Boyboy B. A. G., Ichiyanagi K.*
Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse. Mob DNA 15, 11 (2024) [Pubmed]
Uno Y.*, Matsubara K., Inoue J., Inazawa J., Shinohara A., Koshimoto C., Ichiyanagi K., Matsuda Y.*
Diversity and evolution of highly repetitive DNA sequences constituting chromosome-site specific heterochromatin in two Gerbillinae species. Cytogenet Genome Res 163, 42-51 (2023) [Pubmed]
Kobayashi M.*, Kanbe F., Ishii R., Tsubouchi H., Hirai K., Miyasaka Y., Ohno T., Oda H., Ikeda S., Katoh H., Ichiyanagi K., Ishikawa A., Murai A., Horio F.
C3H/HeNSlc mouse with low phospholipid transfer protein expression showed dyslipidemia. Sci Rep 13, 13813 (2023) [Pubmed]
Hirata M., Ichiyanagi T., Katoh H., Hashimoto T., Suzuki H., Nitta H., Kawase M., Nakai R., Imamura M., Ichiyanagi K.*
Sequence divergence and retrotransposon insertion underlie interspecific epigenetic differences in primates. Mol Biol Evol 39, msac208 (2022) [Pubmed]
Kawase M., Ichiyanagi K.*
The expression dynamics of piRNAs derived from male germline piRNA clusters and retrotransposons. Front Cell Dev Biol 10, 868746 (2022) [Pubmed]
Fukuda K., Makino Y., Kaneko S., Shimura C., Okada Y., Ichiyanagi K., Shinkai Y.*
Transcriptional states of retroelement-inserted regions and specific KRAB zinc finger protein association are correlated with DNA methylation of retroelements in human male germ cells. eLife 11, e76822 (2022) [Pubmed]
Inatomi T., Matsuda S., Ishiuchi T., Do Y., Nakayama M., Abe S., Kasho K., Wanrooij S., Nakada K., Ichiyanagi K., Sasaki H., Yasukawa T.*, Kang D.*
TFB2M and POLRMT are essential for mammalian mitochondrial DNA replication. Biochim Biophys Acta Mol Cell Res 1869, 119167 (2022) [Pubmed]
Mori Y., Ichiyanagi K.*
melRNA-seq for expression analysis of SINE RNAs and other medium-length noncoding RNAs. Mob DNA 12, 15 (2021) [Pubmed]
Ichiyanagi T., Katoh H., Mori Y., Hirafuku K., Boyboy B. A., Kawase M., Ichiyanagi K.*
B2 SINE copies serve as a transposable boundary of DNA methylation and histone modifications in the mouse. Mol Biol Evol 38, 2380-2395 (2021) [Pubmed]
Kimprasit T., Nunome M., Iida K., Murakami Y., Wong M.L., Wu C.H., Kobayashi R., Hengjan Y., Takemae H., Yonemitsu K., Kuwata R., Shimoda H., Si L., Sohn J.H., Asakawa S., Ichiyanagi K., Maeda K., Oh H.S., Mizutani T., Kimura J., Iida A., Hondo E.*
Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia . PLoS One 16, e0244006 (2021) [Pubmed]
Kinoshita K., Suzuki T., Koike M., Nishida C., Koike A., Nunome M., Uemura T., Ichiyanagi K., Matsuda Y.*
Deletions of IHH and NHEJ1 cause chondrodystrophy 1 and embryonic lethality
in the Creeper chicken. Commun Biol 3, 144 (2020) [Pubmed]
Ohishi H., Au Yeung W.K., Unoki M., Ichiyanagi K., Fukuda K., Shoji M., Shirane K., Chiba H., Sado T., Sasaki H.*
Characterization of genetic-origin-dependent monoallelic expression in
mouse embryonic stem cells. Genes Cells 25, 54-65 (2020) [Pubmed]
Hiramoto T., Tahara M., Liao J., Soda Y., Miura Y., Kurita R., Hamana H., Inoue K., Kohara H., Miyamoto S., Hijikata Y., Okano S., Yamaguchi Y., Oda Y., Ichiyanagi K.,
Toh H., Sasaki H., Kishi H., Ryo A., Muraguchi A., Takeda M., Tani K.* Non-transmissible MV Vector with Segmented RNA Genome Establishes Different Types of iPSCs from Hematopoietic Cells. Mol Ther 28, 129-141 (2020) [Pubmed]
Inoguchi Y., Ichiyanagi K., Ohishi H., Maeda Y., Sonoda N., Ogawa Y., Inoguchi T., Sasaki H.*
Poorly controlled diabetes during pregnancy and lactation activates the Foxo1 pathway and causes glucose intolerance in adult offspring. Sci Rep 9, 10181 (2019) [Pubmed]
Wakisaka K. T., Tanaka R., Hirashima T., Muraoka Y., Azuma Y., Yoshida H., Tokuda T., Asada S., Suda K., Ichiyanagi K., Ohno S., Itoh M., Yamaguchi M.*.
Novel roles of Drosophila FUS and Aub responsible for piRNA biogenesis in neuronal disorders. Brain Res 1708, 207-219 (2019)[Pubmed]
Matsuda S., Yasukawa T.*, Sakaguchi Y, Ichiyanagi K., Unoki M., Gotoh K., Fukuda K., Sasaki H., Suzuki T., Kan D.*.
Accurate estimation of 5-methylcytosine in mammalian mitochondrial DNA. Sci Rep 8, 5801 (2018)[Pubmed]
Kuroki S., Nakai Y., Maeda R., Okashita N., Akiyoshi M, Yamaguchi Y., Kitano S., Miyachi H.,Nakato R., Ichiyanagi K., Shirahige K., Kimura H., Shinkai Y, Tachibana M.*.
Combined loss of JMJD1A and JMJD1B reveals critical roles for H3K9 demethylation
in the maintenance of embryonic stem cells and early embryogenesis. Stem Cell Rep 10, 1340-1354 (2018) [Pubmed]
Wakisaka K.*, Ichiyanagi K., Ohno S., and Ito M.
Association of zygotic piRNAs derived from paternal P elements with hybrid
dysgenesis in Drosophila melanogaster. Mob DNA 9, 7 (2018) [Pubmed]
Shimosuga K., Fukuda K., Sasaki H., and Ichiyanagi K.*
Locus-specific hypomethylation of the mouse IAP retrotransposon is associated with transcription factor-binding sites. Mob DNA 8, 20 (2017) [Pubmed]
Wakisaka K.*, Ichiyanagi K., Ohno S., and Ito M.
Diversity of P-element piRNA production among M’ and Q strains and its association with P-M hybrid dysgenesis in Drosophila melanogaster. Mob DNA 8, 13 (2017) [Pubmed]
Inoue K., Ichiyanagi K.*, Fukuda K., Glinka M., and Sasaki H.*
Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice. PLoS Genet 13, e1006926 (2017) [Pubmed]
Fukuda K., Inoguchi Y., Ichiyanagi K.*, Ichiyanagi T., Go Y., Nagano M., Yanagawa Y., Takaesu N., Ohkawa Y., Imai H., and Sasaki H.*
Evolution of the sperm methylome of primates is associated with retrotransposon insertions and genome instability. Hum Mol Genet 26, 3508-3519 (2017) [Pubmed]
Iida K., Kobayashi R., Hengjan Y., Nagata N., Yonemitsu K., Nunome M., Kuwata R., Suzuki K., Ichiyanagi K., Maeda K., OhmoriY., and Hondo E.*
The genetic diversity of D-loop sequences in eastern bent-winged bats (Miniopterus fuliginosus) living in Wakayama Prefecture, Japan. J Vet Med Sci 79, 1142-1145 (2017) [Pubmed]
Kobayashi M., Kato H., Hada H., Itoh-Nakadai A., Fujiwara T., Muto A., Inoguchi Y., Ichiyanagi K., Houjou W., Tomosugi N., Sasaki H., Harigae H., Igarashi K.*
Iron-heme-Bach1 axis is involved in erythroblast adaptation to iron deficiency. Haematologica 102, 454-465 (2017) [Pubmed]
Toh H., Shirane K., Miura F., Kubo N. Ichiyanagi K., Hayashi K., Saitou M., Suyama M., Ito T., and Sasaki H*.
Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing. BMC Genomics 18, 31 (2017) [Pubmed]
Hayashi M., Maehara K., Harada A., Semba Y., Kudo K., Takahashi H., Oki S., Meno C., Ichiyanagi K., Akashi K., and Ohkawa Y*.
Chd5 regulates MuERV-L/MERVL expression in mouse embryonic stem cells via H3K27me3 modification and histone H3.1/H3.2. J Cell Biochem 117, 780-792 (2016) [Pubmed]
Ichiyanagi T., Ichiyanagi K., Ogawa A., Kuramochi-Miyagawa S., Nakano T., Chuma S., Sasaki H., and Udono H.*
HSP90α plays an important role in piRNA biogenesis and retrotransposon repression in mouse. Nucleic Acids Res 42, 11903-11911 (2014) [Pubmed]
Ichiyanagi T., Ichiyanagi K., Miyake M., and Sasaki H.*
Accumulation and loss of non-CpG methylation during male germ-cell development. Nucleic Acids Res 41, 738-745 (2013) [Pubmed]
Fukuda K., Ichiyanagi K.*, Yamada Y., Go Y., Udono T., Wada S., Maeda M., Soejima H., Saitou N., Ito T., and Sasaki H.*
DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes. J Hum Genet 58, 446-454 (2013) [Pubmed]
Umemori J., Mori A., Ichiyanagi K., Uno T., and Koide T.*
Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome. BMC Genomics 14, 455 (2013) [Pubmed]
Yamamoto Y., Watanabe T., Hoki Y., Shirane K., Li Y., Ichiyanagi K., Kuramochi- Miyagawa S., Toyoda A., Fujiyama A., Oginuma M., Suzuki H., Sado T., Nakano T., and Sasaki, H*
Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus. Genome Res 23, 292-299 (2013) [Pubmed]
Nitta H., Unoki M., Ichiyanagi K., Kosho T., Shigemura T., Takahashi H., Velasco G., Francastel C., Picard C., Kubota T., and Sasaki H.*
Three novel ZBTB24 mutations identified in Japanese and Cape Verdean type 2 ICF syndrome patients. J Hum Genet 58:455-460 (2013) [Pubmed]
Ichiyanagi K.*
Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site: A concern for DNA modification studies using restriction endonucleases Epigenetics 7, 131-136 (2012) [Pubmed]
Ichiyanagi K.*, Li Y., Watanabe T., Ichiyanagi T., Fukuda K., Kitayama J., Yamamoto Y., Kuramochi-Miyagawa S., Nakano T., Yabuta Y., Seki Y., Saitou M., and Sasaki H.
Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. Genome Res 21, 2058-2066 (2011) [Pubmed]
Watanabe T., Tomizawa S., Mitsuya K., Totoki Y., Yamamoto Y., Kuramochi-Miyagawa S., Iida N., Hoki Y., Murphy P.J., Toyoda A., Gotoh K., Hiura H., Arima T., Fujiyama A., Sado T., Shibata T., Nakano T., Lin H., Ichiyanagi K., Soloway P. D., and Sasaki H.*
Role for piRNAs and non-coding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science 332, 848-852 (2011)[Pubmed]
Suzuki J., Yamaguchi K., Kajikawa M., Ichiyanagi K., Adachi N., Koyama H., Takeda S., and Okada N.*
Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition. PLoS Genet 5, e1000461 (2009)[Pubmed]
Ichiyanagi K. and Okada N.*
Mobility pathways for vertebrate L1, L2, CR1, and RTE clade retrotransposons. Mol Biol Evol 25,1148-1157 (2008)[Pubmed]
Ichiyanagi K., Nakajima R., Kajikawa M., and Okada N.*
Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts. Genome Res 17, 33-41 (2007) [Pubmed]
Ichiyanagi K., Nishihara H., Duvernell D. D., and Okada N.*
Acquisition of endonuclease specificity during evolution of L1 retrotransposon. Mol Biol Evol 24, 2009-2015 (2007) [Pubmed]
Honda H., Ichiyanagi,K., Suzuki J., Ono T., Koyama H., Kajikawa M., and Okada N.*
A new system for analyzing LINE retrotransposition in the chicken DT40 cell line widely used for reverse genetics. Gene 395, 116-124 (2007) [Pubmed]
Ichiyanagi K., and Okada N.*
Genomic alterations upon integration of zebrafish L1 elements revealed by the TANT method. Gene 383, 108-116 (2006) [Pubmed]
Kajikawa M., Ichiyanagi K., Tanaka N., and Okada N.*
Isolation and characterization of active LINE and SINEs from the eel. Mol Biol Evol 22, 673-682 (2005) [Pubmed]
Conlan L. H., Stanger M. J., Ichiyanagi K., and Belfort M.*
Localization, mobility and fidelity of retrotransposed Group II introns in rRNA genes. Nucleic Acids Res 33, 5262-5270 (2005) [Pubmed]
Ichiyanagi K., Beauregard A., and Belfort M.*
A bacterial group II intron favors retrotransposition into plasmid targets. Proc Natl Acad Sci USA 100, 15742-15747 (2003) [Pubmed]
Ichiyanagi K., Beauregard A., Lawrence S., Smith D., Cousineau B., and Belfort M.*
Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets. Mol Microbiol 46, 1259-1272 (2002) [Pubmed]
Ichiyanagi K., Ishino Y., Ariyoshi M., Komori K., and Morikawa K.*
Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI. J Mol Biol 300, 889-901 (2000) [Pubmed]
Komori K., Fujita N., Ichiyanagi K., Shinagawa H., Morikawa K., and Ishino Y.*
PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus. I. Purification and identification of the homing-type endonuclease activities. Nucleic Acids Res 27, 4167-4174 (1999) [Pubmed]
Komori K., Ichiyanagi K., Morikawa K., and Ishino Y.*
PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus. II. Characterization Of the binding and cleavage abilities by site-directed mutagenesis. Nucleic Acids Res 27, 4175-4182 (1999) [Pubmed]
Ichiyanagi K., Iwasaki H., Hishida T., and Shinagawa H.*
Mutational analysis on structure-function relationship of a Holliday junction specific endonuclease RuvC. Genes Cells 3, 575-586 (1998) [Pubmed]
Reviews
Ichiyanagi K.*, Ikeda Y., and Saito K.
The sixth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements. Mobile DNA 14, 22 (2023) [Journal Page]
Kawase M. and Ichiyanagi K.*
Mouse retrotransposons: sequence structure, evolutional age, genomic distribution, and function. Genes Genet Syst 98, 337-351 (2023) [Pubmed]
Ichiyanagi K.* and Saito K.
The fifth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements. Mobile DNA 13, 3 (2022) [Journal Page]
Ohtani H.* and Iwasaki Y. W.*
Rewiring of chromatin state and gene expression by transposable elements. Dev Growth Differ 63, 262-273 (2021) [Pubmed]
Ichiyanagi K.* and Saito K.
TE studies in Japan: The forth Japanese meeting on host-transposon interactions. Mobile DNA 10, 11 (2019) [Journal Page]
Ichiyanagi K.*
TE studies in Japan: The third Japanese meeting on host-transposon interactions. Mobile DNA 7, 26 (2016) [Journal Page]
Ichiyanagi K.*
Regulating Pol III transcription to change Pol II transcriptome. Cell Cycle 13, 3625-3626 (2014) [Pubmed]
Ichiyanagi K.*
Transposable elements in eukaryotic genomes: epigenetic regulation by the host and functionalization for the host. Genes Genet Syst 88, 1 (2013) [Pubmed]
Ichiyanagi K.*
Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs. Genes Genet Syst 88, 19-29 (2013) [Pubmed]
