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Kubo N, Uehara R, Uemura S, Ohishi H, Shirane K, Sasaki H. Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells. Nat Commun 2024; 15:3266. [PMID: 38627502 PMCID: PMC11021467 DOI: 10.1038/s41467-024-47699-2] [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: 09/15/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
DNA methyltransferase 3A (DNMT3A) and its catalytically inactive cofactor DNA methyltransferase 3-Like (DNMT3L) proteins form functional heterotetramers to deposit DNA methylation in mammalian germ cells. While both proteins have an ATRX-DNMT3-DNMT3L (ADD) domain that recognizes histone H3 tail unmethylated at lysine-4 (H3K4me0), the combined and differential roles of the domains in the two proteins have not been fully defined in vivo. Here we investigate DNA methylation landscapes in female and male germ cells derived from mice with loss-of-function amino acid substitutions in the ADD domains of DNMT3A and/or DNMT3L. Mutations in either the DNMT3A-ADD or the DNMT3L-ADD domain moderately decrease global CG methylation levels, but to different degrees, in both germ cells. Furthermore, when the ADD domains of both DNMT3A and DNMT3L lose their functions, the CG methylation levels are much more reduced, especially in oocytes, comparable to the impact of the Dnmt3a/3L knockout. In contrast, aberrant accumulation of non-CG methylation occurs at thousands of genomic regions in the double mutant oocytes and spermatozoa. These results highlight the critical role of the ADD-H3K4me0 binding in proper CG and non-CG methylation in germ cells and the various impacts of the ADD domains of the two proteins.
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Affiliation(s)
- Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Ryuji Uehara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hiroaki Ohishi
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenjiro Shirane
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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Uehara R, Au Yeung WK, Toriyama K, Ohishi H, Kubo N, Toh H, Suetake I, Shirane K, Sasaki H. The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes. PLoS Genet 2023; 19:e1010855. [PMID: 37527244 PMCID: PMC10393158 DOI: 10.1371/journal.pgen.1010855] [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: 01/13/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Establishment of a proper DNA methylation landscape in mammalian oocytes is important for maternal imprinting and embryonic development. De novo DNA methylation in oocytes is mediated by the DNA methyltransferase DNMT3A, which has an ATRX-DNMT3-DNMT3L (ADD) domain that interacts with histone H3 tail unmethylated at lysine-4 (H3K4me0). The domain normally blocks the methyltransferase domain via intramolecular interaction and binding to histone H3K4me0 releases the autoinhibition. However, H3K4me0 is widespread in chromatin and the role of the ADD-histone interaction has not been studied in vivo. We herein show that amino-acid substitutions in the ADD domain of mouse DNMT3A cause dwarfism. Oocytes derived from homozygous females show mosaic loss of CG methylation and almost complete loss of non-CG methylation. Embryos derived from such oocytes die in mid-to-late gestation, with stochastic and often all-or-none-type CG-methylation loss at imprinting control regions and misexpression of the linked genes. The stochastic loss is a two-step process, with loss occurring in cleavage-stage embryos and regaining occurring after implantation. These results highlight an important role for the ADD domain in efficient, and likely processive, de novo CG methylation and pose a model for stochastic inheritance of epigenetic perturbations in germ cells to the next generation.
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Affiliation(s)
- Ryuji Uehara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keisuke Toriyama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Isao Suetake
- Department of Nutrition Science, Nakamura Gakuen University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Shirane K, Lorincz M. Epigenetic mechanisms governing female and male germline development in mammals. Sex Dev 2023:000529336. [PMID: 36702107 DOI: 10.1159/000529336] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/22/2023] [Indexed: 01/28/2023] Open
Abstract
Background DNA methylation (DNAme) and histone post-translational modifications (PTMs) play an integral role in the transcriptional regulation of specific sets of genes and retrotransposons. In turn, these chromatin marks are essential for cellular reprogramming, including during germline development. While DNAme is stably propagated in most somatic tissues, this epigenetic mark undergoes cycles of widespread erasure and re-establishment in the early embryo as well as in the germline. Summary De novo DNAme occurs at distinct developmental stages in male and female germ cells; before birth in prospermatogonia (PSG) and after birth in growing oocytes. Furthermore, while only ~40% of the mouse genome is methylated in mature oocytes, ~80% of the genome is methylated in mature sperm. Here, we review recent epigenome studies which reveal a complex interplay between histone PTMs and de novo DNAme in shaping the sexually dimorphic profiles of DNAme observed in mature gametes in the mouse, including in intergenic regions as well as at imprinted gametic differentially methylated regions (gDMRs). We discuss the dynamics and distribution of key histone PTMs in male and female germ cells, including H3K36me2/me3, H3K4me3 and H3K27me3, and the implications of positive and negative crosstalk between these PTMs and the DNAme machinery. Finally, we reflect on how the sex-specific epigenetic landscapes observed in the mouse germline impact transcriptional regulation in both the gametes and the early embryo. Key Messages Investigation of the roles of chromatin modifying enzymes and the interplay between the chromatin marks that they deposit in germ cells has been facilitated by analyses of conventional or germline-specific knockout mice, combined with low-input genome-wide profiling methods that have been developed in recent years. While clearly informative, these findings generally reflect "snapshots" of chromatin states derived from analyses of cells analyzed in bulk at a specific period in development. Technological advances and novel experimental models will be required to further refine our understanding of the underlying mechanism and order of establishment of chromatin marks and the impact of sexually dimorphic epigenetic patterning on transcription and other nuclear processes in germ cells, the early embryo and beyond.
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Lu Y, Nagamori I, Kobayashi H, Kojima-Kita K, Shirane K, Chang HY, Nishimura T, Koyano T, Yu Z, Castañeda JM, Matsuyama M, Kuramochi-Miyagawa S, Matzuk MM, Ikawa M. ADAD2 functions in spermiogenesis and piRNA biogenesis in mice. Andrology 2023; 11:698-709. [PMID: 36698249 PMCID: PMC10073342 DOI: 10.1111/andr.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/17/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
BACKGROUND Adenosine deaminase domain containing 2 (ADAD2) is a testis-specific protein composed of a double-stranded RNA binding domain and a non-catalytic adenosine deaminase domain. A recent study showed that ADAD2 is indispensable for the male reproduction in mice. However, the detailed functions of ADAD2 remain elusive. OBJECTIVES This study aimed to investigate the cause of male sterility in Adad2 mutant mice and to understand the molecular functions of ADAD2. MATERIALS AND METHODS Adad2 homozygous mutant mouse lines, Adad2-/- and Adad2Δ/Δ , were generated by CRISPR/Cas9. Western blotting and immunohistochemistry were used to reveal the expression and subcellular localization of ADAD2. Co-immunoprecipitation tandem mass spectrometry was employed to determine the ADAD2-interacting proteins in mouse testes. RNA-sequencing analyses were carried out to analyze the transcriptome and PIWI-interacting RNA (piRNA) populations in wildtype and Adad2 mutant testes. RESULTS Adad2-/- and Adad2Δ/Δ mice exhibit male-specific sterility because of abnormal spermiogenesis. ADAD2 interacts with multiple RNA-binding proteins involved in piRNA biogenesis, including MILI, MIWI, RNF17, and YTHDC2. ADAD2 co-localizes and forms novel granules with RNF17 in spermatocytes. Ablation of ADAD2 impairs the formation of RNF17 granules, decreases the number of cluster-derived pachytene piRNAs, and increases expression of ping-pong-derived piRNAs. DISCUSSION AND CONCLUSION In collaboration with RNF17 and other RNA-binding proteins in spermatocytes, ADAD2 directly or indirectly functions in piRNA biogenesis.
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Affiliation(s)
- Yonggang Lu
- Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ippei Nagamori
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Nara, Japan
| | - Kanako Kojima-Kita
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kenjiro Shirane
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hsin-Yi Chang
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Toru Nishimura
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Takayuki Koyano
- Division of Molecular Genetics, Shigei Medical Research Institute, Okayama, Japan
| | - Zhifeng Yu
- Center for Drug Discovery and Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Julio M Castañeda
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, Okayama, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Martin M Matzuk
- Center for Drug Discovery and Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Masahito Ikawa
- Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Graduate School of Medicine, Osaka University, Osaka, Japan.,Laboratory of Reproductive Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
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5
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Abstract
Epigenetic marks including DNA methylation (DNAme) play a critical role in the transcriptional regulation of genes and retrotransposons. Defects in DNAme are detected in infertility, imprinting disorders and congenital diseases in humans, highlighting the broad importance of this epigenetic mark in both development and disease. While DNAme in terminally differentiated cells is stably propagated following cell division by the maintenance DNAme machinery, widespread erasure and subsequent de novo establishment of this epigenetic mark occur early in embryonic development as well as in germ cell development. Combined with deep sequencing, low-input methods that have been developed in the past several years have enabled high-resolution and genome-wide mapping of both DNAme and histone post-translational modifications (PTMs) in rare cell populations including developing germ cells. Epigenome studies using these novel methods reveal an unprecedented view of the dynamic chromatin landscape during germ cell development. Furthermore, integrative analysis of chromatin marks in normal germ cells and in those deficient in chromatin-modifying enzymes uncovers a critical interplay between histone PTMs and de novo DNAme in the germline. This review discusses work on mechanisms of the erasure and subsequent de novo DNAme in mouse germ cells as well as the outstanding questions relating to the regulation of the dynamic chromatin landscape in germ cells.
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Affiliation(s)
- Kenjiro Shirane
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University
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Naitou Y, Nagamatsu G, Hamazaki N, Shirane K, Hayashi M, Hayashi M, Kobayashi S, Hayashi K. Dual role of Ovol2 on the germ cell lineage segregation during gastrulation in mouse embryogenesis. Development 2022; 149:274415. [DOI: 10.1242/dev.200319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
ABSTRACT
In mammals, primordial germ cells (PGCs), the origin of the germ line, are specified from the epiblast at the posterior region where gastrulation simultaneously occurs, yet the functional relationship between PGC specification and gastrulation remains unclear. Here, we show that OVOL2, a transcription factor conserved across the animal kingdom, balances these major developmental processes by repressing the epithelial-to-mesenchymal transition (EMT) that drives gastrulation and the upregulation of genes associated with PGC specification. Ovol2a, a splice variant encoding a repressor domain, directly regulates EMT-related genes and, consequently, induces re-acquisition of potential pluripotency during PGC specification, whereas Ovol2b, another splice variant missing the repressor domain, directly upregulates genes associated with PGC specification. Taken together, these results elucidate the molecular mechanism underlying allocation of the germ line among epiblast cells differentiating into somatic cells through gastrulation.
This article has an associated ‘The people behind the papers’ interview.
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Affiliation(s)
- Yuki Naitou
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Go Nagamatsu
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuhiko Hamazaki
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kenjiro Shirane
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masafumi Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Makoto Hayashi
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Satoru Kobayashi
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Germline Genetics, Graduate School of Medicine, Osaka University, Suita 565-0871, Osaka, Japan
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Mochizuki K, Sharif J, Shirane K, Uranishi K, Bogutz AB, Janssen SM, Suzuki A, Okuda A, Koseki H, Lorincz MC. Repression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing. Nat Commun 2021; 12:7020. [PMID: 34857746 PMCID: PMC8639735 DOI: 10.1038/s41467-021-27345-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 04/07/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023] Open
Abstract
Silencing of a subset of germline genes is dependent upon DNA methylation (DNAme) post-implantation. However, these genes are generally hypomethylated in the blastocyst, implicating alternative repressive pathways before implantation. Indeed, in embryonic stem cells (ESCs), an overlapping set of genes, including germline "genome-defence" (GGD) genes, are upregulated following deletion of the H3K9 methyltransferase SETDB1 or subunits of the non-canonical PRC1 complex PRC1.6. Here, we show that in pre-implantation embryos and naïve ESCs (nESCs), hypomethylated promoters of germline genes bound by the PRC1.6 DNA-binding subunits MGA/MAX/E2F6 are enriched for RING1B-dependent H2AK119ub1 and H3K9me3. Accordingly, repression of these genes in nESCs shows a greater dependence on PRC1.6 than DNAme. In contrast, GGD genes are hypermethylated in epiblast-like cells (EpiLCs) and their silencing is dependent upon SETDB1, PRC1.6/RING1B and DNAme, with H3K9me3 and DNAme establishment dependent upon MGA binding. Thus, GGD genes are initially repressed by PRC1.6, with DNAme subsequently engaged in post-implantation embryos.
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Affiliation(s)
- Kentaro Mochizuki
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Kenjiro Shirane
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Kousuke Uranishi
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Aaron B Bogutz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ayumu Suzuki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo ward, Chiba, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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Karahan G, Chan D, Shirane K, McClatchie T, Janssen S, Baltz JM, Lorincz M, Trasler J. Paternal MTHFR deficiency leads to hypomethylation of young retrotransposons and reproductive decline across two successive generations. Development 2021; 148:dev199492. [PMID: 34128976 PMCID: PMC8276981 DOI: 10.1242/dev.199492] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/01/2021] [Indexed: 12/17/2022]
Abstract
5,10-Methylenetetrahydrofolate reductase (MTHFR) is a crucial enzyme in the folate metabolic pathway with a key role in generating methyl groups. As MTHFR deficiency impacts male fertility and sperm DNA methylation, there is the potential for epimutations to be passed to the next generation. Here, we assessed whether the impact of MTHFR deficiency on testis morphology and sperm DNA methylation is exacerbated across generations in mouse. Although MTHFR deficiency in F1 fathers has only minor effects on sperm counts and testis weights and histology, F2 generation sons show further deterioration in reproductive parameters. Extensive loss of DNA methylation is observed in both F1 and F2 sperm, with >80% of sites shared between generations, suggestive of regions consistently susceptible to MTHFR deficiency. These regions are generally methylated during late embryonic germ cell development and are enriched in young retrotransposons. As retrotransposons are resistant to reprogramming of DNA methylation in embryonic germ cells, their hypomethylated state in the sperm of F1 males could contribute to the worsening reproductive phenotype observed in F2 MTHFR-deficient males, compatible with the intergenerational passage of epimutations.
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Affiliation(s)
- Gurbet Karahan
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Kenjiro Shirane
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Taylor McClatchie
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Departments of Obstetrics and Gynecology and Cellular and Molecular Medicine, University of Ottawa Faculty of Medicine, Ottawa, ON K1H 8M5, Canada
| | - Sanne Janssen
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jay M. Baltz
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Departments of Obstetrics and Gynecology and Cellular and Molecular Medicine, University of Ottawa Faculty of Medicine, Ottawa, ON K1H 8M5, Canada
| | - Matthew Lorincz
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacquetta Trasler
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3A 1A3, Canada
- Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
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9
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Kibe K, Shirane K, Ohishi H, Uemura S, Toh H, Sasaki H. The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes. PLoS Genet 2021; 17:e1009570. [PMID: 34048432 PMCID: PMC8162659 DOI: 10.1371/journal.pgen.1009570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/28/2022] Open
Abstract
DNA methylation at CG sites is important for gene regulation and embryonic development. In mouse oocytes, de novo CG methylation requires preceding transcription-coupled histone mark H3K36me3 and is mediated by a DNA methyltransferase DNMT3A. DNMT3A has a PWWP domain, which recognizes H3K36me2/3, and heterozygous mutations in this domain, including D329A substitution, cause aberrant CG hypermethylation of regions marked by H3K27me3 in somatic cells, leading to a dwarfism phenotype. We herein demonstrate that D329A homozygous mice show greater CG hypermethylation and severer dwarfism. In oocytes, D329A substitution did not affect CG methylation of H3K36me2/3-marked regions, including maternally methylated imprinting control regions; rather, it caused aberrant hypermethylation in regions lacking H3K36me2/3, including H3K27me3-marked regions. Thus, the role of the PWWP domain in CG methylation seems similar in somatic cells and oocytes; however, there were cell-type-specific differences in affected regions. The major satellite repeat was also hypermethylated in mutant oocytes. Contrary to the CA hypomethylation in somatic cells, the mutation caused hypermethylation at CH sites, including CA sites. Surprisingly, oocytes expressing only the mutated protein could support embryonic and postnatal development. Our study reveals that the DNMT3A PWWP domain is important for suppressing aberrant CG hypermethylation in both somatic cells and oocytes but that D329A mutation has little impact on the developmental potential of oocytes.
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Affiliation(s)
- Kanako Kibe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- * E-mail:
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10
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Ohishi H, Au Yeung WK, Unoki M, Ichiyanagi K, Fukuda K, Maenohara S, Shirane K, Chiba H, Sado T, Sasaki H. Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells. Genes Cells 2019; 25:54-64. [PMID: 31733167 DOI: 10.1111/gtc.12736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/19/2022]
Abstract
Monoallelic gene expression occurs in various mammalian cells and can be regulated genetically, epigenetically and/or stochastically. We identified 145 monoallelically expressed genes (MoEGs), including seven known imprinted genes, in mouse embryonic stem cells (ESCs) derived from reciprocal F1 hybrid blastocysts and cultured in 2i/LIF. As all MoEGs except for the imprinted genes were expressed in a genetic-origin-dependent manner, we focused on this class of MoEGs for mechanistic studies. We showed that a majority of the genetic-origin-dependent MoEGs identified in 2i/LIF ESCs remain monoallelically expressed in serum/LIF ESCs, but become more relaxed or even biallelically expressed upon differentiation. These MoEGs and their regulatory regions were highly enriched for single nucleotide polymorphisms. In addition, some MoEGs were associated with retrotransposon insertions/deletions, consistent with the fact that certain retrotransposons act as regulatory elements in pluripotent stem cells. Interestingly, most MoEGs showed allelic differences in enrichment of histone H3K27me and H3K4me marks, linking allelic epigenetic differences and monoallelic expression. In contrast, there was little or no allelic difference in CpG methylation or H3K9me. Taken together, our study highlights the impact of genetic variation including single nucleotide polymorphisms and retrotransposon insertions/deletions on monoallelic epigenetic marks and expression in ESCs.
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Affiliation(s)
- Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN, Wako, Japan
| | - Shoji Maenohara
- Gynecology Service, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Kenjiro Shirane
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Hatsune Chiba
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, KINDAI University, Nara, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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11
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Yamashiro C, Sasaki K, Yabuta Y, Kojima Y, Nakamura T, Okamoto I, Yokobayashi S, Murase Y, Ishikura Y, Shirane K, Sasaki H, Yamamoto T, Saitou M. Generation of human oogonia from induced pluripotent stem cells in vitro. Science 2018; 362:356-360. [PMID: 30237246 DOI: 10.1126/science.aat1674] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Abstract
Human in vitro gametogenesis may transform reproductive medicine. Human pluripotent stem cells (hPSCs) have been induced into primordial germ cell-like cells (hPGCLCs); however, further differentiation to a mature germ cell has not been achieved. Here, we show that hPGCLCs differentiate progressively into oogonia-like cells during a long-term in vitro culture (approximately 4 months) in xenogeneic reconstituted ovaries with mouse embryonic ovarian somatic cells. The hPGCLC-derived oogonia display hallmarks of epigenetic reprogramming-genome-wide DNA demethylation, imprint erasure, and extinguishment of aberrant DNA methylation in hPSCs-and acquire an immediate precursory state for meiotic recombination. Furthermore, the inactive X chromosome shows a progressive demethylation and reactivation, albeit partially. These findings establish the germline competence of hPSCs and provide a critical step toward human in vitro gametogenesis.
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Affiliation(s)
- Chika Yamashiro
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kotaro Sasaki
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukihiro Yabuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoji Kojima
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tomonori Nakamura
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ikuhiro Okamoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shihori Yokobayashi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yusuke Murase
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukiko Ishikura
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenjiro Shirane
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.,Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.,Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takuya Yamamoto
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), AMED, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan. .,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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12
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Brind'Amour J, Kobayashi H, Richard Albert J, Shirane K, Sakashita A, Kamio A, Bogutz A, Koike T, Karimi MM, Lefebvre L, Kono T, Lorincz MC. LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nat Commun 2018; 9:3331. [PMID: 30127397 PMCID: PMC6102241 DOI: 10.1038/s41467-018-05841-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/26/2018] [Indexed: 12/29/2022] Open
Abstract
De novo DNA methylation (DNAme) during mouse oogenesis occurs within transcribed regions enriched for H3K36me3. As many oocyte transcripts originate in long terminal repeats (LTRs), which are heterogeneous even between closely related mammals, we examined whether species-specific LTR-initiated transcription units (LITs) shape the oocyte methylome. Here we identify thousands of syntenic regions in mouse, rat, and human that show divergent DNAme associated with private LITs, many of which initiate in lineage-specific LTR retrotransposons. Furthermore, CpG island (CGI) promoters methylated in mouse and/or rat, but not human oocytes, are embedded within rodent-specific LITs and vice versa. Notably, at a subset of such CGI promoters, DNAme persists on the maternal genome in fertilized and parthenogenetic mouse blastocysts or in human placenta, indicative of species-specific epigenetic inheritance. Polymorphic LITs are also responsible for disparate DNAme at promoter CGIs in distantly related mouse strains, revealing that LITs also promote intra-species divergence in CGI DNAme.
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Affiliation(s)
- Julie Brind'Amour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan.
| | - Julien Richard Albert
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kenjiro Shirane
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Akihiko Sakashita
- Department of BioScience, Tokyo University of Agriculture, Tokyo, 113-0033, Japan
- Division of Reproductive Sciences, Cincinnati's Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Asuka Kamio
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Aaron Bogutz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tasuku Koike
- Department of BioScience, Tokyo University of Agriculture, Tokyo, 113-0033, Japan
| | - Mohammad M Karimi
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- MRC London Institute of Medical Sciences, Imperial College, London, W12 0NN, UK
| | - Louis Lefebvre
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tomohiro Kono
- Department of BioScience, Tokyo University of Agriculture, Tokyo, 113-0033, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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13
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Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell 2017; 22:50-63.e6. [PMID: 29249463 DOI: 10.1016/j.stem.2017.11.004] [Citation(s) in RCA: 464] [Impact Index Per Article: 66.3] [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: 05/16/2017] [Revised: 09/20/2017] [Accepted: 11/02/2017] [Indexed: 11/25/2022]
Abstract
Trophoblast cells play an essential role in the interactions between the fetus and mother. Mouse trophoblast stem (TS) cells have been derived and used as the best in vitro model for molecular and functional analysis of mouse trophoblast lineages, but attempts to derive human TS cells have so far been unsuccessful. Here we show that activation of Wingless/Integrated (Wnt) and EGF and inhibition of TGF-β, histone deacetylase (HDAC), and Rho-associated protein kinase (ROCK) enable long-term culture of human villous cytotrophoblast (CT) cells. The resulting cell lines have the capacity to give rise to the three major trophoblast lineages, which show transcriptomes similar to those of the corresponding primary trophoblast cells. Importantly, equivalent cell lines can be derived from human blastocysts. Our data strongly suggest that the CT- and blastocyst-derived cell lines are human TS cells, which will provide a powerful tool to study human trophoblast development and function.
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Affiliation(s)
- Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Sato
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Sota Takahashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuka Kabayama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
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14
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Ohta H, Kurimoto K, Okamoto I, Nakamura T, Yabuta Y, Miyauchi H, Yamamoto T, Okuno Y, Hagiwara M, Shirane K, Sasaki H, Saitou M. In vitro expansion of mouse primordial germ cell-like cells recapitulates an epigenetic blank slate. EMBO J 2017; 36:1888-1907. [PMID: 28559416 DOI: 10.15252/embj.201695862] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [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: 10/11/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 12/22/2022] Open
Abstract
The expansion of primordial germ cells (PGCs), the precursors for the oocytes and spermatozoa, is a key challenge in reproductive biology/medicine. Using a chemical screening exploiting PGC-like cells (PGCLCs) induced from mouse embryonic stem cells (ESCs), we here identify key signaling pathways critical for PGCLC proliferation. We show that the combinatorial application of Forskolin and Rolipram, which stimulate cAMP signaling via different mechanisms, expands PGCLCs up to ~50-fold in culture. The expanded PGCLCs maintain robust capacity for spermatogenesis, rescuing the fertility of infertile mice. Strikingly, during expansion, PGCLCs comprehensively erase their DNA methylome, including parental imprints, in a manner that precisely recapitulates genome-wide DNA demethylation in gonadal germ cells, while essentially maintaining their identity as sexually uncommitted PGCs, apparently through appropriate histone modifications. By establishing a paradigm for PGCLC expansion, our system reconstitutes the epigenetic "blank slate" of the germ line, an immediate precursory state for sexually dimorphic differentiation.
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Affiliation(s)
- Hiroshi Ohta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan .,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Kazuki Kurimoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Ikuhiro Okamoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Tomonori Nakamura
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Yukihiro Yabuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Hidetaka Miyauchi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, Japan.,AMED-CREST, AMED, Chiyoda-ku, Tokyo, Japan
| | - Yukiko Okuno
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Epigenome Network Research Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan.,Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Epigenome Network Research Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan .,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.,Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, Japan
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15
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Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H. Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing. BMC Genomics 2017; 18:31. [PMID: 28056787 PMCID: PMC5217569 DOI: 10.1186/s12864-016-3392-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 12/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-bisulfite adaptor tagging sequencing (PBAT-seq), uses the power of high-throughput DNA sequencers and provides genome-wide DNA methylation profiles at single-base resolution. However, the accuracy and consistency of WGBS outputs in relation to the operating conditions of high-throughput sequencers have not been explored. RESULTS We have used the Illumina HiSeq platform for our PBAT-based WGBS, and found that different versions of HiSeq Control Software (HCS) and Real-Time Analysis (RTA) installed on the system provided different global CpG methylation levels (approximately 5% overall difference) for the same libraries. This problem was reproduced multiple times with different WGBS libraries and likely to be associated with the low sequence diversity of bisulfite-converted DNA. We found that HCS was the major determinant in the observed differences. To determine which version of HCS is most suitable for WGBS, we used substrates with predetermined CpG methylation levels, and found that HCS v2.0.5 is the best among the examined versions. HCS v2.0.12 showed the poorest performance and provided artificially lower CpG methylation levels when 5-methylcytosine is read as guanine (first read of PBAT-seq and second read of MethylC-seq). In addition, paired-end sequencing of low diversity libraries using HCS v2.2.38 or the latest HCS v2.2.58 was greatly affected by cluster densities. CONCLUSIONS Software updates in the Illumina HiSeq platform can affect the outputs from low-diversity sequencing libraries such as WGBS libraries. More recent versions are not necessarily the better, and HCS v2.0.5 is currently the best for WGBS among the examined HCS versions. Thus, together with other experimental conditions, special care has to be taken on this point when CpG methylation levels are to be compared between different samples by WGBS.
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Affiliation(s)
- Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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16
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Ishikura Y, Yabuta Y, Ohta H, Hayashi K, Nakamura T, Okamoto I, Yamamoto T, Kurimoto K, Shirane K, Sasaki H, Saitou M. In Vitro Derivation and Propagation of Spermatogonial Stem Cell Activity from Mouse Pluripotent Stem Cells. Cell Rep 2016; 17:2789-2804. [DOI: 10.1016/j.celrep.2016.11.026] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/23/2016] [Accepted: 11/02/2016] [Indexed: 01/11/2023] Open
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17
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Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T. Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta. Am J Hum Genet 2016; 99:1045-1058. [PMID: 27843122 DOI: 10.1016/j.ajhg.2016.08.021] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/31/2016] [Indexed: 10/20/2022] Open
Abstract
DNA methylation is globally reprogrammed after fertilization, and as a result, the parental genomes have similar DNA-methylation profiles after implantation except at the germline differentially methylated regions (gDMRs). We and others have previously shown that human blastocysts might contain thousands of transient maternally methylated gDMRs (transient mDMRs), whose maternal methylation is lost in embryonic tissues after implantation. In this study, we performed genome-wide allelic DNA methylation analyses of purified trophoblast cells from human placentas and, surprisingly, found that more than one-quarter of the transient-in-embryo mDMRs maintained their maternally biased DNA methylation. RNA-sequencing-based allelic expression analyses revealed that some of the placenta-specific mDMRs were associated with expression of imprinted genes (e.g., TIGAR, SLC4A7, PROSER2-AS1, and KLHDC10), and three imprinted gene clusters were identified. This approach also identified some X-linked gDMRs. Comparisons of the data with those from other mammals revealed that genomic imprinting in the placenta is highly variable. These findings highlight the incomplete erasure of germline DNA methylation in the human placenta; understanding this erasure is important for understanding normal placental development and the pathogenesis of developmental disorders with imprinting effects.
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18
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Ikematsu H, Chong Y, Shirane K, Toh H, Sasaki H, Matsumoto S, Noda N, Hotta T, Uchiumi T, Kang D. [Neuraminidase Amino Acid Sequences of Influenza A/H3N2 and B Viruses Isolated from Influenza Patients in the 2014/15 Japanese Influenza Season]. Fukuoka Igaku Zasshi 2016; 107:98-104. [PMID: 29210538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Neuraminidase (NA) is a surface protein essential for influenza virus replication. NA inhibitors are commonly used for the treatment of influenza patients in Japan. Several mutations that reduce the effect of NA inhibitors have been reported. We sequenced the whole NA segment of isolated virus from influenza patients and investigated the relation between the NA amino acid sequence and the 50% inhibitory concentration (IC_50) of four NA inhibitors. MATERIALS AND METHODS Forty A/H3N2 and 19 B influenza virus isolated from patients in the 2014/15 influenza season were analyzed. The IC_50 was determined by a neuraminidase inhibition assay using a fluorescent substrate. Viral RNA was amplified by RT-PCR and the genome was sequenced using a next generation sequencer. The deduced amino acid sequences were analyzed. RESULTS There was no AA change in the NA catalytic site of the A/H3N2 and B viruses isolated in the 2014-15 influenza season. There was no significant relation between the NA amino acids and the IC_50 of the four NA inhibitors for A/H3N2 or B viruses. CONCLUSION The catalytic site of NA was highly conserved for these A/H3N2 and B viruses. No emergence of NA amino acid mutations related to the sensitivity of the four currently used NA inhibitors was observed.
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Kubo N, Toh H, Shirane K, Shirakawa T, Kobayashi H, Sato T, Sone H, Sato Y, Tomizawa SI, Tsurusaki Y, Shibata H, Saitsu H, Suzuki Y, Matsumoto N, Suyama M, Kono T, Ohbo K, Sasaki H. DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis. BMC Genomics 2015; 16:624. [PMID: 26290333 PMCID: PMC4546090 DOI: 10.1186/s12864-015-1833-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [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: 04/09/2015] [Accepted: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
Background In the male germline, neonatal prospermatogonia give rise to spermatogonia, which include stem cell population (undifferentiated spermatogonia) that supports continuous spermatogenesis in adults. Although the levels of DNA methyltransferases change dynamically in the neonatal and early postnatal male germ cells, detailed genome-wide DNA methylation profiles of these cells during the stem cell formation and differentiation have not been reported. Results To understand the regulation of spermatogonial stem cell formation and differentiation, we examined the DNA methylation and gene expression dynamics of male mouse germ cells at the critical stages: neonatal prospermatogonia, and early postntal (day 7) undifferentiated and differentiating spermatogonia. We found large partially methylated domains similar to those found in cancer cells and placenta in all these germ cells, and high levels of non-CG methylation and 5-hydroxymethylcytosines in neonatal prospermatogonia. Although the global CG methylation levels were stable in early postnatal male germ cells, and despite the reported scarcity of differential methylation in the adult spermatogonial stem cells, we identified many regions showing stage-specific differential methylation in and around genes important for stem cell function and spermatogenesis. These regions contained binding sites for specific transcription factors including the SOX family members. Conclusions Our findings show a distinctive and dynamic regulation of DNA methylation during spermatogonial stem cell formation and differentiation in the neonatal and early postnatal testes. Furthermore, we revealed a unique accumulation and distribution of non-CG methylation and 5hmC marks in neonatal prospermatogonia. These findings contrast with the reported scarcity of differential methylation in adult spermatogonial stem cell differentiation and represent a unique phase of male germ cell development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1833-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,Research Institute for Disease of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takayuki Shirakawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Tetsuya Sato
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hidetoshi Sone
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Yasuyuki Sato
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Shin-ichi Tomizawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8568, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tomohiro Kono
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan.,Department of BioScience, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Kazuyuki Ohbo
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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Ikematsu H, Chong Y, Shirane K, Toh H, Sasaki H, Koga Y, Matsumoto S, Hotta T, Uchiumi T, Kang D. [Analysis of the Neuraminidase Amino Acid Sequences of Influenza A/H1N1pdm09, A/H3N2, and B Viruses Isolated from Influenza Patients in the 2013/14 Japanese Influenza Season]. Fukuoka Igaku Zasshi 2015; 106:231-239. [PMID: 26630841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND Neuraminidase (NA) is an essential surface protein for influenza virus replication. NA inhibitors are commonly used for the treatment of influenza patients in Japan. Several mutations that reduce the effect of NA inhibitors have been reported. We sequenced the whole NA segment of isolated virus from influenza patients and investigated the relation between the NA amino acid sequence and the 50% inhibitory concentration (IC50) of four NA inhibitors. MATERIALS AND METHODS A total of 20 viruses that showed high or low IC50 of NA inhibitors were selected from A/H1N1pdm09, A/H3N2, and B isolates from the viruses isolated from patients in the 2013-14 influenza season. Viral RNA was extracted and RT-PCR was done. The amplified genome was sequenced using a next generation sequencer", and the deduced amino acid sequences were analyzed. RESULTS Two A/H1N1pdm09 viruses that showed very high IC50 for oseltamivir (150 nM and 130 nM) contained the H275Y mutation. Otherwise, no significant relation was found between the NA amino acids and the IC50 of the four NA inhibitors. There was no significant relation between the NA amino acids and the IC50 of the four NA inhibitors for A/H3N2 viruses. The B viruses that showed a high IC50 for oseltamivir and laninamivir shared some amino acids. The B viruses that showed a high IC50 of zanamivir and peramivir also shared some amino acids. They were different from the shared amino acids found for oseltamivir and laninamivir. CONCLUSION The previously reported H275Y mutation that causes oseltamivir resistance was found in the two A/H1N1pdm09 viruses that showed a very high IC50 for oseltamivir. No additional NA amino acid sequences related to the IC50 of the four NA inhibitors was found. The meaning of the shared amino acids among B viruses that showed a high IC50 would be an interesting target for further investigation.
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21
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Ikematsu H, Chong Y, Shirane K, Toh H, Sasaki H, Koga Y, Urata M, Hotta T, Uchiumi T, Kang D. [Analysis of influenza A/H3N2 neuraminidase genes obtained from influenza patients in the 2011/12 and 2012/13 seasons in Japan]. Fukuoka Igaku Zasshi 2015; 106:16-22. [PMID: 25942938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND Influenza virus has neuraminidase (NA), a surface protein with enzymatic activity that is essential for virus replication. Mutation may affect the effectiveness of NA inhibitors that are used for the treatment of influenza patients. In this study, we determined the NA gene sequences from the clinical isolates of influenza patients to examine the chronological genetic changes and the relation to drug susceptibility. METHODS For 96 A/H3N2 virus isolates the 50% inhibitory concentration (IC50) (48 each from the 2011-12 and 12-13 influenza seasons) was measured. RT-PCR was done with extracted viral RNA, followed by nucleotide sequencing. RESULTS One putative amino acid mutation, D151N, was found in an NA activity-related cite in five of ninety-six tested isolate. The mutation did not affect the IC50 value. The mutations identified at amino acid positions 387 and 400 were statistically correlated with an increased IC50 value, although the change was less than ten times, suggesting no significant difference in the clinical effectiveness. A small number .of isolates showed mutation in the T and/or B cell epitope region of NA. CONCLUSION No mutation that affected the IC50 value or effectiveness of NAIs was detected. Antigenic mutations of NA, which influence the selection of epidemic strains, were not determined. Continuous observation will be necessary to further clarify the genetic features of NA.
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Liu S, Brind'Amour J, Karimi MM, Shirane K, Bogutz A, Lefebvre L, Sasaki H, Shinkai Y, Lorincz MC. Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells. Genes Dev 2014; 28:2041-55. [PMID: 25228647 PMCID: PMC4173156 DOI: 10.1101/gad.244848.114] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transcription of endogenous retroviruses is inhibited by de novo DNA methylation during gametogenesis, and DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes. Liu et al. find that germline-specific conditional knockout of the H3K9 methyltransferase SETDB1 yields a decrease of H3K9me3 and H3K27me3 marks and DNA methylation at H3K9me3-enriched retrotransposon families. Setdb1 deficiency is associated with a reduced number of male E13.5 PGCs and postnatal hypogonadism in both sexes. Therefore, SETDB1 is an essential guardian against proviral expression prior to the onset of de novo DNA methylation in the germline. Transcription of endogenous retroviruses (ERVs) is inhibited by de novo DNA methylation during gametogenesis, a process initiated after birth in oocytes and at approximately embryonic day 15.5 (E15.5) in prospermatogonia. Earlier in germline development, the genome, including most retrotransposons, is progressively demethylated. Young ERVK and ERV1 elements, however, retain intermediate methylation levels. As DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes, we determined whether retrotransposons are marked by H3K9me3 and H3K27me3 using a recently developed low-input ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) method. Although these repressive histone modifications are found predominantly on distinct genomic regions in E13.5 PGCs, they concurrently mark partially methylated long terminal repeats (LTRs) and LINE1 elements. Germline-specific conditional knockout of the H3K9 methyltransferase SETDB1 yields a decrease of both marks and DNA methylation at H3K9me3-enriched retrotransposon families. Strikingly, Setdb1 knockout E13.5 PGCs show concomitant derepression of many marked ERVs, including intracisternal A particle (IAP), ETn, and ERVK10C elements, and ERV-proximal genes, a subset in a sex-dependent manner. Furthermore, Setdb1 deficiency is associated with a reduced number of male E13.5 PGCs and postnatal hypogonadism in both sexes. Taken together, these observations reveal that SETDB1 is an essential guardian against proviral expression prior to the onset of de novo DNA methylation in the germline.
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Affiliation(s)
- Sheng Liu
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan
| | - Julie Brind'Amour
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan
| | - Mohammad M Karimi
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan; Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Aaron Bogutz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan
| | - Louis Lefebvre
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Yoichi Shinkai
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan; Cellular Memory Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan;
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Tagawa M, Shirane K, Yu L, Sato T, Furukawa S, Mizuguchi H, Kuji R, Kawamura K, Takahashi N, Kato K, Hayakawa S, Sawada S, Furukawa K. Enhanced expression of the β4-galactosyltransferase 2 gene impairs mammalian tumor growth. Cancer Gene Ther 2014; 21:219-27. [DOI: 10.1038/cgt.2014.21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 01/09/2023]
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24
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Shirane K, Kuji R, Tareyanagi C, Sato T, Kobayashi Y, Furukawa S, Murata T, Kubota S, Ishikawa Y, Segawa K, Furukawa K. Gene expression levels of 4-galactosyltransferase 5 correlate with the tumorigenic potentials of B16-F10 mouse melanoma cells. Glycobiology 2014; 24:532-41. [DOI: 10.1093/glycob/cwu021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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25
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Li Y, Miyanari Y, Shirane K, Nitta H, Kubota T, Ohashi H, Okamoto A, Sasaki H. Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes. Nucleic Acids Res 2013; 41:e186. [PMID: 23990328 PMCID: PMC3799461 DOI: 10.1093/nar/gkt766] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [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] [Indexed: 12/11/2022] Open
Abstract
Methylation-specific fluorescence in situ hybridization (MeFISH) was developed for microscopic visualization of DNA methylation status at specific repeat sequences in individual cells. MeFISH is based on the differential reactivity of 5-methylcytosine and cytosine in target DNA for interstrand complex formation with osmium and bipyridine-containing nucleic acids (ICON). Cell nuclei and chromosomes hybridized with fluorescence-labeled ICON probes for mouse major and minor satellite repeats were treated with osmium for crosslinking. After denaturation, fluorescent signals were retained specifically at satellite repeats in wild-type, but not in DNA methyltransferase triple-knockout (negative control) mouse embryonic stem cells. Moreover, using MeFISH, we successfully detected hypomethylated satellite repeats in cells from patients with immunodeficiency, centromeric instability and facial anomalies syndrome and 5-hydroxymethylated satellite repeats in male germ cells, the latter of which had been considered to be unmethylated based on anti-5-methylcytosine antibody staining. MeFISH will be suitable for a wide range of applications in epigenetics research and medical diagnosis.
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Affiliation(s)
- Yufeng Li
- Division of Epigenomics and Development, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka 812-8582, Japan, The Cancer Institute, Tangshan People's Hospital, Hebei 063001, China, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, F-67404 Illkirch, Cité Universitaire de Strasbourg, France, Department of Epigenetics Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi 409-3898, Japan, Division of Medical Genetics, Saitama Children's Medical Center, Saitama 339-8551, Japan and Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 113-8656, Japan
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Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 2013; 9:e1003439. [PMID: 23637617 PMCID: PMC3630097 DOI: 10.1371/journal.pgen.1003439] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 02/23/2013] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in normal mammalian development, retrotransposon silencing, and cellular reprogramming. Although methylation mainly occurs on the cytosine in a CG site, non-CG methylation is prevalent in pluripotent stem cells, brain, and oocytes. We previously identified non-CG methylation in several CG-rich regions in mouse germinal vesicle oocytes (GVOs), but the overall distribution of non-CG methylation and the enzymes responsible for this modification are unknown. Using amplification-free whole-genome bisulfite sequencing, which can be used with minute amounts of DNA, we constructed the base-resolution methylome maps of GVOs, non-growing oocytes (NGOs), and mutant GVOs lacking the DNA methyltransferase Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3L. We found that nearly two-thirds of all methylcytosines occur in a non-CG context in GVOs. The distribution of non-CG methylation closely resembled that of CG methylation throughout the genome and showed clear enrichment in gene bodies. Compared to NGOs, GVOs were over four times more methylated at non-CG sites, indicating that non-CG methylation accumulates during oocyte growth. Lack of Dnmt3a or Dnmt3L resulted in a global reduction in both CG and non-CG methylation, showing that non-CG methylation depends on the Dnmt3a-Dnmt3L complex. Dnmt3b was dispensable. Of note, lack of Dnmt1 resulted in a slight decrease in CG methylation, suggesting that this maintenance enzyme plays a role in non-dividing oocytes. Dnmt1 may act on CG sites that remain hemimethylated in the de novo methylation process. Our results provide a basis for understanding the mechanisms and significance of non-CG methylation in mammalian oocytes.
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Affiliation(s)
- Kenjiro Shirane
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
| | - Hisato Kobayashi
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Fumihito Miura
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hatsune Chiba
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ito
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- * E-mail:
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Yamamoto Y, Watanabe T, Hoki Y, Shirane K, Li Y, Ichiiyanagi K, Kuramochi-Miyagawa S, Toyoda A, Fujiyama A, Oginuma M, Suzuki H, Sado T, Nakano T, Sasaki H. Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus. Genome Res 2012; 23:292-9. [PMID: 23132912 PMCID: PMC3561870 DOI: 10.1101/gr.137224.112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [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: 01/10/2023]
Abstract
In germ cells, early embryos, and stem cells of animals, PIWI-interacting RNAs (piRNAs) have an important role in silencing retrotransposons, which are vicious genomic parasites, through transcriptional and post-transcriptional mechanisms. To examine whether the piRNA pathway can be used to silence genes of interest in germ cells, we have generated knock-in mice in which a foreign DNA fragment was inserted into a region generating pachytene piRNAs. The knock-in sequence was transcribed, and the resulting RNA was processed to yield piRNAs in postnatal testes. When reporter genes possessing a sequence complementary to portions of the knock-in sequence were introduced, they were greatly repressed after the time of pachytene piRNA generation. This repression mainly occurred at the post-transcriptional level, as degradation of the reporter RNAs was accelerated. Our results show that the piRNA pathway can be used as a tool for sequence-specific gene silencing in germ cells and support the idea that the piRNA generating regions serve as traps for retrotransposons, enabling the host cell to generate piRNAs against active retrotransposons.
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Affiliation(s)
- Yasuhiro Yamamoto
- Division of Epigenomics, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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Ide R, Mizoue T, Fujino Y, Kubo T, Pham TM, Shirane K, Ogimoto I, Tokui N, Yoshimura T. Oral Symptoms Predict Mortality: a Prospective Study in Japan. J Dent Res 2008; 87:485-9. [DOI: 10.1177/154405910808700510] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Several studies have reported positive associations between oral infections and systemic diseases. The purpose of the present study was to evaluate the effects of oral symptoms on mortality from cardiovascular disease (CVD) and pneumonia. Using data from a cohort study in Japan, we analyzed 4,139 individuals aged 40–79 years. The baseline questionnaire included the following items related to oral symptoms: ‘sensitive teeth’, ‘difficulty in chewing tough food substances’, ‘bleeding gums’, and ‘mouth feels sticky’. We used the Cox proportional hazard model to estimate hazard ratios (HRs) and 95% confidence intervals (95%CIs) for mortality, after adjustments for lifestyle, socio-economic factors, and history of diseases. Persons complaining that their ‘mouth feels sticky’ had a two-fold higher risk of pneumonia (HR = 2.1; 95%CI, 1.2–3.6), while those complaining of ‘sensitive teeth’ had a lower risk of CVD (HR = 0.4; 95%CI, 0.2–0.9). Some oral symptoms may be predictors of mortality from pneumonia and CVD.
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Affiliation(s)
- R. Ide
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - T. Mizoue
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - Y. Fujino
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - T. Kubo
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - T.-M. Pham
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - K. Shirane
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - I. Ogimoto
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - N. Tokui
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
| | - T. Yoshimura
- Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
- Department of Epidemiology and International Health, Research Institute, International Medical Center of Japan, Tokyo
- Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
- Asahi Kasei, Nobeoka Office Health Care Center, Miyazaki, Japan
- St. Mary’s Hospital, Kurume, Japan
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Guo S, Sato T, Shirane K, Furukawa K. Galactosylation of N-linked oligosaccharides by human beta-1,4-galactosyltransferases I, II, III, IV, V, and VI expressed in Sf-9 cells. Glycobiology 2001; 11:813-20. [PMID: 11588157 DOI: 10.1093/glycob/11.10.813] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [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: 01/08/2023] Open
Abstract
Several studies showed that Sf-9 cells can synthesize the galactosylated N-linked oligosaccharides if beta-1,4-galactosyltransferase (beta-1,4-GalT) is supplied. The full-length human beta-1,4-GalT I, II, III, IV, V, and VI cDNAs were independently transfected into Sf-9 cells, and the galactosylation of endogenous membrane glycoproteins was examined by lectin blot analysis using Ricinus communis agglutinin-I (RCA-I), which preferentially interacts with oligosaccharides terminated with Galbeta1-->4GlcNAc group. Several RCA-I-reactive bands appeared in all of the gene-transfected cells, and disappeared on treatment of blots with beta-1,4-galactosidase or N-glycanase prior to incubation with lectin. Introduction of the antisense beta-1,4-GalT II and V cDNAs separately into human colorectal adenocarcinoma SW480 cells, in which beta-1,4-GalT I, II, and V genes were expressed, resulted in the reduction of RCA-I binding toward N-linked oligosaccharides of the membrane glycoproteins. Differences were found in their K(m) values toward UDP-Gal and GlcNAcbeta-S-pNP and in their acceptor specificities toward oligosaccharides with the GlcNAcbeta1-->4(GlcNAcbeta1-->2)Man branch and with the GlcNAcbeta1-->6(GlcNAcbeta1-->2)Man branch. These results indicate that beta-1,4-GalTs II, III, IV, V, and VI are involved in the N-linked oligosaccharide biosynthesis cooperatively but not in a redundant manner with beta-1,4-GalT I within cells.
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Affiliation(s)
- S Guo
- Department of Biosignal Research, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
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30
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Sato T, Shirane K, Kido M, Furukawa K. Correlated gene expression between beta-1,4-galactosyltransferase V and N-acetylglucosaminyltransferase V in human cancer cell lines. Biochem Biophys Res Commun 2000; 276:1019-23. [PMID: 11027584 DOI: 10.1006/bbrc.2000.3594] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [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: 01/28/2023]
Abstract
Since our previous study showed that the gene expression level of beta-1,4-galactosyltransferase (beta-1,4-GalT) V is only increased in mouse NIH3T3 transformant and that beta-1,4-GalT V preferentially galactosylates the GlcNAcbeta1 --> 6Man branch of oligosaccharides [Shirane et al. (1999) Biochem. Biophys. Res. Commun. 265, 434-438], whether its gene expression is correlated with malignant transformation was investigated. Northern blot analysis of beta-1, 4-GalTs I, II, III, IV, V, and VI and N-acetylglucosaminyltransferase (GlcNAcT)V in human cancer cell lines showed that the gene expression levels of beta-1,4-GalT V but not other beta-1,4-GalTs are strongly correlated with those of GlcNAcT V whose activity was shown to increase by malignant transformation. These results indicate that beta-1,4-GalT V is involved in the galactosylation of highly branched oligosaccharides characteristic of malignantly transformed cells.
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Affiliation(s)
- T Sato
- Department of Biosignal Research, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, 173-0015, Japan
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31
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Shirane K, Sato T, Segawa K, Furukawa K. Involvement of beta-1,4-galactosyltransferase V in malignant transformation-associated changes in glycosylation. Biochem Biophys Res Commun 1999; 265:434-8. [PMID: 10558885 DOI: 10.1006/bbrc.1999.1684] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [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: 01/01/2023]
Abstract
In spite of marked changes in the glycosylation upon malignant transformation of cells, no biological significance of beta-1, 4-galactosyltransferase (beta-1,4-GalT) activities has been elucidated. When beta-1,4-GalT activities toward 1 mM GlcNAcbeta-S-pNP were determined using homogenates of NIH3T3 and its transformant, MTAg, MTAg contained 1.3 times higher activities. Northern blot analysis, however, revealed that the beta-1,4-GalT V gene expression increases by three times with a decrease in that of beta-1,4-GalT II by one-fifth and without significant changes in those of other beta-1,4-GalTs in MTAg. Analysis of beta-1,4-GalT V acceptor-specificity showed that the GlcNAcbeta1-->6Man group of the GlcNAcbeta1-->6(GlcNAbeta1-->2)Manalpha1- branch is galactosylated. These results indicate that changes in beta-1,4-GalT II and V activities are important for the altered glycosylation.
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Affiliation(s)
- K Shirane
- Department of Biosignal Research, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, 173-0015, Japan
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Abstract
Nitric oxide, a gaseous free NO radical (.NO) generated in particulate-free gas-phase main-stream smoke of cigarettes, was observed with electrical spin resonance (ESR) using a spin trapping technique. N-Methyl-D-glucamine-dithiocarbamate (MGD)2-Fe2+ complex was used for the NO radical spin trapper in aqueous solution. The intensity of the ESR signal of the spin adduct formed by bubbling smoke from one cigarette increased gradually with time over 2 hours at about 20 degrees C and was constant for 2 days or longer. The time course of the production of the NO radical followed the rate equation y = 1520(1-e-0.018t) for the first-order reaction up to around 25 min after mixing of Fe2+ solution and then slowly approached the maximum value determined by the concentration of the spin adduct. These findings suggest that NO radical is produced slowly from NO radical donors such as amine .NO complexes, peroxinitrite (ONOO-), and other reactants such as nitrogen oxides (NOx), which are produced from the smoke of tobacco leaves, and suggest that its generation could be involved in the decomposition or cleavage of such substances.
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Affiliation(s)
- K Shinagawa
- Department of Preventive Medicine and Environmental Health, Osaka City University Medical School, Japan.
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Shirane K, Furukawa K, Fukuchi K, Yamazaki H, Tsuji M, Okamoto Y. Effects of N-3554S, a polyprenyl phosphate, on B16-F10 mouse melanoma cells. Biochim Biophys Acta 1995; 1268:285-92. [PMID: 7548227 DOI: 10.1016/0167-4889(95)00087-9] [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] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
N-3554S, an optically active S-isomer of alpha-dihydrodecaprenyl phosphate, reduced the tumorigenicity of cultured B16-F10 mouse melanoma cells probably by affecting protein N-glycosylation. Accordingly, membrane glycoprotein samples were prepared from the melanoma cells cultured with or without N-3554S, and amounts and structures of N-linked sugar chains were determined. Analyses of the N-linked oligosaccharides released by hydrazinolysis from these samples and reduced with NaB3H4 revealed that the N-3554S-treated cells contain 1.5-1.8 times as much oligosaccharides as the control cells, and the relative amounts of high-mannose-type and bi-, tri- and tetra-antennary complex-type sugar chains are almost the same between two samples. Western blot analysis, however, showed that binding of L-PHA, which binds to oligosaccharides with the GlcNAc beta 1-->6(GlcNAc beta 1-->2)Man structure, is significantly reduced in 90 K, 96 K, 140 K, 155 K and 180 K glycoproteins in N-3554S-treated cells. Immunoblot analysis showed that the 140 K glycoprotein could be a fibronectin receptor. It was also shown that N-3554S treatment enhances the adhesiveness of the cells to fibronectin. These results indicate that N-3554S affects N-glycosylation of membrane glycoproteins and alters the cell surface properties of B16-F10 cells.
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Affiliation(s)
- K Shirane
- Pharmaceutical Research Center, Nisshin Flour Milling Co., Ltd., Saitama, Japan
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Kawakubo I, Funazaki J, Shirane K, Yoshizawa A. Integrated optical-disk pickup that uses a focusing grating coupler with a high numerical aperture. Appl Opt 1994; 33:6855-6859. [PMID: 20941232 DOI: 10.1364/ao.33.006855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
An integrated optical-disk pickup that uses a focusing grating coupler with a numerical aperture of 0.45 (a focal length of 1.0 mm and an aperture of 1.0 mm × 0.8 mm) was developed, and the readout signal on an International Standards Organization (ISO) -formatted 90-mm optical disk was detected by the pickup. The signal-amplitude ratio of the minimum-limit data pattern to the maximum was 0.53 on the innermost track. It meets the requirement on the signal resolution for optical-disk storage devices.
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Shirane K, Nakagomi O. Interspecies transmission of animal rotaviruses to humans as evidenced by phylogenetic analysis of the hypervariable region of the VP4 protein. Microbiol Immunol 1994; 38:823-6. [PMID: 7869963 DOI: 10.1111/j.1348-0421.1994.tb01865.x] [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: 01/27/2023]
Abstract
A phylogenetic tree constructed for the hypervariable region (aa 71-203) of the VP4 protein of 28 human and animal rotaviruses that were previously reported to belong to 13 distinct VP4 genotypes revealed unique positions of human rotavirus strains HCR3 and Ro1845, together with feline strain FRV64 and canine strains K9 and CU-1, in the animal rotavirus lineages, lending strong support to the view that both HCR3 and Ro1845 were of animal rotavirus origin.
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Affiliation(s)
- K Shirane
- Department of Microbiology, Akita University School of Medicine, Japan
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Abe Y, Shirane K, Yokosawa H, Matsushita H, Mitta M, Kato I, Ishii S. Asparaginyl endopeptidase of jack bean seeds. Purification, characterization, and high utility in protein sequence analysis. J Biol Chem 1993; 268:3525-9. [PMID: 8429028] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Asparaginyl endopeptidase was highly purified from mature seeds of the jack bean (Canavalia ensiformis). The final enzyme preparation showed a single peak in high-performance liquid chromatography on a reversed-phase column, and the material in the peak gave the following NH2-terminal amino acid sequence on Edman degradation for 25 cycles: H-Glu-Val-Gly-Thr-Arg-Trp-Ala-Val-Leu-Val-Ala-Gly-Ser-Asn-Gly-Tyr-Gly-Asn-Tyr- Arg-His-Gln-Ala-Asp-Val-. Behavior of the enzyme toward various protease inhibitors suggested that it belongs to a family of cysteine proteases. Strict substrate specificity of this enzyme was verified by the use of 14 polypeptide substrates including those derived from proteins. Almost all the peptide bonds on the carboxyl side of Asn residues were susceptible to the enzyme. The exceptions were cases where the residue was at the NH2 terminus or the second position from the NH2 terminus of substrates and where it was N-glycosylated Asn. Peptide bonds on the carboxyl side of any other amino acid residues were not cleaved. These properties promise the high utility of this novel endopeptidase in protein sequence analysis. Identity of jack bean asparaginyl endopeptidase with a processing enzyme responsible for maturation of concanavalin A from its precursor is also discussed.
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Affiliation(s)
- Y Abe
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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Abe Y, Shirane K, Yokosawa H, Matsushita H, Mitta M, Kato I, Ishii S. Asparaginyl endopeptidase of jack bean seeds. Purification, characterization, and high utility in protein sequence analysis. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53726-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Shirane K, Tokimoto T, Yamaguchi Y. Chemical model of reaction cascades induced by activated enzymes or catalysts. Two-step cascades in visual transduction. Biophys J 1990; 57:163-7. [PMID: 2153420 PMCID: PMC1280654 DOI: 10.1016/s0006-3495(90)82518-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [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: 12/30/2022] Open
Abstract
A dissipative system is approximated by a nonlinear rate equation: Z congruent to K1Z - K2Z3 (K2 greater than 0), in which the right side is derived from -delta G/delta Z of Taylor's series of the thermodynamic potential given by Gibbs' function G(Tc, Pc) (Z) at about the critical point C(Tc, Pc) of the control variables (parameters) T and P. The stability or instability of the system is treated by the changes in the control parameters. In the case that T not equal to P not equal to 0 in the steady state, Z = 0, and T and P pass the point C, K1 becomes negative. By this change, the G function is convex at Z = 0 and each product is created rapidly with concentration or number of the molecules Z = ([K1]/K2)1/2. This dynamic theory is applied to enzyme cascades. Based on cyclic GMP (cGMP) hypothesis in visual transduction, the cascade hydrolysis of cGMP of vertebrates is analyzed by dividing it into two-step reaction cascades: The initial process is that metarhodopsin II catalyzes the exchange of GDP for GTP by transducin (Gtd) and that GTP-Gtd complex is hydrolyzed to GDP-Gtd complex. In the following cascade cGMP is hydrolyzed with amplification of phosphodiesterase (PDE) activated by the removal of the small inhibitory subunit. The quantity of the hydrolysis of cGMP is estimated as approximately 5 x 10(4-5) molecules per photolyzed rhodopsin semiempirically, and this coincides well with experiments.
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Affiliation(s)
- K Shirane
- Biophysics Laboratory, Osaka City University Medical School, Japan
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Biyajima M, Shirane K, Suzuki N. Analyses of moments in pseudorapidity intervals at sqrt s =546 GeV by means of two probability distributions in pure-birth process. Int J Clin Exp Med 1988; 37:1824-1829. [PMID: 9958875 DOI: 10.1103/physrevd.37.1824] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
The ligands of Ca2+-Cu2+-phosphatidylserine (PS) complexes in membrane networks at the water-oil interface through the symmetry breaking instability and the head groups of PS molecules were changed into a solid-like state. A first step in this transition is described by the following scheme in one unit in which the molar ratio is Ca2+: Cu2+: PS = 1:2:4; [Oh]+2[Oh]*----3[Oh]*, where [Oh]* denotes a little distorted ligand structure [LnM2+...2H2O] from [LnM2+2H2O], where Ln is PS molecules (n = 2 to Cu2+ and 4 to Ca2+). All the ligands are changed to [D4h] by the unit-unit interaction due to the network formation; [Oh]*----[D4h]. The whole system is equivalent to Schlögl's scheme and is given by a cubic state equation for suitable variables transformations: x = -x3 - ux - v, where x corresponds to the concentration of [Oh]*, and u and v are related to rate constants in the first and the second steps, and they also depend on the initial [Oh] and the final [D4h] concentrations. This system is transferred into a new state with a cusp catastrophe.
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Affiliation(s)
- K Shirane
- Biophysics Laboratory, Osaka City University Medical School, Japan
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Abstract
Some reaction cascades in biological systems are analyzed by a self-organized chemical model, an autocatalytic reaction. This model is described by the coupling of a primary system which stabilizes the initial stage of the reaction rapidly and a partial system which controls the primary system slowly. By the internal force caused by a trigger above the threshold, the coupled system in near-equilibrium is broken and changed into a new state. From the rate equation for the coupled system, a dimensionless nonlinear state equation, n = -n3 - un - v, is derived, where n is the concentration of intermediate, and u, v are dynamic variables of the system. This equation is similar to a nonequilibrium tri-molecular reaction. By using this chemical network theory, fibrin polymerization. F + F----fm----fp + X, where F is a fibrinogen molecule, fm is a fibrin monomer, fp is fibrin polymer, and X is small peptides released from fibrinogen, is discussed as an excellent example of the enzyme reaction cascade.
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Affiliation(s)
- T Tokimoto
- Department of Physiology, Osaka City University Medical School, Japan
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Biyajima M, Shirane K, Terazawa O. Calculations of standard-Higgs-boson production cross sections in e+e- collisions by means of a reasonable set of parameters. Int J Clin Exp Med 1987; 36:2161-2164. [PMID: 9958413 DOI: 10.1103/physrevd.36.2161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
Based on Haken's theory, self-organization or synergetics is discussed using chemical dynamics to represent an autocatalytic reaction. In a simple case the changes in a self-organizing system are given by a set of two rate equations for a primary and a partial system. When these systems mutually form a feedback loop under the adiabatic condition, the rate equation of self-organization is described by a generalized Gibbs' free energy change delta U (delta x) followed by the reaction. The sign of the parameter k'3 (k0-kex; k0, kex: rate constants with or without an external stimulus) determines the instability of the coupled system in quasi-equilibrium (k'3 approximately greater than 0; k0 greater than kex). When the product exceeds the threshold (k'3 less than 0; k0 less than kex), the system transfers into a new state, or a phase transition appears. Considering the Boltzmann distribution, the transition parameter k'3 is evaluated by an average distribution of the states and the instability is discussed using the reaction velocities vqe and vqe in the quasi-equilibrium state. As an example of this model membrane excitation is discussed briefly.
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Abstract
Thermotropic and inotropic phase transitions have been analysed with a dynamic theory on a self-organization. An equation of motion of a molecular assembly with strong interactions may be approximately described as: dQ/dt' congruent to -K1Q-K3Q3, where Q is a displacement from the equilibrium point Q0(identical to 0) in a vibrational state, K1 is a transition parameter. When the parameter K1 concerned with an internal driving force (partial system) changes from positive to negative through the potential bifurcation, the system transfers to a new stable state breaking down the symmetry. Such a sign change of K1 serves as a trigger to a phase transition. Using Weiss' approximation, we have evaluated the change of K1 by a function of temperature, kappa (T-TC), and have obtained the critical temperature TC of thermotropic phase transition. We have furthermore treated inotropic phase transition caused by the binding of divalent cations like Ca2+ using the function kappa (T-beta TC), where beta is a shift parameter of the critical temperature.
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Nanri S, Akita H, Jozaki K, Iwata S, Iwasaki Y, Tojo M, Hotta M, Yamashita N, Sunakawa K, Oikawa T, Osano M, Ichihashi Y, Ishikawa K, Kanemitsu T, Ri S, Shirane K, Kanki K, Kawai S, Saito N. [Fundamental and clinical studies of cefotaxime in neonates and immature infants]. Jpn J Antibiot 1982; 35:1749-60. [PMID: 6294356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cefotaxime (CTX) was used in the treatment and prophylaxis of infections in neonates and immature infants. The following results were obtained. 1. Mean serum concentrations (bioassay) 30 minutes after a single intravenous injection of about 20 mg/kg of CTX were 44.5 mcg/ml in neonates and 47.2 mcg/ml in immature infants aged 0-3 days, 45.8 mcg/ml in neonates and 56.4 mcg/ml in an immature infant aged 4-7 days and 40.6 mcg/ml in neonates and 38.1 mcg/ml in immature infants aged 8 or more days. Six hour values were respectively 10.9 mcg/ml, 17.0 mcg/ml, 4.6 mcg/ml, 13.4 mcg/ml, 3.8 mcg/ml and 2.7 mcg/ml. 2. Mean serum concentration half-lives were 3.0 hours in neonates and 3.2 hours in immature infants aged 0-3 days, 1.8 hours in neonates and 3.2 hours in an immature infant aged 4-7 days, and 1.5 hours in neonates and 1.6 hours in immature infants aged 8 or more days. 3. Urinary recovery rates were 0.8-78.0% for 0-6 hours after treatment. 4. Adequate clinical efficacy can be expected by the intravenous injection of CTX in doses of 20 mg/kg 2 times daily, every 12 hours, in neonates and immature infants aged 0-3 days, 20 mg/kg 3 times daily, every 8 hours, in neonates and immature infants aged 4-7 days, and 20 mg/kg 3 to 4 times daily, every 6-8 hours, in neonates and immature infants aged 8 or more days. 5. The clinical efficacy of CTX was good in all 4 cases of sepsis (including suspected case), excellent in 1 case of urinary tract infection, and good in all 4 cases of fever of unknown origin for a cure rate of 100%. 6. Adverse reactions were not noted in any cases.
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