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Nomura A, Kobayashi T, Seo W, Ohno-Oishi M, Kakugawa K, Muroi S, Yoshida H, Endo TA, Moro K, Taniuchi I. Identification of a novel enhancer essential for Satb1 expression in T H2 cells and activated ILC2s. Life Sci Alliance 2023; 6:e202301897. [PMID: 37193606 PMCID: PMC10189277 DOI: 10.26508/lsa.202301897] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023] Open
Abstract
The genome organizer, special AT-rich binding protein-1 (SATB1), functions to globally regulate gene networks during primary T cell development and plays a pivotal role in lineage specification in CD4+ helper-, CD8+ cytotoxic-, and FOXP3+ regulatory-T cell subsets. However, it remains unclear how Satb1 gene expression is controlled, particularly in effector T cell function. Here, by using a novel reporter mouse strain expressing SATB1-Venus and genome editing, we have identified a cis-regulatory enhancer, essential for maintaining Satb1 expression specifically in TH2 cells. This enhancer is occupied by STAT6 and interacts with Satb1 promoters through chromatin looping in TH2 cells. Reduction of Satb1 expression, by the lack of this enhancer, resulted in elevated IL-5 expression in TH2 cells. In addition, we found that Satb1 is induced in activated group 2 innate lymphoid cells (ILC2s) through this enhancer. Collectively, these results provide novel insights into how Satb1 expression is regulated in TH2 cells and ILC2s during type 2 immune responses.
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Affiliation(s)
- Aneela Nomura
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Tetsuro Kobayashi
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Wooseok Seo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Michiko Ohno-Oishi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Kiyokazu Kakugawa
- Laboratory for Immune Crosstalk, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Sawako Muroi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Hideyuki Yoshida
- Laboratory for YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Kazuyo Moro
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
- Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School for Medicine, Osaka University, Osaka, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
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2
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Masui O, Corbel C, Nagao K, Endo TA, Kezuka F, Diabangouaya P, Nakayama M, Kumon M, Koseki Y, Obuse C, Koseki H, Heard E. Polycomb repressive complexes 1 and 2 are each essential for maintenance of X inactivation in extra-embryonic lineages. Nat Cell Biol 2023; 25:134-144. [PMID: 36635505 DOI: 10.1038/s41556-022-01047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/08/2022] [Indexed: 01/14/2023]
Abstract
In female mammals, one of the two X chromosomes becomes inactivated during development by X-chromosome inactivation (XCI). Although Polycomb repressive complex (PRC) 1 and PRC2 have both been implicated in gene silencing, their exact roles in XCI during in vivo development have remained elusive. To this end, we have studied mouse embryos lacking either PRC1 or PRC2. Here we demonstrate that the loss of either PRC has a substantial impact on maintenance of gene silencing on the inactive X chromosome (Xi) in extra-embryonic tissues, with overlapping yet different genes affected, indicating potentially independent roles of the two complexes. Importantly, a lack of PRC1 does not affect PRC2/H3K27me3 accumulation and a lack of PRC2 does not impact PRC1/H2AK119ub1 accumulation on the Xi. Thus PRC1 and PRC2 contribute independently to the maintenance of XCI in early post-implantation extra-embryonic lineages, revealing that both Polycomb complexes can be directly involved and differently deployed in XCI.
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Affiliation(s)
- Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Catherine Corbel
- Unité de Génétique et Biologie du Développement, Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Paris, France
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Fuyuko Kezuka
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Patricia Diabangouaya
- Unité de Génétique et Biologie du Développement, Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Paris, France
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Mami Kumon
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Edith Heard
- Unité de Génétique et Biologie du Développement, Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Paris, France. .,Collège de France, Paris, France. .,European Molecular Biology Laboratory (EMBL), Directors' research unit, Heidelberg, Germany.
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3
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Vincent SA, Kim JM, Pérez-Salamó I, To TK, Torii C, Ishida J, Tanaka M, Endo TA, Bhat P, Devlin PF, Seki M, Devoto A. Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response. BMC Biol 2022; 20:83. [PMID: 35399062 PMCID: PMC8996529 DOI: 10.1186/s12915-022-01273-8] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. RESULTS We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. CONCLUSIONS The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.
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Affiliation(s)
- Stacey A Vincent
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Jong-Myong Kim
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Ac-Planta Inc., 2-16-9 Yushima, Bunkyo-ku, Tokyo, 113-0034, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Imma Pérez-Salamó
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Taiko Kim To
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chieko Torii
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ishida
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takaho A Endo
- Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Present address: Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Prajwal Bhat
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Paul F Devlin
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Alessandra Devoto
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
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4
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Ohinata Y, Endo TA, Sugishita H, Watanabe T, Iizuka Y, Kawamoto Y, Saraya A, Kumon M, Koseki Y, Kondo T, Ohara O, Koseki H. Establishment of mouse stem cells that can recapitulate the developmental potential of primitive endoderm. Science 2022; 375:574-578. [PMID: 35113719 DOI: 10.1126/science.aay3325] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The mammalian blastocyst consists of three distinct cell types: epiblast, trophoblast (TB), and primitive endoderm (PrE). Although embryonic stem cells (ESCs) and trophoblast stem cells (TSCs) retain the functional properties of epiblast and TB, respectively, stem cells that fully recapitulate the developmental potential of PrE have not been established. Here, we report derivation of primitive endoderm stem cells (PrESCs) in mice. PrESCs recapitulate properties of embryonic day 4.5 founder PrE, are efficiently incorporated into PrE upon blastocyst injection, generate functionally competent PrE-derived tissues, and support fetal development of PrE-depleted blastocysts in chimeras. Furthermore, PrESCs can establish interactions with ESCs and TSCs and generate descendants with yolk sac-like structures in utero. Establishment of PrESCs will enable the elucidation of the mechanisms for PrE specification and subsequent pre- and postimplantation development.
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Affiliation(s)
- Yasuhide Ohinata
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo ward, Chiba 260-8670, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroki Sugishita
- Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Watanabe
- Laboratory for Integrative Genomics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yusuke Iizuka
- Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yurie Kawamoto
- Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Atsunori Saraya
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo ward, Chiba 260-8670, Japan
| | - Mami Kumon
- Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.,Facility for Clinical Omics Analysis, Kazusa DNA Research Institure, 2-6-7 Kazusakamatori, Kisarazu, Chiba 292-0818, Japan
| | - Haruhiko Koseki
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo ward, Chiba 260-8670, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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5
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Takahashi S, Nobuhisa I, Saito K, Gerel M, Itabashi A, Harada K, Osawa M, Endo TA, Iwama A, Taga T. Sox17-mediated expression of adherent molecules is required for the maintenance of undifferentiated hematopoietic cluster formation in midgestation mouse embryos. Differentiation 2020; 115:53-61. [PMID: 32891959 DOI: 10.1016/j.diff.2020.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/30/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022]
Abstract
Hematopoietic stem cell-containing intra-aortic hematopoietic cell clusters (IAHCs) emerge in the dorsal aorta of the aorta-gonad-mesonephros (AGM) region during midgestation mouse embryos. We previously showed that transduction of Sox17 in CD45lowc-Kithigh cells, which are one component of IAHCs, maintained the cluster formation and the undifferentiated state, but the mechanism of the cluster formation by Sox17 has not been clarified. By microarray gene expression analysis, we found that genes for vascular endothelial-cadherin (VE-cad) and endothelial cell-selective adhesion molecule (ESAM) were expressed at high levels in Sox17-transduced c-Kit+ cells. Here we show the functional role of these adhesion molecules in the formation of IAHCs and the maintenance of the undifferentiated state by in vitro experiments. We detected VE-cad and ESAM expression in endothelial cells of dorsal aorta and IAHCs in E10.5 embryos by whole mount immunohistochemistry. Cells with the middle expression level of VE-cad and the low expression level of ESAM had the highest colony-forming ability. Tamoxifen-dependent nuclear translocation of Sox17-ERT fusion protein induced the formation of cell clusters and the expression of Cdh5 (VE-cad) and ESAM genes. We showed the induction of the Cdh5 (VE-cad) and ESAM expression and the direct interaction of Sox17 with their promoter by luciferase assay and chromatin immunoprecipitation assay, respectively. Moreover, shRNA-mediated knockdown of either Cdh5 (VE-cad) or ESAM gene in Sox17-transduced cells decreased the multilineage-colony forming potential. These findings suggest that VE-cad and ESAM play an important role in the high hematopoietic activity of IAHCs and cluster formation.
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Affiliation(s)
- Satomi Takahashi
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ikuo Nobuhisa
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Kiyoka Saito
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Melig Gerel
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ayumi Itabashi
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kaho Harada
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Mitsujiro Osawa
- Clinical Application Department, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Takaho A Endo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuya Taga
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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6
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Nishizono H, Darwish M, Endo TA, Uno K, Abe H, Yasuda R. Glycine receptor α4 subunit facilitates the early embryonic development in mice. Reproduction 2019; 159:41. [PMID: 31689234 DOI: 10.1530/rep-19-0312] [Citation(s) in RCA: 9] [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: 07/15/2019] [Accepted: 11/05/2019] [Indexed: 11/08/2022]
Abstract
Oviduct fluid is essential for the fertilization and subsequent preimplantation development. Glycine is abundant in oviduct fluid and is reported to be critical for preimplantation development of fertilized eggs in mammals. However, the mechanism by which glycine exerts its action on fertilized eggs is yet to be understood. Here we show that glycine regulates the preimplantation development of mouse fertilized eggs via glycine receptors. Among them, the alpha-4 subunit (Glra4) and the β subunit are expressed in mouse fertilized eggs, and lacking Glra4 inhibits embryonic development to the blastocyst stage, decreases the number of cells in the blastocysts and the litter size. Thus, we identify a novel function of the glycine receptor, which is considered to act mainly as a neurotransmitter receptor, as a regulator of embryonic development and our data provide new insights into the interactions between oviduct milieu and mammalian fertilized egg.
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Affiliation(s)
- Hirofumi Nishizono
- Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA.,Life Science Research Center, University of Toyama, Toyama, Japan.,Department of Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Japan
| | - Mohamed Darwish
- Department of Behavioral Physiology, Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan.,Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kyosuke Uno
- Laboratory of Molecular Pharmacology, Faculty of Pharmaceutical Science, Setsunan University, Hirakata, Japan
| | - Hiroyuki Abe
- Department of Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Japan
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
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7
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Han SK, Qi X, Sugihara K, Dang JH, Endo TA, Miller KL, Kim ED, Miura T, Torii KU. MUTE Directly Orchestrates Cell-State Switch and the Single Symmetric Division to Create Stomata. Dev Cell 2018; 45:303-315.e5. [PMID: 29738710 DOI: 10.1016/j.devcel.2018.04.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [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: 12/20/2017] [Revised: 03/20/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Precise cell division control is critical for developmental patterning. For the differentiation of a functional stoma, a cellular valve for efficient gas exchange, the single symmetric division of an immediate precursor is absolutely essential. Yet, the mechanism governing this event remains unclear. Here we report comprehensive inventories of gene expression by the Arabidopsis bHLH protein MUTE, a potent inducer of stomatal differentiation. MUTE switches the gene expression program initiated by SPEECHLESS. MUTE directly induces a suite of cell-cycle genes, including CYCD5;1, in which introduced expression triggers the symmetric divisions of arrested precursor cells in mute, and their transcriptional repressors, FAMA and FOUR LIPS. The regulatory network initiated by MUTE represents an incoherent type 1 feed-forward loop. Our mathematical modeling and experimental perturbations support a notion that MUTE orchestrates a transcriptional cascade leading to a tightly restricted pulse of cell-cycle gene expression, thereby ensuring the single cell division to create functional stomata.
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Affiliation(s)
- Soon-Ki Han
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Xingyun Qi
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Kei Sugihara
- Department of Anatomy and Cell Biology, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Jonathan H Dang
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kristen L Miller
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Eun-Deok Kim
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Takashi Miura
- Department of Anatomy and Cell Biology, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Keiko U Torii
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan.
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8
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Chikaraishi K, Takenobu H, Sugino RP, Mukae K, Akter J, Haruta M, Kurosumi M, Endo TA, Koseki H, Shimojo N, Ohira M, Kamijo T. CFC1 is a cancer stemness-regulating factor in neuroblastoma. Oncotarget 2018; 8:45046-45059. [PMID: 28620148 PMCID: PMC5542166 DOI: 10.18632/oncotarget.18464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 12/06/2016] [Accepted: 05/28/2017] [Indexed: 01/06/2023] Open
Abstract
Background Despite the use of aggressive therapy, survival rates among high-risk neuroblastoma (NB) patients remain poor. Cancer stem cells (CSCs) are considered to be critically involved in the recurrence and metastasis of NB and are isolated as NB spheres. Methods The gene expression profiling of adherent (control) and sphere-forming primary NB cells was conducted using a gene expression microarray. CFC1, which functions in the development of embryos and decides the left-right axis, was strongly expressed in sphere-forming cells only and was related to the unfavorable prognosis of NB patients. The knockdown and overexpression of CFC1 were performed using a lentiviral system in NB cell lines. Sphere formation, cell proliferation, colony formation in soft agar, and xenograft tumor formation were analyzed. Results The overexpression of CFC1 increased sphere formation, cell growth, and colony formation. These phenotypes, particularly sphere formation, and xenograft tumor formation were significantly suppressed by the knockdown of CFC1. CFC1 inhibited Activin A-induced NB cell differentiation and Smad2 phosphorylation in NB cell lines, indicating its involvement in tumorigenesis related to EGF-CFC co-receptor family molecule pathways. Collectively, these results indicate that CFC1 is a candidate molecule for the development of CSC-targeted therapy for NB.
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Affiliation(s)
- Koji Chikaraishi
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Department of Pediatrics, Chiba University, Chiba, Japan
| | - Hisanori Takenobu
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ryuichi P Sugino
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Kyosuke Mukae
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Jesmin Akter
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | | | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Naoki Shimojo
- Department of Pediatrics, Chiba University, Chiba, Japan
| | - Miki Ohira
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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9
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Miyai T, Takano J, Endo TA, Kawakami E, Agata Y, Motomura Y, Kubo M, Kashima Y, Suzuki Y, Kawamoto H, Ikawa T. Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells. Genes Dev 2018; 32:112-126. [PMID: 29440259 PMCID: PMC5830925 DOI: 10.1101/gad.309575.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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] [Received: 11/13/2017] [Accepted: 12/29/2017] [Indexed: 02/04/2023]
Abstract
Miyai et al. used multipotent progenitors harboring a tamoxifen-inducible form of Id3—where virtually all cells became B cells within 6 d by withdrawing 4-OHT—to identify a three-step transcription factor network model during specification of multipotent progenitors toward the B-cell lineage. Stem cell fate is orchestrated by core transcription factors (TFs) and epigenetic modifications. Although regulatory genes that control cell type specification are identified, the transcriptional circuit and the cross-talk among regulatory factors during cell fate decisions remain poorly understood. To identify the “time-lapse” TF networks during B-lineage commitment, we used multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system in which virtually all cells became B cells within 6 d by simply withdrawing 4-hydroxytamoxifen (4-OHT). Transcriptome and epigenome analysis at multiple time points revealed that ∼10%–30% of differentially expressed genes were virtually controlled by the core TFs, including E2A, EBF1, and PAX5. Strikingly, we found unexpected transcriptional priming before the onset of the key TF program. Inhibition of the immediate early genes such as Nr4a2, Klf4, and Egr1 severely impaired the generation of B cells. Integration of multiple data sets, including transcriptome, protein interactome, and epigenome profiles, identified three representative transcriptional circuits. Single-cell RNA sequencing (RNA-seq) analysis of lymphoid progenitors in bone marrow strongly supported the three-step TF network model during specification of multipotent progenitors toward B-cell lineage in vivo. Thus, our findings will provide a blueprint for studying the normal and neoplastic development of B lymphocytes.
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Affiliation(s)
- Tomohiro Miyai
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Disease Biology Group, Medical Science Innovation Hub Program, RIKEN Cluster for Science and Technology Hub, Yokohama 230-0045, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Junichiro Takano
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Immune Regulation Research, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba 260-8670, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Eiryo Kawakami
- Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Healthcare and Medical Data-Driven AI-based Predictive Reasoning Development Unit, Medical Science Innovation Hub Program, RIKEN Cluster for Science and Technology Hub, Yokohama 230-0045, Japan
| | - Yasutoshi Agata
- Department of Biochemistry and Molecular Biology, Shiga University of Medical School, Shiga 520-2192, Japan
| | - Yasutaka Motomura
- Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda 278-0022, Japan.,Laboratory for Cytokine Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masato Kubo
- Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda 278-0022, Japan.,Laboratory for Cytokine Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yukie Kashima
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 272-8562, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 272-8562, Japan
| | - Hiroshi Kawamoto
- Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Tomokatsu Ikawa
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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10
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Tenno M, Kojo S, Lawir DF, Hess I, Shiroguchi K, Ebihara T, Endo TA, Muroi S, Satoh R, Kawamoto H, Boehm T, Taniuchi I. Cbfβ2 controls differentiation of and confers homing capacity to prethymic progenitors. J Exp Med 2018; 215:595-610. [PMID: 29343500 PMCID: PMC5789415 DOI: 10.1084/jem.20171221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 07/11/2017] [Revised: 10/28/2017] [Accepted: 12/13/2017] [Indexed: 01/05/2023] Open
Abstract
Tenno et al. show that an evolutionarily conserved alternative splicing event in the Cbfb gene generates Cbfβ2, which forms a functionally distinct transcription factor complex underlying the differentiation of extrathymic T cell progenitors, including induction of the principal thymus-homing receptor, Ccr9. Multipotent hematopoietic progenitors must acquire thymus-homing capacity to initiate T lymphocyte development. Despite its importance, the transcriptional program underlying this process remains elusive. Cbfβ forms transcription factor complexes with Runx proteins, and here we show that Cbfβ2, encoded by an RNA splice variant of the Cbfb gene, is essential for extrathymic differentiation of T cell progenitors. Furthermore, Cbfβ2 endows extrathymic progenitors with thymus-homing capacity by inducing expression of the principal thymus-homing receptor, Ccr9. This occurs via direct binding of Cbfβ2 to cell type–specific enhancers, as is observed in Rorγt induction during differentiation of lymphoid tissue inducer cells by activation of an intronic enhancer. As in mice, an alternative splicing event in zebrafish generates a Cbfβ2-specific mRNA, important for ccr9 expression. Thus, despite phylogenetically and ontogenetically variable sites of origin of T cell progenitors, their robust thymus-homing capacity is ensured by an evolutionarily conserved mechanism emerging from functional diversification of Runx transcription factor complexes by acquisition of a novel splice variant.
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Affiliation(s)
- Mari Tenno
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Satoshi Kojo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Divine-Fondzenyuy Lawir
- Department of Developmental Immunology, Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Isabell Hess
- Department of Developmental Immunology, Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Katsuyuki Shiroguchi
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Laboratory for Integrative Omics, RIKEN Quantitative Biology Center, Osaka, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama, Japan
| | - Takashi Ebihara
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Sawako Muroi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Rumi Satoh
- Laboratory for Lymphocyte Development, RIKEN Center for Allergy and Immunology, Yokohama, Japan
| | - Hiroshi Kawamoto
- Laboratory for Lymphocyte Development, RIKEN Center for Allergy and Immunology, Yokohama, Japan
| | - Thomas Boehm
- Department of Developmental Immunology, Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
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11
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Yakushiji-Kaminatsui N, Kondo T, Hironaka KI, Sharif J, Endo TA, Nakayama M, Masui O, Koseki Y, Kondo K, Ohara O, Vidal M, Morishita Y, Koseki H. Variant PRC1 competes with retinoic acid-related signals to repress Meis2 in distal forelimb bud. Development 2018; 145:dev.166348. [DOI: 10.1242/dev.166348] [Citation(s) in RCA: 9] [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] [Received: 04/04/2018] [Accepted: 08/28/2018] [Indexed: 12/12/2022]
Abstract
Suppression of Meis genes in the distal limb bud is required for Proximal-Distal (PD) specification of the forelimb. Polycomb group (PcG) factors play a role in downregulation of retinoic acid (RA)-related signals in the distal forelimb bud, causing Meis repression. It is, however, not known if downregulation of RA-related signals and PcG-mediated proximal genes repression are functionally linked. Here, we reveal that PcG factors and RA-related signals antagonize each other to polarize Meis2 expression along the PD axis. With mathematical modeling and simulation, we propose that PcG factors are required to adjust the threshold for RA-related signaling to regulate Meis2 expression. Finally, we show that a variant Polycomb repressive complex 1 (PRC1), incorporating PCGF3 and PCGF5, represses Meis2 expression in the distal limb bud. Taken together, we reveal a previously unknown link between PcG proteins and downregulation of RA-related signals to mediate the phase transition of Meis2 transcriptional status during forelimb specification.
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Affiliation(s)
- Nayuta Yakushiji-Kaminatsui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Ken-ichi Hironaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0033, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takaho A. Endo
- Laboratory for Integrative Genomics, RIKEN-IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Manabu Nakayama
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kaori Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN-IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biológicas, Department of Cellular and Molecular Biology, Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Yoshihiro Morishita
- Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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12
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Kojo S, Tanaka H, Endo TA, Muroi S, Liu Y, Seo W, Tenno M, Kakugawa K, Naoe Y, Nair K, Moro K, Katsuragi Y, Kanai A, Inaba T, Egawa T, Venkatesh B, Minoda A, Kominami R, Taniuchi I. Priming of lineage-specifying genes by Bcl11b is required for lineage choice in post-selection thymocytes. Nat Commun 2017; 8:702. [PMID: 28951542 PMCID: PMC5615048 DOI: 10.1038/s41467-017-00768-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 01/24/2017] [Accepted: 07/27/2017] [Indexed: 12/05/2022] Open
Abstract
T-lineage committed precursor thymocytes are screened by a fate-determination process mediated via T cell receptor (TCR) signals for differentiation into distinct lineages. However, it remains unclear whether any antecedent event is required to couple TCR signals with the transcriptional program governing lineage decisions. Here we show that Bcl11b, known as a T-lineage commitment factor, is essential for proper expression of ThPOK and Runx3, central regulators for the CD4-helper/CD8-cytotoxic lineage choice. Loss of Bcl11b results in random expression of these factors and, thereby, lineage scrambling that is disconnected from TCR restriction by MHC. Initial Thpok repression by Bcl11b prior to the pre-selection stage is independent of a known silencer for Thpok, and requires the last zinc-finger motif in Bcl11b protein, which by contrast is dispensable for T-lineage commitment. Collectively, our findings shed new light on the function of Bcl11b in priming lineage-specifying genes to integrate TCR signals into subsequent transcriptional regulatory mechanisms. CD4 and CD8 T cells develop in the thymus with their transcription programs controlled by ThPOK and Runx3, respectively. Here the authors show that a pre-commitment event modulated by the transcription factor, Bcl11b, is required for the proper expression of ThPOK and Runx3 and correct CD4/CD8 lineage commitment.
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Affiliation(s)
- Satoshi Kojo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hirokazu Tanaka
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sawako Muroi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Ye Liu
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Wooseok Seo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mari Tenno
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kiyokazu Kakugawa
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yoshinori Naoe
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Krutula Nair
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kazuyo Moro
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yoshinori Katsuragi
- Division of Molecular Biology, Department of Molecular Genetics, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8510, Japan
| | - Akinori Kanai
- Department of Molecular Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima, 734-8553, Japan
| | - Takeshi Egawa
- Department of Pathology and Immunology, School of Medicine, Washington University School of Medicine, 660 S Euclid, Saint Louis, 63110, MO, USA
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, 138673, Singapore
| | - Aki Minoda
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Ryo Kominami
- Division of Molecular Biology, Department of Molecular Genetics, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8510, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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13
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Hayatsu N, Miyao T, Tachibana M, Murakami R, Kimura A, Kato T, Kawakami E, Endo TA, Setoguchi R, Watarai H, Nishikawa T, Yasuda T, Yoshida H, Hori S. Analyses of a Mutant Foxp3 Allele Reveal BATF as a Critical Transcription Factor in the Differentiation and Accumulation of Tissue Regulatory T Cells. Immunity 2017; 47:268-283.e9. [PMID: 28778586 DOI: 10.1016/j.immuni.2017.07.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [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: 11/22/2016] [Revised: 05/02/2017] [Accepted: 07/10/2017] [Indexed: 12/25/2022]
Abstract
Foxp3 controls the development and function of regulatory T (Treg) cells, but it remains elusive how Foxp3 functions in vivo. Here, we established mouse models harboring three unique missense Foxp3 mutations that were identified in patients with the autoimmune disease IPEX. The I363V and R397W mutations were loss-of-function mutations, causing multi-organ inflammation by globally compromising Treg cell physiology. By contrast, the A384T mutation induced a distinctive tissue-restricted inflammation by specifically impairing the ability of Treg cells to compete with pathogenic T cells in certain non-lymphoid tissues. Mechanistically, repressed BATF expression contributed to these A384T effects. At the molecular level, the A384T mutation altered Foxp3 interactions with its specific target genes including Batf by broadening its DNA-binding specificity. Our findings identify BATF as a critical regulator of tissue Treg cells and suggest that sequence-specific perturbations of Foxp3-DNA interactions can influence specific facets of Treg cell physiology and the immunopathologies they regulate.
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Affiliation(s)
- Norihito Hayatsu
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Takahisa Miyao
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Masashi Tachibana
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Ryuichi Murakami
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan; Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiko Kimura
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Takako Kato
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Eiryo Kawakami
- Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan; Disease Biology Group, RIKEN Medical Sciences Innovation Hub Program, Kanagawa 230-0045, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Ruka Setoguchi
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Hiroshi Watarai
- Division of Stem Cell Cellomics, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takeshi Nishikawa
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Takuwa Yasuda
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Hisahiro Yoshida
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Shohei Hori
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan; Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
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14
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Kim JM, To TK, Matsui A, Tanoi K, Kobayashi NI, Matsuda F, Habu Y, Ogawa D, Sakamoto T, Matsunaga S, Bashir K, Rasheed S, Ando M, Takeda H, Kawaura K, Kusano M, Fukushima A, Endo TA, Kuromori T, Ishida J, Morosawa T, Tanaka M, Torii C, Takebayashi Y, Sakakibara H, Ogihara Y, Saito K, Shinozaki K, Devoto A, Seki M. Acetate-mediated novel survival strategy against drought in plants. Nat Plants 2017; 3:17097. [PMID: 28650429 DOI: 10.1038/nplants.2017.97] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/25/2017] [Indexed: 05/19/2023]
Abstract
Water deficit caused by global climate changes seriously endangers the survival of organisms and crop productivity, and increases environmental deterioration1,2. Plants' resistance to drought involves global reprogramming of transcription, cellular metabolism, hormone signalling and chromatin modification3-8. However, how these regulatory responses are coordinated via the various pathways, and the underlying mechanisms, are largely unknown. Herein, we report an essential drought-responsive network in which plants trigger a dynamic metabolic flux conversion from glycolysis into acetate synthesis to stimulate the jasmonate (JA) signalling pathway to confer drought tolerance. In Arabidopsis, the ON/OFF switching of this whole network is directly dependent on histone deacetylase HDA6. In addition, exogenous acetic acid promotes de novo JA synthesis and enrichment of histone H4 acetylation, which influences the priming of the JA signalling pathway for plant drought tolerance. This novel acetate function is evolutionarily conserved as a survival strategy against environmental changes in plants. Furthermore, the external application of acetic acid successfully enhanced the drought tolerance in Arabidopsis, rapeseed, maize, rice and wheat plants. Our findings highlight a radically new survival strategy that exploits an epigenetic switch of metabolic flux conversion and hormone signalling by which plants adapt to drought.
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Affiliation(s)
- Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Taiko Kim To
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Natsuko I Kobayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Fumio Matsuda
- Metabolic Engineering Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5, Yamadaoka, Suita, Osaka 565-0871, Japan
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yoshiki Habu
- Plant Physiology Research Unit, Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Daisuke Ogawa
- Breeding Strategies Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Sultana Rasheed
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Marina Ando
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Hiroko Takeda
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Miyako Kusano
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Atsushi Fukushima
- Metabolome Informatics Research Team, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Centre for Integrative Medical Sciences, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Kuromori
- Gene Discovery Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Junko Ishida
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Taeko Morosawa
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Chieko Torii
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yumiko Takebayashi
- Plant Productivity System Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- Plant Productivity System Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Alessandra Devoto
- School of Biological Sciences, Plant Molecular Sciences, Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
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15
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Kawasaki H, Kasai H, Endo TA, Ashizaki K, Yasuda F, Amagai M, Ebihara T. The classification of atopic dermatitis patients using machine learning method, based on the therapeutic outcome for the proactive treatment. J Dermatol Sci 2017. [DOI: 10.1016/j.jdermsci.2017.02.112] [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: 10/19/2022]
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16
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Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma KW, Ito S, Sharif J, Endoh T, Onaga N, Nakayama M, Ishikura T, Masui O, Kessler BM, Suda T, Ohara O, Okuda A, Klose RJ, Koseki H. Correction: PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. eLife 2017; 6. [PMID: 28440749 PMCID: PMC5404914 DOI: 10.7554/elife.27970] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 11/23/2022] Open
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17
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Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma KW, Ito S, Sharif J, Endoh T, Onaga N, Nakayama M, Ishikura T, Masui O, Kessler BM, Suda T, Ohara O, Okuda A, Klose R, Koseki H. PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. eLife 2017; 6:21064. [PMID: 28304275 PMCID: PMC5375644 DOI: 10.7554/elife.21064] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [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: 09/01/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022] Open
Abstract
The ring finger protein PCGF6 (polycomb group ring finger 6) interacts with RING1A/B and E2F6 associated factors to form a non-canonical PRC1 (polycomb repressive complex 1) known as PCGF6-PRC1. Here, we demonstrate that PCGF6-PRC1 plays a role in repressing a subset of PRC1 target genes by recruiting RING1B and mediating downstream mono-ubiquitination of histone H2A. PCGF6-PRC1 bound loci are highly enriched for promoters of germ cell-related genes in mouse embryonic stem cells (ESCs). Conditional ablation of Pcgf6 in ESCs leads to robust de-repression of such germ cell-related genes, in turn affecting cell growth and viability. We also find a role for PCGF6 in pre- and peri-implantation mouse embryonic development. We further show that a heterodimer of the transcription factors MAX and MGA recruits PCGF6 to target loci. PCGF6 thus links sequence specific target recognition by the MAX/MGA complex to PRC1-dependent transcriptional silencing of germ cell-specific genes in pluripotent stem cells.
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Affiliation(s)
- Mitsuhiro Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Shinga
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Anca Farcas
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Kit-Wan Ma
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Tamie Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Naoko Onaga
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Benedikt M Kessler
- Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Toshio Suda
- Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Robert Klose
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
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18
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Dashtsoodol N, Shigeura T, Aihara M, Ozawa R, Kojo S, Harada M, Endo TA, Watanabe T, Ohara O, Taniguchi M. Alternative pathway for the development of Vα14+ NKT cells directly from CD4–CD8– thymocytes that bypasses the CD4+CD8+ stage. Nat Immunol 2017; 18:274-282. [DOI: 10.1038/ni.3668] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/19/2016] [Indexed: 12/12/2022]
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19
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Ikawa T, Masuda K, Endo TA, Endo M, Isono K, Koseki Y, Nakagawa R, Kometani K, Takano J, Agata Y, Katsura Y, Kurosaki T, Vidal M, Koseki H, Kawamoto H. Conversion of T cells to B cells by inactivation of polycomb-mediated epigenetic suppression of the B-lineage program. Genes Dev 2016; 30:2475-2485. [PMID: 27913604 PMCID: PMC5159663 DOI: 10.1101/gad.290593.116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 09/12/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022]
Abstract
Ikawa et al. report that the inactivation of polycomb-mediated epigenetic regulation results in the conversion of T-lineage progenitors to the B-cell fate. This arrest was almost completely cancelled by additional deletion of Pax5. In general, cell fate is determined primarily by transcription factors, followed by epigenetic mechanisms fixing the status. While the importance of transcription factors controlling cell fate has been well characterized, epigenetic regulation of cell fate maintenance remains to be elucidated. Here we provide an obvious fate conversion case, in which the inactivation of polycomb-medicated epigenetic regulation results in conversion of T-lineage progenitors to the B-cell fate. In T-cell-specific Ring1A/B-deficient mice, T-cell development was severely blocked at an immature stage. We found that these developmentally arrested T-cell precursors gave rise to functional B cells upon transfer to immunodeficient mice. We further demonstrated that the arrest was almost completely canceled by additional deletion of Pax5. These results indicate that the maintenance of T-cell fate critically requires epigenetic suppression of the B-lineage gene program.
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Affiliation(s)
- Tomokatsu Ikawa
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama 230-0045, Japan.,PRESTO (Precursory Research for Embryonic Science and Technology), Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Kyoko Masuda
- Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama 230-0045, Japan.,Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Mitsuhiro Endo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kyoichi Isono
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Rinako Nakagawa
- Laboratory for Lymphocyte Differentiation, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Kohei Kometani
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Junichiro Takano
- Laboratory for Immune Regeneration, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yasutoshi Agata
- Department of Immunology and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yoshimoto Katsura
- Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama 230-0045, Japan.,Division of Cell Regeneration and Transplantation, Advanced Medical Research Center, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Tomohiro Kurosaki
- Laboratory for Lymphocyte Differentiation, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, 28040 Madrid, Spain
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Hiroshi Kawamoto
- Laboratory for Lymphocyte Development, RIKEN Research Center for Allergy and Immunology, Yokohama 230-0045, Japan.,Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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20
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Takikita S, Muro R, Takai T, Otsubo T, Kawamura YI, Dohi T, Oda H, Kitajima M, Oshima K, Hattori M, Endo TA, Toyoda T, Weis J, Shinkai Y, Suzuki H. A Histone Methyltransferase ESET Is Critical for T Cell Development. J Immunol 2016; 197:2269-79. [PMID: 27511731 DOI: 10.4049/jimmunol.1502486] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/08/2016] [Indexed: 12/15/2022]
Abstract
ESET/SETDB1, one of the major histone methyltransferases, catalyzes histone 3 lysine 9 (H3K9) trimethylation. ESET is critical for suppressing expression of retroviral elements in embryonic stem cells; however, its role in the immune system is not known. We found that thymocyte-specific deletion of ESET caused impaired T cell development, with CD8 lineage cells being most severely affected. Increased apoptosis of CD8 single-positive cells was observed, and TCR-induced ERK activation was severely inhibited in ESET(-/-) thymocytes. Genome-wide comprehensive analysis of mRNA expression and H3K9 trimethylation revealed that ESET regulates expression of numerous genes in thymocytes. Among them, FcγRIIB, whose signaling can inhibit ERK activation, was strongly and ectopically expressed in ESET(-/-) thymocytes. Indeed, genetic depletion of FcγRIIB in ESET(-/-) thymocytes rescued impaired ERK activation and partially restored defective positive selection in ESET(-/-) mice. Therefore, impaired T cell development in ESET(-/-) mice is partly due to the aberrant expression of FcγRIIB. Collectively, to our knowledge, we identify ESET as the first trimethylated H3K9 histone methyltransferase playing a crucial role in T cell development.
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Affiliation(s)
- Shoichi Takikita
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Ryunosuke Muro
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Toshiyuki Takai
- Department of Experimental Immunology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Takeshi Otsubo
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Yuki I Kawamura
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Taeko Dohi
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Hiroyo Oda
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Masayuki Kitajima
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan
| | - Kenshiro Oshima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, University of Tokyo, Kashiwa, Chiba 272-8561, Japan
| | - Masahira Hattori
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, University of Tokyo, Kashiwa, Chiba 272-8561, Japan; Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Takaho A Endo
- Integrated Database Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tetsuro Toyoda
- Integrated Database Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
| | - John Weis
- Division of Cell Biology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132; Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132; and
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Harumi Suzuki
- Department of Immunology and Pathology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba 272-8516, Japan;
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21
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Yamada D, Iyoda T, Vizcardo R, Shimizu K, Sato Y, Endo TA, Kitahara G, Okoshi M, Kobayashi M, Sakurai M, Ohara O, Taniguchi M, Koseki H, Fujii SI. Efficient Regeneration of Human Vα24 + Invariant Natural Killer T Cells and Their Anti-Tumor Activity In Vivo. Stem Cells 2016; 34:2852-2860. [PMID: 27422351 DOI: 10.1002/stem.2465] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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: 04/27/2016] [Revised: 06/14/2016] [Accepted: 06/30/2016] [Indexed: 01/31/2023]
Abstract
Reprogramming of antigen-specific T lymphocytes into induced pluripotent stem cells (iPSCs) and their subsequent re-differentiation has enabled expansion of functional T lymphocytes in vitro, thus opening up new approaches for immunotherapy of cancer and other diseases. In this study, we have established a robust protocol to reprogram human invariant NKT (Vα24+ iNKT) cells, which have been shown to act as cellular adjuvants and thus exert anti-tumor activity in mice and humans, and to re-differentiate the iNKT cell-derived iPSCs into functional iNKT cells. These iPSC-derived iNKT cells (iPS-Vα24+ iNKT cells) can be activated by ligand-pulsed dendritic cells (DCs) and produce a large amount of interferon-γ upon activation, as much as parental Vα24+ iNKT cells, but exhibit even better cytotoxic activity against various tumor cell lines. The iPS-Vα24+ iNKT cells possess significant anti-tumor activity in tumor-bearing mice and can activate autologous NK cells upon activation by ligand-pulsed DCs in the NOG mouse model in vivo, further extending their therapeutic potential. This study thus provides a first proof of concept for the clinical application of human iPS-Vα24+ iNKT cells for cancer immunotherapy. Stem Cells 2016;34:2852-2860.
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Affiliation(s)
- Daisuke Yamada
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Tomonori Iyoda
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS)
| | - Raul Vizcardo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS)
| | - Yusuke Sato
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS)
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Genta Kitahara
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Momoko Okoshi
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Midori Kobayashi
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Maki Sakurai
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS)
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Masaru Taniguchi
- Laboratory for Immunoregulation, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Japan
| | - Shin-Ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Science (IMS)
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22
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Sumitomo JI, Emori C, Matsuno Y, Ueno M, Kawasaki K, Endo TA, Shiroguchi K, Fujii W, Naito K, Sugiura K. Mouse oocytes suppress miR-322-5p expression in ovarian granulosa cells. J Reprod Dev 2016; 62:393-9. [PMID: 27180925 PMCID: PMC5005186 DOI: 10.1262/jrd.2015-161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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] [Indexed: 01/01/2023] Open
Abstract
This study tested the hypothesis that oocyte-derived paracrine factors (ODPFs)
regulate miRNA expression in mouse granulosa cells. Expression of mmu-miR-322-5p
(miR-322) was higher in mural granulosa cells (MGCs) than in cumulus cells of the
Graafian follicles. The expression levels of miR-322 decreased when cumulus cells or
MGCs were co-cultured with oocytes denuded of their cumulus cells. Inhibition of
SMAD2/3 signaling by SB431542 increased miR-322 expression by cumulus-oocyte
complexes (COCs). Moreover, the cumulus cells but not the MGCs in
Bmp15–/–/Gdf9+/– (double-mutant) mice
exhibited higher miR-322 expression than those of wild-type mice. Taken together,
these results show that ODPFs suppress the expression of miR-322 in cumulus cells.
Gene ontology analysis of putative miR-322 targets whose expression was detected in
MGCs with RNA-sequencing suggested that multiple biological processes are affected by
miR-322 in MGCs. These results demonstrate that ODPFs regulate miRNA expression in
granulosa cells and that this regulation may participate in the differential control
of cumulus cell versus MGC functions. Therefore, the ODPF-mediated regulation of
cumulus cells takes place at both transcriptional and post-transcriptional
levels.
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Affiliation(s)
- Jun-Ichi Sumitomo
- Laboratory of Applied Genetics, Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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23
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Yakushiji-Kaminatsui N, Kondo T, Endo TA, Koseki Y, Kondo K, Ohara O, Vidal M, Koseki H. RING1 contributes to early proximal-distal specification of the forelimb bud by restricting Meis2 expression. Development 2015; 143:276-85. [DOI: 10.1242/dev.127506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/08/2015] [Indexed: 12/30/2022]
Abstract
Polycomb group (PcG) proteins play a pivotal role in silencing development-related genes and help to maintain various stem and precursor cells and regulate their differentiation. PcG factors also regulate dynamic and complex regional specification, particularly in mammals, but this activity is mechanistically not well understood. In this study, we focused on proximal-distal (PD) patterning of the forelimb bud to elucidate how PcG factors contribute to a regional specification process that depends on developmental signals. Depletion of RING1 proteins, which are essential components of the Polycomb repressive complex-1 (PRC1), led to severe defects in forelimb formation along the PD axis. We show that preferential defects in early distal specification in Ring1-deficient forelimb buds accompany failures in repression of proximal signal circuitry bound by RING1B, including Meis2/1, and activation of distal signal circuitry in the prospective distal region. Additional deletion of Meis2 induced partial restoration of distal gene expression and limb formation seen in the Ring1-deficient mice, suggesting a critical role for RING1-dependent repression of Meis2 and likely Meis1 for distal specification. We suggest that the RING1/MEIS2/1 axis is regulated by early PD signals and contributes to initiation or maintenance of the distal signal circuitry.
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Affiliation(s)
- Nayuta Yakushiji-Kaminatsui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Takaho A. Endo
- Laboratory for Integrative Genomics, RIKEN IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kaori Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biológicas, Department of Cellular and Molecular Biology, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Abstract
RNA sequencing (RNA-seq) provides information not only about the level of expression of individual genes but also about genomic sequences of host cells. When we use transcriptome data with whole-genome single nucleotide polymorphism (SNP) variant information, the allele frequency can show the genetic composition of the cell population and/or chromosomal aberrations. Here, I show how SNPs in mRNAs can be used to evaluate RNA-seq experiments by focusing on RNA-seq data based on a recently retracted paper on stimulus-triggered acquisition of pluripotency (STAP) cells. The analysis indicated that different types of cells and chromosomal abnormalities might have been erroneously included in the dataset. This re-evaluation showed that observing allele frequencies could help in assessing the quality of samples during a study and with retrospective evaluation of experimental quality.
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Affiliation(s)
- Takaho A Endo
- RIKEN Center for Integrative Medical Science (IMS-RIKEN), 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan
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25
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Kim JM, To TK, Tanaka M, Endo TA, Matsui A, Ishida J, Robertson FC, Toyoda T, Seki M. Highly reproducible ChIP-on-chip analysis to identify genome-wide protein binding and chromatin status in Arabidopsis thaliana. Methods Mol Biol 2014; 1062:405-26. [PMID: 24057379 DOI: 10.1007/978-1-62703-580-4_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gene activity is regulated via chromatin dynamics in eukaryotes. In plants, alterations of histone modifications are correlated with gene regulation for development, vernalization, and abiotic stress responses. Using ChIP, ChIP-on-chip, and ChIP-seq analyses, the direct binding regions of transcription factors and alterations of histone modifications can be identified on a genome-wide level. We have established reliable and reproducible ChIP and ChIP-on-chip methods that have been optimized for the Arabidopsis model system. These methods are not only useful for identifying the direct binding of transcription factors and chromatin status but also for scanning the regulatory network in Arabidopsis.
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Affiliation(s)
- Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Japan
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26
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Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, Nakanishi Y, Uetake C, Kato K, Kato T, Takahashi M, Fukuda NN, Murakami S, Miyauchi E, Hino S, Atarashi K, Onawa S, Fujimura Y, Lockett T, Clarke JM, Topping DL, Tomita M, Hori S, Ohara O, Morita T, Koseki H, Kikuchi J, Honda K, Hase K, Ohno H. Erratum: Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2014. [DOI: 10.1038/nature13041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Kondo T, Isono K, Kondo K, Endo TA, Itohara S, Vidal M, Koseki H. Polycomb potentiates meis2 activation in midbrain by mediating interaction of the promoter with a tissue-specific enhancer. Dev Cell 2013. [PMID: 24374176 DOI: 10.1016/j.devcel.20 13.11.021] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Polycomb-group (PcG) proteins mediate repression of developmental regulators in a reversible manner, contributing to their spatiotemporally regulated expression. However, it is poorly understood how PcG-repressed genes are activated by developmental cues. Here, we used the mouse Meis2 gene as a model to identify a role of a tissue-specific enhancer in removing PcG from the promoter. Meis2 repression in early development depends on binding of RING1B, an essential E3 component of PcG, to its promoter, coupled with its association with another RING1B-binding site (RBS) at the 3' end of the Meis2 gene. During early midbrain development, a midbrain-specific enhancer (MBE) transiently associates with the promoter-RBS, forming a promoter-MBE-RBS tripartite interaction in a RING1-dependent manner. Subsequently, RING1B-bound RBS dissociates from the tripartite complex, leaving promoter-MBE engagement to activate Meis2 expression. This study therefore demonstrates that PcG and/or related factors play a role in Meis2 activation by regulating the topological transition of cis-regulatory elements.
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Affiliation(s)
- Takashi Kondo
- Developmental Genetics Laboratory, RIKEN-IMS, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; CREST, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Kondo Research Unit, RIKEN-BSI, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Kyoichi Isono
- Developmental Genetics Laboratory, RIKEN-IMS, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kaori Kondo
- Developmental Genetics Laboratory, RIKEN-IMS, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; CREST, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Kondo Research Unit, RIKEN-BSI, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takaho A Endo
- Integrative Genomics Laboratory, RIKEN-IMS, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shigeyoshi Itohara
- Laboratory of Behavioral Genetics, RIKEN-BSI, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biológicas, Department of Cellular and Molecular Biology, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Haruhiko Koseki
- Developmental Genetics Laboratory, RIKEN-IMS, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; CREST, Japan Science and Technology Agency, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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28
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Otani J, Kimura H, Sharif J, Endo TA, Mishima Y, Kawakami T, Koseki H, Shirakawa M, Suetake I, Tajima S. Cell cycle-dependent turnover of 5-hydroxymethyl cytosine in mouse embryonic stem cells. PLoS One 2013; 8:e82961. [PMID: 24340069 PMCID: PMC3858372 DOI: 10.1371/journal.pone.0082961] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/30/2013] [Indexed: 11/29/2022] Open
Abstract
Hydroxymethylcytosine in the genome is reported to be an intermediate of demethylation. In the present study, we demonstrated that maintenance methyltransferase Dnmt1 scarcely catalyzed hemi-hydroxymethylated DNA and that the hemi-hydroxymethylated DNA was not selectively recognized by the SRA domain of Uhrf1, indicating that hydroxymethylcytosine is diluted in a replication-dependent manner. A high level of 5-hydroxymethylcytosine in mouse embryonic stem cells was produced from the methylcytosine supplied mainly by de novo-type DNA methyltransferases Dnmt3a and Dnmt3b. The promoter regions of the HoxA gene cluster showed a high hydroxymethylation level whilst the methylcytosine level was quite low, suggesting that methylated CpG is actively hydroxylated during proliferation. All the results indicate that removal and production of hydroxymethylcytosine are regulated in replication-dependent manners in mouse embryonic stem cells.
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Affiliation(s)
- Junji Otani
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Hironobu Kimura
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Jafar Sharif
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takaho A. Endo
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Yuichi Mishima
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Masahiro Shirakawa
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Isao Suetake
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Shoji Tajima
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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29
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Isono K, Endo TA, Ku M, Yamada D, Suzuki R, Sharif J, Ishikura T, Toyoda T, Bernstein BE, Koseki H. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev Cell 2013; 26:565-77. [PMID: 24091011 DOI: 10.1016/j.devcel.2013.08.016] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/29/2013] [Accepted: 08/19/2013] [Indexed: 01/01/2023]
Abstract
The Polycomb-group (PcG) repressive complex-1 (PRC1) forms microscopically visible clusters in nuclei; however, the impact of this cluster formation on transcriptional regulation and the underlying mechanisms that regulate this process remain obscure. Here, we report that the sterile alpha motif (SAM) domain of a PRC1 core component Phc2 plays an essential role for PRC1 clustering through head-to-tail macromolecular polymerization, which is associated with stable target binding of PRC1/PRC2 and robust gene silencing activity. We propose a role for SAM domain polymerization in this repression by two distinct mechanisms: first, through capturing and/or retaining PRC1 at the PcG targets, and second, by strengthening the interactions between PRC1 and PRC2 to stabilize transcriptional repression. Our findings reveal a regulatory mechanism mediated by SAM domain polymerization for PcG-mediated repression of developmental loci that enables a robust yet reversible gene repression program during development.
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Affiliation(s)
- Kyoichi Isono
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS-RCAI), 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan; CREST, Japan Science and Technology Agency, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan; PREST, Japan Science and Technology Agency, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan.
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30
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Miyazaki H, Higashimoto K, Yada Y, Endo TA, Sharif J, Komori T, Matsuda M, Koseki Y, Nakayama M, Soejima H, Handa H, Koseki H, Hirose S, Nishioka K. Ash1l methylates Lys36 of histone H3 independently of transcriptional elongation to counteract polycomb silencing. PLoS Genet 2013; 9:e1003897. [PMID: 24244179 PMCID: PMC3820749 DOI: 10.1371/journal.pgen.1003897] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 09/03/2013] [Indexed: 12/27/2022] Open
Abstract
Molecular mechanisms for the establishment of transcriptional memory are poorly understood. 5,6-dichloro-1-D-ribofuranosyl-benzimidazole (DRB) is a P-TEFb kinase inhibitor that artificially induces the poised RNA polymerase II (RNAPII), thereby manifesting intermediate steps for the establishment of transcriptional activation. Here, using genetics and DRB, we show that mammalian Absent, small, or homeotic discs 1-like (Ash1l), a member of the trithorax group proteins, methylates Lys36 of histone H3 to promote the establishment of Hox gene expression by counteracting Polycomb silencing. Importantly, we found that Ash1l-dependent Lys36 di-, tri-methylation of histone H3 in a coding region and exclusion of Polycomb group proteins occur independently of transcriptional elongation in embryonic stem (ES) cells, although both were previously thought to be consequences of transcription. Genome-wide analyses of histone H3 Lys36 methylation under DRB treatment have suggested that binding of the retinoic acid receptor (RAR) to a certain genomic region promotes trimethylation in the RAR-associated gene independent of its ongoing transcription. Moreover, DRB treatment unveils a parallel response between Lys36 methylation of histone H3 and occupancy of either Tip60 or Mof in a region-dependent manner. We also found that Brg1 is another key player involved in the response. Our results uncover a novel regulatory cascade orchestrated by Ash1l with RAR and provide insights into mechanisms underlying the establishment of the transcriptional activation that counteracts Polycomb silencing.
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Affiliation(s)
- Hitomi Miyazaki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi City, Saitama, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
| | - Yukari Yada
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
| | - Takaho A. Endo
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Jafar Sharif
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Toshiharu Komori
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama City, Kanagawa, Japan
| | - Masashi Matsuda
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Yoko Koseki
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Manabu Nakayama
- Laboratory of Medical Genomics, Department of Human Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu City, Chiba, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
| | - Hiroshi Handa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama City, Kanagawa, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi City, Saitama, Japan
| | - Susumu Hirose
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
| | - Kenichi Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi City, Saitama, Japan
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
- * E-mail:
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31
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Sharif J, Endo TA, Ito S, Ohara O, Koseki H. Embracing change to remain the same: conservation of polycomb functions despite divergence of binding motifs among species. Curr Opin Cell Biol 2013; 25:305-13. [PMID: 23478215 DOI: 10.1016/j.ceb.2013.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 02/17/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
Polycomb-group (PcG) proteins are evolutionarily conserved developmental regulators among species. In flies, PcG factors bind discrete DNA motifs known as the PREs (polycomb response elements); while in mammals they exhibit a marked preference for CpG islands (CGIs) that are unmethylated CpG-rich stretches in the genome. In this review, we discuss that despite the lack of similarities in DNA sequence both PREs and CGIs share many common properties and suggest that these could play a role for recruitment of PcG molecules into these loci. Further, in light of the antagonistic relationship between polycomb and DNA methylation pathways in mammals, we construct a model by compartmentalizing the genome into several representative categories and propose that the polycomb factors are the most suited to regulate development associated genes because of the robust yet reversible nature of PcG mediated transcriptional repression.
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Affiliation(s)
- Jafar Sharif
- Developmental Genetics Group, RIKEN Research Center for Allergy & Immunology (RCAI), 1-7-22 Suehiuro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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32
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Itoh Y, Moriyama Y, Hasegawa T, Endo TA, Toyoda T, Gotoh Y. Scratch regulates neuronal migration onset via an epithelial-mesenchymal transition-like mechanism. Nat Neurosci 2013; 16:416-25. [PMID: 23434913 DOI: 10.1038/nn.3336] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/23/2013] [Indexed: 12/15/2022]
Abstract
During neocortical development, the neuroepithelial or neural precursor cells that commit to neuronal fate need to delaminate and start migration toward the pial surface. However, the mechanism that couples neuronal fate commitment to detachment from the neuroepithelium remains largely unknown. Here we show that Scratch1 and Scratch2, members of the Snail superfamily of transcription factors, are expressed upon neuronal fate commitment under the control of proneural genes and promote apical process detachment and radial migration in the developing mouse neocortex. Scratch-induced delamination from the apical surface was mediated by transcriptional repression of the adhesion molecule E-cadherin. These findings suggest that Scratch proteins constitute a molecular link between neuronal fate commitment and the onset of neuronal migration. On the basis of their similarity to proteins involved in the epithelial-mesenchymal transition (EMT), we propose that Scratch proteins mediate the conversion of neuroepithelial cells to migrating neurons or intermediate neuronal progenitors through an EMT-related mechanism.
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Affiliation(s)
- Yasuhiro Itoh
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan.
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33
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Endoh M, Endo TA, Endoh T, Isono KI, Sharif J, Ohara O, Toyoda T, Ito T, Eskeland R, Bickmore WA, Vidal M, Bernstein BE, Koseki H. Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. PLoS Genet 2012; 8:e1002774. [PMID: 22844243 PMCID: PMC3405999 DOI: 10.1371/journal.pgen.1002774] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 05/04/2012] [Indexed: 01/08/2023] Open
Abstract
Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing mono-ubiquitination of histone H2A (H2AK119u1) and trimethylation of H3 lysine 27 (H3K27me3), respectively. Compared to H3K27me3, localization and the role of H2AK119u1 are not fully understood in ESCs. Here we present genome-wide H2AK119u1 maps in ESCs and identify a group of genes at which H2AK119u1 is deposited in a Ring1-dependent manner. These genes are a distinctive subset of genes with H3K27me3 enrichment and are the central targets of Polycomb silencing that are required to maintain ESC identity. We further show that the H2A ubiquitination activity of PRC1 is dispensable for its target binding and its activity to compact chromatin at Hox loci, but is indispensable for efficient repression of target genes and thereby ESC maintenance. These data demonstrate that multiple effector mechanisms including H2A ubiquitination and chromatin compaction combine to mediate PRC1-dependent repression of genes that are crucial for the maintenance of ESC identity. Utilization of these diverse effector mechanisms might provide a means to maintain a repressive state that is robust yet highly responsive to developmental cues during ES cell self-renewal and differentiation. Polycomb-group (PcG) proteins play essential roles in the epigenetic regulation of gene expression during development. PcG proteins form two distinct multimeric complexes, PRC1 and PRC2. In the widely accepted hierarchical model, PRC2 is recruited to specific genomic locations and catalyzes trimethylation of H3 lysine 27 (H3K27me3), thereby creating binding sites for PRC1, which then catalyzes mono-ubiquitination of histone H2A (H2AK119u1). Recently, PRC1 has been shown to be able to compact chromatin structure at target loci independently of its histone ubiquitination activity. Therefore, the role of H2AK119u1 still remains unclear. To gain insight into this issue, we used ChIP-on-chip analysis to map H2AK119u1 genome-wide in mouse ES cells (ESCs). The data demonstrate that H2AK119u1 occupies a distinctive subset of genes with H3K27me3 enrichment. These genes are the central targets of Polycomb silencing to maintain ESC identity. We further show that the H2A ubiquitination activity of PRC1 is dispensable for its target binding and its activity to compact chromatin at Hox loci, but is indispensable for efficient repression of target genes and therefore ESC maintenance. We propose that multiple effector mechanisms including H2A ubiquitination and chromatin compaction combine to mediate PRC1-dependent repression of developmental genes to maintain the identity of ESCs.
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Affiliation(s)
- Mitsuhiro Endoh
- Laboratory for Developmental Genetics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Yokohama, Japan
- * E-mail: (ME); (HK)
| | - Takaho A. Endo
- RIKEN Bioinformatics and System Engineering Division, Yokohama, Japan
| | - Tamie Endoh
- Laboratory for Developmental Genetics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Kyo-ichi Isono
- Laboratory for Developmental Genetics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Osamu Ohara
- Laboratories for Immunogenomics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Tetsuro Toyoda
- RIKEN Bioinformatics and System Engineering Division, Yokohama, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Ragnhild Eskeland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Miguel Vidal
- Cell Proliferation and Development, Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Research Unit for Immunoepigenetics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Bradley E. Bernstein
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Yokohama, Japan
- * E-mail: (ME); (HK)
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Koseki H, Endoh M, Endo TA. O12. Polycomb-dependent regulation for differentiation programs of stem cells and progenitors. Differentiation 2010. [DOI: 10.1016/j.diff.2010.09.155] [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]
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35
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Watarai H, Fujii SI, Yamada D, Rybouchkin A, Sakata S, Nagata Y, Iida-Kobayashi M, Sekine-Kondo E, Shimizu K, Shozaki Y, Sharif J, Matsuda M, Mochiduki S, Hasegawa T, Kitahara G, Endo TA, Toyoda T, Ohara O, Harigaya KI, Koseki H, Taniguchi M. Murine induced pluripotent stem cells can be derived from and differentiate into natural killer T cells. J Clin Invest 2010; 120:2610-8. [PMID: 20516640 DOI: 10.1172/jci42027] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 04/14/2010] [Indexed: 01/04/2023] Open
Abstract
NKT cells demonstrate antitumor activity when activated to produce Th1 cytokines by DCs loaded with alpha-galactosylceramide, the prototypic NKT cell-activating glycolipid antigen. However, most patients do not have sufficient numbers of NKT cells to induce an effective immune response in this context, indicating a need for a source of NKT cells that could be used to supplement the endogenous cell population. Induced pluripotent stem cells (iPSCs) hold tremendous potential for cell-replacement therapy, but whether it is possible to generate functionally competent NKT cells from iPSCs has not been rigorously assessed. In this study, we successfully derived iPSCs both from embryonic fibroblasts from mice harboring functional NKT cell-specific rearranged T cell receptor loci in the germline and from splenic NKT cells from WT adult mice. These iPSCs could be differentiated into NKT cells in vitro and secreted large amounts of the Th1 cytokine IFN-gamma. Importantly, iPSC-derived NKT cells recapitulated the known adjuvant effects of natural NKT cells and suppressed tumor growth in vivo. These studies demonstrate the feasibility of expanding functionally competent NKT cells via an iPSC phase, an approach that may be adapted for NKT cell-targeted therapy in humans.
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Affiliation(s)
- Hiroshi Watarai
- RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan
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Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J, Tanaka M, Endo TA, Mochizuki Y, Toyoda T, Kamiya Y, Shinozaki K, Nambara E, Seki M. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant J 2010; 62:39-51. [PMID: 20088898 DOI: 10.1111/j.1365-313x.2010.04135.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The phytohormone abscisic acid (ABA) plays important roles in the induction and maintenance of seed dormancy. Although application of exogenous ABA inhibits germination, the effects of exogenous ABA on ABA-mediated gene transcription differ from those of endogenous ABA. To understand how endogenous ABA regulates the transcriptomes in seeds, we performed comprehensive expression analyses using whole-genome Affymetrix tiling arrays in two ABA metabolism mutants - an ABA-deficient mutant (aba2) and an ABA over-accumulation mutant (cyp707a1a2a3 triple mutant). Hierarchical clustering and principal components analyses showed that differences in endogenous ABA levels do not influence global expression of stored mRNA in dry seeds. However, the transcriptome after seed imbibition was related to endogenous ABA levels in both types of mutant. Endogenous ABA-regulated genes expressed in imbibed seeds included those encoding key ABA signaling factors and gibberellin-related components. In addition, cohorts of ABA-upregulated genes partially resembled those of dormant genes, whereas ABA-downregulated genes were partially overlapped with after-ripening-regulated genes. Bioinformatic analyses revealed that 6105 novel genes [non-Arabidopsis Genome Initiative (AGI) transcriptional units (TUs)] were expressed from unannotated regions. Interestingly, approximately 97% of non-AGI TUs possibly encoded hypothetical non-protein-coding RNAs, including a large number of antisense RNAs. In dry and imbibed seeds, global expression profiles of non-AGI TUs were similar to those of AGI genes. For both non-AGI TUs and AGI code genes, we identified those that were regulated differently in embryo and endosperm tissues. Our results suggest that transcription in Arabidopsis seeds is more complex and dynamic than previously thought.
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Hirabayashi Y, Suzki N, Tsuboi M, Endo TA, Toyoda T, Shinga J, Koseki H, Vidal M, Gotoh Y. Polycomb limits the neurogenic competence of neural precursor cells to promote astrogenic fate transition. Neuron 2009; 63:600-13. [PMID: 19755104 DOI: 10.1016/j.neuron.2009.08.021] [Citation(s) in RCA: 332] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 08/20/2009] [Accepted: 08/20/2009] [Indexed: 11/26/2022]
Abstract
During neocortical development, neural precursor cells (NPCs, or neural stem cells) produce neurons first and astrocytes later. Although the timing of the fate switch from neurogenic to astrogenic is critical for determining the number of neurons, the mechanisms are not fully understood. Here, we show that the polycomb group complex (PcG) restricts neurogenic competence of NPCs and promotes the transition of NPC fate from neurogenic to astrogenic. Inactivation of PcG by knockout of the Ring1B or Ezh2 gene or Eed knockdown prolonged the neurogenic phase of NPCs and delayed the onset of the astrogenic phase. Moreover, PcG was found to repress the promoter of the proneural gene neurogenin1 in a developmental-stage-dependent manner. These results demonstrate a role of PcG: the temporal regulation of NPC fate.
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Affiliation(s)
- Yusuke Hirabayashi
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
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Matsushima A, Kobayashi N, Mochizuki Y, Ishii M, Kawaguchi S, Endo TA, Umetsu R, Makita Y, Toyoda T. OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. Nucleic Acids Res 2009; 37:W57-62. [PMID: 19528066 PMCID: PMC2703975 DOI: 10.1093/nar/gkp404] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. It is an open source tool capable of regulating multiple user data access to each dataset to allow multiple users to have their own integrative view of both their unpublished and published datasets, so that the maintenance costs related to supplying each collaborator exclusively with their own private data are significantly reduced. OmicBrowse supports DAS1 imports and exports of annotations to Internet site servers worldwide. We also provide a data-download named OmicDownload server that interactively selects datasets and filters the data on the selected datasets. Our OmicBrowse server has been freely available at http://omicspace.riken.jp/ since its launch in 2003. The OmicBrowse source code is downloadable from http://sourceforge.net/projects/omicbrowse/.
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Affiliation(s)
- Akihiro Matsushima
- Bioinformatics and Systems Engineering division (BASE), RIKEN (The Institute of Physical and Chemical Research), 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Mano S, Endo TA, Oka A, Ozawa A, Gojobori T, Inoko H. Detecting linkage between a trait and a marker in a random mating population without pedigree record. PLoS One 2009; 4:e4956. [PMID: 19308260 PMCID: PMC2655708 DOI: 10.1371/journal.pone.0004956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/27/2008] [Accepted: 02/20/2009] [Indexed: 11/18/2022] Open
Abstract
Modern linkage-based approaches employing extended pedigrees are becoming powerful tools for localizing complex quantitative trait loci. For these linkage mapping methods, it is necessary to reconstruct extended pedigrees which include living individuals, using extensive pedigree records. Unfortunately, such records are not always easy to obtain and application of the linkage-based approaches has been restricted. Within a finite population under random mating, latent inbreeding rather than non-random inbreeding by consanguineous marriages is expected to occur and is attributable to coalescence in a finite population. Interestingly, it has been revealed that significant random inbreeding exists even in general human populations. Random inbreeding should be used to detect the hidden coancestry between individuals for a particular chromosomal position and it could also have application in linkage mapping methods. Here we present a novel method, named finite population based linkage mapping (FPL) method, to detect linkage between a quantitative trait and a marker via random inbreeding in a finite population without pedigree records. We show how to estimate coancestry for a chromosomal position between individuals by using multipoint Bayesian estimation. Subsequently, we describe the FPL method for detecting linkage via interval mapping method using a nonparametric test. We show that the FPL method does work via simulated data. For a random sample from a finite population, the FPL method is more powerful than a standard pedigree-based linkage mapping method with using genotypes of all parents of the sample. In addition, the FPL method was demonstrated by actual microsatellite genotype data of 750 Japanese individuals that are unrelated according to pedigree records to map a known Psoriasis susceptible locus. For samples without pedigree records, it was suggested that the FPL method require limited number of individuals, therefore would be better than other methods using thousands of individuals.
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Affiliation(s)
- Shuhei Mano
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan.
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Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kawashima M, Satou M, Kim JM, Kobayashi N, Toyoda T, Shinozaki K, Seki M. Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol 2008; 49:1135-49. [PMID: 18625610 DOI: 10.1093/pcp/pcn101] [Citation(s) in RCA: 330] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants respond and adapt to drought, cold and high-salinity stresses in order to survive. In this study, we applied Arabidopsis Affymetrix tiling arrays to study the whole genome transcriptome under drought, cold, high-salinity and ABA treatment conditions. The bioinformatic analysis using the tiling array data showed that 7,719 non-AGI transcriptional units (TUs) exist in the unannotated "intergenic" regions of Arabidopsis genome. These include 1,275 and 181 TUs that are induced and downregulated, respectively, by the stress or ABA treatments. Most of the non-AGI TUs are hypothetical non-protein-coding RNAs. About 80% of the non-AGI TUs belong to pairs of the fully overlapping sense-antisense transcripts (fSATs). Significant linear correlation between the expression ratios (treated/untreated) of the sense TUs and the ratios of the antisense TUs was observed in the SATs of AGI code/non-AGI TU. We studied the biogenesis mechanisms of the stress- or ABA-inducible antisense RNAs and found that the expression of sense TUs is necessary for the stress- or ABA-inducible expression of the antisense TUs in the fSATs (AGI code/non-AGI TU).
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Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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Endoh M, Endo TA, Endoh T, Fujimura YI, Ohara O, Toyoda T, Otte AP, Okano M, Brockdorff N, Vidal M, Koseki H. Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity. Development 2008; 135:1513-24. [PMID: 18339675 DOI: 10.1242/dev.014340] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Polycomb group (PcG) proteins mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes 1 (PRC1) and 2 (PRC2). Although PRC2 has been shown to share target genes with the core transcription network, including Oct3/4, to maintain embryonic stem (ES) cells, it is still unclear whether PcG proteins and the core transcription network are functionally linked. Here, we identify an essential role for the core PRC1 components Ring1A/B in repressing developmental regulators in mouse ES cells and, thereby, in maintaining ES cell identity. A significant proportion of the PRC1 target genes are also repressed by Oct3/4. We demonstrate that engagement of PRC1 at target genes is Oct3/4-dependent, whereas engagement of Oct3/4 is PRC1-independent. Moreover, upon differentiation induced by Gata6 expression, most of the Ring1A/B target genes are derepressed and the binding of Ring1A/B to their target loci is also decreased. Collectively, these results indicate that Ring1A/B-mediated Polycomb silencing functions downstream of the core transcriptional regulatory circuitry to maintain ES cell identity.
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Affiliation(s)
- Mitsuhiro Endoh
- RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan
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Abstract
MOTIVATION Developing a new method of assembling small sequences based on sequencing by hybridization with many positive and negative faults. First, an interpretation of a generic traveling salesman problem is provided (i.e. finding the shortest route for visiting many cities), using genetic algorithms. Second, positive errors are excluded before assembly by a sanitization process. RESULTS The present method outperforms those described in previous studies, in terms of both time and accuracy. AVAILABILITY http://kamit.med.u-tokai.ac.jp/~takaho/sbh/index.html
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Affiliation(s)
- Takaho A Endo
- Division of Molecular Life Sciences, Department of Genetic Information, School of Medicine, Tokai University, Bouseidai, Isehara, Kanagawa, 259-1193, Japan.
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Endo TA, Masuhara M, Yokouchi M, Suzuki R, Sakamoto H, Mitsui K, Matsumoto A, Tanimura S, Ohtsubo M, Misawa H, Miyazaki T, Leonor N, Taniguchi T, Fujita T, Kanakura Y, Komiya S, Yoshimura A. A new protein containing an SH2 domain that inhibits JAK kinases. Nature 1997; 387:921-4. [PMID: 9202126 DOI: 10.1038/43213] [Citation(s) in RCA: 1065] [Impact Index Per Article: 39.4] [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: 02/04/2023]
Abstract
The proliferation and differentiation of cells of many lineages are regulated by secreted proteins known as cytokines. Cytokines exert their biological effect through binding to cell-surface receptors that are associated with one or more members of the JAK family of cytoplasmic tyrosine kinases. Cytokine-induced receptor dimerization leads to the activation of JAKs, rapid tyrosine-phosphorylation of the cytoplasmic domains, and subsequent recruitment of various signalling proteins, including members of the STAT family of transcription factors, to the receptor complex. Using the yeast two-hybrid system, we have now isolated a new SH2-domain-containing protein, JAB, which is a JAK-binding protein that interacts with the Jak2 tyrosine-kinase JH1 domain. JAB is structurally related to CIS, a cytokine-inducible SH2 protein. Interaction of JAB with Jak1, Jak2 or Jak3 markedly reduces their tyrosine-kinase activity and suppresses the tyrosine-phosphorylation and activation of STATs. JAB and CIS appear to function as negative regulators in the JAK signalling pathway.
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Affiliation(s)
- T A Endo
- Institute of Life Science, Kurume University, Aikawamachi, Japan
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Endo TA, Kobayashi T, Ohki K. A Chinese hamster ovary cell mutant resistant to phosphatidylserine is defective in transbilayer movement of cell surface phosphatidylserine. Exp Cell Res 1996; 228:341-6. [PMID: 8912728 DOI: 10.1006/excr.1996.0334] [Citation(s) in RCA: 5] [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: 02/03/2023]
Abstract
A mammalian plasma membrane protein(s) which catalyzes ATP-dependent transbilayer movement (flip-flop) of phosphatidylserine (PS) has been suggested to be involved in the formation and maintenance of membrane lipid asymmetry. Flip-flop of PS in the cell surface of nucleated cells was first described by O. C. Martin and R. E. Pagano (1987, J. Biol. Chem. 262, 5890-5898). It has been suggested that flip-flop is involved in the internalization of exogenous PS in cultured cells. In the present study we report that incubation with an excess amount of PS is cytotoxic to Chinese hamster ovary (CHO) cells, while the same amount of phosphatidylcholine gives no effect. This effect allowed us to obtain PS-resistant cells among mutagenized CHO cells. Endocytosis-independent internalization of exogenous fluorescent PS analog was defective in 40% of the PS-resistant mutants. One of the mutants, PSR (phosphatidylserine resistant) 406 was further characterized. Unlike wild-type CHO cells, this mutant did not transport fluorescent PS significantly at 15 degrees C. Fluorescent PS was not metabolized at 15 degrees C in either wild-type or mutant cells. These results suggest that transbilayer movement of cell surface PS is defective in PS-resistant cells.
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Affiliation(s)
- T A Endo
- Department of Physics, Tohoku University, Sendai, Japan
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