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Abstract
Retrotransposons are transposable elements that are transposed via transcription and reverse transcription. Their copies have accumulated in the genome of mammals, occupying approximately 40% of mammalian genomic mass. These copies are often involved in numerous phenomena, such as chromatin spatial organization, gene expression, development and disease, and have been recognized as a driving force in evolution. Different organisms have gained specific retrotransposon subfamilies and retrotransposed copies, such as hundreds of Mus-specific subfamilies with diverse sequences and genomic locations. Despite this complexity, basic information is still necessary for present-day genomic and epigenomic studies. Herein, we describe the characteristics of each subfamily of Mus-specific retrotransposons in terms of sequence structure, phylogenetic relationships, evolutionary age, and preference for A or B compartments of chromatin.
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Affiliation(s)
- Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
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Uno Y, Matsubara K, Inoue J, Inazawa J, Shinohara A, Koshimoto C, Ichiyanagi K, Matsuda Y. Diversity and Evolution of Highly Repetitive DNA Sequences Constituting Chromosome Site-Specific Heterochromatin in Two Gerbillinae Species. Cytogenet Genome Res 2023; 163:42-51. [PMID: 37708873 DOI: 10.1159/000533716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals.
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Affiliation(s)
- Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazumi Matsubara
- Department of Environmental Biology, College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Jun Inoue
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akio Shinohara
- Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Chihiro Koshimoto
- Department of Biotechnology, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoichi Matsuda
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Kobayashi M, Kanbe F, Ishii R, Tsubouchi H, Hirai K, Miyasaka Y, Ohno T, Oda H, Ikeda S, Katoh H, Ichiyanagi K, Ishikawa A, Murai A, Horio F. C3H/HeNSlc mouse with low phospholipid transfer protein expression showed dyslipidemia. Sci Rep 2023; 13:13813. [PMID: 37620514 PMCID: PMC10449841 DOI: 10.1038/s41598-023-40917-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
High serum levels of triglycerides (TG) and low levels of high-density lipoprotein cholesterol (HDL-C) increase the risk of coronary heart disease in humans. Herein, we first reported that the C3H/HeNSlc (C3H-S) mouse, a C3H/HeN-derived substrain, is a novel model for dyslipidemia. C3H-S showed hypertriglyceridemia and low total cholesterol (TC), HDL-C, and phospholipid (PL) concentrations. To identify the gene locus causing dyslipidemia in C3H-S, we performed genetic analysis. In F2 intercrosses between C3H-S mice and strains with normal serum lipids, the locus associated with serum lipids was identified as 163-168 Mb on chromosome 2. The phospholipid transfer protein (Pltp) gene was a candidate gene within this locus. Pltp expression and serum PLTP activity were markedly lower in C3H-S mice. Pltp expression was negatively correlated with serum TG and positively correlated with serum TC and HDL-C in F2 mice. Genome sequencing analysis revealed that an endogenous retrovirus (ERV) sequence called intracisternal A particle was inserted into intron 12 of Pltp in C3H-S. These results suggest that ERV insertion within Pltp causes aberrant splicing, leading to reduced Pltp expression in C3H-S. This study demonstrated the contribution of C3H-S to our understanding of the relationship between TG, TC, and PL metabolism via PLTP.
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Affiliation(s)
- Misato Kobayashi
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan.
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan.
| | - Fumi Kanbe
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Reika Ishii
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Hiroki Tsubouchi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Kana Hirai
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Yuki Miyasaka
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Hiroaki Oda
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Saiko Ikeda
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan
| | - Hirokazu Katoh
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Akira Ishikawa
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Atsushi Murai
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Fumihiko Horio
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
- Department of Life Studies and Environmental Science, Nagoya Women's University, Aichi, Japan
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Hirata M, Ichiyanagi T, Katoh H, Hashimoto T, Suzuki H, Nitta H, Kawase M, Nakai R, Imamura M, Ichiyanagi K. Sequence divergence and retrotransposon insertion underlie interspecific epigenetic differences in primates. Mol Biol Evol 2022; 39:msac208. [PMID: 36219870 PMCID: PMC9577543 DOI: 10.1093/molbev/msac208] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/27/2022] [Accepted: 09/21/2022] [Indexed: 11/14/2022] Open
Abstract
Changes in the epigenome can affect the phenotype without the presence of changes in the genomic sequence. Given the high identity of the human and chimpanzee genome sequences, a substantial portion of their phenotypic divergence likely arises from epigenomic differences between the two species. In this study, the transcriptome and epigenome were determined for induced pluripotent stem cells (iPSCs) generated from human and chimpanzee individuals. The transcriptome and epigenomes for trimethylated histone H3 at lysine-4 (H3K4me3) and lysine-27 (H3K27me3) showed high levels of similarity between the two species. However, there were some differences in histone modifications. Although such regions, in general, did not show significant enrichment of interspecies nucleotide variations, gains in binding motifs for pluripotency-related transcription factors, especially POU5F1 and SOX2, were frequently found in species-specific H3K4me3 regions. We also revealed that species-specific insertions of retrotransposons, including the LTR5_Hs subfamily in human and a newly identified LTR5_Pt subfamily in chimpanzee, created species-specific H3K4me3 regions associated with increased expression of nearby genes. Human iPSCs have more species-specific H3K27me3 regions, resulting in more abundant bivalent domains. Only a limited number of these species-specific H3K4me3 and H3K27me3 regions overlap with species-biased enhancers in cranial neural crest cells, suggesting that differences in the epigenetic state of developmental enhancers appear late in development. Therefore, iPSCs serve as a suitable starting material for studying evolutionary changes in epigenome dynamics during development.
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Affiliation(s)
- Mayu Hirata
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoko Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirokazu Katoh
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Takuma Hashimoto
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hikaru Suzuki
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirohisa Nitta
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Risako Nakai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Masanori Imamura
- Molecular Biology Section, Department of Cellular and Molecular Biology, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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Ichiyanagi K. The regulatory mechanisms that make mature sperm cells in the mouse. Gene 2022; 97:1. [PMID: 35665700 DOI: 10.1266/ggs.97.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
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Kawase M, Ichiyanagi K. The Expression Dynamics of piRNAs Derived From Male Germline piRNA Clusters and Retrotransposons. Front Cell Dev Biol 2022; 10:868746. [PMID: 35646920 PMCID: PMC9130748 DOI: 10.3389/fcell.2022.868746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022] Open
Abstract
In mammals, germ cells produce a class of small regulatory RNAs called PIWI-interacting RNAs or piRNAs, which are 25–32 nucleotides in length. The profile of testicular piRNAs changes during development. The piRNAs detected in fetal testes at embryonic day 13.5 and later are called fetal piRNAs. The piRNAs detected in testes in a period where germ cells do not yet enter the pachytene stage of meiotic prophase I are called pre-pachytene piRNAs, whereas those in testes at later postnatal days are called pachytene piRNAs. Here, to elucidate the exact expression dynamics of these piRNAs during development, we compared piRNAs present in male germ cells at different stages, which were purified by fluorescence-activated cell sorting, and those in embryonic testes. The analysis identified three distinct groups of piRNA clusters: prospermatogonial, early, and late clusters. piRNA length was largely correlated with the repertoire of PIWI-like proteins in respective germ cells; however, the late piRNA clusters tended to generate longer (PIWIL1-type) piRNAs, whereas the early clusters tended to generate shorter (PIWIL2-type) piRNAs, suggesting a cluster- or sequence-dependent mechanism for loading onto PIWI-like proteins. Retrotransposon-derived piRNAs, particularly evolutionary young retrotransposons, were abundantly produced in prospermatogonia, however, their abundance declined as development proceeded. Thus, in later stages, retrotransposon-derived piRNAs were not enriched with those from evolutionary young elements. The results revealed that, depending on the piRNA clusters from which they are derived, longer PIWIL1-type piRNAs are produced earlier, and shorter PIWIL2-type piRNAs remain in a longer period, than previously thought.
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Affiliation(s)
- Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Fukuda K, Makino Y, Kaneko S, Shimura C, Okada Y, Ichiyanagi K, Shinkai Y. Transcriptional states of retroelement-inserted regions and specific KRAB zinc finger protein association are correlated with DNA methylation of retroelements in human male germ cells. eLife 2022; 11:76822. [PMID: 35315771 PMCID: PMC8967385 DOI: 10.7554/elife.76822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
Abstract
DNA methylation, repressive histone modifications, and PIWI-interacting RNAs are essential for controlling retroelement silencing in mammalian germ lines. Dysregulation of retroelement silencing is associated with male sterility. Although retroelement silencing mechanisms have been extensively studied in mouse germ cells, little progress has been made in humans. Here, we show that the Krüppel-associated box domain zinc finger proteins are associated with DNA methylation of retroelements in human primordial germ cells. Further, we show that the hominoid-specific retroelement SINE-VNTR-Alus (SVA) is subjected to transcription-directed de novo DNA methylation during human spermatogenesis. The degree of de novo DNA methylation in SVAs varies among human individuals, which confers significant inter-individual epigenetic variation in sperm. Collectively, our results highlight potential molecular mechanisms for the regulation of retroelements in human male germ cells.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN, Wako, Japan
| | - Yoshinori Makino
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Satoru Kaneko
- Department of Obstetrics and Gynecology, Tokyo Dental College Ichikawa General Hospital, Ichikawa, Japan
| | | | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
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Ichiyanagi K, Saito K. The fifth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements. Mob DNA 2022; 13:3. [PMID: 35027075 PMCID: PMC8756742 DOI: 10.1186/s13100-022-00261-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/01/2022] [Indexed: 12/02/2022] Open
Abstract
The fifth Japanese meeting on host–transposon interactions, titled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs),” was held online on August 26–27, 2021. The meeting was supported by National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense systems against TE mobility by chromatin and RNA modifications and protein-protein interactions. Here, we present the highlights of the talks.
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Affiliation(s)
- Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Kuniaki Saito
- Invertebrate Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
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Inatomi T, Matsuda S, Ishiuchi T, Do Y, Nakayama M, Abe S, Kasho K, Wanrooij S, Nakada K, Ichiyanagi K, Sasaki H, Yasukawa T, Kang D. TFB2M and POLRMT are essential for mammalian mitochondrial DNA replication. Biochim Biophys Acta Mol Cell Res 2021; 1869:119167. [PMID: 34744028 DOI: 10.1016/j.bbamcr.2021.119167] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
Abstract
Two classes of replication intermediates have been observed from mitochondrial DNA (mtDNA) in many mammalian tissue and cells with two-dimensional agarose gel electrophoresis. One is assigned to leading-strand synthesis in the absence of synchronous lagging-strand synthesis (strand-asynchronous replication), and the other has properties of coupled leading- and lagging-strand synthesis (strand-coupled replication). While strand-asynchronous replication is primed by long noncoding RNA synthesized from a defined transcription initiation site, little is known about the commencement of strand-coupled replication. To investigate it, we attempted to abolish strand-asynchronous replication in cultured human cybrid cells by knocking out the components of the transcription initiation complexes, mitochondrial transcription factor B2 (TFB2M/mtTFB2) and mitochondrial RNA polymerase (POLRMT/mtRNAP). Unexpectedly, removal of either protein resulted in complete mtDNA loss, demonstrating for the first time that TFB2M and POLRMT are indispensable for the maintenance of human mtDNA. Moreover, a lack of TFB2M could not be compensated for by mitochondrial transcription factor B1 (TFB1M/mtTFB1). These findings indicate that TFB2M and POLRMT are crucial for the priming of not only strand-asynchronous but also strand-coupled replication, providing deeper insights into the molecular basis of mtDNA replication initiation.
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Affiliation(s)
- Teppei Inatomi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shigeru Matsuda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryocho, Aoba-ku, Sendai-shi, Miyagi 980-8575, Japan
| | - Takashi Ishiuchi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Masunari Nakayama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shusaku Abe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Kazutoshi Kasho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba-shi, Ibaraki 305-8572, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya-shi, Aichi 464-8601, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
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Ichiyanagi T, Katoh H, Mori Y, Hirafuku K, Boyboy BA, Kawase M, Ichiyanagi K. B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and Histone Modifications in the Mouse. Mol Biol Evol 2021; 38:2380-2395. [PMID: 33592095 PMCID: PMC8136502 DOI: 10.1093/molbev/msab033] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
More than one million copies of short interspersed elements (SINEs), a class of retrotransposons, are present in the mammalian genomes, particularly within gene-rich genomic regions. Evidence has accumulated that ancient SINE sequences have acquired new binding sites for transcription factors (TFs) through multiple mutations following retrotransposition, and as a result have rewired the host regulatory network during the course of evolution. However, it remains unclear whether currently active SINEs contribute to the expansion of TF binding sites. To study the mobility, expression, and function of SINE copies, we first identified about 2,000 insertional polymorphisms of SINE B1 and B2 families within Mus musculus. Using a novel RNA sequencing method designated as melRNA-seq, we detected the expression of SINEs in male germ cells at both the subfamily and genomic copy levels: the vast majority of B1 RNAs originated from evolutionarily young subfamilies, whereas B2 RNAs originated from both young and old subfamilies. DNA methylation and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses in liver revealed that polymorphic B2 insertions served as a boundary element inhibiting the expansion of DNA hypomethylated and histone hyperacetylated regions, and decreased the expression of neighboring genes. Moreover, genomic B2 copies were enriched at the boundary of various histone modifications, and chromatin insulator protein, CCCTC-binding factor, a well-known chromatin boundary protein, bound to >100 polymorphic and >10,000 non-polymorphic B2 insertions. These results suggest that the currently active B2 copies are mobile boundary elements that can modulate chromatin modifications and gene expression, and are likely involved in epigenomic and phenotypic diversification of the mouse species.
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Affiliation(s)
- Tomoko Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirokazu Katoh
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshinobu Mori
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Keigo Hirafuku
- The Jikei University Hospital, Minato-ku, Tokyo 105-8471, Japan
| | - Beverly Ann Boyboy
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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Kimprasit T, Nunome M, Iida K, Murakami Y, Wong ML, Wu CH, Kobayashi R, Hengjan Y, Takemae H, Yonemitsu K, Kuwata R, Shimoda H, Si L, Sohn JH, Asakawa S, Ichiyanagi K, Maeda K, Oh HS, Mizutani T, Kimura J, Iida A, Hondo E. Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia. PLoS One 2021; 16:e0244006. [PMID: 33444317 PMCID: PMC7808576 DOI: 10.1371/journal.pone.0244006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/25/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.
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Affiliation(s)
- Thachawech Kimprasit
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Keisuke Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Min-Liang Wong
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Hsin Wu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yupadee Hengjan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hitoshi Takemae
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzo Yonemitsu
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Lifan Si
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, China
| | - Joon-Hyuk Sohn
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hong-Shik Oh
- Institute of Science Education, Jeju National University, Jeju, Korea
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Junpei Kimura
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Atsuo Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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12
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Kinoshita K, Suzuki T, Koike M, Nishida C, Koike A, Nunome M, Uemura T, Ichiyanagi K, Matsuda Y. Combined deletions of IHH and NHEJ1 cause chondrodystrophy and embryonic lethality in the Creeper chicken. Commun Biol 2020; 3:144. [PMID: 32214226 PMCID: PMC7096424 DOI: 10.1038/s42003-020-0870-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 02/27/2020] [Indexed: 11/18/2022] Open
Abstract
The Creeper (Cp) chicken is characterized by chondrodystrophy in Cp/+ heterozygotes and embryonic lethality in Cp/Cp homozygotes. However, the genes underlying the phenotypes have not been fully known. Here, we show that a 25 kb deletion on chromosome 7, which contains the Indian hedgehog (IHH) and non-homologous end-joining factor 1 (NHEJ1) genes, is responsible for the Cp trait in Japanese bantam chickens. IHH is essential for chondrocyte maturation and is downregulated in the Cp/+ embryos and completely lost in the Cp/Cp embryos. This indicates that chondrodystrophy is caused by the loss of IHH and that chondrocyte maturation is delayed in Cp/+ heterozygotes. The Cp/Cp homozygotes exhibit impaired DNA double-strand break (DSB) repair due to the loss of NHEJ1, resulting in DSB accumulation in the vascular and nervous systems, which leads to apoptosis and early embryonic death. Kinoshita et al find that the classical Creeper (Cp) phenotype in chicken is caused by a deletion containing not only the gene encoding Indian hedgehog, previously implicated in the Cp trait, but also the NHEJ1 gene encoding a DNA repair factor. They show that early death in Cp/Cp chicken is caused by impaired DNA repair and abnormalities of the vascular and nervous systems.
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Affiliation(s)
- Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Takayuki Suzuki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Manabu Koike
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Inage-ku, Chiba, 263-8555, Japan
| | - Chizuko Nishida
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido, 060-0808, Japan
| | - Aki Koike
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Inage-ku, Chiba, 263-8555, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Takeo Uemura
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan. .,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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13
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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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14
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Hiramoto T, Tahara M, Liao J, Soda Y, Miura Y, Kurita R, Hamana H, Inoue K, Kohara H, Miyamoto S, Hijikata Y, Okano S, Yamaguchi Y, Oda Y, Ichiyanagi K, Toh H, Sasaki H, Kishi H, Ryo A, Muraguchi A, Takeda M, Tani K. Non-transmissible MV Vector with Segmented RNA Genome Establishes Different Types of iPSCs from Hematopoietic Cells. Mol Ther 2019; 28:129-141. [PMID: 31677955 DOI: 10.1016/j.ymthe.2019.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 01/11/2023] Open
Abstract
Recent advances in gene therapy technologies have enabled the treatment of congenital disorders and cancers and facilitated the development of innovative methods, including induced pluripotent stem cell (iPSC) production and genome editing. We recently developed a novel non-transmissible and non-integrating measles virus (MV) vector capable of transferring multiple genes simultaneously into a wide range of cells through the CD46 and CD150 receptors. The MV vector expresses four genes for iPSC generation and the GFP gene for a period of time sufficient to establish iPSCs from human fibroblasts as well as peripheral blood T cells. The transgenes were expressed differentially depending on their gene order in the vector. Human hematopoietic stem/progenitor cells were directly and efficiently reprogrammed to naive-like cells that could proliferate and differentiate into primed iPSCs by the same method used to establish primed iPSCs from other cell types. The novel MV vector has several advantages for establishing iPSCs and potential future applications in gene therapy.
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Affiliation(s)
- Takafumi Hiramoto
- Department of Biochemistry, Jichi Medical University, Tochigi 329-0498, Japan
| | - Maino Tahara
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Jiyuan Liao
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasushi Soda
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshie Miura
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Ryo Kurita
- Central Blood Institute (Blood Service Headquarters), Japanese Red Cross Society, Tokyo 135-8521, Japan
| | - Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kota Inoue
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroshi Kohara
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Shohei Miyamoto
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasuki Hijikata
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Shinji Okano
- Section of Pathology, Department of Morphological Biology, Fukuoka Dental College, Fukuoka 814-0193, Japan
| | | | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hidehiro Toh
- Division of Epigenetics and Development, Medical Institute of Bioregulation, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroyuki Sasaki
- Division of Epigenetics and Development, Medical Institute of Bioregulation, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University, Kanagawa 236-0004, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo 208-0011, Japan.
| | - Kenzaburo Tani
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.
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15
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Inoguchi Y, Ichiyanagi K, Ohishi H, Maeda Y, Sonoda N, Ogawa Y, Inoguchi T, Sasaki H. Poorly controlled diabetes during pregnancy and lactation activates the Foxo1 pathway and causes glucose intolerance in adult offspring. Sci Rep 2019; 9:10181. [PMID: 31308441 PMCID: PMC6629688 DOI: 10.1038/s41598-019-46638-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 03/22/2019] [Accepted: 07/01/2019] [Indexed: 12/26/2022] Open
Abstract
Exposure to maternal diabetes during pregnancy results in diabetes in offspring, but its underlying mechanisms are unclear. Here, we investigated the phenotype and molecular defects of the offspring of poorly controlled diabetic female mice generated by streptozotocin (STZ) administration. Offspring was exposed to maternal diabetes during pregnancy and lactation. The body weight of STZ offspring was lower than that of control offspring at birth and in adulthood, and glucose tolerance was impaired in adult STZ offspring. Interestingly, the phenotype was more pronounced in male offspring. We next investigated the morphology of islets and expression of β cell-related genes, but no significant changes were observed. However, transcriptome analysis of the liver revealed activation of the fork head box protein O1 (Foxo1) pathway in STZ male offspring. Notably, two key gluconeogenesis enzyme genes, glucose 6 phosphatase catalytic subunit (G6pc) and phosphoenolpyruvate carboxykinase 1 (Pck1), were upregulated. Consistent with this finding, phosphorylation of Foxo1 was decreased in the liver of STZ male offspring. These changes were not obvious in female offspring. The activation of Foxo1 and gluconeogenesis in the liver may have contributed to the impaired glucose tolerance of STZ male offspring.
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Affiliation(s)
- Yukihiro Inoguchi
- Division of Epigenomics and Development, Department of Molecular and Structural Biology Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan. .,Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Department of Molecular and Structural Biology Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Department of Molecular and Structural Biology Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasutaka Maeda
- Clinical Research Center for Diabetes, Clinic Masae Minami, Fukuoka, Japan
| | - Noriyuki Sonoda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Molecular and Cellular Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | | | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Department of Molecular and Structural Biology Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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16
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Gusyev MA, Morgenstern U, Nishihara T, Hayashi T, Akata N, Ichiyanagi K, Sugimoto A, Hasegawa A, Stewart MK. Evaluating anthropogenic and environmental tritium effects using precipitation and Hokkaido snowpack at selected coastal locations in Asia. Sci Total Environ 2019; 659:1307-1321. [PMID: 31096342 DOI: 10.1016/j.scitotenv.2018.12.342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/22/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Tritium dating requires a good understanding of the tritium and water inputs into hydrologic systems, including their main trends due to latitudinal, seasonal and altitudinal effects. Although tritium reached ambient levels at the end of the 20th century, tritium released from nuclear facilities and bomb tests since then has the potential to confound use of tritium for age dating. We therefore collected precipitation and snowpack samples for tritium analysis to confirm that tritium levels in Japanese precipitation had not exceeded ambient levels following the North Korean nuclear tests in January 6th 2016 and September 3rd 2017. As the result, the highest tritium concentration was 5.52(±0.27)TU at samples collected from January 8 to 11th at one Honshu and four Hokkaido locations and samples collected at six Honshu locations had 8.01(±1.5)TU from September 6 to 19th 2017. Confirming ambient tritium concentrations after both events we investigated the latitude tritium effect at selected coastal stations in Asia, indicating a break of latitude trend around Tokyo area, and established the latitude scaling factors to the north and south of the Tokyo area data. The seasonal trend was investigated during the winter-spring 2016 in precipitation samples confirming the higher spring tritium compared with winter continental tritium values. The altitude effect on tritium and stable (18O and 2H) isotopes was observed in Hokkaido snowpack, which had tritium concentrations ranging between 4.08 and 5.93 TU during March-April, and demonstrated two trends for western and central Hokkaido mountain ranges. Using established latitude and altitude scaling factors with the long-term continuous time-series of monthly Tokyo area tritium we estimated the annual weighted tritium at 110 meteorological stations in Japan with monthly precipitation demonstrating the applicability of this approach for future tritium-tracer studies across Asia.
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Affiliation(s)
- M A Gusyev
- International Centre for Water Hazard and Risk Management (ICHARM)/National Graduate Institute for Policy Studies (GRIPS), Public Works Research Institute (PWRI), Tsukuba 305-8516, Japan.
| | | | - T Nishihara
- Civil Engineering Research Institute for Cold Region (CERI), PWRI, Sapporo 062-8602, Japan
| | - T Hayashi
- Akita University, Akita 010-8502, Japan
| | - N Akata
- National Institute for Fusion Science (NIFS), Toki 509-5292, Japan
| | | | - A Sugimoto
- Hokkaido University, Sapporo 060-0808, Japan
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17
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Abstract
The fourth Japanese meeting entitled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs)” was held on August 20–21, 2018 at the National Institute of Genetics (NIG), Mishima, Japan. The meeting was supported by NIG, and its objective was to bring together researchers who study the diverse roles of TEs in genome evolution, as well as host defense systems against TE mobility, such as chromatin modifications, small RNAs, and others. Here, we present the highlights of the talks given by 14 invited speakers. Organizers: Kenji Ichiyanagi (chief), Kuniaki Saito, and Tetsuji Kakutani.
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Affiliation(s)
- Kenji Ichiyanagi
- 1Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Kuniaki Saito
- 2Invertebrate Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540 Japan
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18
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Kuroki S, Nakai Y, Maeda R, Okashita N, Akiyoshi M, Yamaguchi Y, Kitano S, Miyachi H, Nakato R, Ichiyanagi K, Shirahige K, Kimura H, Shinkai Y, Tachibana M. Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis. Stem Cell Reports 2018. [PMID: 29526734 PMCID: PMC5998703 DOI: 10.1016/j.stemcr.2018.02.002] [Citation(s) in RCA: 18] [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] [Indexed: 11/25/2022] Open
Abstract
Histone H3 lysine 9 (H3K9) methylation is unevenly distributed in mammalian chromosomes. However, the molecular mechanism controlling the uneven distribution and its biological significance remain to be elucidated. Here, we show that JMJD1A and JMJD1B preferentially target H3K9 demethylation of gene-dense regions of chromosomes, thereby establishing an H3K9 hypomethylation state in euchromatin. JMJD1A/JMJD1B-deficient embryos died soon after implantation accompanying epiblast cell death. Furthermore, combined loss of JMJD1A and JMJD1B caused perturbed expression of metabolic genes and rapid cell death in embryonic stem cells (ESCs). These results indicate that JMJD1A/JMJD1B-meditated H3K9 demethylation has critical roles for early embryogenesis and ESC maintenance. Finally, genetic rescue experiments clarified that H3K9 overmethylation by G9A was the cause of the cell death and perturbed gene expression of JMJD1A/JMJD1B-depleted ESCs. We summarized that JMJD1A and JMJD1B, in combination, ensure early embryogenesis and ESC viability by establishing the correct H3K9 methylated epigenome.
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Affiliation(s)
- Shunsuke Kuroki
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Yuji Nakai
- Institute for Food Sciences, Hirosaki University, 2-1-1 Yanagawa, Aomori 038-0012, Japan
| | - Ryo Maeda
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Naoki Okashita
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Mika Akiyoshi
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Yutaro Yamaguchi
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Satsuki Kitano
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Hitoshi Miyachi
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, The University of Tokyo, 1-1-1 Yayoi, Bonkyo-ku, Tokyo 113-0032, Japan
| | - Kenji Ichiyanagi
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, The University of Tokyo, 1-1-1 Yayoi, Bonkyo-ku, Tokyo 113-0032, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Makoto Tachibana
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan; Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8597, Japan.
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19
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Wakisaka KT, Ichiyanagi K, Ohno S, Itoh M. Association of zygotic piRNAs derived from paternal P elements with hybrid dysgenesis in Drosophila melanogaster. Mob DNA 2018; 9:7. [PMID: 29441132 PMCID: PMC5800288 DOI: 10.1186/s13100-018-0110-y] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/15/2018] [Indexed: 01/27/2023] Open
Abstract
Background P-element transposition in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster. Maternally deposited piRNAs suppress P-element transposition in the progeny, linking them to P-M phenotypes; however, the role of zygotic piRNAs derived from paternal P elements is poorly understood. Results To elucidate the molecular basis of P-element suppression by zygotic factors, we investigated the genomic constitution and P-element piRNA production derived from fathers. As a result, we characterized males of naturally derived Q, M’ and P strains, which show different capacities for the P-element mobilizations introduced after hybridizations with M-strain females. The amounts of piRNAs produced in ovaries of F1 hybrids varied among the strains and were influenced by the characteristics of the piRNA clusters that harbored the P elements. Importantly, while both the Q- and M’-strain fathers restrict the P-element mobilization in ovaries of their daughters, the Q-strain fathers supported the production of the highest piRNA expression in the ovaries of their daughters, and the M’ strain carries KP elements in transcriptionally active regions directing the highest expression of KP elements in their daughters. Interestingly, the zygotic P-element piRNAs, but not the KP element mRNA, contributed to the variations in P transposition immunity in the granddaughters. Conclusions The piRNA-cluster-embedded P elements and the transcriptionally active KP elements from the paternal genome are both important suppressors of P element activities that are co-inherited by the progeny. Expression levels of the P-element piRNA and KP-element mRNA vary among F1 progeny due to the constitution of the paternal genome, and are involved in phenotypic variation in the subsequent generation. Electronic supplementary material The online version of this article (10.1186/s13100-018-0110-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Tsuji Wakisaka
- 1Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan
| | - Kenji Ichiyanagi
- 2Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Seiko Ohno
- 3Center for Epidemiologic Research in Asia, Shiga Univesity of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Masanobu Itoh
- 1Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan.,4Center for Advanced Insect Research Promotion (CAIRP), Kyoto Institute of Technology, Kyoto, 606-8585 Japan
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20
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Shimosuga KI, Fukuda K, Sasaki H, Ichiyanagi K. Locus-specific hypomethylation of the mouse IAP retrotransposon is associated with transcription factor-binding sites. Mob DNA 2017; 8:20. [PMID: 29255492 PMCID: PMC5729234 DOI: 10.1186/s13100-017-0105-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/01/2017] [Indexed: 01/23/2023] Open
Abstract
Background Intracisternal A particle (IAP) is one of the most transpositionally active retrotransposons in the mouse genome, but its expression varies between cell types. This variation is believed to arise from differences in the epigenetic state (e.g., DNA methylation) of the 5′ long terminal repeat (LTR), where transcription starts. However, owing to the high copy number and high sequence similarity between copies, it is difficult to analyze the epigenetic states of individual IAP LTRs in a comprehensive manner. Results We have developed a method called Target Enrichment after Post-Bisulfite Adaptor Tagging (TEPBAT) to analyze the DNA methylation states of a large number of individual retrotransposon copies at once. Using this method, we determined the DNA methylation levels of >8500 copies of genomic IAP LTRs (almost all copies that we aimed to target by the PCR primers) in the sperm and tail. This revealed that the vast majority of the LTRs were heavily methylated in both sperm and tail; however, hypomethylated copies were more frequently found in the sperm than in the tail. Interestingly, most of these hypomethylated LTRs were solo-type, belonged to specific IAP subfamilies, and carried binding sites for transcription factors (TFs) that are active in male germ cells. Conclusions The current study revealed subfamily- and locus-specific hypomethylation of IAP LTRs, and suggests that binding of TFs is involved in the protection from DNA methylation, whereas the IAP internal sequence enhances methylation. Furthermore, the study demonstrated that TEPBAT offers a cost-effective method for a variety of DNA methylome studies that focus on retrotransposon sequences. Electronic supplementary material The online version of this article (10.1186/s13100-017-0105-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ken-Ichi Shimosuga
- Division of Epigenomics and Development, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 Japan.,Trygroup Incorporated, 1-8-10 Kudankita, Chiyoda-ku, Tokyo, 102-0073 Japan
| | - Kei Fukuda
- Division of Epigenomics and Development, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 Japan.,Cellular Memory Laboratory, RIKEN, Wako, Saitama, 351-0198 Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582 Japan.,Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
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21
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Wakisaka KT, Ichiyanagi K, Ohno S, Itoh M. Diversity of P-element piRNA production among M' and Q strains and its association with P-M hybrid dysgenesis in Drosophila melanogaster. Mob DNA 2017; 8:13. [PMID: 29075336 PMCID: PMC5654125 DOI: 10.1186/s13100-017-0096-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/13/2017] [Indexed: 01/24/2023] Open
Abstract
Background Transposition of P elements in the genome causes P–M hybrid dysgenesis in Drosophila melanogaster. For the P strain, the P–M phenotypes are associated with the ability to express a class of small RNAs, called piwi-interacting small RNAs (piRNAs), that suppress the P elements in female gonads. However, little is known about the extent to which piRNAs are involved in the P–M hybrid dysgenesis in M′ and Q strains, which show different abilities to regulate the P elements from P strains. Results To elucidate the molecular basis of the suppression of paternally inherited P elements, we analyzed the mRNA and piRNA levels of P elements in the F1 progeny between males of a P strain and nine-line females of M′ or Q strains (M′ or Q progenies). M′ progenies showed the hybrid dysgenesis phenotype, while Q progenies did not. Consistently, the levels of P-element mRNA in both the ovaries and F1 embryos were higher in M′ progenies than in Q progenies, indicating that the M′ progenies have a weaker ability to suppress P-element expression. The level of P-element mRNA was inversely correlated to the level of piRNAs in F1 embryos. Importantly, the M′ progenies were characterized by a lower abundance of P-element piRNAs in both young ovaries and F1 embryonic bodies. The Q progenies showed various levels of piRNAs in both young ovaries and F1 embryonic bodies despite all of the Q progenies suppressing P-element transposition in their gonad. Conclusions Our results are consistent with an idea that the level of P-element piRNAs is a determinant for dividing strain types between M′ and Q and that the suppression mechanisms of transposable elements, including piRNAs, are varied between natural populations. Electronic supplementary material The online version of this article (10.1186/s13100-017-0096-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Tsuji Wakisaka
- Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo, Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Seiko Ohno
- Center for Epidemiologic Research in Asia, Shiga Univesity of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Masanobu Itoh
- Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo, Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan.,Center for Advanced Insect Research Promotion (CAIRP), Kyoto Institute of Technology, Kyoto, 606-8585 Japan
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22
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Fukuda K, Inoguchi Y, Ichiyanagi K, Ichiyanagi T, Go Y, Nagano M, Yanagawa Y, Takaesu N, Ohkawa Y, Imai H, Sasaki H. Evolution of the sperm methylome of primates is associated with retrotransposon insertions and genome instability. Hum Mol Genet 2017. [DOI: 10.1093/hmg/ddx236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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23
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Iida K, Kobayashi R, Hengjan Y, Nagata N, Yonemitsu K, Nunome M, Kuwata R, Suzuki K, Ichiyanagi K, Maeda K, Ohmori Y, Hondo E. The genetic diversity of D-loop sequences in eastern bent-winged bats (Miniopterus fuliginosus) living in Wakayama Prefecture, Japan. J Vet Med Sci 2017; 79:1142-1145. [PMID: 28484149 PMCID: PMC5487797 DOI: 10.1292/jvms.17-0152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 12/02/2022] Open
Abstract
The eastern bent-winged bat (Miniopterus fuliginosus) is an
insectivorous bat that lives in the caves, throughout Japan [11]. The bats aggregate in cave in populations of tens to thousands of
individuals. We examined the mitochondrial D-loop sequences of bats in Wakayama, Japan,
and divided them into 35 haplotypes. The sequences of 3 haplotypes in Wakayama were the
same as those of 10 Miniopterus fuliginosus individuals living in China.
Given the substitution rate of the D-loop region, we speculated that the bats had moved
between Japan and China within the last 16,000 years. We could not determine how the bats
crossed the sea; however, it is possible that the bats undergo dynamic movement widely
throughout East Asia.
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Affiliation(s)
- Keisuke Iida
- Laboratory of Animal Morphology, Faculty of Agriculture, Nagoya University, Nagoya 464-8601, Japan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yupadee Hengjan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Nao Nagata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Kenzo Yonemitsu
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Kazuo Suzuki
- Hikiiwa Park Center, Tanabe, Wakayama 646-0051, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Yasushige Ohmori
- Laboratory of Animal Morphology, Faculty of Agriculture, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Faculty of Agriculture, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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24
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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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Abstract
The third Japanese meeting entitled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements (TEs)” was held on 5–6 September 2016 at National Institute of Genetics (NIG), Mishima, Japan. Supported by NIG, the goal of the meeting was to bring together researchers who study diverse biological phenomena such as schizophrenia, carcinogenesis, cellular reprograming, skin function, placental formation, plant mutagenesis and epigenetics, and small RNA-mediated heterochromatinization, where TEs are involved in various ways. The meeting included 13 invited speakers. Here we present highlights of these invited talks.
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26
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Kobayashi M, Kato H, Hada H, Itoh-Nakadai A, Fujiwara T, Muto A, Inoguchi Y, Ichiyanagi K, Hojo W, Tomosugi N, Sasaki H, Harigae H, Igarashi K. Iron-heme-Bach1 axis is involved in erythroblast adaptation to iron deficiency. Haematologica 2016; 102:454-465. [PMID: 27927768 PMCID: PMC5394953 DOI: 10.3324/haematol.2016.151043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 06/15/2016] [Accepted: 12/01/2016] [Indexed: 12/21/2022] Open
Abstract
Iron plays the central role in oxygen transport by erythrocytes as a constituent of heme and hemoglobin. The importance of iron and heme is also to be found in their regulatory roles during erythroblast maturation. The transcription factor Bach1 may be involved in their regulatory roles since it is deactivated by direct binding of heme. To address whether Bach1 is involved in the responses of erythroblasts to iron status, low iron conditions that induced severe iron deficiency in mice were established. Under iron deficiency, extensive gene expression changes and mitophagy disorder were induced during maturation of erythroblasts. Bach1−/− mice showed more severe iron deficiency anemia in the developmental phase of mice and a retarded recovery once iron was replenished when compared with wild-type mice. In the absence of Bach1, the expression of globin genes and Hmox1 (encoding heme oxygenase-1) was de-repressed in erythroblasts under iron deficiency, suggesting that Bach1 represses these genes in erythroblasts under iron deficiency to balance the levels of heme and globin. Moreover, an increase in genome-wide DNA methylation was observed in erythroblasts of Bach1−/− mice under iron deficiency. These findings reveal the principle role of iron as a regulator of gene expression in erythroblast maturation and suggest that the iron-heme-Bach1 axis is important for a proper adaptation of erythroblast to iron deficiency to avoid toxic aggregates of non-heme globin.
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Affiliation(s)
- Masahiro Kobayashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroki Kato
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroshi Hada
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ari Itoh-Nakadai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan.,Department of Experimental Immunology, Institute of Development, Aging and Cancer, Tohoku University, Japan
| | - Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akihiko Muto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Yukihiro Inoguchi
- 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.,Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Wataru Hojo
- Department of Research and Development, Cellspect Co. Ltd., Morioka, Japan
| | - Naohisa Tomosugi
- Division of Systems Bioscience for Drug Discovery, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
| | - Hiroyuki Sasaki
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan.,Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan .,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan.,Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai, Japan
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27
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Affiliation(s)
- Kenji Ichiyanagi
- a Division of Epigenomics and Development; Medical Institute of Bioregulation ; Kyushu University ; Higashiku , Fukuoka , Japan
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28
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Hayashi M, Maehara K, Harada A, Semba Y, Kudo K, Takahashi H, Oki S, Meno C, Ichiyanagi K, Akashi K, Ohkawa Y. Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2. J Cell Biochem 2015; 117:780-92. [PMID: 26359639 DOI: 10.1002/jcb.25368] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 12/12/2022]
Abstract
Chd5 is an essential factor for neuronal differentiation and spermatogenesis and is a known tumor suppressor. H3K27me3 and H3K4un are modifications recognized by Chd5; however, it remains unclear how Chd5 remodels chromatin structure. We completely disrupted the Chd5 locus using the CRISPR-Cas9 system to generate a 52 kbp long deletion and analyzed Chd5 function in mouse embryonic stem cells. Our findings show that Chd5 represses murine endogenous retrovirus-L (MuERV-L/MERVL), an endogenous retrovirus-derived retrotransposon, by regulating H3K27me3 and H3.1/H3.2 function.
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Affiliation(s)
- Masayasu Hayashi
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Akihito Harada
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuichiro Semba
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.,Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Kensuke Kudo
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.,Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hidehisa Takahashi
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Hokkaido 060-8638, Japan
| | - Shinya Oki
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
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29
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Ichiyanagi T, Ichiyanagi K, Ogawa A, Kuramochi-Miyagawa S, Nakano T, Chuma S, Sasaki H, Udono H. HSP90α plays an important role in piRNA biogenesis and retrotransposon repression in mouse. Nucleic Acids Res 2014; 42:11903-11. [PMID: 25262350 PMCID: PMC4231750 DOI: 10.1093/nar/gku881] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
HSP90, found in all kingdoms of life, is a major chaperone protein regulating many client proteins. We demonstrated that HSP90α, one of two paralogs duplicated in vertebrates, plays an important role in the biogenesis of fetal PIWI-interacting RNAs (piRNA), which act against the transposon activities, in mouse male germ cells. The knockout mutation of Hsp90α resulted in a large reduction in the expression of primary and secondary piRNAs and mislocalization of MIWI2, a PIWI homolog. Whereas the mutation in Fkbp6 encoding a co-chaperone reduced piRNAs of 28–32 nucleotides in length, the Hsp90α mutation reduced piRNAs of 24–32 nucleotides, suggesting the presence of both FKBP6-dependent and -independent actions of HSP90α. Although DNA methylation and mRNA levels of L1 retrotransposon were largely unchanged in the Hsp90α mutant testes, the L1-encoded protein was increased, suggesting the presence of post-transcriptional regulation. This study revealed the specialized function of the HSP90α isofom in the piRNA biogenesis and repression of retrotransposons during the development of male germ cells in mammals.
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Affiliation(s)
- Tomoko Ichiyanagi
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Kita-ku, Okayama 700-8558, Japan Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ayako Ogawa
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Toru Nakano
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Shinichiro Chuma
- Department of Development and Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Kita-ku, Okayama 700-8558, Japan
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Ichiyanagi K. Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs. Genes Genet Syst 2014; 88:19-29. [PMID: 23676707 DOI: 10.1266/ggs.88.19] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Short interspersed elements (SINEs) are a class of retrotransposons, which amplify their copy numbers in their host genomes by retrotransposition. More than a million copies of SINEs are present in a mammalian genome, constituting over 10% of the total genomic sequence. In contrast to the other two classes of retrotransposons, long interspersed elements (LINEs) and long terminal repeat (LTR) elements, SINEs are transcribed by RNA polymerase III. However, like LINEs and LTR elements, the SINE transcription is likely regulated by epigenetic mechanisms such as DNA methylation, at least for human Alu and mouse B1. Whereas SINEs and other transposable elements have long been thought as selfish or junk DNA, recent studies have revealed that they play functional roles at their genomic locations, for example, as distal enhancers, chromatin boundaries and binding sites of many transcription factors. These activities imply that SINE retrotransposition has shaped the regulatory network and chromatin landscape of their hosts. Whereas it is thought that the epigenetic mechanisms were originated as a host defense system against proliferation of parasitic elements, this review discusses a possibility that the same mechanisms are also used to regulate the SINE-derived functions.
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Affiliation(s)
- Kenji Ichiyanagi
- Division of Epigenomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Umemori J, Mori A, Ichiyanagi K, Uno T, Koide T. Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome. BMC Genomics 2013; 14:455. [PMID: 23834397 PMCID: PMC3722088 DOI: 10.1186/1471-2164-14-455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 07/05/2013] [Indexed: 11/14/2022] Open
Abstract
Background Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. Results We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (>70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the CNV-type core elements have a longer evolutionary history than constant-type core elements in SD13M. Conclusions Our methodology for the identification of repetitive core sequences simplifies characterization of the structures of large SDs and detailed analysis of CNV. The results of detailed structural and quantitative analyses in this study might help to elucidate the biological role of one of the SDs on chromosome 13.
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Affiliation(s)
- Juzoh Umemori
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Nitta H, Unoki M, Ichiyanagi K, Kosho T, Shigemura T, Takahashi H, Velasco G, Francastel C, Picard C, Kubota T, Sasaki H. Three novel ZBTB24 mutations identified in Japanese and Cape Verdean type 2 ICF syndrome patients. J Hum Genet 2013; 58:455-60. [DOI: 10.1038/jhg.2013.56] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/30/2013] [Accepted: 05/07/2013] [Indexed: 11/09/2022]
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Ichiyanagi K. Transposable elements in eukaryotic genomes: epigenetic regulation by the host and functionalization for the host. Genes Genet Syst 2013; 88:1. [PMID: 23676704 DOI: 10.1266/ggs.88.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Kenji Ichiyanagi
- Department of Epigenomics, Medical Institute of Bioregulation, Kyushu University, Japan
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Abstract
DNA methylation is a well-characterized epigenetic modification involved in gene regulation and transposon silencing in mammals. It mainly occurs on cytosines at CpG sites but methylation at non-CpG sites is frequently observed in embryonic stem cells, induced pluriotent stem cells, oocytes and the brain. The biological significance of non-CpG methylation is unknown. Here, we show that non-CpG methylation is also present in male germ cells, within and around B1 retrotransposon sequences interspersed in the mouse genome. It accumulates in mitotically arrested fetal prospermatogonia and reaches the highest level by birth in a Dnmt3l-dependent manner. The preferential site of non-CpG methylation is CpA, especially CpApG and CpApC. Although CpApG (and CpTpG) sites contain cytosines at symmetrical positions, hairpin-bisulfite sequencing reveals that they are hemimethylated, suggesting the absence of a template-dependent copying mechanism. Indeed, the level of non-CpG methylation decreases after the resumption of mitosis in the neonatal period, whereas that of CpG methylation does not. The cells eventually lose non-CpG methylation by the time they become spermatogonia. Our results show that non-CpG methylation accumulates in non-replicating, arrested cells but is not maintained in mitotically dividing cells during male germ-cell development.
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Affiliation(s)
- Tomoko Ichiyanagi
- Division of Epigenomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Ichiyanagi K. Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site: a concern for DNA modification studies using restriction endonucleases. Epigenetics 2012; 7:131-6. [PMID: 22395461 DOI: 10.4161/epi.7.2.18909] [Citation(s) in RCA: 12] [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] [Indexed: 11/19/2022] Open
Abstract
In mammalian genomic DNA, cytosine methylation predominantly occurs at CpG dinucleotides and provides epigenetic information. In some cells, 5-methyl-cytosine (5-mC) can be further converted to 5-hydroxymethyl-cytosine (5-hmC) by the ten-eleven translocation family of proteins. MspI restriction endonuclease has been used to analyze these modified cytosines. However, the kinetic analysis in this study revealed that MspI activity is dramatically decreased by symmetrical hydroxymethylation of its recognition sequence and partly inhibited by hemi-hydroxymethylation, whereas TaqI and HaeIII are relatively resistant to hydroxymethylation. Therefore, DNA modification studies that use MspI, for example, reduced representation bisulfite shotgun sequencing, quantitative analysis of 5-hmC, and cleavage-sensitivity analysis, should be carefully interpreted.
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Affiliation(s)
- Kenji Ichiyanagi
- Division of Epigenomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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Ichiyanagi K, Li Y, Li Y, Watanabe T, Ichiyanagi T, Fukuda K, Kitayama J, Yamamoto Y, Kuramochi-Miyagawa S, Nakano T, Yabuta Y, Seki Y, Saitou M, Sasaki H. Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. Genome Res 2011; 21:2058-66. [PMID: 22042642 PMCID: PMC3227096 DOI: 10.1101/gr.123679.111] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 08/23/2011] [Indexed: 12/13/2022]
Abstract
In mammals, germ cells undergo striking dynamic changes in DNA methylation during their development. However, the dynamics and mode of methylation are poorly understood for short interspersed elements (SINEs) dispersed throughout the genome. We investigated the DNA methylation status of mouse B1 SINEs in male germ cells at different developmental stages. B1 elements showed a large locus-to-locus variation in methylation; loci close to RNA polymerase II promoters were hypomethylated, while most others were hypermethylated. Interestingly, a mutation that eliminates Piwi-interacting RNAs (piRNAs), which are involved in methylation of long interspersed elements (LINEs), did not affect the level of B1 methylation, implying a piRNA-independent mechanism. Methylation at B1 loci in SINE-poor genomic domains showed a higher dependency on the de novo DNA methyltransferase DNMT3A but not on DNMT3B, suggesting that DNMT3A plays a major role in methylation of these domains. We also found that many genes specifically expressed in the testis possess B1 elements in their promoters, suggesting the involvement of B1 methylation in transcriptional regulation. Taken altogether, our results not only reveal the dynamics and mode of SINE methylation but also suggest how the DNA methylation profile is created in the germline by a pair of DNA methyltransferases.
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Affiliation(s)
- Kenji Ichiyanagi
- Division of Epigenomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Watanabe T, Tomizawa SI, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H. Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science 2011; 332:848-52. [PMID: 21566194 DOI: 10.1126/science.1203919] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genomic imprinting causes parental origin-specific monoallelic gene expression through differential DNA methylation established in the parental germ line. However, the mechanisms underlying how specific sequences are selectively methylated are not fully understood. We have found that the components of the PIWI-interacting RNA (piRNA) pathway are required for de novo methylation of the differentially methylated region (DMR) of the imprinted mouse Rasgrf1 locus, but not other paternally imprinted loci. A retrotransposon sequence within a noncoding RNA spanning the DMR was targeted by piRNAs generated from a different locus. A direct repeat in the DMR, which is required for the methylation and imprinting of Rasgrf1, served as a promoter for this RNA. We propose a model in which piRNAs and a target RNA direct the sequence-specific methylation of Rasgrf1.
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Affiliation(s)
- Toshiaki Watanabe
- Division of Human Genetics and Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan.
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Ichiyanagi K, Sato T, Nozawa S, Kim KH, Lee JH, Choi J, Tomita A, Ichikawa H, Adachi S, Ihee H, Koshihara S. 100 ps time-resolved solution scattering utilizing a wide-bandwidth X-ray beam from multilayer optics. J Synchrotron Radiat 2009; 16:391-394. [PMID: 19395804 PMCID: PMC2678014 DOI: 10.1107/s0909049509005986] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 02/19/2009] [Indexed: 05/27/2023]
Abstract
100 ps time-resolved X-ray solution-scattering capabilities have been developed using multilayer optics at the beamline NW14A, Photon Factory Advanced Ring, KEK. X-ray pulses with an energy bandwidth of DeltaE/E = 1-5% are generated by reflecting X-ray pulses (DeltaE/E = 15%) through multilayer optics, made of W/B(4)C or depth-graded Ru/C on silicon substrate. This tailor-made wide-bandwidth X-ray pulse provides high-quality solution-scattering data for obtaining photo-induced molecular reaction dynamics. The time-resolved solution scattering of CH(2)I(2) in methanol is demonstrated as a typical example.
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Affiliation(s)
- K. Ichiyanagi
- Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - T. Sato
- Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- Tokyo Institute of Technology, 2-12-1 Oh-okayama, Megro-ku, Tokyo 152-8551, Japan
| | - S. Nozawa
- Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - K. H. Kim
- Center for Time-Resolved Diffraction, Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - J. H. Lee
- Center for Time-Resolved Diffraction, Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - J. Choi
- Center for Time-Resolved Diffraction, Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - A. Tomita
- Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- Tokyo Institute of Technology, 2-12-1 Oh-okayama, Megro-ku, Tokyo 152-8551, Japan
| | - H. Ichikawa
- Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - S. Adachi
- Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - H. Ihee
- Center for Time-Resolved Diffraction, Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - S. Koshihara
- Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- Tokyo Institute of Technology, 2-12-1 Oh-okayama, Megro-ku, Tokyo 152-8551, Japan
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Suzuki J, Yamaguchi K, Kajikawa M, Ichiyanagi K, Adachi N, Koyama H, Takeda S, Okada N. Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition. PLoS Genet 2009; 5:e1000461. [PMID: 19390601 PMCID: PMC2666801 DOI: 10.1371/journal.pgen.1000461] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 03/26/2009] [Indexed: 11/24/2022] Open
Abstract
Long interspersed elements (LINEs) are transposable elements that proliferate within eukaryotic genomes, having a large impact on eukaryotic genome evolution. LINEs mobilize via a process called retrotransposition. Although the role of the LINE-encoded protein(s) in retrotransposition has been extensively investigated, the participation of host-encoded factors in retrotransposition remains unclear. To address this issue, we examined retrotransposition frequencies of two structurally different LINEs—zebrafish ZfL2-2 and human L1—in knockout chicken DT40 cell lines deficient in genes involved in the non-homologous end-joining (NHEJ) repair of DNA and in human HeLa cells treated with a drug that inhibits NHEJ. Deficiencies of NHEJ proteins decreased retrotransposition frequencies of both LINEs in these cells, suggesting that NHEJ is involved in LINE retrotransposition. More precise characterization of ZfL2-2 insertions in DT40 cells permitted us to consider the possibility of dual roles for NHEJ in LINE retrotransposition, namely to ensure efficient integration of LINEs and to restrict their full-length formation. Long interspersed elements (LINEs) are transposable elements that mobilize and amplify their own copies within eukaryotic genomes. Although LINEs had been considered as “junk” DNA, recent studies have suggested that the LINE-induced alterations of host chromosomes are a major driving force for eukaryotic genome evolution. LINEs mobilize via a mechanism called retrotransposition, in which transcribed LINE RNA is reverse transcribed into DNA that is then integrated into the host chromosome. Although the role of LINE-encoded proteins in retrotransposition has been revealed, the participation of host-encoded proteins has not been well investigated. Here, using knockout chicken DT40 cell lines, we present genetic evidence that the host-encoded proteins involved in repair of DNA double-strand breaks participate in LINE retrotransposition. More precise characterization of LINE insertions in DT40 cells suggested dual roles for these host DNA repair proteins in LINE retrotransposition; one function is required for efficient integration of LINEs and the other restricts their full-length formation.
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Affiliation(s)
- Jun Suzuki
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, Japan
| | - Katsumi Yamaguchi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, Japan
| | - Masaki Kajikawa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, Japan
- * E-mail: (MK); (NO)
| | - Kenji Ichiyanagi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Noritaka Adachi
- International Graduate School of Arts and Sciences, Yokohama City University, Kanazawa-ku, Yokohama, Kanagawa, Japan
| | - Hideki Koyama
- International Graduate School of Arts and Sciences, Yokohama City University, Kanazawa-ku, Yokohama, Kanagawa, Japan
| | - Shunichi Takeda
- Radiation Genetics, Graduate School of Medicine, Kyoto University, Konoe Yoshida, Kyoto, Kyoto, Japan
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, Japan
- * E-mail: (MK); (NO)
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Tomita A, Sato T, Ichiyanagi K, Nozawa S, Ichikawa H, Chollet M, Kawai F, Park SY, Koshihara S, Adachi S. Slow ligand migration dynamics in carbonmonoxy myoglobin at cryogenic temperature. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308088545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Sato T, Nozawa S, Ichiyanagi K, Tomita A, Ichikawa H, Chollet M, Fujii H, Adachi S, Koshihara S. 100 ps time-resolved X-ray absorption fine structure of Fe II(1,10-phenanthroline) 3. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308093446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Fudeyasu H, Ichiyanagi K, Sugimoto A, Yoshimura K, Ueta A, Yamanaka MD, Ozawa K. Isotope ratios of precipitation and water vapor observed in Typhoon Shanshan. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jd009313] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Autonomous non-long terminal repeat retrotransposons (NLRs) are ubiquitous mobile genetic elements that insert their DNA copies at new locations by retrotransposition. In vertebrates, there are 4 NLR clades, L1, L2, CR1, and RTE, which diverged in the Precambrian era. It has been demonstrated that retrotransposition of L1 and L2 members proceeds via coordinated reactions of targeted DNA cleavage and reverse transcription catalyzed by the NLR-encoded proteins, which are followed by the joining of the 5' (upstream) junction. However, the study on the mobility pathways for vertebrate NLRs is so far limited to L1 and L2. In this report, using target analysis of nested transposons for genomic copies, we studied retrotransposition pathways for a variety of vertebrate NLRs, including those of the L1, L2, CR1, and RTE clades in the human, cow, opossum, chicken, and zebrafish genomes. Thus, this study constitutes the first comprehensive analysis of NLR retrotransposition products in vertebrates. Our data revealed that these elements share similar mechanisms for the cleavages of the 2 target DNA strands and for the initiation of reverse transcription. Possible endonuclease-independent insertions were also identified. Overall, our results suggest the existence of multiple retrotransposition pathways that are conserved among the diverse NLR clades in various vertebrate hosts.
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Affiliation(s)
- Kenji Ichiyanagi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
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Abstract
L1 is the most proliferative autonomous retroelement that comprises about 20% of mammalian genomes. Why L1s have proliferated so extensively in mammalian genomes is an important yet unsolved question. L1 copies are amplified via retrotransposition, in which the DNA cleavage specificity by the L1-encoded endonuclease (EN) primarily dictates sites of insertion. Whereas mammalian L1s show target preference for 5'-TTAAAA-3', other L1-like elements exhibit various degrees of target specificity. To gain insights on diversification of the EN specificity during L1 evolution, ENs of zebrafish L1 elements were analyzed here. We revealed that they form 3 discrete clades, M, F, and Tx1, which is in stark contrast to a single L1 clade in mammalian species. Interestingly, zebrafish clade M elements cluster as a sister group of mammalian L1s and show target-site preference for 5'-TTAAAA-3'. In contrast, elements of the clade F, the immediate outgroup of the clade M, show little specificity. We identified certain clade-specific amino acid residues in EN, many of which are located in the cleft that recognizes the substrate, suggesting that these amino acid alterations have generated 2 types of ENs with different substrate specificities. The distribution pattern of the 3 clades suggests a possibility that the acquisition of target specificity by the L1 ENs improved the L1 fitness under the circumstances in mammalian hosts.
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Affiliation(s)
- Kenji Ichiyanagi
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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Tian L, Yao T, MacClune K, White JWC, Schilla A, Vaughn B, Vachon R, Ichiyanagi K. Stable isotopic variations in west China: A consideration of moisture sources. ACTA ACUST UNITED AC 2007. [DOI: 10.1029/2006jd007718] [Citation(s) in RCA: 370] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lide Tian
- Laboratory of Land Surface Processes Monitoring; Institute of Tibetan Plateau Research; Beijing China
- Stable Isotope Laboratory, Institute of Arctic and Alpine Research; University of Colorado; Boulder Colorado USA
- Key Laboratory of Cryosphere and Environment, Cold and Arid Regions Environment and Engineering Research Institute; Chinese Academy of Science; Lanzhou China
| | - Tandong Yao
- Laboratory of Land Surface Processes Monitoring; Institute of Tibetan Plateau Research; Beijing China
| | - K. MacClune
- Stable Isotope Laboratory, Institute of Arctic and Alpine Research; University of Colorado; Boulder Colorado USA
| | - J. W. C. White
- Stable Isotope Laboratory, Institute of Arctic and Alpine Research; University of Colorado; Boulder Colorado USA
| | - A. Schilla
- Stable Isotope Laboratory, Institute of Arctic and Alpine Research; University of Colorado; Boulder Colorado USA
| | - B. Vaughn
- Stable Isotope Laboratory, Institute of Arctic and Alpine Research; University of Colorado; Boulder Colorado USA
| | - R. Vachon
- Stable Isotope Laboratory, Institute of Arctic and Alpine Research; University of Colorado; Boulder Colorado USA
| | - K. Ichiyanagi
- Institute of Observational Research for Global Change; Yokosuka Japan
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Honda H, Ichiyanagi K, Suzuki J, Ono T, Koyama H, Kajikawa M, Okada N. A new system for analyzing LINE retrotransposition in the chicken DT40 cell line widely used for reverse genetics. Gene 2007; 395:116-24. [PMID: 17434692 DOI: 10.1016/j.gene.2007.02.017] [Citation(s) in RCA: 4] [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] [Received: 09/14/2006] [Revised: 02/14/2007] [Accepted: 02/19/2007] [Indexed: 11/15/2022]
Abstract
Long interspersed elements (LINEs) are autonomous transposable elements that proliferate via retrotransposition, which involves reverse transcription of LINE RNAs. It is anticipated that LINE retrotransposition requires both LINE-encoded proteins and host-encoded proteins. However, identification of the host factors, their roles, and the steps at which they act on retrotransposition are poorly understood because of the lack of an appropriate genetic system to study LINE retrotransposition in a series of mutant hosts. To construct such a genetic system, we applied the retrotransposition-indicative cassette method to DT40 cells, a chicken cell line for which a variety of isogenic mutants have been established by gene targeting. Because DT40 cells are non-adherent, we utilized a selective soft agarose medium to allow the formation of colonies of cells that had undergone LINE retrotransposition. Colony formation was completely dependent on the activities of the LINE-encoded proteins and on the presence of the essential 3' region of the LINE RNA. Moreover, the selected colonies indeed carried retrotransposed LINE copies in their chromosomes, with integration features similar to those of genomic (native) LINE copies. This method thus allows the authentic selection of LINE-retrotransposed cells and the approximate recapitulation of retrotransposition events that occur in nature. Therefore, the DT40 cell system established here provides a powerful tool for the elucidation of LINE retrotransposition pathways, the host factors involved, and their roles.
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Affiliation(s)
- Hiroshi Honda
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-21 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Abstract
Autonomous non-long-terminal-repeat retrotransposons (NLRs) proliferate by retrotransposition via coordinated reactions of target DNA cleavage and reverse transcription by a mechanism called target-primed reverse transcription (TPRT). Whereas this mechanism guarantees the covalent attachment of the NLR and its target site at the 3' junction, mechanisms for the joining at the 5' junction have been conjectural. To better understand the retrotransposition pathways, we analyzed target-NLR junctions of zebrafish NLRs with a new method of identifying genomic copies that reside within other transposons, termed "target analysis of nested transposons" (TANT). Application of the TANT method revealed various features of the zebrafish NLR integrants; for example, half of the integrants carry extra nucleotides at the 5' junction, which is in stark contrast to the major human NLR, LINE-1. Interestingly, in a cell culture assay, retrotransposition of the zebrafish NLR in heterologous human cells did not bear extra 5' nucleotides, indicating that the choice of the 5' joining pathway is affected by the host. Our results suggest that several pathways exist for NLR retrotransposition and argue in favor of host protein involvement. With genomic sequence information accumulating exponentially, our data demonstrate the general applicability of the TANT method for the analysis of a wide variety of retrotransposons.
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Affiliation(s)
- Kenji Ichiyanagi
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Ryo Nakajima
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Masaki Kajikawa
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Norihiro Okada
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
- Corresponding author.E-mail fax: 81-45-924-5835
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48
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Ichiyanagi K, Okada N. Genomic alterations upon integration of zebrafish L1 elements revealed by the TANT method. Gene 2006; 383:108-16. [PMID: 17049188 DOI: 10.1016/j.gene.2006.07.038] [Citation(s) in RCA: 6] [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] [Received: 06/06/2006] [Revised: 07/07/2006] [Accepted: 07/07/2006] [Indexed: 11/25/2022]
Abstract
Transposable elements, or transposons, constitute substantial portions of eukaryotic genomes and have contributed to the diversity and functions of the genomes. Bioinformatic analysis of target junctions of genomic transposon copies can provide insights into their mobility mechanisms and consequent genomic alterations, but definitive identification of the target junctions remains difficult despite the steady accumulation of genomic sequence information. To overcome this difficulty, we recently developed a method termed "the target analysis of nested transposons" (TANT), which anatomizes junction features of numerous genomic copies of transposons that reside within other transposons. Whereas the mammalian long interspersed nuclear element (LINE)-1 (L1), a retrotransposon, has been proposed to make a considerable impact on host genomes, the mobility and impact of non-mammalian L1s are poorly understood. In the present study, we analyzed genomic copies of zebrafish L1 elements by using the TANT method. Some copies exhibited the features of integration that are similar to those of mammalian L1s. The zebrafish L1 retrotransposition reaction, however, frequently truncated the target-site DNA by up to 0.6 kb and produced a new sequence at LINE-target junctions. Moreover, our data suggest that L1 retrotransposition can be used to repair double-strand DNA breaks (DSBs). These results imply that L1s have had considerable impact on the evolution of the zebrafish genome.
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Affiliation(s)
- Kenji Ichiyanagi
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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49
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Abstract
BACKGROUND Although there is lymphatic flow into the popliteal fossa from a skin tumor located in the lower leg, popliteal metastasis is extremely rare. Recently, sentinel lymph nodes outside traditional nodal basins have been identified. This study investigated the incidence of sentinel nodes in the popliteal region and the indication for biopsy. METHODS Fourteen patients with various skin cancers involving the lower extremities (nine melanomas, four squamous cell carcinomas, and one sweat gland carcinoma) underwent lymphoscintigraphy and excision with sentinel lymph node biopsy. RESULTS In all 14 patients, hot spots showed accumulation in the groin region. Five of 14 patients (36%) demonstrated popliteal sentinel nodes in addition to the inguinal nodes. Three of five popliteal sentinel nodes were histologically studied. A patient with acral melanoma demonstrated micrometastasis of melanoma cells in a popliteal node but not in the groin node. CONCLUSION This study demonstrates that sentinel lymph nodes located in the popliteal fossa are frequently detected by lymphoscintigraphy and that biopsy should be performed if popliteal nodes are identified.
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Affiliation(s)
- Naohito Hatta
- Department of Dermatology, Kanazawa University School of Medicine, Takara-machi, Kanazawa, Japan.
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50
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Abstract
We previously showed that the group II Lactococcus lactis Ll.LtrB intron could retrotranspose into ectopic locations on the genome of its native host. Two integration events, which had been mapped to unique sequences, were localized in the present study to separate copies of the six L.lactis 23S rRNA genes, within operon B or D. Although further movement within the bacterial chromosome was undetectable, the retrotransposed introns were able to re-integrate into their original homing site provided on a plasmid. This finding indicates not only that retrotransposed group II introns retain mobility properties, but also that movement occurs back into sequence that is heterologous to the sequence of the chromosomal location. Sequence analysis of the retrotransposed introns and the secondary mobility events back to the homing site showed that the introns retain sequence integrity. These results are illuminating, since the reverse transcriptase (RT) of the intron-encoded protein, LtrA, has no known proofreading function, yet the mobility events have a low error rate. Enzymatic digests were used to monitor sequence changes from the wild-type intron. The results indicate that retromobility events have approximately 10(-5) misincorporations per nucleotide inserted. In contrast to the high RT error rates for retroviruses that must escape host defenses, the infrequent mutations of group II introns would ensure intron spread through retention of sequences essential for mobility.
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Affiliation(s)
- Lori H Conlan
- Wadsworth Center, Center for Medical Science, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12208, USA
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