Updated on 2024/04/18

写真a

 
NAGAKI Kiyotaka
 
Organization
Institute of Plant Science and Resources Associate Professor
Position
Associate Professor
External link

Degree

  • 博士(理学) ( 横浜市立大学 )

Research Interests

  • Chromosome

  • repetitive DNA sequences

  • epigenetics

  • centromere

  • heterochromatin

  • 動原体

  • ヘテロクロマチン

  • 染色体

  • エピジェネティクス

  • 反復配列

  • セントロメア

Research Areas

  • Life Science / Genetics

Professional Memberships

Committee Memberships

  • 日本遺伝学会   評議員  

    2017 - 2020.12   

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  • 財団法人染色体学会   理事  

    2016   

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  • 染色体学会   評議員  

    2007 - 2016   

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    Committee type:Academic society

    染色体学会

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Papers

  • Phenotypic effects of Am genomes in nascent synthetic hexaploids derived from interspecific crosses between durum and wild einkorn wheat Reviewed

    Asami Michikawa, Moeko Okada, Tatsuya M. Ikeda, Kiyotaka Nagaki, Kentaro Yoshida, Shigeo Takumi

    PLOS ONE   18 ( 4 )   e0284408 - e0284408   2023.4

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    Publishing type:Research paper (scientific journal)   Publisher:Public Library of Science (PLoS)  

    Allopolyploid speciation is a major evolutionary process in wheat (Triticum spp.) and the related Aegilops species. The generation of synthetic polyploids by interspecific crosses artificially reproduces the allopolyploidization of wheat and its relatives. These synthetic polyploids allow breeders to introduce agriculturally important traits into durum and common wheat cultivars. This study aimed to evaluate the genetic and phenotypic diversity in wild einkorn Triticum monococcum ssp. aegilopoides (Link) Thell., to generate a set of synthetic hexaploid lines containing the various Am genomes from wild einkorn, and to reveal their trait characteristics. We examined the genetic diversity of 43 wild einkorn accessions using simple sequence repeat markers covering all the chromosomes and revealed two genetically divergent lineages, L1 and L2. The genetic divergence between these lineages was linked to their phenotypic divergence and their habitats. L1 accessions were characterized by early flowering, fewer spikelets, and large spikelets compared to L2 accessions. These trait differences could have resulted from adaptation to their different habitats. We then developed 42 synthetic hexaploids containing the AABBAmAm genome through interspecific crosses between T. turgidum cv. Langdon (AABB genome) as the female parent and the wild einkorn accessions (AmAm genome) as the male parents. Two of the 42 AABBAmAm synthetic hexaploids exhibited hybrid dwarfness. The phenotypic divergence between L1 and L2 accessions of wild einkorn, especially for days to flowering and spikelet-related traits, significantly reflected phenotypic differences in the synthetic hexaploids. The differences in plant height and internodes between the lineages were more distinct in the hexaploid backgrounds. Furthermore, the AABBAmAm synthetic hexaploids had longer spikelets and grains, long awns, high plant heights, soft grains, and late flowering, which are distinct from other synthetic hexaploid wheat lines such as AABBDD. Utilization of various Am genomes of wild einkorn resulted in wide phenotypic diversity in the AABBAmAm synthetic hexaploids and provides promising new breeding materials for wheat.

    DOI: 10.1371/journal.pone.0284408

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  • Effectiveness of Create ML in microscopy image classifications: a simple and inexpensive deep learning pipeline for non-data scientists. Reviewed International journal

    Kiyotaka Nagaki, Tomoyuki Furuta, Naoki Yamaji, Daichi Kuniyoshi, Megumi Ishihara, Yuji Kishima, Minoru Murata, Atsushi Hoshino, Hirotomo Takatsuka

    Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology   29 ( 3-4 )   361 - 371   2021.12

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    Observing chromosomes is a time-consuming and labor-intensive process, and chromosomes have been analyzed manually for many years. In the last decade, automated acquisition systems for microscopic images have advanced dramatically due to advances in their controlling computer systems, and nowadays, it is possible to automatically acquire sets of tiling-images consisting of large number, more than 1000, of images from large areas of specimens. However, there has been no simple and inexpensive system to efficiently select images containing mitotic cells among these images. In this paper, a classification system of chromosomal images by deep learning artificial intelligence (AI) that can be easily handled by non-data scientists was applied. With this system, models suitable for our own samples could be easily built on a Macintosh computer with Create ML. As examples, models constructed by learning using chromosome images derived from various plant species were able to classify images containing mitotic cells among samples from plant species not used for learning in addition to samples from the species used. The system also worked for cells in tissue sections and tetrads. Since this system is inexpensive and can be easily trained via deep learning using scientists' own samples, it can be used not only for chromosomal image analysis but also for analysis of other biology-related images.

    DOI: 10.1007/s10577-021-09676-z

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  • Application of CRISPR/Cas9 to visualize defined genomic sequences in fixed chromosomes and nuclei

    Takayoshi Ishii, Kiyotaka Nagaki, Andreas Houben

    Cytogenomics   147 - 153   2021

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    Publishing type:Part of collection (book)   Publisher:Elsevier  

    DOI: 10.1016/b978-0-12-823579-9.00007-2

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  • Decrosslinking enables visualization of RNA-guided endonuclease?in situ labeling signals for DNA sequences in plant tissues. Reviewed

    Kiyotaka Nagaki, Naoki Yamaji

    Journal of Experimental Botany   71 ( 6 )   1792 - 1800   2020.3

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    DOI: 10.1093/jxb/erz534

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  • ePro-ClearSee: a simple immunohistochemical method that does not require sectioning of plant samples Reviewed

    Kiyotaka Nagaki, Naoki Yamaji, Minoru Murata

    SCIENTIFIC REPORTS   7   42203 - 14   2017.2

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    Investigations into the epigenetic status of individual cells within tissues can produce both epigenetic data for different cell types and positional information of the cells. Thus, these investigations are important for understanding the intra-and inter-cellular control systems of developmental and environmental responses in plants. However, a simple method to detect epigenetic modifications of individual cells in plant tissues is not yet available because detection of the modifications requires immunohistochemistry using specific antibodies. In this study, we developed a simple immunohistochemical method that does not require sectioning to investigate epigenetic modifications. This method uses a clearing system to detect methylated histones, acetylated histones, methylated DNA and/or centromeric histone H3 variants. Analyses of four dicots and five monocots indicated that this method provides a universal technique to investigate epigenetic modifications in diverse plant species.

    DOI: 10.1038/srep42203

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  • Analysis of epigenetic modifications in plant tissues by a novel clearing method Reviewed

    Nagaki Kiyotaka, Yamaji Naoki, Murata Minoru

    Genes & Genetic Systems   91 ( 6 )   346   2016

  • Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat Reviewed

    Kiyotaka Nagaki, Keisuke Tanaka, Naoki Yamaji, Hisato Kobayashi, Minoru Murata

    Frontiers in Plant Science   6 ( OCTOBER )   912   2015.10

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Frontiers Research Foundation  

    The kinetochore is a protein complex including kinetochore-specific proteins that plays a role in chromatid segregation during mitosis and meiosis. The complex associates with centromeric DNA sequences that are usually species-specific. In plant species, tandem repeats including satellite DNA sequences and retrotransposons have been reported as centromeric DNA sequences. In this study on sunflowers, a cDNA-encoding centromere-specific histone H3 (CENH3) was isolated from a cDNA pool from a seedling, and an antibody was raised against a peptide synthesized from the deduced cDNA. The antibody specifically recognized the sunflower CENH3 (HaCENH3) and showed centromeric signals by immunostaining and immunohistochemical staining analysis. The antibody was also applied in chromatin immunoprecipitation (ChIP)-Seq to isolate centromeric DNA sequences and two different types of repetitive DNA sequences were identified. One was a long interspersed nuclear element (LINE)-like sequence, which showed centromere-specific signals on almost all chromosomes in sunflowers. This is the first report of a centromeric LINE sequence, suggesting possible centromere targeting ability. Another type of identified repetitive DNA was a tandem repeat sequence with a 187-bp unit that was found only on a pair of chromosomes. The HaCENH3 content of the tandem repeats was estimated to be much higher than that of the LINE, which implies centromere evolution from LINE-based centromeres to more stable tandem-repeat-based centromeres. In addition, the epigenetic status of the sunflower centromeres was investigated by immunohistochemical staining and ChIP, and it was found that centromeres were heterochromatic.

    DOI: 10.3389/fpls.2015.00912

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  • Epigenomic modification in rice controls meiotic recombination and segregation distortion

    Yoshiki Habu, Tsuyu Ando, Sachie Ito, Kiyotaka Nagaki, Naoki Kishimoto, Fumio Taguchi-Shiobara, Hisataka Numa, Katsushi Yamaguchi, Shuji Shigenobu, Minoru Murata, Tetsuo Meshi, Masahiro Yano

    MOLECULAR BREEDING   35 ( 4 )   644 - 653   2015.4

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    The low frequency of meiotic recombination in chromosomal regions other than hotspots is a general obstacle to efficient breeding. A number of active genes are present in recombination-repressed centromeric regions in higher eukaryotes, suggesting that suppression of meiotic recombination prevents shuffling of genes within a centromeric region. In this study, by using an inter-subspecific cross of Oryza sativa L., we show that modification of inactive chromatin states by either genetic or chemical inhibition of chromatin modifying proteins induced changes in both the position of meiotic recombination and, unexpectedly, the pattern of segregation distortion of parental alleles. Antisense knockdown of rice homologues of DECREASE IN DNA METHYLATION1, which is required for the maintenance of heterochromatin in Arabidopsis thaliana, induced a recombination hotspot in a centromeric region accompanied by a steep increase in the proportion of heterozygotes. Our results describe a previously undocumented phenomenon in which artificial chromatin modification could be used to change the pattern of segregation distortion in rice and open up novel possibilities for efficient crop breeding.

    DOI: 10.1007/s11032-015-0299-0

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  • Modification of centromere structure: a promising approach for haploid line production in plant breeding

    Ahmet L. Tek, Robert M. Stupar, Kiyotaka Nagaki

    TURKISH JOURNAL OF AGRICULTURE AND FORESTRY   39 ( 4 )   557 - 562   2015

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    Language:English   Publisher:TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY  

    Breeding based on doubled-haploid approaches has recently become a common tool for accelerating crop improvement in many plant species. However, many plant species do not have a reliable method for haploid induction. A promising new approach involving centromere engineering has recently been proposed to overcome this limitation. Here we provide a perspective of this novel method for the production of haploid plants, which was originally described in the model plant species Arabidopsis thaliana. Centromeres, known to be critical for the accurate distribution of chromosomes in every cell division, have now become a novel target for crop improvement by enabling doubled-haploid technologies.

    DOI: 10.3906/tar-1405-137

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  • Identification of the centromere-specific histone H3 variant in Lotus japonicus

    Ahmet L. Tek, Kazunari Kashihara, Minoru Murata, Kiyotaka Nagaki

    GENE   538 ( 1 )   8 - 11   2014.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

    The centromere is a structurally and functionally specialized region present on every eukaryotic chromosome. Lotus japorticus is a model legume species for which there is very limited information on the centromere structure. Here we cloned and characterized the L. japonicus homolog of the centromere-specific histone H3 gene (LjCenH3) encoding a 159-amino acid protein. Using an Agrobacterium-based transformation system, LjCenH3 tagged with a green fluorescent protein was transferred into L. japonicus cells. The centromeric position of LjCENH3 protein was revealed on L. japonicus metaphase chromosomes by an immunofiuorescence assay. The identification of LjCenH3 as a critical centromere landmark could pave the way for a better understanding of centromere structure in this model and other agriculturally important legume species. Published by Elsevier B.V.

    DOI: 10.1016/j.gene.2014.01.034

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  • Identification and characterization of functional centromeres of the common bean Reviewed

    Aiko Iwata, Ahmet L. Tek, Manon M.S. Richard, Brian Abernathy, Artur Fonsêca, Jeremy Schmutz, Nicolas W.G. Chen, Vincent Thareau, Ghislaine Magdelenat, Yupeng Li, Minoru Murata, Andrea Pedrosa-Harand, Valérie Geffroy, Kiyotaka Nagaki, Scott A. Jackson

    Plant Journal   76 ( 1 )   47 - 60   2013.10

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    In higher eukaryotes, centromeres are typically composed of megabase-sized arrays of satellite repeats that evolve rapidly and homogenize within a species' genome. Despite the importance of centromeres, our knowledge is limited to a few model species. We conducted a comprehensive analysis of common bean (Phaseolus vulgaris) centromeric satellite DNA using genomic data, fluorescence in situ hybridization (FISH), immunofluorescence and chromatin immunoprecipitation (ChIP). Two unrelated centromere-specific satellite repeats, CentPv1 and CentPv2, and the common bean centromere-specific histone H3 (PvCENH3) were identified. FISH showed that CentPv1 and CentPv2 are predominantly located at subsets of eight and three centromeres, respectively. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of CentPv1 and CentPv2 at centromeres. Genomic analysis revealed several interesting features of CentPv1 and CentPv2: (i) CentPv1 is organized into an higher-order repeat structure, named Nazca, of 528 bp, whereas CentPv2 is composed of tandemly organized monomers
    (ii) CentPv1 and CentPv2 have undergone chromosome-specific homogenization
    and (iii) CentPv1 and CentPv2 are not likely to be commingled in the genome. These findings suggest that two distinct sets of centromere sequences have evolved independently within the common bean genome, and provide insight into centromere satellite evolution. © 2013 The Authors The Plant Journal © 2013 John Wiley &amp
    Sons Ltd.

    DOI: 10.1111/tpj.12269

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  • Tobacco karyotyping by accurate centromere identification and novel repetitive DNA localization

    Fukashi Shibata, Kiyotaka Nagaki, Etsuko Yokota, Minoru Murata

    CHROMOSOME RESEARCH   21 ( 4 )   375 - 381   2013.7

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    Tobacco (Nicotiana tabacum) is an amphidiploid species (2n = 4x = 48, genome constitution SSTT) derived from a natural hybrid between Nicotiana sylvestris (2n = 2x = 24, SS) and Nicotiana tomentosiformis (2n = 2x = 24, TT). Genomic in situ hybridization (GISH), using the genomic DNA from these ancestral species as probes, revealed the chromosomal origins (S or T) and the occurrence of intergenomic translocations in N. tabacum. Fluorescence in situ hybridization (FISH) was also used to distinguish between chromosomes. However, the use of repetitive DNA sequences as probes for FISH analysis is limited by an inability to identify all chromosomes. In addition to this limitation, the occurrence of chromosomal tertiary constrictions can easily lead to the misclassification of chromosomes. To overcome these issues, immunostaining with anti-N. tabacum centromere-specific histone H3 antibody was carried out to determine the centromere position of each chromosome, followed by FISH analysis with ten distinct repetitive DNA probes. This approach allowed us to identify 22 of the 24 chromosome pairs in N. tabacum and revealed novel intergenomic chromosome rearrangements and B-chromosome-like minichromosomes. Hence, the combination of immunostaining with FISH and GISH is critical to accurately karyotype tobacco.

    DOI: 10.1007/s10577-013-9363-y

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  • Generation of an artificial ring chromosome in Arabidopsis by Cre/LoxP-mediated recombination Reviewed

    Minoru Murata, Fukashi Shibata, Akiko Hironaka, Kazunari Kashihara, Satoru Fujimoto, Etsuko Yokota, Kiyotaka Nagaki

    PLANT JOURNAL   74 ( 3 )   363 - 371   2013.5

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    A eukaryotic chromosome consists of a centromere, two telomeres and a number of replication origins, and artificial chromosomes' may be created in yeast and mammals when these three elements are artificially joined and introduced into cells. Plant artificial chromosomes (PACs) have been suggested as new vectors for the development of new crops and as tools for basic research on chromosomes. However, indisputable PAC formation has not yet been confirmed. Here, we present a method for generating PACs in the model plant Arabidopsis thaliana using the Cre/LoxP and Activator/Dissociation element systems. The successfully generated PAC, designated AtARC1 (A.thaliana artificial ring chromosome1), originated from a centromeric edge of the long arm of chromosome2, but its size (2.85Mb) is much smaller than that of the original chromosome (26.3Mb). Although AtARC1 contains only a short centromere domain consisting of 180bp repeats approximately 250kb in length, compared with the 3Mb domain on the original chromosome2, centromere-specific histone H3 (HTR12) was detected on the centromeric region. This result supported the observed stability of the PAC during mitosis in the absence of selection, and transmission of the PAC to the next generation through meiosis. Because AtARC1 contains a unique LoxP site driven by the CaMV 35S promoter, it is possible to introduce a selectable marker and desired transgenes into AtARC1 at the LoxP site using Cre recombinase. Therefore, AtARC1 meets the criteria for a PAC and is a promising vector.

    DOI: 10.1111/tpj.12128

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  • Chromosome Dynamics Visualized with an Anti-Centromeric Histone H3 Antibody in Allium

    Kiyotaka Nagaki, Maki Yamamoto, Naoki Yamaji, Yasuhiko Mukai, Minoru Murata

    PLOS ONE   7 ( 12 )   e51315   2012.12

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:PUBLIC LIBRARY SCIENCE  

    Due to the ease with which chromosomes can be observed, the Allium species, and onion in particular, have been familiar materials employed in cytogenetic experiments in biology. In this study, centromeric histone H3 (CENH3)-coding cDNAs were identified in four Allium species (onion, welsh onion, garlic and garlic chives) and cloned. Anti-CENH3 antibody was then raised against a deduced amino acid sequence of CENH3 of welsh onion. The antibody recognized all CENH3 orthologs of the Allium species tested. Immunostaining with the antibody enabled clear visualization of chromosome behavior during mitosis in the species. Furthermore, three-dimensional (3D) observation of mitotic cell division was achieved by subjecting root sections to immunohistochemical techniques. The 3D dynamics of the cells and position of cell-cycle marker proteins (CENH3 and alpha-tubulin) were clearly revealed by immunohistochemical staining with the antibodies. The immunohistochemical analysis made it possible to establish an overview of the location of dividing cells in the root tissues. This breakthrough in technique, in addition to the two centromeric DNA sequences isolated from welsh onion by chromatin immuno-precipitation using the antibody, should lead to a better understanding of plant cell division. A phylogenetic analysis of Allium CENH3s together with the previously reported plant CENH3s showed two separate clades for monocot species tested. One clade was made from CENH3s of the Allium species with those of Poaceae species, and the other from CENH3s of a holocentric species (Luzula nivea). These data may imply functional differences of CENH3s between holocentric and monocentric species. Centromeric localization of DNA sequences isolated from welsh onion by chromatin immunoprecipitation (ChIP) using the antibody was confirmed by fluorescence in situ hybridization and ChIP-quantitative PCR.

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  • Nondisjunction in Favor of a Chromosome: The Mechanism of Rye B Chromosome Drive during Pollen Mitosis Reviewed

    Ali M. Banaei-Moghaddam, Veit Schubert, Katrin Kumke, Oda Weiss, Sonja Klemme, Kiyotaka Nagaki, Jiri Macas, Monica Gonzalez-Sanchez, Victoria Heredia, Diana Gomez-Revilla, Miriam Gonzalez-Garcia, Juan M. Vega, Maria J. Puertas, Andreas Houben

    PLANT CELL   24 ( 10 )   4124 - 4134   2012.10

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    B chromosomes (Bs) are supernumerary components of the genome and do not confer any advantages on the organisms that harbor them. The maintenance of Bs in natural populations is possible by their transmission at higher than Mendelian frequencies. Although drive is the key for understanding B chromosomes, the mechanism is largely unknown. We provide direct insights into the cellular mechanism of B chromosome drive in the male gametophyte of rye (Secale cereale). We found that nondisjunction of Bs is accompanied by centromere activity and is likely caused by extended cohesion of the B sister chromatids. The B centromere originated from an A centromere, which accumulated B-specific repeats and rearrangements. Because of unequal spindle formation at the first pollen mitosis, nondisjoined B chromatids preferentially become located toward the generative pole. The failure to resolve pericentromeric cohesion is under the control of the B-specific nondisjunction control region. Hence, a combination of nondisjunction and unequal spindle formation at first pollen mitosis results in the accumulation of Bs in the generative nucleus and therefore ensures their transmission at a higher than expected rate to the next generation.

    DOI: 10.1105/tpc.112.105270

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  • Isolation of centromeric-tandem repetitive DNA sequences by chromatin affinity purification using a HaloTag7-fused centromere-specific histone H3 in tobacco

    Kiyotaka Nagaki, Fukashi Shibata, Asaka Kanatani, Kazunari Kashihara, Minoru Murata

    PLANT CELL REPORTS   31 ( 4 )   771 - 779   2012.4

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    The centromere is a multi-functional complex comprising centromeric DNA and a number of proteins. To isolate unidentified centromeric DNA sequences, centromere-specific histone H3 variants (CENH3) and chromatin immunoprecipitation (ChIP) have been utilized in some plant species. However, anti-CENH3 antibody for ChIP must be raised in each species because of its species specificity. Production of the antibodies is time-consuming and costly, and it is not easy to produce ChIP-grade antibodies. In this study, we applied a HaloTag7-based chromatin affinity purification system to isolate centromeric DNA sequences in tobacco. This system required no specific antibody, and made it possible to apply a highly stringent wash to remove contaminated DNA. As a result, we succeeded in isolating five tandem repetitive DNA sequences in addition to the centromeric retrotransposons that were previously identified by ChIP. Three of the tandem repeats were centromere-specific sequences located on different chromosomes. These results confirm the validity of the HaloTag7-based chromatin affinity purification system as an alternative method to ChIP for isolating unknown centromeric DNA sequences. The discovery of more than two chromosome-specific centromeric DNA sequences indicates the mosaic structure of tobacco centromeres.

    DOI: 10.1007/s00299-011-1198-4

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  • Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat

    Ahmet L. Tek, Kazunari Kashihara, Minoru Murata, Kiyotaka Nagaki

    CHROMOSOME RESEARCH   19 ( 8 )   969 - 978   2011.11

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    The centromere plays an essential role for proper chromosome segregation during cell division and usually harbors long arrays of tandem repeated satellite DNA sequences. Although this function is conserved among eukaryotes, the sequences of centromeric DNA repeats are variable. Most of our understanding of functional centromeres, which are defined by localization of a centromere-specific histone H3 (CENH3) protein, comes from model organisms. The components of the functional centromere in legumes are poorly known. The genus Astragalus is a member of the legumes and bears the largest numbers of species among angiosperms. Therefore, we studied the components of centromeres in Astragalus sinicus. We identified the CenH3 homolog of A. sinicus, AsCenH3 that is the most compact in size among higher eukaryotes. A CENH3-based assay revealed the functional centromeric DNA sequences from A. sinicus, called CentAs. The CentAs repeat is localized in A. sinicus centromeres, and comprises an AT-rich tandem repeat with a monomer size of 20 nucleotides.

    DOI: 10.1007/s10577-011-9247-y

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  • Stability of monocentric and dicentric ring minichromosomes in Arabidopsis

    Etsuko Yokota, Fukashi Shibata, Kiyotaka Nagaki, Minoru Murata

    CHROMOSOME RESEARCH   19 ( 8 )   999 - 1012   2011.11

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    A dicentric ring minichromosome (mini delta) was identified in transgenic Arabidopsis thaliana and added to a wild type as a supernumerary chromosome. This line is relatively stable and has been maintained for generations, notwithstanding its ring and dicentric structure. To determine the mechanism for stable transmission of mini delta, the structure and behavior of two new types of ring minichromosomes (mini delta 1 and mini delta 1-1) derived from mini delta were investigated. Fluorescence in situ hybridization analysis revealed that mini delta 1 is dicentric just like mini delta, whereas mini delta 1-1 is monocentric. The estimated sizes of mini delta 1 and mini delta 1-1 were 3.8 similar to 5.0 and 1.7 Mb, respectively. The sizes of the two centromeres on mini delta 1 were identical (ca. 270 kb) and similar to that of mini delta 1-1 (ca. 250 kb). Mini delta 1 was relatively stable during mitosis and meiosis, as is mini delta, whereas mini delta 1-1 was unstable during mitosis, and the number of minichromosomes per cell varied. This possibly resulted from misdivision caused by a short centromere on monocentric mini delta 1-1. Transmission through the female was quite limited for all three ring minichromosomes (0-3.2%), whereas that through the male was relatively high (15.4-27.3%) compared with that of other supernumerary chromosomes in Arabidopsis. Ring structure without telomeres itself seems not to limit the female transmission.

    DOI: 10.1007/s10577-011-9250-3

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  • Coexistence of NtCENH3 and two retrotransposons in tobacco centromeres

    Kiyotaka Nagaki, Fukashi Shibata, Go Suzuki, Asaka Kanatani, Souichi Ozaki, Akiko Hironaka, Kazunari Kashihara, Minoru Murata

    CHROMOSOME RESEARCH   19 ( 5 )   591 - 605   2011.7

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:SPRINGER  

    Although a centromeric DNA fragment of tobacco (Nicotiana tabacum), Nt2-7, has been reported, the overall structure of the centromeres remains unknown. To characterize the centromeric DNA sequences, we conducted a chromatin immunoprecipitation assay using anti-NtCENH3 antibody and chromatins isolated from two ancestral diploid species (Nicotiana sylvestris and Nicotiana tomentosiformis) of N. tabacum and isolated a 178-pb fragment, Nto1 from N. tomentosiformis, as a novel centromeric DNA. Fluorescence in situ hybridization (FISH) showed that Nto1 localizes on 24 out of 48 chromosomes in some cells of a BY-2 cell line. To identify the origins of the Nt2-7 and Nto1, a tobacco bacterial artificial chromosome (BAC) library was constructed from N. tabacum, and then screened by polymerase chain reaction (PCR) with primer sets designed from the Nt2-7 and Not1 DNA sequences. Twelve BAC clones were found to localize on the centromeric regions by FISH. We selected three BAC clones for sequencing and identified two centromeric retrotransposons, NtCR and NtoCR, the DNA sequences of which are similar to that of Nt2-7 and Nto1, respectively. Quantitative PCR analysis using coprecipitated DNA with anti-NtCENH3 clearly showed coexistence of NtCENH3 with both retrotransposons. These results indicate the possibility that these two retrotransposons act as centromeric DNA sequences in tobacco. NtoCR was found to be specific to N. tomentosiformis and T genome of N. tabacum, and a NtCR-like centromeric retrotransposon (TGRIV) exists in tomato. This specificity suggests that the times of amplification of these centromeric retrotransposons were different.

    DOI: 10.1007/s10577-011-9219-2

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  • Meiosis-Specific Loading of the Centromere-Specific Histone CENH3 in Arabidopsis thaliana

    Maruthachalam Ravi, Fukashi Shibata, Joseph S. Ramahi, Kiyotaka Nagaki, Changbin Chen, Minoru Murata, Simon W. L. Chan

    PLOS GENETICS   7 ( 6 )   e1002121   2011.6

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    Centromere behavior is specialized in meiosis I, so that sister chromatids of homologous chromosomes are pulled toward the same side of the spindle (through kinetochore mono-orientation) and chromosome number is reduced. Factors required for mono-orientation have been identified in yeast. However, comparatively little is known about how meiotic centromere behavior is specialized in animals and plants that typically have large tandem repeat centromeres. Kinetochores are nucleated by the centromere-specific histone CENH3. Unlike conventional histone H3s, CENH3 is rapidly evolving, particularly in its N-terminal tail domain. Here we describe chimeric variants of CENH3 with alterations in the N-terminal tail that are specifically defective in meiosis. Arabidopsis thaliana cenh3 mutants expressing a GFP-tagged chimeric protein containing the H3 N-terminal tail and the CENH3 C-terminus (termed GFP-tailswap) are sterile because of random meiotic chromosome segregation. These defects result from the specific depletion of GFP-tailswap protein from meiotic kinetochores, which contrasts with its normal localization in mitotic cells. Loss of the GFP-tailswap CENH3 variant in meiosis affects recruitment of the essential kinetochore protein MIS12. Our findings suggest that CENH3 loading dynamics might be regulated differently in mitosis and meiosis. As further support for our hypothesis, we show that GFP-tailswap protein is recruited back to centromeres in a subset of pollen grains in GFP-tailswap once they resume haploid mitosis. Meiotic recruitment of the GFP-tailswap CENH3 variant is not restored by removal of the meiosis-specific cohesin subunit REC8. Our results reveal the existence of a specialized loading pathway for CENH3 during meiosis that is likely to involve the hypervariable N-terminal tail. Meiosis-specific CENH3 dynamics may play a role in modulating meiotic centromere behavior.

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  • CENH3 distribution and differential chromatin modifications during pollen development in rye (Secale cereale L.)

    Andreas Houben, Katrin Kumke, Kiyotaka Nagaki, Gerd Hause

    CHROMOSOME RESEARCH   19 ( 4 )   471 - 480   2011.5

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    Microgametogenesis in angiosperms results in two structurally and functionally different cells, one generative cell, which subsequently forms the sperm cells, and the vegetative cell. We analysed the chromatin properties of both types of nuclei after first and second pollen mitosis in rye (Secale cereale). The condensed chromatin of generative nuclei is ear-marked by an enhanced level of histone H3K4/K9 dimethylation and H3K9 acetylation. The less condensed vegetative nuclei are RNA polymerase II positive. Trimethylation of H3K27 is not involved in transcriptional downregulation of genes located in generative nuclei as H3K27me3 was exclusively detected in the vegetative nuclei. The global level of DNA methylation does not differ between both types of pollen nuclei. In rye, unlike in Arabidopsis thaliana (Ingouff et al. Curr Biol 17:1032-1037 2007; Schoft et al. EMBO Rep 10:1015-1021 2009), centromeric histone H3 is not excluded from the chromatin of the vegetative nucleus and the condensation degree of centromeric and subtelomeric regions did not differ between the generative and vegetative nuclei. Differences between rye and A. thaliana data suggest that the chromatin organization in mature nuclei of pollen grains is not universal across angiosperms.

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  • Holocentric Chromosomes of Luzula elegans Are Characterized by a Longitudinal Centromere Groove, Chromosome Bending, and a Terminal Nucleolus Organizer Region

    S. Heckmann, E. Schroeder-Reiter, K. Kumke, L. Ma, K. Nagaki, M. Murata, G. Wanner, A. Houben

    CYTOGENETIC AND GENOME RESEARCH   134 ( 3 )   220 - 228   2011

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    The structure of holocentric chromosomes was analyzed in mitotic cells of Luzula elegans. Light and scanning electron microscopy observations provided evidence for the existence of a longitudinal groove along each sister chromatid. The centromere-specific histone H3 variant, CENH3, colocalized with this groove and with microtubule attachment sites. The terminal chromosomal regions were CENH3-negative. During metaphase to anaphase transition, L. elegans chromosomes typically curved to a sickle-like shape, a process that is likely to be influenced by the pulling forces of microtubules along the holocentric axis towards the corresponding microtubule organizing regions. A single pair of 45S rDNA sites, situated distal to Arabidopsis-telomere repeats, was observed at the terminal region of one chromosome pair. We suggest that the 45S rDNA position in distal centromere-free regions could be required to ensure chromosome stability. Copyright (C) 2011 S. Karger AG, Basel

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  • Minichromosome stability induced by partial genome duplication in Arabidopsis thaliana

    Etsuko Yokota, Kiyotaka Nagaki, Minoru Murata

    CHROMOSOMA   119 ( 4 )   361 - 369   2010.8

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    Two partially reconstructed karyotypes (RK1 and RK2) of Arabidopsis thaliana have been established from a transformant, in which four structurally changed chromosomes (alpha, beta, gamma, and delta) were involved. Both karyotypes are composed of 12 chromosomes, 2n - 1 '' + 3 '' + 4 '' + 5 '' + alpha '' + gamma '' - 12 for RK1 and 2n 3 '' + 4 '' + 5 '' + alpha + beta '' + gamma '' - 12 for RK2, and these chromosome constitutions were relatively stable at least for three generations. Pairing at meiosis was limited to the homologues ( 1, 3, 4, 5, alpha, beta, or gamma), and no pairing occurred among non- homologous chromosomes in both karyotypes. For minichromosome a (mini alpha), precocious separation at metaphase I was frequently observed in RK2, as found for other minichromosomes, but was rare in RK1. This stable paring of mini alpha was possibly caused by duplication of the terminal tip of chromosome 1 that is characteristic of RK1.

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  • Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon

    Ahmet L. Tek, Kazunari Kashihara, Minoru Murata, Kiyotaka Nagaki

    CHROMOSOME RESEARCH   18 ( 3 )   337 - 347   2010.4

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    The centromere as a kinetochore assembly site is fundamental to the partitioning of genetic material during cell division. In order to determine the functional centromeres of soybean, we characterized the soybean centromere-specific histone H3 (GmCENH3) protein and developed an antibody against the N-terminal end. Using this antibody, we cloned centromere-associated DNA sequences by chromatin immunoprecipitation. Our analyses indicate that soybean centromeres are composed of two distinct satellite repeats (GmCent-1 and GmCent-4) and retrotransposon-related sequences (GmCR). The possible allopolyploid origin of the soybean genome is discussed in view of the centromeric satellite sequences present.

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  • Centromere targeting of alien CENH3s in Arabidopsis and tobacco cells

    Kiyotaka Nagaki, Kaori Terada, Munenori Wakimoto, Kazunari Kashihara, Minoru Murata

    CHROMOSOME RESEARCH   18 ( 2 )   203 - 211   2010.2

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    The centromere is a region utilized for spindle attachment on a eukaryotic chromosome and essential for accurate chromatid segregation. In most eukaryotes, centromeres have specific DNA sequences and are capable of assembling specific proteins to form a complex called the kinetochore. Among these proteins, centromeric histone H3 (CENH3) is one of the most fundamental, since CENH3s have been found in all investigated functional centromeres and recruits other centromeric proteins. In this study, the localization of alien CENH3s were analyzed in Arabidopsis and tobacco-cultured cells to determine the interaction between species-specific centromeric DNA and CENH3. Results showed that CENH3 of Arabidopsis and tobacco were localized on centromeres in the tobacco-cultured cells, unlike the case with CENH3 of rice and Luzula. In addition to these CENH3s, CENH3 of Luzula was partially localized in the Arabidopsis cultured cells. These data suggest that only evolutionally close CENH3s are able to target centromeres in alien species. Furthermore, the ability to target alien centromeres of histone fold domains was investigated using amino-terminal deleted CENH3s.

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  • Characterization of the two centromeric proteins CENP-C and MIS12 in Nicotiana species

    Kiyotaka Nagaki, Kazunari Kashihara, Minoru Murata

    CHROMOSOME RESEARCH   17 ( 6 )   719 - 726   2009.8

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    Centromeres play an important role in chromosome transmission in eukaryotes and comprise specific DNA and proteins that form complexes called kinetochores. In tobacco, although a centromere-specific histone H3 (NtCENH3) and centromeric DNA sequence (Nt2-7) have been identified, no other kinetochore components have been determined. In this study, we isolated and characterized cDNAs encoding two centromeric proteins CENP-C and MIS12 from Nicotiana tabaccum. Two CENP-C homologues, NtCENP-C-1 and -2, isolated from N. tabaccum were similar to CENP-C from N. sylvestris and N. tomentosiformis, respectively. Similarly, two Mis12 homologues, NtMIS12-1 and -2, in N. tabaccum were shown to originate from N. sylvestris and N. tomentosiformis, respectively. Both respective homologues for CENP-C and Mis12 were expressed at the same level. This indicates that in a tetraploid species, N. tabaccum, two ancestral genes encoding the centromeric proteins participate equally in the functioning of centromeres.

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  • A centromeric DNA sequence colocalized with a centromere-specific histone H3 in tobacco

    Kiyotaka Nagaki, Kazunari Kashihara, Minoru Murata

    CHROMOSOMA   118 ( 2 )   249 - 257   2009.4

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    Centromeres play an important role in segregating chromosomes into daughter cells, and centromeric DNA assembles specific proteins to form a complex referred to as the kinetochore. Among these proteins, centromere-specific histone H3 (CENH3) is one of the most characterized and found to be located only on active centromeres. We isolated four different CENH3-coding complementary DNAs (cDNAs), two from Nicotiana tabaccum and one each from the ancestral diploid species, Nicotiana sylvestris and Nicotiana tomentosiformis and raised an antibody against N-terminal amino acid sequences deduced from the cDNAs. Immunostaining with the antibody revealed the preferential centromere localization, indicating that the cDNAs cloned in this study encode authentic tobacco CENH3. A tobacco centromeric DNA sequence (Nt2-7) was also identified by chromatin immunoprecipitation cloning using the antibody.

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  • Components and structures of plant centromeres.

    Kiyotaka Nagaki

    Chromosome Science   12 ( 1 )   5 - 11   2009

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    Centromeres are functional chromosomal loci involved in an overall process that delivers sister chromatids equally into daughter cells during mitosis and meiosis. A complex of centromeric DNA and proteins is formed at the primary constriction point, and is referred to as the kinetochore. Since this function is essential for all eukaryotes, the process and centromeric proteins involved are conserved among eukaryotes. On the other hand, the DNA components and structures of centromeres are highly variable among eukaryotes. In the last decade, a plethora of investigations concerning plant centromeric components including centromeric DNA and proteins have been conducted which have shed light on these enigmatic chromosomal regions and associated functions. In this review, an overview of plant centromeric components including centromeric proteins (CENP-C, centromere specific histone H3 variants, and MIS12) and centromeric DNA and structures of plant centromeres (Arabidopsis, rice, and Luzula) are presented.

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  • CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley

    Andreas Houben, Elizabeth Schroeder-Reiter, Kiyotaka Nagaki, Shuhei Nasuda, Gerhard Wanner, Minoru Murata, Takashi R. Endo

    CHROMOSOMA   116 ( 3 )   275 - 283   2007.6

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    The chromosomal location of centromere-specific histone H3 (CENH3) is the assembly site for the kinetochore complex of active centromeres. Chromatin immunoprecipitation data indicated that CENH3 interacts in barley with cereba, a centromeric retroelement (CR)-like element conserved among cereal centromeres and barley-specific GC-rich centromeric satellite sequences. Anti-CENH3 signals on extended chromatin fibers always colocalized with the centromeric sequences but did not encompass the entire area covered by such centromeric repeats. This indicates that the CENH3 protein is bound only to a fraction of the centromeric repeats. At mitotic metaphase, CENH3, histone H3, and serine 10 phosphorylated histone H3 predominated within distinct structural subdomains of the centromere, as demonstrated by immunogold labeling for high resolution scanning electron microscopy.

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  • Characterization of two centromere-specific histone H3 homologues from tobacco Reviewed

    Kiyotaka Nagaki, Kazunari Kashihara, Minoru Murata

    CHROMOSOME RESEARCH   15   60 - 61   2007

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  • Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-polymerase chain reaction

    Amy C. Luce, Anupma Sharma, Oliver S. B. Mollere, Thomas K. Wolfgruber, Kiyotaka Nagaki, Jiming Jiang, Gernot G. Presting, R. Kelly Dawe

    GENETICS   174 ( 2 )   1057 - 1061   2006.10

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    Centromeres are difficult to map even in species where genetic resolution is excellent. Here we show that functions between repeats provide reliable single-copy markets for recombinant inbred mapping within centromeres and pericentromeric heterochromatin. Repeat function mapping was combined will anti-CENH3-mediated ChIP to provide a definitive map position for maize centromere 8.

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  • Transcription and histone modifications in the recombination-free region spanning a rice centromere

    HH Yan, WW Jin, K Nagaki, SL Tian, S Ouyang, CR Buell, PB Talbert, S Henikoff, JM Jiang

    PLANT CELL   17 ( 12 )   3227 - 3238   2005.12

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    Centromeres are sites of spindle attachment for chromosome segregation. During meiosis, recombination is absent at centromeres and surrounding regions. To understand the molecular basis for recombination suppression, we have comprehensively annotated the 3.5-Mb region that spans a fully sequenced rice centromere. Although transcriptional analysis showed that the 750-kb CENH3-containing core is relatively deficient in genes, the recombination-free region differs little in gene density from flanking regions that recombine. Likewise, the density of transposable elements is similar between the recombination-free region and flanking regions. We also measured levels of histone H4 acetylation and histone H3 methylation at 176 genes within the 3.5-Mb span. Active genes showed enrichment of H4 acetylation and H3K4 dimethylation as expected, including genes within the core. Our inability to detect sequence or histone modification features that distinguish recombination-free regions from flanking regions that recombine suggest that recombination suppression is an epigenetic feature of centromeres maintained by the assembly of CENH3-containing nucleosomes within the core. CENH3-containing centrochromatin does not appear to be distinguished by a unique combination of H3 and H4 modifications. Rather, the varied distribution of histone modifications might reflect the composition and abundance of sequence elements that inhabit centromeric DNA.

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  • Visualization of diffuse centromeres with centromere-specific histone H3 in the holocentric plant Luzula nivea

    K Nagaki, K Kashihara, M Murata

    PLANT CELL   17 ( 7 )   1886 - 1893   2005.7

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    Although holocentric species are scattered throughout the plant and animal kingdoms, only holocentric chromosomes of the nematode worm Caenorhabditis elegans have been analyzed with centromeric protein markers. In an effort to determine the holocentric structure in plants, we investigated the snowy woodrush Luzula nivea. From the young roots, a cDNA encoding a putative centromere-specific histone H3 (LnCENH3) was successfully isolated based on sequence similarity among plant CENH3s. The deduced amino acid sequence was then used to raise an anti-LnCENH3 antibody. Immunostaining clearly revealed the diffuse centromere-like structure that appears in the linear shape at prophase to telophase. Furthermore, it was shown that the amount of LnCENH3 decreased significantly at interphase. The polar side positioning on each chromatid at metaphase to anaphase also confirmed that LnCENH3 represents one of the centromere-specific proteins in L. nivea. These data from L. nivea are compared with those from C. elegans, and common features of holocentric chromosomes are discussed.

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  • Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice

    K Nagaki, P Neumann, DF Zhang, S Ouyang, CR Buell, ZK Cheng, JM Jiang

    MOLECULAR BIOLOGY AND EVOLUTION   22 ( 4 )   845 - 855   2005.4

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    The centromeric retrotransposon (CR) family in the grass species is one of few Ty3-gypsy groups of retroelements that preferentially transpose into highly specialized chromosomal domains. It has been demonstrated in both rice and maize that CRR (CR of rice) and CRM (CR of maize) elements are intermingled with centromeric satellite DNA and are highly concentrated within cytologically defined centromeres. We collected all of the CRR elements from rice chromosomes 1, 4, 8, and 10 that have been sequenced to high quality. Phylogenetic analysis revealed that the CRR elements are structurally diverged into four subfamilies, including two autonomous subfamilies (CRR1 and CRR2) and two nonautonomous subfamilies (noaCRR1 and noaCRR2). The CRR1/CRR2 elements contain all characteristic protein domains required for retrotransposition. In contrast, the noaCRR elements have different structures, containing only a gag or gag-pro domain or no open reading frames. The CRR and noaCRR elements share substantial sequence similarity in regions required for DNA replication and for recognition by integrase during retrotransposition. These data, coupled with the presence of young noaCRR elements in the rice genome and similar chromosomal distribution patterns between noaCRR1 and CRR1/CRR2 elements, suggest that the noaCRR elements were likely mobilized through the retrotransposition machinery from the autonomous CRR elements. Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed.

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  • Characterization of CENH3 and centromere-associated DNA sequences in sugarcane

    K Nagaki, M Murata

    CHROMOSOME RESEARCH   13 ( 2 )   195 - 203   2005.1

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    Centromere-specific histone H3 (CENH3) has been used to detect active centromeres, and to analyse the DNA sequences closely associated with the centromere, because they localize only in active centromeres and bind directly to the DNA. In maize and rice, the centromeric retrotransposons (CR) are shown to be closely associated with their own CENH3 whereas no such association was found in Arabidopsis thaliana. In this study, this sort of association was investigated in sugarcane. Two expressed sequence tag groups encoding putative sugarcane CENH3 (SoCENH3) were found in a sugarcane-expressed sequence tag database. Their deduced amino acid sequences were similar to these of the CENH3s in rice and maize. An antibody against rice CENH3 seemed to crossreact with the SoCENH3s, and stained sugarcane centromeres. A set of immunoprecipitation tests was conducted with the antibody and chromatin from the sugarcane genome to reveal CENH3-associated DNA sequences in sugarcane. Centromeric tandem repeats (SCEN) and centromeric retrotransposons of sugarcane (CRS) were significantly precipitated with the antibody, meaning these repeats are directly interacting with CENH3 in sugarcane centromeres.

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  • Maize centromeres: Organization and functional adaptation in the genetic background of oat

    WW Jin, Melo, JR, K Nagaki, PB Talbert, S Henikoff, RK Dawe, JM Jiang

    PLANT CELL   16 ( 3 )   571 - 581   2004.3

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    Centromeric DNA sequences in multicellular eukaryotes are often highly repetitive and are not unique to a specific centromere or to centromeres at all. Thus, it is a major challenge to study the fine structure of individual plant centromeres. We used a DNA fiber-fluorescence in situ hybridization approach to study individual maize (Zea mays) centromeres using oat (Avena sativa)-maize chromosome addition lines. The maize centromere-specific satellite repeat CentC in the addition lines allowed us to delineate the size and organization of centromeric DNA of individual maize chromosomes. We demonstrate that the cores of maize centromeres contain mainly CentC arrays and clusters of a centromere-specific retrotransposon, CRM. CentC and CRM sequences are highly intermingled. The amount of CentC/CRM sequence varies from similar to300 to >2800 kb among different centromeres. The association of CentC and CRM with centromeric histone H3 (CENH3) was visualized by a sequential detection procedure on stretched centromeres. The analysis revealed that CENH3 is always associated with CentC and CRM but that not all CentC or CRM sequences are associated with CENH3. We further demonstrate that in the chromosomal addition lines in which two CenH3 genes were present, one from oat and one from maize, the oat CENH3 was consistently incorporated by the maize centromeres.

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  • Sequencing of a rice centromere uncovers active genes

    K Nagaki, ZK Cheng, S Ouyang, PB Talbert, M Kim, KM Jones, S Henikoff, CR Buell, JM Jiang

    NATURE GENETICS   36 ( 2 )   138 - 145   2004.2

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    Centromeres are the last frontiers of complex eukaryotic genomes, consisting of highly repetitive sequences that resist mapping, cloning and sequencing. The centromere of rice Chromosome 8 (Cen8) has an unusually low abundance of highly repetitive satellite DNA, which allowed us to determine its sequence. A region of similar to750 kb in Cen8 binds rice CENH3, the centromere-specific H3 histone. CENH3 binding is contained within a larger region that has abundant dimethylation of histone H3 at Lys9 (H3-Lys9), consistent with Cen8 being embedded in heterochromatin. Fourteen predicted and at least four active genes are interspersed in Cen8, along with CENH3 binding sites. The retrotransposons located in and outside of the CENH3 binding domain have similar ages and structural dynamics. These results suggest that Cen8 may represent an intermediate stage in the evolution of centromeres from genic regions, as in human neocentromeres, to fully mature centromeres that accumulate megabases of homogeneous satellite arrays.

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  • Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres

    K Nagaki, PB Talbert, CX Zhong, RK Dawe, S Henikoff, JM Jiang

    GENETICS   163 ( 3 )   1221 - 1225   2003.3

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    The centromeres of Arabidopsis thaliana chromosomes contain megabases of complex DNA consisting of numerous types of repetitive DNA elements. We developed a chromatin immunoprecipitation (ChIP) technique using an antibody against the centromeric H3 histone, HTR12, in Arabidopsis. ChIP assays showed that the 180-bp centromeric satellite repeat was precipitated with the antibody, suggesting that this repeat is the key component of the centromere/kinctochore complex in Arabidopsis.

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  • Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres

    K Nagaki, JQ Song, RM Stupar, AS Parokonny, QP Yuan, S Ouyang, J Liu, J Hsiao, KM Jones, RK Dawe, CR Buell, JM Jiang

    GENETICS   163 ( 2 )   759 - 770   2003.2

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    We sequenced two maize bacterial artificial chromosome (BAC) clones anchored by the centromere-specific satellite repeat CentC. The two BACs, consisting of similar to200 kb of cytologically defined centromeric DNA, are composed exclusively of satellite sequences and retrotransposons that can be classified as centromere specific or noncentromere specific on the basis of their distribution in the maize genome. Sequence analysis suggests that the original maize sequences were composed of CentC arrays that were expanded by retrotransposon invasions. Seven centromere-specific retrotransposons of maize (CRM) were found in BAC 16H10. The CRM elements inserted randomly into either CentC monomers or other retrotransposons. Sequence comparisons of the long terminal repeats (LTRs) of individual CRM elements indicated that these elements transposed within the last 1.22 million years. We observed that all of the previously reported centromere-specific retrotransposons in rice and barley, which belong to the same family as the CRM elements, also recently transposed with the oldest element having transposed similar to3.8 million years ago. Highly conserved sequence motifs were found in the LTRs of the centromere-specific retrotransposons in the grass species, suggesting that the LTRs may be important for the centromere specificity of this retrotransposon family.

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  • Centromeric retroelements and satellites interact with maize kinetochore protein CENH3

    CX Zhong, JB Marshall, C Topp, R Mroczek, A Kato, K Nagaki, JA Birchler, JM Jiang, RK Dawe

    PLANT CELL   14 ( 11 )   2825 - 2836   2002.11

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    Maize centromeres are composed of CentC tandem repeat arrays, centromeric retrotransposons (CRs), and a variety of other repeats. One particularly well-conserved CR element, CRM, occurs primarily as complete and uninterrupted elements and is interspersed thoroughly with CentC at the light microscopic level. To determine if these major centromeric DNAs are part of the functional centromere/kinetochore complex, we generated antiserum to maize centromeric histone H3 (CENH3). CENH3, a highly conserved protein that replaces histone H3 in centromeres, is thought to recruit many of the proteins required for chromosome movement. CENH3 is present throughout the cell cycle and colocalizes with the kinetochore protein CENPC in meiotic cells. Chromatin immunoprecipitation demonstrates that CentC and CRM interact specifically with CENH3, whereas knob repeats and Tekay retroelements do not. Approximately 38 and 33% of CentC and CRM are precipitated in the chromatin immunoprecipitation assay, consistent with data showing that much, but not all, of CENH3 colocalizes with CentC.

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  • Tetrad-FISH analysis reveals recombination suppression by interstitial heterochromatin sequences in rye (Secale cereale)

    N Kagawa, K Nagaki, H Tsujimoto

    MOLECULAR GENETICS AND GENOMICS   267 ( 1 )   10 - 15   2002.3

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    Tetrad analysis is a genetic method that can locate genes and centromeres on a linkage map with a high degree of precision. Despite its effectiveness and accuracy, application of this method is generally limited to fungi, algae and mosses. Here we demonstrate a new method of tetrad analysis that is applicable to other organisms. This combines tetrad analysis with fluorescence in situ hybridization (FISH), and is thus referred to as tetrad-FISH analysis. We demonstrate the effectiveness of this method using tetrads of rye, Secale cereale. The rye strain JNK contains interstitial heterochromatin in a region of Chromosome 2R. We have previously cloned the tandemly repeated sequence forming this heterochromatin in the plasmid pScJNK. We performed FISH using pScJNK as the probe on tetrads obtained from heterozygotes for the heterochromatin region. The frequency of tetrads demonstrating positive signals in two cells that are diagonally opposite one another must correspond to the frequency of recombination in the interval between the heterochromatin and the centromere. Comparison between the results of tetrad-FISH analysis and linkage maps based on RFLP markers clearly indicated that heterochromatin strongly suppresses recombination of whole chromosomal regions. We discuss the effectiveness of tetrad-FISH analysis, particularly for the localization of functional centromeres in linkage maps.

    DOI: 10.1007/s00438-001-0634-5

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  • Amplification of the Afa-family repetitive sequences in the evolution of the D and A genomes in wheat and its relatives

    Kiyotaka Nagaki, Hisashi Tsujimoto

    The Botanica   51   18 - 28   2001

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  • A tandem repetitive sequence located in the centromeric region of common wheat (Triticum aestivum) chromosomes

    M Kishii, K Nagaki, H Tsujimoto

    CHROMOSOME RESEARCH   9 ( 5 )   417 - 428   2001

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    Although TaiI-family sequences are present in the subtelomeric region of Leymus racemosus, it became apparent in the present study that such sequences are also present in the centromeric region of common wheat (Triticum aestivum). These sequences hybridized to all chromosomes with various degrees of signal strength. FISH using TaiI and Ty3/gypsy, a conservative sequence in cereal centromeres, revealed a complicated arrangement of both sequences in all wheat chromosomes at once. Unlike the Arabidopsis centromeres characterized by massive tandem arrays of 180-bp family with flanking paracentromeric retrotransposons in all chromosomes, wheat chromosomes showed various arrangement patterns of TaiI and Ty3/gypsy sequences depending on the chromosome; TaiI-family sequences were scattered in many wheat centromeres as isolated colonies instead of forming uninterrupted solid tandem arrays. This pattern may have resulted from retrotransposon insertion within pre-existing TaiI-tandem arrays or a two-step amplification mechanism of the TaiI family where each TaiI colony was amplified to form arrays independently after the insertion of TaiI-family sequences along the entire centromere. Although sequence analysis of centromeric TaiI repeats in wheat and subtelomeric TaiI repeats in L. racemosus showed variable and conservative regions between the two repeats, they did not show a distinctive difference phylogenically. The widespread presence of tandem repetitive sequences in the eucaryotic centromere suggests a significant role for them in centromeric formation.

    DOI: 10.1023/A:1016739719421

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  • Development of an efficient maintenance and screening system for large-insert genomic DNA libraries of hexaploid wheat in a transformation-competent artificial chromosome (TAC) vector

    YG Liu, K Nagaki, M Fujita, K Kawaura, M Uozumi, Y Ogihara

    PLANT JOURNAL   23 ( 5 )   687 - 695   2000.9

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    Three large-insert genomic DNA libraries of common wheat, Triticum aestivum cv. Chinese Spring, were constructed in a newly developed transformation-competent artificial chromosome (TAC) vector, pYLTAC17, which accepts and maintains large genomic DNA fragments stably in both Escherichia coli and Agrobacterium tumefaciens. The vector contains the cis sequence required for Agrobacterium-mediated gene transfer into grasses. The average insert sizes of the three genomic libraries were approximately 46, 65 and 120 kbp, covering three haploid genome equivalents. Genomic libraries were stored as frozen cultures in a 96-well format, each well containing approximately 300-600 colonies (12 plates for small library, four for medium-size library and four for large library). In each of the libraries, approximately 80% of the colonies harbored genomic DNA inserts of > 50 kbp. TAC clones containing gene(s) of interest were identified by the pooled PCR technique. Once the target TAC clones were isolated, they could be immediately transferred into grass genomes with the Agrobacterium system. Five clones containing the thionin type I genes (single copy per genome), corresponding to each of the three genomes (A, B and D), were successfully selected by the pooled PCR method, in addition to an STS marker (aWG464; single copy per genome) and CAB (a multigene family). TAC libraries constructed as described here can be used to isolate genomic clones containing target genes, and to carry out genome walking for positional cloning.

    DOI: 10.1046/j.1365-313X.2000.00827.x

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  • Tandem repetitive Afa-family sequences from Leymus racemosus and Psathyrostachys juncea (Poaceae)

    K Nagaki, M Kishii, H Tsujimoto, T Sasakuma

    GENOME   42 ( 6 )   1258 - 1260   1999.12

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    Tandem repetitive Afa-family sequences of 340 bp are known to occur in wheat and related species of tribe Triticeae. We isolated six and three Afa-family sequences from Leymus racemosus and Psathyrostachys juncea, respectively, both of which are perennial species. The sequences account for 0.5% and 0.2% of L. racemosus and P. juncea genomes, respectively, and using in situ hybridization were located in subtelomeric and interstitial regions of L. racemosus chromosomes. These sequences are clustered with those of Elymus trachycaulus in the phylogenetic tree. Our findings indicate that the Afa-family sequences have been amplified at least twice in the lineage of L. racemosus, P. juncea, and E. trachycaulus.

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  • De novo synthesis of telomere sequences at the healed breakpoints of wheat deletion chromosomes

    H Tsujimoto, N Usami, K Hasegawa, T Yamada, K Nagaki, T Sasakuma

    MOLECULAR AND GENERAL GENETICS   262 ( 4-5 )   851 - 856   1999.12

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    When chromosomes are broken, the breakpoints become highly unstable and acquire the ability to fuse-with other broken ends. The breakpoints are, however, eventually stabilized, and, therefore, the broken chromosomes are transmitted to the daughter cells without further morphological change. This phenomenon, known as "healing of breakpoints", involves the addition of repetitive telomere sequences at the breakpoints by telomerase, the enzyme that normally synthesizes the telomere sequence at normal chromosome terminals. In many higher organisms, however, this property has not been well investigated. In this study, we examined the telomere sequences in wheat deletion lines with breakpoints on chromosome 1B. Lines that had breakpoints around the nucleolar organizer region were first selected on the basis of cytological observations, and the precise breakpoints were determined by mapping a fragment of rDNA and RFLP markers. In three lines - in addition to one previously reported - the DNA fragments encompassing the breakpoints were amplified by PCR using primers located in the rDNA and in telomere sequences. The DNA sequences provide insight into the properties of the telomerase activity at the breakpoints. The telomere sequences initiated from 2- to 4-nucleotide motifs in the original ribosomal DNA sequence which are also found in the repeat unit characteristic of telomere sequences. No specific sequences or structures were observed at or around the breakpoints. At all of the four breakpoints investigated, the newly synthesized telomere sequences contained considerable numbers of atypical telomere sequence units, particularly TTAGGG, which is the common unit of mammalian telomere sequences. Based on these results, we discuss the ability of plant telomerase to initiate the de novo synthesis of telomere sequences at internal breakpoints.

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  • Exclusive localization of tandem repetitive sequences in subtelomeric heterochromatin regions of Leymus racemosus (Poaceae, Triticeae)

    M Kishii, K Nagaki, H Tsujimoto, T Sasakuma

    CHROMOSOME RESEARCH   7 ( 7 )   519 - 529   1999

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    Two kinds of tandem repetitive sequences were isolated from Leymus racemosus (Lam.) Tzvelev. One of them was classified in the 350-bp family originally isolated from Secale. The other was a novel repetitive sequence family, named 'TaiI family', which consisted of a repeat unit of 570 bp. Fluorescence in-situ hybridization of the chromosomes of L. racemosus indicated that both families were located in subtelomeric heterochromatin and that the 350-bp family and TaiI family occupied different heterochromatin regions. In addition, even homologous chromosomes did not show the same patterns of TaiI and 350-bp families. The combination of these two families of repetitive sequences, together with Afa-family sequences and rDNAs, helps to identify the ten homologous chromosome pairs of L. racemosus. From these data, we proposed a karyotype of L. racemosus and compared it with other karyotypes already reported.

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  • A novel repetitive sequence, termed the JNK repeat family, located on an extra heterochromatic region of chromosome 2R of Japanese rye

    K Nagaki, H Tsujimoto, T Sasakuma

    CHROMOSOME RESEARCH   7 ( 2 )   95 - 101   1999

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    Among cultivated rye, Secale cereale L., collected in Japan, we found an extra heterochromatin on the long-arm interstitial region of chromosome 2R. This extra heterochromatin was polymorphic in the population. The plants with the extra heterochromatin showed a specific DNA fragment of 1.2 kb in digests prepared with the restriction enzyme DraI. The fragment was cloned and used as a probe for fluorescent in-situ hybridization (FISH). The clone, pScJNK1, showed a hybridization signal at the extra heterochromatic region. The segregation of the number of signals corresponded to the number of the extra heterochromatin of the 2R chromosome, indicating that the sequence might construct the heterochromatin. Southern hybridization using the clone as a probe showed a ladder pattern, suggesting that the sequence was a tandem repeat. Three sequences homologous to pScJNK1 were isolated; these were 1192-1232 bp, 44.7-45.9% in GC content, highly homologous (> 93%) with each other, and did not show any significant homology to other sequences in a DNA database. Slot blot hybridization using pScJNK1 as a probe indicated that there were about 4000 copies of the sequence in the haploid genome carrying the extra heterochromatin, whereas less than 20 copies existed in the genome without the heterochromatin. Southern hybridization using MspI and HapII indicated that all of the second cytosine nucleotides in CCGG sites in the sequence were methylated in the extra heterochromatin.

    DOI: 10.1023/A:1009226612818

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  • Dynamics of tandem repetitive Afa-family sequences in triticeae, wheat-related species

    K Nagaki, H Tsujimoto, T Sasakuma

    JOURNAL OF MOLECULAR EVOLUTION   47 ( 2 )   183 - 189   1998.8

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    The Afa-family sequences in wheat-related species, Triticeae, are tandem repetitive sequences of 340 bp. All the analyzed Triticeae species carried the sequences in their genomes, though the copy numbers varied about 100-fold among the species. The nucleotide fragments amplified by PCR were cloned and sequenced, and their behavior in the evolution of Triticeae was analyzed by the neighbor-joining (NJ) method. The sequences in genomes with many copies of this family clustered at independent branches of the phylogenic tree, whereas the sequences in genomes with a few copies did not. This may suggest that Afa-family sequences had amplified several times in the evolution of Triticeae, each using a limited number of different master copies. In addition, the sequences of the A and B genomes of hexaploid common wheat indicated that the Afa-family sequences had not evolved in a concerted manner between the genomes. Furthermore, the sequences of each chromosome of the D genome of this species indicated that the sequences had amplified on all over the D-genome chromosomes in a short period.

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  • H genome specific repetitive sequence, pEt2, of Elymus trachycaulus in part of afa family of triticeae

    Kiyotaka Nagaki, Hisashi Tsujimoto, Tetsuo Sasakuma

    Genome   41 ( 1 )   134 - 136   1998

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    The H genome specific repetitive sequence of Elymus trachycaulus, pEt2, consists of three units of a 337-339 bp repeat aligned in tandem. The sequence is homologous to Afa-family sequences that are widely distributed in the genomes of Triticeae (Gramineae) species.

    DOI: 10.1139/gen-41-1-134

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  • A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions

    Kiyotaka Nagaki, Hisashi Tsujimoto, Tetsuo Sasakuma

    Chromosome Research   6 ( 4 )   295 - 302   1998

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    Tandem repetitive sequences consisting of 140-bp repetitive units were cloned from sugar cane genomic DNA and designated the SCEN family. In situ hybridization revealed that they were located on the centromeric region of almost all of the chromosomes of sugar cane. The 140-bp sequence included three CENP-B box-like sequences. Phylogenetic analysis of the members of the SCEN family revealed that the sequences had 75% homology with each other, on average, and that the sequences could not be further classified into smaller subfamilies. The copy number of the sequence was estimated to be 2.6 x 105 per haploid sugar cane genome and, therefore, 4.6 x 103 or 630 kb per chromosome on average.

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  • Identification of individual barley chromosomes based on repetitive sequences: Conservative distribution of Afa-family repetitive sequences on the chromosomes of barley and wheat

    H Tsujimoto, Y Mukai, K Akagawa, K Nagaki, J Fujigaki, M Yamamoto, T Sasakuma

    GENES & GENETIC SYSTEMS   72 ( 5 )   303 - 309   1997.10

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    The Afa-family repetitive sequences were isolated from barley (Hordeum vulgare, 2n = 14) and cloned as pHvA14. This sequence distinguished each barley chromosome by in situ hybridization. Double color fluorescence in situ hybridization using pHvA14 and 5S rDNA or HvRT-family sequence (subtelomeric sequence of barley) allocated individual barley chromosomes showing a specific pattern. of pHvA14 to chromosome 1H to 7H. As the case of the D genome chromosomes of Aegilops squarrosa and common wheat (Triticum aestivum) hybridized by its Afa-family sequences, the signals of pHvA14 in barley chromosomes tended to appear in the distal regions that do not carry many chromosome band markers. In the telomeric regions these signals always placed in more proximal portions than those of HvRT-family. Based on the distribution patterns of Afa-family sequences in the chromosomes of barley and D genome chromosomes of wheat,we discuss a possible mechanism of amplification of the repetitive sequences during the evolution of Triticeae. In addition, we show here that HvRT-family also could be used to distinguish individual barley chromosomes from the patterns of in situ hybridization.

    DOI: 10.1266/ggs.72.303

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  • Molecular characterization of a tandem repeat, Afa family, and its distribution among Triticeae

    K. Nagaki, H. Tsujimoto, K. Isono, T. Sasakuma

    Genome   38 ( 3 )   479 - 486   1995

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    DOI: 10.1139/g95-063

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Books

  • Cytogenomics

    ( Role: Joint author)

    Elsevier  2021.5 

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  • Essential Genetics and Genomics 7th Eddition

    ( Role: Joint translator)

    2021.1 

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  • Chromosome and genomic engineering in plants, Methods in Molecular Biology

    Humana Press  2016 

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  • はじめての染色体-植物染色体写真集&実験マニュアル-

    Apple  2014 

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  • The First Chromosomes

    Apple  2012 

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  • The First Chromosomes

    Apple  2012 

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  • Centromere, Progress in Molecular and Subcellular Biology 48.

    Springer-Verlag Berlin Heidelbarg  2009 

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  • 細胞工学別冊・植物細胞工学シリーズ24、植物のエピジェネティクス

    秀潤社  2008 

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MISC

  • 細胞遺伝学の新潮流-より速く、より広く、より細かく、そして創出へ、古くて新しいゲノムの見える化技術 Invited

    石井孝佳, 長岐清孝, 菊池真司

    化学と生物   ( 58 )   606 - 613   2020.11

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  • 植物透明化によるエピジェネティック修飾の解析 Invited

    長岐清孝

    月刊バイオインダストリー   ( 7 )   1 - 8   2017.7

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  • Research on post-fertilization barriers in the context of plant breeding

    19 ( 1 )   35 - 40   2017.3

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  • Transmission control of plant artificial ring chromosome in Arabidopsis thaliana

    Minoru Murata, Asaka Kanatani, Kazunari Kashihara, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   91 ( 6 )   342 - 342   2016.12

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  • Attempts to generate artificial ring chromosomes in rice

    Minoru Murata, Asaka Kanatani, Kazunari Kashihara, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   90 ( 6 )   402 - 402   2015.12

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  • Analysis of epigenetic marks on plant chromosomes -from micro to macro-

    Kiyotaka Nagaki, Naoki Yamaji, Keisuke Tanaka, Hisato Kobayashi, Minoru Murata

    GENES & GENETIC SYSTEMS   90 ( 6 )   374 - 374   2015.12

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  • Generation of a stable 1-Mb-sized artificial ring chromosome in Arabidopsis

    Minoru Murata, Asaka Kanatani, Kazunari Kashihara, Akiko Hironaka, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   89 ( 6 )   304 - 304   2014.12

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  • Development of a novel method for identifying centromeric DNA sequences

    Kiyotaka Nagaki, Keisuke Tanaka, Ryo Matsushima, Hisato Kobayashi, Minoru Murata

    GENES & GENETIC SYSTEMS   89 ( 6 )   304 - 304   2014.12

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  • Analyses of kinetochore components of legume species

    Ahmet Latif Tek, Kazunari Kashihara, Minoru Murata, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   88 ( 6 )   388 - 388   2013.12

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  • Stability of artificial ring chromosomes in Arabidopsis thaliana

    Fukashi Shibata, Kiyotaka Nagaki, Minoru Murata

    GENES & GENETIC SYSTEMS   88 ( 6 )   388 - 388   2013.12

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  • Utilization of centromeric histone H3 for chromosome observation in Allium species

    Kiyotaka Nagaki, Maki Yamamoto, Yasuhiko Mukai, Minoru Murata

    GENES & GENETIC SYSTEMS   87 ( 6 )   409 - 409   2012.12

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  • Induction of chromosomal rearrangements and genome stability in Arabidopsis

    Minoru Murata, Fukashi Shibata, Satoru Fujimoto, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   87 ( 6 )   394 - 394   2012.12

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  • Mega-base scale chromosomal rearrangements induced by Cre/LoxP-mediated recombinations in Arabidopsis

    Minoru Murata, Fukashi Shibata, Akiko Hironaka, Kazunari Kashihara, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   86 ( 6 )   434 - 434   2011.12

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  • Karyotyping of tobacco by immnunolabeling and FISH, and a discovery of mini B-chromosome

    Fukashi Shibata, Etsuko Yokota, Minoru Murata, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   86 ( 6 )   434 - 434   2011.12

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  • A mosaic structure of centromeric DNA in tobacco

    Kiyotaka Nagaki, Fukasi Shibata, Minoru Murata

    GENES & GENETIC SYSTEMS   86 ( 6 )   434 - 434   2011.12

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  • Gene expression on induced partial genome duplications in Arabidopsis thaliana

    Minoru Murata, Etsuko Yokota, Kiyotaka Nagaki

    GENES & GENETIC SYSTEMS   85 ( 6 )   418 - 418   2010.12

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  • Evolutionally close alien CENH3s are able to target centromeres in Arabidopsis and tobacco cells

    Kiyotaka Nagaki, Kaori Terada, Munenori Wakimoto, Kazunari Kashihara, Minoru Murata

    GENES & GENETIC SYSTEMS   85 ( 6 )   418 - 418   2010.12

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  • Chromatin modification controls segregation distortion

    Yoshiki Habu, Tsuyu Ando, Sachie Ito, Kiyotaka Nagaki, Fumio Taguchi-Shiobara, Masahiro Yano

    GENES & GENETIC SYSTEMS   85 ( 6 )   417 - 417   2010.12

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  • Isolation of a tobacco centromeric DNA sequence using chromatin immunoprecipitation

    Kiyotaka Nagaki, Kazunari Kashihara, Go Suzuki, Minoru Murata

    GENES & GENETIC SYSTEMS   84 ( 6 )   472 - 472   2009.12

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  • A microchromosome derived from the mini ring chromosome delta in Arabidopsis thaliana

    Etsuko Yokota, Kiyotaka Nagaki, Minoru Murata

    GENES & GENETIC SYSTEMS   83 ( 6 )   511 - 511   2008.12

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  • Epigenetics in centromeres

    Kiyotaka Nagaki, Kazunari Kashihara, Munenori Wakimoto, Kaori Terada, Etsuko Yokota, Minoru Murata

    GENES & GENETIC SYSTEMS   83 ( 6 )   534 - 534   2008.12

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  • Analysis of centromere-specific histone H3 homologues from tobacco

    Kiyotaka Nagaki, Kazunari Kashihara, Minoru Murata

    GENES & GENETIC SYSTEMS   82 ( 6 )   559 - 559   2007.12

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  • O-25. Analysis of CENP-C homologue from tobacco(Abstracts for the oral and the poster presentations,Abstracts of the Joint Meeting: the 58th Annual Meeting of the Society of Chromosome Research and the 17th Annual Meeting of the Chromosome Colloquium) :

    NAGAKI Kiyotaka, KASHIHARA Kazunari, MURATA Minoru

    Chromosome science   10 ( 4 )   120 - 120   2007

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    Other Link: http://id.nii.ac.jp/1141/00107766/

  • Identification and functional analysis of chromosomal passenger proteins in Arabidopsis thaliana

    Mauren Jaudal, Kiyotaka Nagaki, Minoru Murata

    GENES & GENETIC SYSTEMS   81 ( 6 )   431 - 431   2006.12

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  • The rice centromere 8 contains active genes

    NAGAKI Kiyotaka, CHENG Zhukuan, OUYANG Shu, TALBERT Paul B., KIM Mary, M. JONES Kristine, HENIKOFF Steven, BUELL C. Robin, JIANG Jiming

    79 ( 5 )   I   2004.10

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  • Cathy Xiaoyan Zhong, Joshua B. Marshall, Christopher Topp, Rebecca Mroczek, Akio Kato, *Kiyotaka Nagaki, James A. Birchler, Jiming Jiang, and R. Kelly Dawe

    Naoko Kagawa, Kiyotaka Nagaki, Hisashi Tsujimoto

    Molecular Genetics Genomics   267   10 - 15   2002

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  • O-02. Construction of a transformation-competent artificial chromosome (TAC) library for lettuce molecular cytogenetics research(Abstracts of the oral and poster presentations)(The 53rd Annual Meeting of the Society of Chromosome Research) :

    MATOBA Hideyuki, UCHIYAMA Hiroshi, KOYAMA Tetsuo, NAGAKI Kiyotaka, TSUJIMOTO Hisashi, SASAKUMA Tetsuo

    Chromosome science   6 ( 4 )   110 - 110   2002

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  • Naoko Kagawa, *Kiyotaka Nagaki, Hisashi Tsujimoto

    Masahiro Kishii, Kiyotaka Nagaki, Hisashi Tsujimoto

    Chromosome Research   9   417 - 428   2001

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  • Production of wheat haploids by pollination of Job's tears (Coix lachrima-jobi L.)

    MOCHIDA K, NAGAKI K, TSUJIMOTO H, SASAKUMA T

    育種学研究 = Breeding research   2 ( 1 )   142 - 142   2000.4

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  • Cytogenetic variation of tetraploid Leymus species for genetic resource of wheat

    KISHII M, NAGAKI K, TSUJIMOTO H, SASAKUMA T

    育種学研究 = Breeding research   2 ( 1 )   263 - 263   2000.4

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  • Characterization of centromeric regirons of comnron wheat :

    Nagaki Kiyotaka, Kishii Masahiro, Tsujimoto Hisashi

    Chromosome science   4 ( 4 )   124 - 124   2000

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  • Development of genomic in situ hybridization method to Technovit 7100 sections of wheat early embryo :

    MOCHIDA Keiichi, NAGAKI Kiyotaka, TSUJIMOTO Hisashi, SASAKUMA Tetsuo

    Chromosome science   4 ( 4 )   131 - 131   2000

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    Other Link: http://id.nii.ac.jp/1141/00107089/

  • Genome-specific arrangement of Tail-family sequence in Triticeae : localization in either subtelomeric or centromeric region :

    KISHII Masahiro, NAGAKI Kiyotaka, TSUJIMOTO Hisashi

    Chromosome science   4 ( 4 )   131 - 131   2000

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  • Analysis on wheat-Leymus racemosus addition lines by tandem repetitive sequences.

    岸井正浩, 長岐清孝, 辻本寿, 笹隈哲夫

    育種学研究   1   1999

  • Leymus racemosusおよびPsathyrostachys junceaにおけるAfaファミリー反復配列の解析

    長岐清孝, 岸井正浩, 辻本寿, 笹隈哲夫

    日本遺伝学会大会プログラム・予稿集   71st   1999

  • 1. De novo initiation of telomere sequences at the healed break points of wheat deletion chromosomes(Abstracts of the 50th Annual Meeting of the Society of Chromosome Research) :

    TSUJIMOTO Hisashi, USAMI N., HASEGAWA K., YAMADA T., NAGAKI K., SASAKUMA T.

    Chromosome science   3 ( 3 )   140 - 140   1999

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  • The JNK repeat family: A novel repetitive sequence located on an extra C-band region of the chromosome 2R of Japanese rye

    Nagaki K, Tsujimoto H, Sasakuma T

    Proc. 9 Int. Wheat Genet   2   98 - 100   1998

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  • Tandem type repetition arrangement existing in the sugar cane centromere.

    長岐清孝, 辻本寿, 笹隈哲夫

    日本遺伝学会大会プログラム・予稿集   70th   1998

  • Analysis of rye 2R chromosome long arm peculiar repeat sequence.

    長岐清孝, 辻本寿, 笹隈哲夫

    日本遺伝学会大会プログラム・予稿集   69th   1997

  • Repetitive DNA sequences locating on the polymorphic C-band region found in a novel chromosome of rye, Secale cereale(Abstracts of the 48th Annual Meeting of the Society of Chromosome Research) :

    TSUJIMOTO Hisashi, NAGAKI Kiyotaka, SASAKUMA Tetsuo

    Chromosome science   1 ( 2 )   156 - 156   1997

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  • Molecular evolution of Afa family repeat sequence at the wheat run.

    長岐清孝, 辻本寿, 笹隈哲夫

    日本遺伝学会大会プログラム・予稿集   68th   1996

  • VARIABILITY OF AFA-FAMILY SEQUENCES IN DGENOME CHROMOSOMES OF COMMON WHEAT

    NAGAKI K., TSUJIMOTO H., SASAKUMA T.

    70 ( 6 )   717 - 717   1995.12

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  • Genome specific amplification of Afa-family sequence in Triticeae

    Nagaki K, Tsujimoto H, Sasakuma T

    Proc. US-Jpn joint meeting, Modification of gene expression and non-Mendelian inheritance   449 - 454   1995

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  • Variability of Afa family repeated sequence in the wheat D genome in each chromosome.

    長岐清孝, 辻本寿, 笹隈哲夫

    日本遺伝学会大会プログラム・予稿集   67th   1995

  • Identification of progenitor genomes for polyploid species in Triticeae revealed from PCR analysis with Afa-family sequences.

    長岐清孝, 辻本寿, 笹隈哲夫

    育種学雑誌   45   1995

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Presentations

  • 6倍性コムギにおける花器官形成クラスB MADS-box遺伝子の同祖遺伝子特異的エピジェネティック制御

    第39回日本分子生物学会年会  2016 

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  • 6倍性コムギにおける花器官形成クラスB MADS-box遺伝子の同祖遺伝子特異的エピジェネティック制御

    第57回日本植物生理学会年会  2016 

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  • 花成遅延を誘発する細胞質置換パンコムギ系統および正常細胞質系統おけるVRN1同祖遺伝子のヒストンメチル化修飾パターン変異

    一般社団法人日本育種学会 第129回講演会  2016 

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  • パンコムギにおける花器官形成クラス B MADS-box 遺伝子の同祖遺伝子内発現変異はエピジェネティック制御による

    一般社団法人日本育種学会 第130回講演会  2016 

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  • パンコムギにおける花器官形成クラス B MADS-box 遺伝子の同祖遺伝子内発現変異とヒストンのメチル化パターン

    一般社団法人日本育種学会 第129回講演会  2016 

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  • パンコムギにおけるtrithorax-group遺伝子の同定と発現解析

    一般社団法人日本育種学会 第130回講演会  2016 

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  • 倍数性コムギにおける花器官形成MADSボックス遺伝子のエピジェネティック制御

    第8回中国地域育種談話会・第11回ムギ類研究会(共催)  2016 

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  • 花成促進遺伝子VRN1のエピジェネティック制御機構の解明

    第8回中国地域育種談話会・第11回ムギ類研究会(共催)  2016 

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  • 動原体改変による半数体作出

    一般社団法人日本育種学会 第130回講演会  2016 

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  • タバコにおける動原体タンパク質MIS12ホモローグの解析

    第60回染色体学会  2009 

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  • クロマチン免疫沈降によるタバコ動原体DNA配列の単離

    日本遺伝学会第81回大会  2009 

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  • CENH3による動原体のエピジェネティクス

    日本遺伝学会第80回大会  2008 

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  • シロイヌナズナ環状ミニ染色体δ由来の極小染色体

    日本遺伝学会第80回大会  2008 

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  • 植物人工染色体の構築に向けて-動原体とミニクロモソーム-

    日本育種学会第114回講演会  2008 

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  • Visualization and detection of chromatin status by immunostaining and chromatin immunoprecipitation

    The 3rd Asian Chromosome Colloquium 2008  2008 

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  • タバコ動原体特異的ヒストンH3の解析

    日本遺伝学会第79回大会  2007 

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  • タバコにおける動原体タンパク質Cホモローグの解析

    第58回染色体学会・第17回染色体コロキウム2007年合同年会  2007 

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  • Characterization of two centromere-specific histone H3 homologues from tobacco

    16th International Chromosome Conference  2007 

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  • Dynamic changes of centromere-specific histone H3 amount during mitosis in the holocentric plant Luzula nivea

    Plant& Animal Genome XIV  2006 

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  • Identification and functional analysis of chromosomal passenger proteins in Arabidopsis thaliana

    日本遺伝学会・第78回大会  2006 

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  • 植物におけるセントロメアの機能解析

    染色体学会・染色体コロキウム 合同シンポジウム  2006 

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  • 植物の動原体に局在するレトロトランスポゾン

    第28回日本分子生物学会年会  2005 

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  • Sequencing of a native rice centromere reveals active genes

    Plant & animal genome XIII  2005 

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  • サトウキビにおける動原体特異的ヒストンの解析および動原体DNAの同定

    日本育種学会・第107・108回講演会  2005 

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  • セントロメアのパラドックス

    第34回生物進化・細胞遺伝談話会  2005 

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  • 動原体特異的ヒストンH3を用いたルズラ分散型動原体の分子解析

    日本遺伝学会第77回大会  2005 

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  • 高等真核生物最後の秘境「動原体」の探検

    コムギ遺伝学シンポジウム・ムギ類分子生物学研究会 ムギ類合同研究会  2004 

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  • The functional components of rice centromeres

    Plant and Animal Genome XII Conference  2004 

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  • The fine structure of maize centromeres

    Plant & Animal Genome XII Conference  2004 

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  • イネ第8染色体動原体領域の塩基配列の決定とその領域における遺伝子発現とクロマチン状態の解析

    第27回日本分子生物学会年会  2004 

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  • イネ第8染色体動原体領域の塩基配列の解析および機能領域の特定

    日本遺伝学会第76回大会  2004 

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  • Chromatin immunoprecipitation analysis of the centromeric repeats in Arabidopsis thaliana

    Plant and Animal Genome XI Conference  2003 

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  • コムギのゲノム科学 VI TACゲノミックライブラリーを用いたパンコムギ遺伝子のスクリーニング

    第99回 日本育種学会  2001 

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  • コムギのゲノム科学 V TACゲノミックライブラリーを用いたパンコムギ遺伝子のスクリーニング

    第23回 日本分子生物学会  2000 

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  • ジュズダマ花粉の交雑によるコムギ半数体の作出

    第97回 日本育種学会  2000 

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  • コムギのゲノム科学III. Transformation-competent artificial chromosome (TAC)ベクターを用いたパンコムギゲノミックライブラリーの構築と解析

    第97回 日本育種学会  2000 

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  • Construction of large insert genomic dna libraries of common wheat in a transformation-competent artificial chromosome (TAC) vector

    Plant & Animal Genome VIII Conference  2000 

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  • コムギ育種遺伝資源としての四倍性レイムス属の細胞遺伝学的多様性

    第97回 日本育種学会  2000 

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  • コムギ連植物におけるTaiI family反復配列のゲノム特異的配置:染色体末端または動原体への局在

    第51回 染色体学会  2000 

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  • コムギのゲノム科学 IV. TACゲノミックライブラリーを用いたコムギ遺伝子のスクリーニング

    第72回 日本遺伝学会  2000 

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  • コムギ初期胚におけるテクノビット樹脂包埋切片に対するゲノミックin situハイブリダイゼーション法の開発

    第51回 染色体学会  2000 

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  • FISHを利用した植物の四分子分析の可能性

    第51回 染色体学会  2000 

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  • Tetrad FISH分析によるライムギJNK反復配列の動原体からの距離の推定

    第72回 日本遺伝学会  2000 

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  • パンコムギの動原体領域に局在する縦列型反復配列の解析

    第72回 日本遺伝学会  2000 

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  • Leymus racemosusおよびPsathyrostachys junceaにおけるAfaファミリー反復配列の解析

    第71回 日本遺伝学会  1999 

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  • Molecular evolution of a tandem repeat, Afa-family sequences, in Triticeae

    International symposium of the third Yamazaki school "Mobile DNA, telomere and genome evolution"  1999 

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  • 安定化したコムギ染色体切断点におけるテロメア配列の新規合成

    第50回 日本染色体学会  1999 

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  • オオハマニンニク(Leymus racemosus)の反復配列による添加パンコムギ系統の解析

    第96回 日本育種学会  1999 

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  • The JNK repeat family; a novel repetitive sequence located on an extra C-band region of the chromosome 2R of Japanese rye,

    9th international wheat genetics symposium  1998 

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  • サトウキビ動原体に存在する縦列型反復配列

    第70回 日本遺伝学会  1998 

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  • ライムギ2R染色体長腕特異的反復配列の解析

    第69回 日本遺伝学会  1997 

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  • Molecular evolution of tandem repeat, Afa-family sequences, in Triticeae,

    International workshop on analysis and utility of plant chromosome information  1997 

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  • Molecular dynamics of a tandem repeated sequence family in wheat related species

    International symposium plant molecular biology  1997 

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  • Molecular evolution of tandem repetitive Afa-family sequences in Triticeae, wheat-related species

    International molecular evolution symposium ”JUNK DNA”  1997 

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  • Afa ファミリー配列の分子進化

    第68回 日本遺伝学会  1996 

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  • オオムギ・コムギの反復配列の類似性

    第25回 コムギ遺伝学シンポジウム  1996 

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  • Genome specific amplification of Afa-family sequence in Triticeae

    Japan-U.S.A. workshop on "Modification of gene expression and non-mendelian inheritance"  1995 

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  • コムギ D ゲノムの各染色体における Afa ファミリー反復配列の変異性

    第67回 日本遺伝学会  1995 

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  • Discrimination of barley chromosomes by in situ hybridization using Afa-family repetitive sequences

    12th International chromosome conference  1995 

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  • Afa ファミリー配列の構成から見た倍数性コムギの祖先種

    第87回 日本育種学会  1995 

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  • ムギ連における反復配列の分布

    第67回日本遺伝学会  1995 

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  • Afa family反復配列のin situ hybridizationによる全オオムギ染色体の識別

    第45回 染色体学会  1994 

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  • ムギ連植物におけるpAs1およびその類似配列の分子構造の解析

    第66回 日本遺伝学会  1994 

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Works

  • ゲノム編集を用いた半数体作出法の開発

    2015
    -
    2018

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  • 動原体機能低下系統を利用した半数体育種法の確立

    2011
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    2014

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  • マメ科植物の動原体構成要素の同定

    2008
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    2010

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  • 分散型動原体形成機構の解明

    2008
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    2009

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  • タバコ動原体DNA配列の解析および人工染色体形成能の比較

    2008
    -
    2009

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  • タバコにおける動原体複合体構成要素の解析および人工染色体の構築

    2006
    -
    2008

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  • 植物における染色体機能要素の分子的解析と人工染色体の構築

    2000
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    2005

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  • 植物の倍数体におけるゲノム間相互作用の統合的理解

    2000
    -
    2001

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  • ヘテロクロマチン領域形成に関わるDNA配列の解析

    1999
    -
    2001

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Awards

  • 日本遺伝学会奨励賞

    2009  

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  • 染色体学会賞

    2008  

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    Country:Japan

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  • 遺伝学会Best paper賞

    2004  

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    Country:Japan

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Research Projects

  • Analyses of kinetochore/centromere in plants

    2001

      More details

    Grant type:Competitive

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Class subject in charge

  • Analytical Molecular Cytogenetics (2023academic year) Late  - その他

  • Analytical Molecular Cytogenetics (2023academic year) Late  - その他

  • Plant Molecular Cytogenetics (2023academic year) Late  - 木5~8

  • Advanced Study (2023academic year) Other  - その他

  • Specific Research of Bioresources Science (2023academic year) Year-round  - その他

  • Integrated Genomic Breeding (2023academic year) Late  - 木5~8

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  • Seminar in Integrated Genomic Breeding (2023academic year) Late  - その他

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  • Laboratory manuals for plant bioresources research (2023academic year) Prophase  - 火5~8

  • Laboratory manuals for plant bioresources research (2023academic year) Prophase  - 火5~8

  • Analytical Molecular Cytogenetics (2022academic year) Late  - その他

  • Plant Molecular Cytogenetics (2022academic year) Late  - 木5~8

  • Specific Research of Bioresources Science (2022academic year) Year-round  - その他

  • Seminar in Integrated Genomic Breeding (2022academic year) Prophase  - その他

  • Seminar in Integrated Genomic Breeding (2022academic year) Late  - その他

  • Seminar in Integrated Genomic Breeding (2022academic year) Late  - その他

  • Seminar in Integrated Genomic Breeding (2022academic year) Prophase  - その他

  • Laboratory manuals for plant bioresources research (2022academic year) Prophase  - 火5~8

  • Analytical Molecular Cytogenetics (2021academic year) Late  - その他

  • Plant Molecular Cytogenetics (2021academic year) Late  - 木5~8

  • Specific Research of Bioresources Science (2021academic year) Year-round  - その他

  • Seminar in Integrated Genomic Breeding (2021academic year) Prophase  - その他

  • Seminar in Integrated Genomic Breeding (2021academic year) Late  - その他

  • Seminar in Integrated Genomic Breeding (2021academic year) Late  - その他

  • Seminar in Integrated Genomic Breeding (2021academic year) Prophase  - その他

  • Laboratory manuals for plant bioresources research (2021academic year) Prophase  - 火5~8

  • Analytical Molecular Cytogenetics (2020academic year) Late  - その他

  • Plant Molecular Cytogenetics (2020academic year) Late  - その他

  • Specific Research of Bioresources Science (2020academic year) Year-round  - その他

  • Seminar in Molecular Biology of the Nucleus (2020academic year) Prophase  - その他

  • Seminar in Molecular Biology of the Nucleus (2020academic year) Late  - その他

  • Seminar in Integrated Genomic Breeding (2020academic year) Prophase  - その他

  • Seminar in Integrated Genomic Breeding (2020academic year) Late  - その他

  • Seminar in Integrated Genomic Breeding (2020academic year) Late  - その他

  • Seminar in Integrated Genomic Breeding (2020academic year) Prophase  - その他

  • Laboratory manuals for plant bioresources research (2020academic year) Prophase  - その他

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