicalis (X. tropicalis), X. laevis, Nanorana parkeri, by phylogenetic and synteny analyses. Any duplicated hes5 were not found in mammals, whereas hes5 clusters in teleost were conserved although not as many genes as the three frog species. In addition, hes5 cluster-like structure was found in the elephant shark genome, but not found in cyclostomata. Conclusion These data suggest that the hes5 cluster existed in the gnathostome ancestor but became a single gene in mammals. The number of hes5 cluster genes were specifically large in frogs. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01879-6.
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Affiliation(s)
- Aya Kuretani
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayoshi Yamamoto
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Masanori Taira
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Tatsuo Michiue
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
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9
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Abstract
The field of molecular embryology started around 1990 by identifying new genes and analyzing their functions in early vertebrate embryogenesis. Those genes encode transcription factors, signaling molecules, their regulators, etc. Most of those genes are relatively highly expressed in specific regions or exhibit dramatic phenotypes when ectopically expressed or mutated. This review focuses on one of those genes, Lim1/Lhx1, which encodes a transcription factor. Lim1/Lhx1 is a member of the LIM homeodomain (LIM-HD) protein family, and its intimate partner, Ldb1/NLI, binds to two tandem LIM domains of LIM-HDs. The most ancient LIM-HD protein and its partnership with Ldb1 were innovated in the metazoan ancestor by gene fusion combining LIM domains and a homeodomain and by creating the LIM domain-interacting domain (LID) in ancestral Ldb, respectively. The LIM domain has multiple interacting interphases, and Ldb1 has a dimerization domain (DD), the LID, and other interacting domains that bind to Ssbp2/3/4 and the boundary factor, CTCF. By means of these domains, LIM-HD-Ldb1 functions as a hub protein complex, enabling more intricate and elaborate gene regulation. The common, ancestral role of LIM-HD proteins is neuron cell-type specification. Additionally, Lim1/Lhx1 serves crucial roles in the gastrula organizer and in kidney development. Recent studies using Xenopus embryos have revealed Lim1/Lhx1 functions and regulatory mechanisms during development and regeneration, providing insight into evolutionary developmental biology, functional genomics, gene regulatory networks, and regenerative medicine. In this review, we also discuss recent progress at unraveling participation of Ldb1, Ssbp, and CTCF in enhanceosomes, long-distance enhancer-promoter interactions, and trans-interactions between chromosomes.
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Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.
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10
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Mii Y, Nakazato K, Pack CG, Ikeda T, Sako Y, Mochizuki A, Taira M, Takada S. Quantitative analyses reveal extracellular dynamics of Wnt ligands in Xenopus embryos. eLife 2021; 10:55108. [PMID: 33904408 PMCID: PMC8139832 DOI: 10.7554/elife.55108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
The mechanism of intercellular transport of Wnt ligands is still a matter of debate. To better understand this issue, we examined the distribution and dynamics of Wnt8 in Xenopus embryos. While Venus-tagged Wnt8 was found on the surfaces of cells close to Wnt-producing cells, we also detected its dispersal over distances of 15 cell diameters. A combination of fluorescence correlation spectroscopy and quantitative imaging suggested that only a small proportion of Wnt8 ligands diffuses freely, whereas most Wnt8 molecules are bound to cell surfaces. Fluorescence decay after photoconversion showed that Wnt8 ligands bound on cell surfaces decrease exponentially, suggesting a dynamic exchange of bound forms of Wnt ligands. Mathematical modeling based on this exchange recapitulates a graded distribution of bound, but not free, Wnt ligands. Based on these results, we propose that Wnt distribution in tissues is controlled by a dynamic exchange of its abundant bound and rare free populations.
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Affiliation(s)
- Yusuke Mii
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Japan Science and Technology Agency (JST), PRESTO, Kawaguchi, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | - Chan-Gi Pack
- Cellular Informatics Laboratory, RIKEN, Wako, Japan.,ASAN Institute for Life Sciences, ASAN Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Takafumi Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, Wako, Japan
| | - Atsushi Mochizuki
- Theoretical Biology Laboratory, RIKEN, Wako, Japan.,Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Shinji Takada
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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11
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Hasegawa M, Taira M, Kanaya T, Araki K, Watanabe T, Tominaga Y, Kugo Y, Ishida H, Narita A, Ueno T, Ueno T, Sawa Y. Clinical Outcomes for Children with Left Ventricular Noncompaction and Cardiomyopathy. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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12
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Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho KWY. Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. Cell Rep 2020; 27:2962-2977.e5. [PMID: 31167141 PMCID: PMC6610736 DOI: 10.1016/j.celrep.2019.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/30/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Elucidation of the sequence of events underlying the dynamic interaction
between transcription factors and chromatin states is essential. Maternal
transcription factors function at the top of the regulatory hierarchy to specify
the primary germ layers at the onset of zygotic genome activation (ZGA). We
focus on the formation of endoderm progenitor cells and examine the interactions
between maternal transcription factors and chromatin state changes underlying
the cell specification process. Endoderm-specific factors Otx1 and Vegt together
with Foxh1 orchestrate endoderm formation by coordinated binding to select
regulatory regions. These interactions occur before the deposition of enhancer
histone marks around the regulatory regions, and these TFs recruit RNA
polymerase II, regulate enhancer activity, and establish super-enhancers
associated with important endodermal genes. Therefore, maternal transcription
factors Otx1, Vegt, and Foxh1 combinatorially regulate the activity of
super-enhancers, which in turn activate key lineage-specifying genes during
ZGA. How do maternal transcription factors interact with chromatin regions to
coordinate the endodermal gene regulatory program? Paraiso et al. demonstrate
that combinatorial binding of maternal Otx1, Vegt, and Foxh1 to select enhancers
and super-enhancers in the genome controls endodermal cell fate specification
during zygotic gene activation.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Masani Coley
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Norihiro Sudou
- Department of Anatomy, Tokyo Women's Medical University, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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13
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Kondo M, Matsuo M, Igarashi K, Haramoto Y, Yamamoto T, Yasuoka Y, Taira M. De novo transcription of multiple Hox cluster genes takes place simultaneously in early Xenopus tropicalis embryos. Biol Open 2019; 8:bio.038422. [PMID: 30651235 PMCID: PMC6451350 DOI: 10.1242/bio.038422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
hox genes are found as clusters in the genome in most bilaterians. The order of genes in the cluster is supposed to be correlated with the site of expression along the anterior-posterior body axis and the timing of expression during development, and these correlations are called spatial and temporal collinearity, respectively. Here we studied the expression dynamics of all hox genes of the diploid species Xenopus tropicalis in four Hox clusters (A–D) by analyzing high-temporal-resolution RNA-seq databases and the results showed that temporal collinearity is not supported, which is consistent with our previous data from allotetraploid Xenopuslaevis. Because the temporal collinearity hypothesis implicitly assumes the collinear order of gene activation, not mRNA accumulation, we determined for the first time the timing of when new transcripts of hox genes are produced, by detecting pre-spliced RNA in whole embryos with reverse transcription and quantitative PCR (RT-qPCR) for all hoxa genes as well as several selected hoxb, hoxc and hoxd genes. Our analyses showed that, coinciding with the RNA-seq results, hoxa genes started to be transcribed in a non-sequential order, and found that multiple genes start expression almost simultaneously or more posterior genes could be expressed earlier than anterior ones. This tendency was also found in hoxb and hoxc genes. These results suggest that temporal collinearity of hox genes is not held during early development of Xenopus. Summary: qPCR analysis for de novo transcription of hox genes suggest that temporal collinearity is not held for all hox genes during early development of Xenopus tropicalis.
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Affiliation(s)
- Mariko Kondo
- Misaki Marine Biological Station, Graduate School of Science and Center for Marine Biology, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
| | - Megumi Matsuo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kento Igarashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Takayoshi Yamamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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14
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Yasuoka Y, Taira M. Microinjection of DNA Constructs into Xenopus Embryos for Gene Misexpression and cis-Regulatory Module Analysis. Cold Spring Harb Protoc 2019; 2019:pdb.prot097279. [PMID: 30131366 DOI: 10.1101/pdb.prot097279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introducing exogenous DNA into an embryo can promote misexpression of a gene of interest via transcription regulated by an attached enhancer-promoter. This protocol describes plasmid DNA microinjection into Xenopus embryos for misexpression of genes after zygotic gene expression begins. It also describes a method for coinjecting a reporter plasmid with mRNA or antisense morpholinos to perform luciferase reporter assays, which are useful for quantitative analysis of cis-regulatory sequences responding to endogenous or exogenous stimuli in embryos.
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Affiliation(s)
- Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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15
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Yasuoka Y, Tando Y, Kubokawa K, Taira M. Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. Zoological Lett 2019; 5:27. [PMID: 31388442 PMCID: PMC6679436 DOI: 10.1186/s40851-019-0143-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/12/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated. RESULTS To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5' upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5' upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5' region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos. CONCLUSIONS On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5' upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate.
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Affiliation(s)
- Yuuri Yasuoka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yukiko Tando
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Kaoru Kubokawa
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: SIRC, Teikyo University, 2-11-1, Itabashi-ku, Tokyo, 173-8605 Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present address: Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551 Japan
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16
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Narita J, Kogaki S, Ishigaki S, Torigoe F, Ishii R, Ishida H, Ozono K, Taira M, Ueno T, Sawa Y. Prolonged but Successful Weaning from Berlin Heart EXCOR After a Long-term Mechanical Unloading in Infantile DCM. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.1058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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17
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Taira M, Ueno T, Kido T, Kanaya T, Okuda N, Matsunaga Y, Toda K, Kuratani T, Sawa Y. Long Term Results of Mechanical Circulatory Support as Bridge to Transplant in Severe Heart Failure Pediatric Patients. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.1057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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18
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Satou Y, Minami K, Hosono E, Okada H, Yasuoka Y, Shibano T, Tanaka T, Taira M. Phosphorylation states change Otx2 activity for cell proliferation and patterning in the Xenopus embryo. Development 2018; 145:dev.159640. [PMID: 29440302 DOI: 10.1242/dev.159640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/01/2018] [Indexed: 12/19/2022]
Abstract
The homeodomain transcription factor Otx2 has essential roles in head and eye formation via the negative and positive regulation of its target genes, but it remains elusive how this dual activity of Otx2 affects cellular functions. In the current study, we first demonstrated that both exogenous and endogenous Otx2 are phosphorylated at multiple sites. Using Xenopus embryos, we identified three possible cyclin-dependent kinase (Cdk) sites and one Akt site, and analyzed the biological activities of phosphomimetic (4E) and nonphosphorylatable (4A) mutants for those sites. In the neuroectoderm, the 4E but not the 4A mutant downregulated the Cdk inhibitor gene p27xic1 (cdknx) and posterior genes, and promoted cell proliferation, possibly forming a positive-feedback loop consisting of Cdk, Otx2 and p27xic1 for cell proliferation, together with anteriorization. Conversely, the 4A mutant functioned as an activator on its own and upregulated the expression of eye marker genes, resulting in enlarged eyes. Consistent with these results, the interaction of Otx2 with the corepressor Tle1 is suggested to be phosphorylation dependent. These data suggest that Otx2 orchestrates cell proliferation, anteroposterior patterning and eye formation via its phosphorylation state.
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Affiliation(s)
- Yumeko Satou
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kohei Minami
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Erina Hosono
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hajime Okada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuuri Yasuoka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Takashi Shibano
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiaki Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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19
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DeLay BD, Corkins ME, Hanania HL, Salanga M, Deng JM, Sudou N, Taira M, Horb ME, Miller RK. Tissue-Specific Gene Inactivation in Xenopus laevis: Knockout of lhx1 in the Kidney with CRISPR/Cas9. Genetics 2018; 208:673-686. [PMID: 29187504 PMCID: PMC5788530 DOI: 10.1534/genetics.117.300468] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/18/2017] [Indexed: 11/18/2022] Open
Abstract
Studying genes involved in organogenesis is often difficult because many of these genes are also essential for early development. The allotetraploid frog, Xenopus laevis, is commonly used to study developmental processes, but because of the presence of two homeologs for many genes, it has been difficult to use as a genetic model. Few studies have successfully used CRISPR in amphibians, and currently there is no tissue-targeted knockout strategy described in Xenopus The goal of this study is to determine whether CRISPR/Cas9-mediated gene knockout can be targeted to the Xenopus kidney without perturbing essential early gene function. We demonstrate that targeting CRISPR gene editing to the kidney and the eye of F0 embryos is feasible. Our study shows that knockout of both homeologs of lhx1 results in the disruption of kidney development and function but does not lead to early developmental defects. Therefore, targeting of CRISPR to the kidney may not be necessary to bypass the early developmental defects reported upon disruption of Lhx1 protein expression or function by morpholinos, antisense RNA, or dominant negative constructs. We also establish a control for CRISPR in Xenopus by editing a gene (slc45a2) that when knocked out results in albinism without altering kidney development. This study establishes the feasibility of tissue-specific gene knockout in Xenopus, providing a cost-effective and efficient method for assessing the roles of genes implicated in developmental abnormalities that is amenable to high-throughput gene or drug screening techniques.
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Affiliation(s)
- Bridget D DeLay
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030
| | - Mark E Corkins
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030
| | - Hannah L Hanania
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030
- Program in Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
| | - Matthew Salanga
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, Massachusetts 02543
| | - Jian Min Deng
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Norihiro Sudou
- Department of Anatomy, School of Medicine, Tokyo Women's Medical University, 162-8666, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 113-8654, Japan
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, Massachusetts 02543
| | - Rachel K Miller
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, Texas 77030
- Program in Biochemistry and Cell Biology, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, Texas 77030
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20
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Mii Y, Yamamoto T, Takada R, Mizumoto S, Matsuyama M, Yamada S, Takada S, Taira M. Roles of two types of heparan sulfate clusters in Wnt distribution and signaling in Xenopus. Nat Commun 2017; 8:1973. [PMID: 29215008 PMCID: PMC5719454 DOI: 10.1038/s41467-017-02076-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
Wnt proteins direct embryonic patterning, but the regulatory basis of their distribution and signal reception remain unclear. Here, we show that endogenous Wnt8 protein is distributed in a graded manner in Xenopus embryo and accumulated on the cell surface in a punctate manner in association with “N-sulfo-rich heparan sulfate (HS),” not with “N-acetyl-rich HS”. These two types of HS are differentially clustered by attaching to different glypicans as core proteins. N-sulfo-rich HS is frequently internalized and associated with the signaling vesicle, known as the Frizzled/Wnt/LRP6 signalosome, in the presence of Wnt8. Conversely, N-acetyl-rich HS is rarely internalized and accumulates Frzb, a secreted Wnt antagonist. Upon interaction with Frzb, Wnt8 associates with N-acetyl-rich HS, suggesting that N-acetyl-rich HS supports Frzb-mediated antagonism by sequestering Wnt8 from N-sulfo-rich HS. Thus, these two types of HS clusters may constitute a cellular platform for the distribution and signaling of Wnt8. Wnt proteins mediate embryonic development but how protein localization and patterning is regulated is unclear. Here, the authors show that distinct structures with different heparan sulfate modifications (‘N-sulfo-rich’ and ‘N-acetyl-rich’) regulate cellular localization and signal transduction of Wnt8 in Xenopus.
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Affiliation(s)
- Yusuke Mii
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,National Institute for Basic Biology and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, 444-8787, Japan
| | - Takayoshi Yamamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ritsuko Takada
- National Institute for Basic Biology and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi, 468-8503, Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama, 701-0202, Japan
| | - Shuhei Yamada
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi, 468-8503, Japan
| | - Shinji Takada
- National Institute for Basic Biology and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan. .,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, 444-8787, Japan.
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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21
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Kondo M, Yamamoto T, Takahashi S, Taira M. Comprehensive analyses ofhoxgene expression inXenopus laevisembryos and adult tissues. Dev Growth Differ 2017; 59:526-539. [DOI: 10.1111/dgd.12382] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/29/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Mariko Kondo
- Misaki Marine Biological Station; Graduate School of Science and Center for Marine Biology; The University of Tokyo; 1024 Koajiro Misaki Miura Kanagawa 238-0225 Japan
| | - Takayoshi Yamamoto
- Department of Biological Sciences; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shuji Takahashi
- Institute for Amphibian Biology; Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Masanori Taira
- Department of Biological Sciences; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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22
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Inamochi Y, Fueki K, Usui N, Taira M, Wakabayashi N. Adaptive change in chewing-related brain activity while wearing a palatal plate: an functional magnetic resonance imaging study. J Oral Rehabil 2017. [DOI: 10.1111/joor.12541] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Y. Inamochi
- Removable Partial Prosthodontics; Department of Masticatory Function Rehabilitation; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - K. Fueki
- Removable Partial Prosthodontics; Department of Masticatory Function Rehabilitation; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - N. Usui
- Department of Cognitive Neurobiology; The Center for Brain Integration Research; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - M. Taira
- Department of Cognitive Neurobiology; The Center for Brain Integration Research; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - N. Wakabayashi
- Removable Partial Prosthodontics; Department of Masticatory Function Rehabilitation; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
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23
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Suzuki A, Uno Y, Takahashi S, Grimwood J, Schmutz J, Mawaribuchi S, Yoshida H, Takebayashi-Suzuki K, Ito M, Matsuda Y, Rokhsar D, Taira M. Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Dev Biol 2017; 426:236-244. [PMID: 27720224 DOI: 10.1016/j.ydbio.2016.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 01/21/2023]
Abstract
Extracellular factors belonging to the TGF-β family play pivotal roles in the formation and patterning of germ layers during early Xenopus embryogenesis. Here, we show that the vg1 and nodal3 genes of Xenopus laevis are present in gene clusters on chromosomes XLA1L and XLA3L, respectively, and that both gene clusters have been completely lost from the syntenic S chromosome regions. The presence of gene clusters and chromosome-specific gene loss were confirmed by cDNA FISH analyses. Sequence and expression analyses revealed that paralogous genes in the vg1 and nodal3 clusters on the L chromosomes were also altered compared to their Xenopus tropicalis orthologs. X. laevis vg1 and nodal3 paralogs have potentially become pseudogenes or sub-functionalized genes and are expressed at different levels. As X. tropicalis has a single vg1 gene on chromosome XTR1, the ancestral vg1 gene in X. laevis appears to have been expanded on XLA1L. Of note, two reported vg1 genes, vg1(S20) and vg1(P20), reside in the cluster on XLA1L. The nodal3 gene cluster is also present on X. tropicalis chromosome XTR3, but phylogenetic analysis indicates that nodal3 genes in X. laevis and X. tropicalis were independently expanded and/or evolved in concert within each cluster by gene conversion. These findings provide insights into the function and molecular evolution of TGF-β family genes in response to allotetraploidization.
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Affiliation(s)
- Atsushi Suzuki
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Yoshinobu Uno
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Shuji Takahashi
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Shuuji Mawaribuchi
- School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku, Sagamihara 252-0373, Japan
| | - Hitoshi Yoshida
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Kimiko Takebayashi-Suzuki
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Michihiko Ito
- School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku, Sagamihara 252-0373, Japan
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Daniel Rokhsar
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, CA 94720-3200, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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24
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Tanaka T, Ochi H, Takahashi S, Ueno N, Taira M. Genes coding for cyclin-dependent kinase inhibitors are fragile in Xenopus. Dev Biol 2017; 426:291-300. [PMID: 27393661 DOI: 10.1016/j.ydbio.2016.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/16/2016] [Accepted: 06/16/2016] [Indexed: 11/27/2022]
Abstract
Cell proliferation is strictly regulated by the dosage balance among cell-cycle regulators such as CDK/cyclin complexes and CDK-Inhibitors. Even in the allotetraploid genome of Xenopus laevis, the dosage balance must be maintained for animals to stay alive, and the duplicated homeologous genes seem to have gradually changed, through evolution, resulting in the best genes for them to thrive. In the Xenopus laevis genome, while homeologous gene pairs of CDKs are fundamentally maintained and a few cyclin genes are amplified, homeologous gene pairs of the important CDK-Inhibitors, CDKn1c and CDKn2a, are deleted from chromosomes L and S. Although losses of CDKn1c and CDKn2a can lead to diseases in humans, their loss in X. laevis does not affect the animals' health. Also, another gene coding CDKn1b is lost besides CDKn1c and CDKn2a in the genome of Xenopus tropicalis. These findings suggest a high resistance of Xenopus to diseases. We also found that CDKn2c.S expression is higher than that of CDKn2c.L, and a conserved noncoding sequence (CNS) of CDKn2c genomic loci on X. laevis chromosome S and X. tropicalis has an enhancement activity in regulating the different expression. These findings together indicate a surprising fragility of CDK inhibitor gene loci in the Xenopus genome in spite of their importance, and may suggest that factors other than CDK-inhibitors decelerate cell-cycling in Xenopus.
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Affiliation(s)
- Toshiaki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan
| | - Shuji Takahashi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Naoto Ueno
- National Institute for Basic Biology, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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25
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Michiue T, Yamamoto T, Yasuoka Y, Goto T, Ikeda T, Nagura K, Nakayama T, Taira M, Kinoshita T. High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis. Dev Biol 2017; 426:270-290. [DOI: 10.1016/j.ydbio.2016.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
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26
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Watanabe M, Yasuoka Y, Mawaribuchi S, Kuretani A, Ito M, Kondo M, Ochi H, Ogino H, Fukui A, Taira M, Kinoshita T. Conservatism and variability of gene expression profiles among homeologous transcription factors in Xenopus laevis. Dev Biol 2017; 426:301-324. [DOI: 10.1016/j.ydbio.2016.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 07/27/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
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27
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Suzuki A, Yoshida H, van Heeringen SJ, Takebayashi-Suzuki K, Veenstra GJC, Taira M. Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis. Dev Biol 2017; 426:336-359. [DOI: 10.1016/j.ydbio.2016.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/10/2016] [Accepted: 09/19/2016] [Indexed: 12/13/2022]
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28
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Mawaribuchi S, Takahashi S, Wada M, Uno Y, Matsuda Y, Kondo M, Fukui A, Takamatsu N, Taira M, Ito M. Sex chromosome differentiation and the W- and Z-specific loci in Xenopus laevis. Dev Biol 2017; 426:393-400. [DOI: 10.1016/j.ydbio.2016.06.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/09/2016] [Accepted: 06/09/2016] [Indexed: 12/22/2022]
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29
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Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KWY. Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program. Dev Cell 2017; 40:595-607.e4. [PMID: 28325473 PMCID: PMC5434453 DOI: 10.1016/j.devcel.2017.02.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/24/2016] [Accepted: 02/16/2017] [Indexed: 12/14/2022]
Abstract
The interplay between transcription factors and chromatin dictates gene regulatory network activity. Germ layer specification is tightly coupled with zygotic gene activation and, in most metazoans, is dependent upon maternal factors. We explore the dynamic genome-wide interactions of Foxh1, a maternal transcription factor that mediates Nodal/TGF-β signaling, with cis-regulatory modules (CRMs) during mesendodermal specification. Foxh1 marks CRMs during cleavage stages and recruits the co-repressor Tle/Groucho in the early blastula. We highlight a population of CRMs that are continuously occupied by Foxh1 and show that they are marked by H3K4me1, Ep300, and Fox/Sox/Smad motifs, suggesting interplay between these factors in gene regulation. We also propose a molecular "hand-off" between maternal Foxh1 and zygotic Foxa at these CRMs to maintain enhancer activation. Our findings suggest that Foxh1 functions at the top of a hierarchy of interactions by marking developmental genes for activation, beginning with the onset of zygotic gene expression.
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Affiliation(s)
- Rebekah M Charney
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Elmira Forouzmand
- Department of Computer Science, Donald Bren School of Information & Computer Sciences, University of California, Irvine, CA 92697, USA
| | - Jin Sun Cho
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Shuji Takahashi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8526, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ira L Blitz
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Xiaohui Xie
- Department of Computer Science, Donald Bren School of Information & Computer Sciences, University of California, Irvine, CA 92697, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA.
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30
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Shinagawa H, Ono T, Honda E, Sasaki T, Taira M, Iriki A, Kuroda T, Ohyama K. Chewing-side Preference is Involved in Differential Cortical Activation Patterns during Tongue Movements after Bilateral Gum-chewing: a Functional Magnetic Resonance Imaging Study. J Dent Res 2016; 83:762-6. [PMID: 15381715 DOI: 10.1177/154405910408301005] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Contralateral dominance in the activation of the primary sensorimotor cortex (S1/M1) during tongue movements (TMs) has been shown to be associated with a chewing-side preference (CSP). However, little is known about its interaction with chewing-related cortical activation. Functional magnetic resonance imaging was performed before and after gum-chewing in six subjects who exhibited a left CSP to determine the relationship between the CSP and activation patterns in the S1/M1 during TMs. Before the subjects chewed the gum, activation foci were found in the bilateral S1/M1. In the left hemisphere, both signal intensity and the area of activation significantly increased during TMs within 10 min after subjects chewed gum. Moreover, this augmented activation significantly decreased within 20 min during tongue protrusion and leftward movement. In the right hemisphere, there were no marked changes during TMs. These results suggest that bilateral gum-chewing enhances activation of the S1/M1 ipsilateral to the CSP during TMs.
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Affiliation(s)
- H Shinagawa
- Department of Oral/Maxillofacial Radiology, The University of Tokushima, Tokushima 770-8503, Japan.
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31
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Suzuki KIT, Suzuki M, Shigeta M, Fortriede JD, Takahashi S, Mawaribuchi S, Yamamoto T, Taira M, Fukui A. Clustered Xenopus keratin genes: A genomic, transcriptomic, and proteomic analysis. Dev Biol 2016; 426:384-392. [PMID: 27842699 DOI: 10.1016/j.ydbio.2016.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 01/21/2023]
Abstract
Keratin genes belong to the intermediate filament superfamily and their expression is altered following morphological and physiological changes in vertebrate epithelial cells. Keratin genes are divided into two groups, type I and II, and are clustered on vertebrate genomes, including those of Xenopus species. Various keratin genes have been identified and characterized by their unique expression patterns throughout ontogeny in Xenopus laevis; however, compilation of previously reported and newly identified keratin genes in two Xenopus species is required for our further understanding of keratin gene evolution, not only in amphibians but also in all terrestrial vertebrates. In this study, 120 putative type I and II keratin genes in total were identified based on the genome data from two Xenopus species. We revealed that most of these genes are highly clustered on two homeologous chromosomes, XLA9_10 and XLA2 in X. laevis, and XTR10 and XTR2 in X. tropicalis, which are orthologous to those of human, showing conserved synteny among tetrapods. RNA-Seq data from various embryonic stages and adult tissues highlighted the unique expression profiles of orthologous and homeologous keratin genes in developmental stage- and tissue-specific manners. Moreover, we identified dozens of epidermal keratin proteins from the whole embryo, larval skin, tail, and adult skin using shotgun proteomics. In light of our results, we discuss the radiation, diversification, and unique expression of the clustered keratin genes, which are closely related to epidermal development and terrestrial adaptation during amphibian evolution, including Xenopus speciation.
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Affiliation(s)
- Ken-Ichi T Suzuki
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Miyuki Suzuki
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mitsuki Shigeta
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Shuji Takahashi
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Shuuji Mawaribuchi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takashi Yamamoto
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akimasa Fukui
- Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Sapporo 060-0810, Japan.
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32
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Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJC, Fujiyama A, Harland RM, Taira M, Rokhsar DS. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 2016; 538:336-343. [PMID: 27762356 PMCID: PMC5313049 DOI: 10.1038/nature19840] [Citation(s) in RCA: 621] [Impact Index Per Article: 77.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 09/09/2016] [Indexed: 02/07/2023]
Abstract
To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We demonstrate the allotetraploid origin of X. laevis by partitioning its genome into two homeologous subgenomes, marked by distinct families of “fossil” transposable elements. Based on the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged ~34 million years ago (Mya) and combined to form an allotetraploid ~17–18 Mya. 56% of all genes are retained in two homeologous copies. Protein function, gene expression, and the amount of flanking conserved sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
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Affiliation(s)
- Adam M Session
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Yoshinobu Uno
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Taejoon Kwon
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Jarrod A Chapman
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Atsushi Toyoda
- Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Shuji Takahashi
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Akimasa Fukui
- Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Hikosaka
- Division of Human Sciences, Graduate School of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Atsushi Suzuki
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mariko Kondo
- Misaki Marine Biological Station (MMBS), Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Simon J van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Ian Quigley
- Salk Institute, Molecular Neurobiology Laboratory, La Jolla, San Diego, California 92037, USA
| | - Sven Heinz
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, San Diego, California 92037, USA
| | - Hajime Ogino
- Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan
| | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jessica B Lyons
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | | | | | - Yoko Kuroki
- Department of Genome Medicine, National Research Institute for Child Health and Development, NCCHD, 2-10-1, Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Toshiaki Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Minoru Watanabe
- Institute of Institution of Liberal Arts and Fundamental Education, Tokushima University, 1-1 Minamijosanjima-cho, Tokushima 770-8502, Japan
| | - Ozren Bogdanovic
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Georgios Georgiou
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Sarita S Paranjpe
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Ila van Kruijsbergen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Shengquiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Joseph Carlson
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Tsutomu Kinoshita
- Department of Life Science, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, 655 W Baltimore St, Baltimore, Maryland 21201, USA
| | - Shuuji Mawaribuchi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, Tokyo 108-8641, Japan
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Therese Mitros
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Sahar V Mozaffari
- Department of Human Genetics, University of Chicago, 920 E. 58th St, CLSC 431F, Chicago, Illinois 60637, USA
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568, Japan
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Takamasa S Yamamoto
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Chiyo Takagi
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Rebecca Heald
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley California 94720-3200, USA
| | - Kelly Miller
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley California 94720-3200, USA
| | | | - Jacob Kitzman
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle Washington 98195-5065, USA
| | - Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Yumi Izutsu
- Department of Biology, Faculty of Science, Niigata University, 8050, Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Jacques Robert
- Department of Microbiology &Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Joshua Fortriede
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Kevin Burns
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Darwin S Dichmann
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, 655 W Baltimore St, Baltimore, Maryland 21201, USA
| | - Douglas W Houston
- The University of Iowa, Department of Biology, 257 Biology Building, Iowa City, Iowa 52242-1324, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle Washington 98195-5065, USA
| | - Louis DuPasquier
- Department of Zoology and Evolutionary Biology, University of Basel, Basel CH-4051, Switzerland
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Michihiko Ito
- Department of Biological Sciences, School of Science, Kitasato University, 1-15-1 Minamiku, Sagamihara, Kanagawa 252-0373, Japan
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Makoto Asashima
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Naoto Ueno
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Gert Jan C Veenstra
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Asao Fujiyama
- Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Principles of Informatics, National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan.,Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizoka 411-8540, Japan
| | - Richard M Harland
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daniel S Rokhsar
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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Shinozaki T, Imamura Y, Kohashi R, Dezawa K, Nakaya Y, Sato Y, Watanabe K, Morimoto Y, Shizukuishi T, Abe O, Haji T, Tabei K, Taira M. Spatial and Temporal Brain Responses to Noxious Heat Thermal Stimuli in Burning Mouth Syndrome. J Dent Res 2016; 95:1138-46. [DOI: 10.1177/0022034516653580] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Burning mouth syndrome (BMS) is an idiopathic orofacial pain condition. Although the pathophysiology of BMS is not clearly understood, central and peripheral neuropathic mechanisms are thought to be involved. The authors compared brain response to noxious heat stimuli in 16 right-handed women with primary BMS and 15 sex- and age-matched right-handed healthy female controls. A thermal stimulus sequence of 32 °C to 40 °C to 32 °C to 49 °C was repeated 4 times in a cycle. Warm and noxious heat stimuli were delivered with a Peltier thermode placed on the right palm or right lower lip for 32 s each in a session. Functional magnetic resonance imaging data were obtained by recording echoplanar images with a block design. Statistical Parametric Mapping 8 software was used to analyze the data. Patients and controls both reported feeling more pain during palm stimulation than during lip stimulation. Repetition of noxious heat stimulus on the lower lip but not on the palm induced habituation in brain activity in the cingulate cortex without reduction in pain perception. Multiple regression analysis revealed a correlation between perceived pain intensity and suppression of brain activity in the anterior cingulate cortex when the repeated thermal sequence was applied at the lower lip. Furthermore, the response of the parahippocampal area differed in BMS patients and controls when the same repeated thermal sequence was applied at the palm. The authors’ findings indicate that BMS patients show specific brain responses due to impaired function of the central and peripheral nervous systems (clinical trial registration: UMIN000015002).
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Affiliation(s)
- T. Shinozaki
- Department of Oral Diagnostic Sciences, Nihon University School of Dentistry, Tokyo, Japan
- Clinical Research Division, Nihon University Dental Research Center, Tokyo, Japan
| | - Y. Imamura
- Department of Oral Diagnostic Sciences, Nihon University School of Dentistry, Tokyo, Japan
- Clinical Research Division, Nihon University Dental Research Center, Tokyo, Japan
| | - R. Kohashi
- Department of Oral Diagnostic Sciences, Nihon University School of Dentistry, Tokyo, Japan
| | - K. Dezawa
- Department of Oral Diagnostic Sciences, Nihon University School of Dentistry, Tokyo, Japan
| | - Y. Nakaya
- Department of Oral Diagnostic Sciences, Nihon University School of Dentistry, Tokyo, Japan
| | - Y. Sato
- Department of Oral Diagnostic Sciences, Nihon University School of Dentistry, Tokyo, Japan
| | - K. Watanabe
- Department of Oral Diagnostic Sciences, Nihon University School of Dentistry, Tokyo, Japan
| | - Y. Morimoto
- Division of Oral and Maxillofacial Radiology, Kyushu Dental University, Kitakyushu, Japan
| | - T. Shizukuishi
- Department of Radiology, Nihon University School of Medicine, Tokyo, Japan
| | - O. Abe
- Department of Radiology, Nihon University School of Medicine, Tokyo, Japan
| | - T. Haji
- Brain Activity Imaging Center, ATR-Promotions Inc., Osaka, Japan
| | - K. Tabei
- Department of Dementia Prevention and Therapeutics, Mie University Graduate School of Medicine, Tsu, Japan
| | - M. Taira
- Department of Cognitive Neurobiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
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Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M. A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis. Cytogenet Genome Res 2015; 145:187-91. [PMID: 25871511 DOI: 10.1159/000381292] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Xenopus laevis (XLA) is an allotetraploid species which appears to have undergone whole-genome duplication after the interspecific hybridization of 2 diploid species closely related to Silurana/Xenopus tropicalis (XTR). Previous cDNA fluorescence in situ hybridization (FISH) experiments have identified 9 sets of homoeologous chromosomes in X. laevis, in which 8 sets correspond to chromosomes 1-8 of X. tropicalis (XTR1-XTR8), and the last set corresponds to a fusion of XTR9 and XTR10. In addition, recent X. laevis genome sequencing and BAC-FISH experiments support this physiological relationship and show no gross chromosome translocation in the X. laevis karyotype. Therefore, for the benefit of both comparative cytogenetics and genome research, we here propose a new chromosome nomenclature for X. laevis based on the phylogenetic relationship and chromosome length, i.e. XLA1L, XLA1S, XLA2L, XLA2S, and so on, in which the numbering of XLA chromosomes corresponds to that in X. tropicalis and the postfixes 'L' and 'S' stand for 'long' and 'short' chromosomes in the homoeologous pairs, which can be distinguished cytologically by their relative size. The last chromosome set is named XLA9L and XLA9S, in which XLA9 corresponds to both XTR9 and XTR10, and hence, to emphasize the phylogenetic relationship to X. tropicalis, XLA9_10L and XLA9_10S are also used as synonyms.
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Affiliation(s)
- Yoichi Matsuda
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Shoi K, Fueki K, Usui N, Taira M, Wakabayashi N. Influence of posterior dental arch length on brain activity during chewing in patients with mandibular distal extension removable partial dentures. J Oral Rehabil 2014; 41:486-95. [DOI: 10.1111/joor.12169] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 11/28/2022]
Affiliation(s)
- K. Shoi
- Section of Removable Partial Prosthodontics; Department of Masticatory Function Rehabilitation; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - K. Fueki
- Section of Removable Partial Prosthodontics; Department of Masticatory Function Rehabilitation; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - N. Usui
- Department of Cognitive Neurobiology; The Center for Brain Integration Research; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - M. Taira
- Department of Cognitive Neurobiology; The Center for Brain Integration Research; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
| | - N. Wakabayashi
- Section of Removable Partial Prosthodontics; Department of Masticatory Function Rehabilitation; Graduate School of Medical and Dental Sciences; Tokyo Medical and Dental University; Tokyo Japan
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Tsutsumi R, Masoudi M, Takahashi A, Fujii Y, Hayashi T, Kikuchi I, Satou Y, Taira M, Hatakeyama M. YAP and TAZ, Hippo Signaling Targets, Act as a Rheostat for Nuclear SHP2 Function. Dev Cell 2013; 26:658-65. [DOI: 10.1016/j.devcel.2013.08.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 07/09/2013] [Accepted: 08/15/2013] [Indexed: 02/02/2023]
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Kaneta A, Araki T, Taira M, Aomori T, Nagano D, Arai M, Nakamura T, Kurabayashi M, Yamamoto K. CPC-009 Administration of Dabigatran Removed from the Capsule. Eur J Hosp Pharm 2013. [DOI: 10.1136/ejhpharm-2013-000276.466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Yamashita K, Yoshioka Y, Pan H, Taira M, Ogura T, Nagano T, Aoyama M, Nagano K, Abe Y, Kamada H, Tsunoda SI, Aoshima H, Nabeshi H, Yoshikawa T, Tsutsumi Y. Biochemical and hematologic effects of polyvinylpyrrolidone-wrapped fullerene C60 after oral administration. Pharmazie 2013; 68:54-57. [PMID: 23444781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The fullerene C60 is used in consumer products such as cosmetics owing to its antioxidative effects and is being developed for nanomedical applications. However, knowledge regarding the safety of fullerene C60, especially after oral administration, is sparse. Here, we examined the safety of fullerene C60 in mice after 7 d of exposure to orally administered polyvinylpyrrolidone (PVP)-wrapped fullerene C60 (PVP-fullerene C60). Mice treated with PVP-fullerene C60 showed few changes in the plasma levels of various markers of kidney and liver injury and experienced no significant hematologic effects. Furthermore, the histology of the colon of PVP-fullerene C60-treated mice was indistinguishable from that of control mice. These results suggest that PVP-fullerene C60 lacks toxicity after high-dose oral administration and indicate that PVP-fullerene C60 can be considered safe for oral medication. These data provide basic information that likely will facilitate the production of safe and effective forms of fullerene C60.
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Affiliation(s)
- K Yamashita
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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Sudou N, Yamamoto S, Ogino H, Taira M. Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer. Development 2012; 139:1651-61. [PMID: 22492356 DOI: 10.1242/dev.068395] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
How multiple developmental cues are integrated on cis-regulatory modules (CRMs) for cell fate decisions remains uncertain. The Spemann-Mangold organizer in Xenopus embryos expresses the transcription factors Lim1/Lhx1, Otx2, Mix1, Siamois (Sia) and VegT. Reporter analyses using sperm nuclear transplantation and DNA injection showed that cerberus (cer) and goosecoid (gsc) are activated by the aforementioned transcription factors through CRMs conserved between X. laevis and X. tropicalis. ChIP-qPCR analysis for the five transcription factors revealed that cer and gsc CRMs are initially bound by both Sia and VegT at the late blastula stage, and subsequently bound by all five factors at the gastrula stage. At the neurula stage, only binding of Lim1 and Otx2 to the gsc CRM, among others, persists, which corresponds to their co-expression in the prechordal plate. Based on these data, together with detailed expression pattern analysis, we propose a new model of stepwise formation of the organizer, in which (1) maternal VegT and Wnt-induced Sia first bind to CRMs at the blastula stage; then (2) Nodal-inducible Lim1, Otx2, Mix1 and zygotic VegT are bound to CRMs in the dorsal endodermal and mesodermal regions where all these genes are co-expressed; and (3) these two regions are combined at the gastrula stage to form the organizer. Thus, the in vivo dynamics of multiple transcription factors highlight their roles in the initiation and maintenance of gene expression, and also reveal the stepwise integration of maternal, Nodal and Wnt signaling on CRMs of organizer genes to generate the organizer.
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Affiliation(s)
- Norihiro Sudou
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Moriyama Y, Kawanishi T, Nakamura R, Tsukahara T, Sumiyama K, Suster ML, Kawakami K, Toyoda A, Fujiyama A, Yasuoka Y, Nagao Y, Sawatari E, Shimizu A, Wakamatsu Y, Hibi M, Taira M, Okabe M, Naruse K, Hashimoto H, Shimada A, Takeda H. The medaka zic1/zic4 mutant provides molecular insights into teleost caudal fin evolution. Curr Biol 2012; 22:601-7. [PMID: 22386310 DOI: 10.1016/j.cub.2012.01.063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 12/26/2011] [Accepted: 01/31/2012] [Indexed: 10/28/2022]
Abstract
Teleosts have an asymmetrical caudal fin skeleton formed by the upward bending of the caudal-most portion of the body axis, the ural region. This homocercal type of caudal fin ensures powerful and complex locomotion and is regarded as one of the most important innovations for teleosts during adaptive radiation in an aquatic environment. However, the mechanisms that create asymmetric caudal fin remain largely unknown. The spontaneous medaka (teleost fish) mutant, Double anal fin (Da), exhibits a unique symmetrical caudal skeleton that resembles the diphycercal type seen in Polypterus and Coelacanth. We performed a detailed analysis of the Da mutant to obtain molecular insight into caudal fin morphogenesis. We first demonstrate that a large transposon, inserted into the enhancer region of the zic1 and zic4 genes (zic1/zic4) in Da, is associated with the mesoderm-specific loss of their transcription. We then show that zic1/zic4 are strongly expressed in the dorsal part of the ural mesenchyme and thereby induce asymmetric caudal fin development in wild-type embryos, whereas their expression is lost in Da. Comparative analysis further indicates that the dorsal mesoderm expression of zic1/zic4 is conserved in teleosts, highlighting the crucial role of zic1/zic4 in caudal fin morphogenesis.
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Affiliation(s)
- Yuuta Moriyama
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
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Abstract
Gradient formation and signaling ranges of secreted proteins are crucial problems to understand how morphogens work for positional information and patterning in animal development. Yet, extracellular behaviors of secreted signaling molecules remain unexplored compared to their downstream pathways inside the cell. Recent advances in bioimaging make it possible to directly visualize morphogen molecules, and this simple strategy has, at least partly, succeeded in uncovering molecular behaviors of morphogens, such as Wnt (wingless-type MMTV integration site family member) and BMP (bone morphogenetic protein) as well as secreted Wnt binding proteins, sFRPs (secreted Frizzled-related proteins), in embryonic tissues. Here, we review the regulation of Wnt signaling by sFRPs, focusing on extracellular regulation of Wnt ligands in comparison with other morphogens. We also discuss evolutionary aspects with comprehensive syntenic and phylogenetic information about vertebrate sfrp genes. We newly annotated several sfrp genes including sfrp2-like 1 (sfrp2l1) in frogs and fishes and crescent in mammals.
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Affiliation(s)
- Yusuke Mii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Venegas-Ferrín M, Sudou N, Taira M, del Pino EM. Comparison of Lim1 expression in embryos of frogs with different modes of reproduction. Int J Dev Biol 2010; 54:195-202. [PMID: 19876816 DOI: 10.1387/ijdb.092870mv] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A polyclonal antibody was used to detect the expression of the homeodomain protein Lim1 (Lhx1) in embryos of Xenopus laevis, Engystomops randi, Colostethus machalilla and Gastrotheca riobambae. These frogs belong to four separate families, and have differences in their modes of reproduction and developmental rates. The expression of Lim1 in embryos of these frogs resembled the X. laevis expression pattern. Thus, the dorsal blastopore lip, axial mesoderm, pronephros and certain cells of the central nervous system were Lim1-positive in embryos of all frogs. There were, however, time differences; thus, in the mid-gastrula of the rapidly developing embryos of X. laevis and E. randi, the Lim1 protein was simultaneously detected in the prechordal plate (head organizer) and notochord (trunk organizer). In contrast, only the prechordal plate was Lim1-positive during gastrulation in the slow developing embryos of C. machalilla. The notochord elongated and became Lim1-positive after closure of the blastopore in C. machalilla and G. riobambae embryos. The prechordal plate of G. riobambae embryos could not be clearly detected, as the Lim1-signal remained around the blastopore during gastrulation. These observations indicate that the timing of gene expression at the dorsal blastopore lip in embryos of slow developing frogs differs from that of X. laevis. Moreover, the comparison shows that the developmental processes of the head and trunk organizers are basically separable and become dissociated in embryos of the slow developing frog, C. machalilla.
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Affiliation(s)
- Michael Venegas-Ferrín
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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Abstract
Secreted Frizzled-related proteins (sFRPs) are thought to negatively modulate Wnt signalling. Although Wnt proteins are thought to diffuse extracellularly and act as morphogens, little is known about the diffusibility of either Wnts or sFRPs. Here we show that Frzb and Crescent (Cres), which are members of the sFRP family, have the ability to regulate the diffusibility and signalling areas of the Wnt ligands Wnt8 and Wnt11. We found, using the Xenopus embryo, that Wnts do not diffuse effectively, whereas Frzb and Cres spread very widely. Interestingly, Frzb and Cres substantially promoted the diffusion of Wnt8 and Wnt11 through extracellular interactions. Importantly, we show that Wnt8 conveyed by sFRPs can activate canonical Wnt signalling despite the function of sFRPs as Wnt inhibitors, suggesting a novel regulatory system for Wnts by sFRPs.
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Affiliation(s)
- Yusuke Mii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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Takada H, Kawana T, Ito Y, Kikuno RF, Mamada H, Araki T, Koga H, Asashima M, Taira M. The RNA-binding protein Mex3b has a fine-tuning system for mRNA regulation in early Xenopus development. Development 2009; 136:2413-22. [PMID: 19542354 DOI: 10.1242/dev.029165] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Post-transcriptional control by RNA-binding proteins is a precise way to assure appropriate levels of gene expression. Here, we identify a novel mRNA regulatory system involving Mex3b (RKHD3) and demonstrate its role in FGF signaling. mex3b mRNA has a 3' long conserved UTR, named 3'LCU, which contains multiple elements for both mRNA destabilization and translational enhancement. Notably, Mex3b promotes destabilization of its own mRNA by binding to the 3'LCU, thereby forming a negative autoregulatory loop. The combination of positive regulation and negative autoregulation constitutes a fine-tuning system for post-transcriptional control. In early embryogenesis, Mex3b is involved in anteroposterior patterning of the neural plate. Consistent with this, Mex3b can attenuate FGF signaling and destabilize mRNAs for the FGF signaling components Syndecan 2 and Ets1b through their 3' UTRs. These data suggest that the 3'LCU-mediated fine-tuning system determines the appropriate level of mex3b expression, which in turn contributes to neural patterning through regulating FGF signaling.
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Affiliation(s)
- Hitomi Takada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Matsukawa Y, Nagashima M, Kamei S, Tanabe E, Takahashi S, Kojima T, Taira M, Morita K, Matsuura M, Sawada S. Random number generation evaluation in patients with systemic lupus erythematosus indicates a heterogeneous nature of central nervous system vulnerability. Scand J Rheumatol 2009; 35:295-9. [PMID: 16882594 DOI: 10.1080/03009740600556027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
OBJECTIVE To evaluate the vulnerability of the central nervous system (CNS) in patients with systemic lupus erythematosus (SLE). METHODS Forty-eight patients with SLE, 58 with schizophrenia in remission and 39 healthy controls were enrolled in the study. Patients vocally generated 100 numbers in a random fashion, using numbers 0 to 9, and were evaluated with seriality scores. Patients with SLE were subgrouped according to differences in the presence of Raynaud's phenomenon, anti-phospholipid antibody, lupus activity, and a history of neuropsychiatric (NP) lupus, and these patients were also evaluated by comparison with their counterparts. RESULTS In general, patients with SLE showed lower seriality scores than patients with schizophrenia, and higher seriality scores than normal controls. The scores of the patients with a history of NP lupus matched those with schizophrenia, and the scores of never having NP lupus matched those of the healthy controls. CONCLUSIONS CNS vulnerability may be prolonged in patients who have a history of NP lupus even when they appear to be in normal NP status. The damage in random number generation (RNG) observed in patients with a history of NP lupus seemed equal to that found in those with schizophrenia, whereas those patients never having NP lupus appeared to be equal to the controls. The current study suggests a heterogeneous nature of SLE and prolonged damage, especially in CNS vulnerability, when evaluating with RNG.
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Affiliation(s)
- Y Matsukawa
- Division of Haematology and Rheumatology, Department of Medicine, Nihon University of Medicine, Oyaguchi-Kamimachi, Itabashi, 173-8610, Tokyo, Japan.
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Yasuoka Y, Kobayashi M, Kurokawa D, Akasaka K, Saiga H, Taira M. Evolutionary origins of blastoporal expression and organizer activity of the vertebrate gastrula organizer gene lhx1 and its ancient metazoan paralog lhx3. Development 2009; 136:2005-14. [DOI: 10.1242/dev.028530] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Expression of the LIM homeobox gene lhx1 (lim1) is specific to the vertebrate gastrula organizer. Lhx1 functions as a transcriptional regulatory core protein to exert `organizer' activity in Xenopus embryos. Its ancient paralog, lhx3 (lim3),is expressed around the blastopore in amphioxus and ascidian, but not vertebrate, gastrulae. These two genes are thus implicated in organizer evolution, and we addressed the evolutionary origins of their blastoporal expression and organizer activity. Gene expression analysis of organisms ranging from cnidarians to chordates suggests that blastoporal expression has its evolutionary root in or before the ancestral eumetazoan for lhx1,but possibly in the ancestral chordate for lhx3, and that in the ascidian lineage, blastoporal expression of lhx1 ceased, whereas endodermal expression of lhx3 has persisted. Analysis of organizer activity using Xenopus embryos suggests that a co-factor of LIM homeodomain proteins, Ldb, has a conserved function in eumetazoans to activate Lhx1, but that Lhx1 acquired organizer activity in the bilaterian lineage,Lhx3 acquired organizer activity in the deuterostome lineage and ascidian Lhx3 acquired a specific transactivation domain to confer organizer activity on this molecule. Knockdown analysis using cnidarian embryos suggests that Lhx1 is required for chordin expression in the blastoporal region. These data suggest that Lhx1 has been playing fundamental roles in the blastoporal region since the ancestral eumetazoan arose, that it contributed as an`original organizer gene' to the evolution of the vertebrate gastrula organizer, and that Lhx3 could be involved in the establishment of organizer gene networks.
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Affiliation(s)
- Yuuri Yasuoka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaaki Kobayashi
- Department of Biological Sciences, Graduate School of Science and Engineering,Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397,Japan
| | - Daisuke Kurokawa
- Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, 1024 Koajiro, Misaki, Miura Kanagawa, 238-0225, Japan
| | - Koji Akasaka
- Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, 1024 Koajiro, Misaki, Miura Kanagawa, 238-0225, Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences, Graduate School of Science and Engineering,Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397,Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Suga A, Taira M, Nakagawa S. LIM family transcription factors regulate the subtype-specific morphogenesis of retinal horizontal cells at post-migratory stages. Dev Biol 2009; 330:318-28. [PMID: 19361492 DOI: 10.1016/j.ydbio.2009.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 11/17/2022]
Abstract
In the nervous system, transcription factor expression in progenitor and/or nascent neurons regulates cell type specification. Although the functions of these transcription factors at early stages are well established, whether or not they are required during late developmental periods remains an open question. To address this issue, we conditionally manipulated gene expression using a recently developed transposon-mediated gene transfer system combined with in ovo electroporation. In chicken retinas, horizontal cells are classified into three subtypes according to their characteristic neuronal morphology. Two LIM family transcription factors, Lim1 and Isl1, begin to be expressed in a distinct subset of nascent retinal neurons, which results in complementary expression of these genes in mature retinas in type I and type II/III horizontal cells, respectively. Overexpression of Isl1 in post-migratory horizontal cells represses endogenous Lim1 expression and increases the number of neurons with a dendritic morphology characteristic of type II horizontal cells, which normally express Isl1. Inhibition of Lim1 function by expression of a dominant negative form Lim1 perturbs axonal morphogenesis of type I horizontal cells. Therefore, we propose that LIM family transcription factors are required for subtype-specific morphogenesis of horizontal cells at later stages of retinal development.
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Affiliation(s)
- Akiko Suga
- Nakagawa Initiative Research Unit, RIKEN Advanced Science Institute, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
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Kato M, Hasunuma N, Nakayama R, Takeda J, Itami S, Taira M, Manabe M, Osada SI. Progranulin, a secreted tumorigenesis and dementia-related factor, regulates mouse hair growth. J Dermatol Sci 2009; 53:234-6. [DOI: 10.1016/j.jdermsci.2008.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 09/29/2008] [Accepted: 10/04/2008] [Indexed: 01/13/2023]
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Seki N, Yagi S, Suzuki Y, Shimada F, Taira M, Makino H, Amano K, Yagui K, Saito Y, Hashimoto N. Protein tyrosine phosphatase regulation in fibroblasts from patients with an insulin receptor gene mutation. Horm Metab Res 2008; 40:833-7. [PMID: 18925540 DOI: 10.1055/s-0028-1082082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Tyrosine phosphorylation of the insulin receptor is the initial event following receptor binding to insulin, and it induces further tyrosine phosphorylation of various intracellular molecules. This signaling is countered by protein tyrosine phosphatases (PTPases), which reportedly are associated with insulin resistance that can be reduced by regulation of PTPases. Protein tyrosine phosphatase 1B (PTP1B) and leukocyte antigen-related PTPase (LAR) are the PTPases implicated most frequently in insulin resistance and diabetes mellitus. Here, we show that PTP1B and LAR are expressed in human fibroblasts, and we examine the regulation of PTPase activity in fibroblasts from patients with an insulin receptor gene mutation as an in vitro model of insulin resistance. Total PTPase activity was significantly lower in the cytosolic and membrane fractions of fibroblasts with mutations compared with controls (p<0.05). Insulin stimulation of fibroblasts with mutations resulted in a significantly smaller increase in PTP1B activity compared with stimulation of wild-type fibroblasts (p<0.05). This indicates that insulin receptor gene mutations blunt increases in PTPase activity in response to insulin, possibly via a negative feedback mechanism. Our data suggest that the PTPase activity in patients with insulin receptor gene mutation and severe insulin resistance may differ from that in ordinary type 2 diabetes.
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MESH Headings
- Blotting, Western
- Cells, Cultured
- Exons/genetics
- Fibroblasts/enzymology
- Gene Expression Regulation, Enzymologic/genetics
- Gene Expression Regulation, Enzymologic/physiology
- Humans
- Immunoprecipitation
- Insulin/pharmacology
- Insulin Resistance/genetics
- Mutation/physiology
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism
- Protein Tyrosine Phosphatases/biosynthesis
- Protein Tyrosine Phosphatases/genetics
- Receptor, Insulin/genetics
- Receptor-Like Protein Tyrosine Phosphatases, Class 4/genetics
- Receptor-Like Protein Tyrosine Phosphatases, Class 4/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Stimulation, Chemical
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Affiliation(s)
- N Seki
- Clinical Research Center, National Hospital Organization, Chiba-East National Hospital, Chiba, Japan
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