Guo Y, Li TD, Modzelewski AJ, Siomi H.
Retrotransposon renaissance in early embryos
Trends in Genetics 2023. [website]
Sakashita A, Ooga M, Otsuka K, Maezawa S, Takeuchi C, Wakayama S, Wakayama T, Namekawa SH.
Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin
Nucleic Acids Research 2023. gkad479 [website]
doi: 10.1093/nar/gkad479
Sakashita A, Kitano T, Ishizu H, Guo Y, Masuda H, Ariura M, Murano K, Siomi H.
Transcription of MERVL retrotransposons is required for preimplantation embryo development
Nat Genet. 2023. ji2200525 [website]
doi: 10.1038/s41588-023-01324-y
Mise-Omata S, Ikeda M, Takeshita M, Uwamino Y, Wakui M, Arai T, Yoshifuji A, Murano K, Siomi H, Nakagawara K, Ohyagi M, Ando M, Hasegawa N, Saya H, Murata M, Fukunaga K, Namkoong H, Lu X, Yamasaki S, Yoshimura A.
Memory B Cells and Memory T Cells Induced by SARS-CoV-2 Booster Vaccination or Infection Show Different Dynamics and Responsiveness to the Omicron Variant
J Immunol. 2022. ji2200525 [website]
doi: 10.4049/jimmunol.2200525
This is part of the results of the department project termed “the Keio Donner Project for COVID-19″
Li TD, Murano K, Kitano T, Guo Y, Negishi L, Siomi H.
TDP-43 safeguards the embryo genome from L1 retrotransposition
Science Advances. 2022. eabq3806 [website]
doi: 10.1126/sciadv.abq3806
Takeuchi C, Yokoshi M, Kondo S, Shibuya A, Saito K, Fukaya T, Siomi H, Iwasaki YW.
Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers
Nucleic Acids Research. 2022. gkac1034 [website]
doi: 10.1093/nar/gkac1034
Sakashita A, Takeuchi C, Maezawa S, Namekawa SH.
Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts
Epigenomics: Methods and Protocols (Methods in Molecluar Biology). 2022. 2577:123-146 [website]
doi: 10.1007/978-1-0716-2724-2_9
Sakashita A, Ariura M, Namekawa SH.
CRISPR-Mediated Activation of Transposable Elements in Embryonic Stem Cells
piRNA: Methods and Protocols (Methods in Molecluar Biology). 2022. 2509:171-194 [website]
doi: 10.1007/978-1-0716-2380-0_11
Takeuchi C, Murano K, Ishikawa M, Okano H, Iwasaki YW.
Generation of Stable Drosophila Ovarian Somatic Cell Lines Using the piggyBac System
piRNA: Methods and Protocols (Methods in Molecluar Biology). 2022. 2509:143-153 [website]
doi: 10.1007/978-1-0716-2380-0_9
Abe K, Kabe Y, Uchiyama S, Iwasaki YW, Ishizu H, Uwamino Y, Takenouchi T, Uno S, Ishii M, Maruno T, Noda M, Murata M, Hasegawa N, Saya H, Kitagawa Y, Fukunaga K, Amagai M, Siomi H, Suematsu M, Kosaki K, Keio Donner Project.
Pro108Ser mutation of SARS-CoV-2 3CLpro reduces the enzyme activity and ameliorates the clinical severity of COVID-19
Sci Rep. 12(1299) 2022. [website]
DOI 10.1038/s41598-022-05424-3
This is part of the results of the department project termed “the Keio Donner Project for COVID-19″
Murano K, Guo Y, Siomi H.
The emergence of SARS-CoV-2 variants threatens to decrease the efficacy of neutralizing antibodies and vaccines
Biochem Soc Trans. 49(6) 2021. [website]
DOI 10.1042/BST20210859
Hasuwa H, Iwasaki YW, Au Yeung WK, Ishino K, Masuda H, Sasaki H, Siomi H.
Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters
Nat Cell Biol. 2021. [website]
DOI 10.1038/s41556-021-00745-3
Iwasaki YW, Sriswasdi S, Kinugasa Y, Adachi J, Horikoshi Y, Shibuya A, Iwasaki W, Tashiro S, Tomonaga T, Siomi H.
Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci
EMBO J. 2021. e108345 [website]
DOI 10.15252/embj.2021108345
Ohtani H, Iwasaki YW.
Rewiring of chromatin state and gene expression by transposable elements
Dev Growth Differ. 2021. 63:262-273 [website]
DOI 10.1111/dgd.12735
Ishino K, Hasuwa H, Yoshimura J, Iwasaki YW, Nishihara H, Seki NM, Hirano T, Tsuchiya M, Ishizaki H, Masuda H, Kuramoto T, Saito K, Sakakibara Y, Toyoda A, Itoh T, Siomi MC, Morishita S, Siomi H.
Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation
Nucleic Acids Research 2021. 49(5):2700–2720 [website]
DOI 10.1093/nar/gkab059
[golden hamster genome sequence] MD5:c575be09457eaac35d4fe98d80254d53
[golden hamster gff3 annotation] MD5:24c1cfb0ba0c9d20a171d7610fae4ae7
[golden hamster transposon annotation (repeatmasker .out file)] MD5:dbacf099e330b419238c1deaed3ae5ac
Guo Y, Kawaguchi A, Takeshita M, Sekiya T, Hirohama M, Yamashita A, Siomi H, Murano K.
Potent mouse monoclonal antibodies that block SARS-CoV-2 infection
J Biol Chem 2021. 100346 [website]
DOI 10.1016/j.jbc.2021.100346
This is part of the results of the department project termed “the Keio Donner Project for COVID-19″
Onishi R, Sato K, Murano K, Negishi L, Siomi H, Siomi MC.
Piwi suppresses transcription of Brahma-dependent transposons via Maelstrom in ovarian somatic cells
Science Advances 2020. 6: eaaz7420 [website]
DOI 10.1126/sciadv.aaz7420
Takenouchi T, Iwasaki YW, Harada S, Ishizu H, Uwamino Y, Uno S, Osada A, Abe K, Hasegawa N, Murata M, Takebayashi T, Fukunaga K, Saya H, Kitagawa Y, Amagai M, Siomi H, Kosaki K, Keio Donner Project.
Clinical utility of SARS-CoV-2 whole genome sequencing in deciphering source of infection
J Hosp Infect. 2021. 107:40-44 [website]
DOI 10.1016/j.jhin.2020.10.014
This is part of the results of the department project termed “the Keio Donner Project for COVID-19″
Yamanaka S, Kishi Y, Siomi H.
ATAC-seq method applied to embryonic germ cells and neural stem cells from mouse: practical tips and modifications
Epigenetics Methods 2020. 18:371-386 [website]
DOI 10.1016/B978-0-12-819414-0.00018-5
Yamaguchi S, Oe A, Nishida KM, Yamashita K, Kajiya A, Hirano S, Matsumoto N, Dohmae N, Ishitani R, Saito K, Siomi H, Nishimasu H, Siomi MC, Nureki O.
Crystal structure of Drosophila Piwi
Nat Commun. 2020. 11:858 [website]
DOI 10.1038/s41467-020-14687-1
Osumi K, Sato K, Murano K, Siomi H, Siomi M.
Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing
EMBO Rep. 2019. e48296 [website]
DOI 10.15252/embr.201948296
Yamanaka S, Nishihara H, Toh H, Nagai LAE, Hashimoto K, Park SJ, Shibuya A, Suzuki AM, Tanaka Y, Nakai K, Carninci P, Sasaki H, Siomi H.
Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation
Dev Cell. 2019. 51:21–34 [website] [talk]
DOI 10.1016/j.devcel.2019.07.023
Murano K, Iwasaki YW, Ishizu H, Mashiko A, Shibuya A, Kondo S, Adachi S, Suzuki S, Saito K, Natsume T, Siomi MC, Siomi H.
Nuclear RNA export factor variant initiates piRNA‐guided co‐transcriptional silencing
EMBO J. 2019. e102870 [website]
DOI 10.15252/embj.2019102870
Yashiro R, Murota Y, Nishida KM, Yamashiro H, Fujii K, Ogai A, Yamanaka S, Negishi L, Siomi H, Siomi MC.
Piwi Nuclear Localization and Its Regulatory Mechanism in Drosophila Ovarian Somatic Cells
Cell Rep. 2018. 23:3647–3657 [PDF]
DOI 10.1016/j.celrep.2018.05.051
Nishida KM, Sakakibara K, Iwasaki YW, Yamada H, Murakami R, Murota Y, Kawamura T, Kodama T, Siomi H, Siomi MC.
Hierarchical roles of mitochondrial Papi and Zucchini in Bombyx germline piRNA biogenesis
Nature. 2018. 555:260-264 [PDF]
DOI 10.1038/nature25788
Murano K, Iwasaki YW, Siomi H.
Profiling Open Chromatin Structure in the Ovarian Somatic Cells Using ATAC-seq
Argonaute Proteins (Methods in Molecluar Biology). 2018. 1680:165-177 [website]
DOI 10.1007/978-1-4939-7339-2_11
Hasuwa H, Ishino K, Siomi H.
Human PIWI (HIWI) is an azoospermia factor
SCIENCE CHINA Life Sciences. 2017. Available online 11 August [website]
DOI 10.1007/s11427-017-9149-0
Iwasaki YW, Ishino K, Siomi H.
Deep sequencing and high-throughput analysis of PIWI-associated small RNAs
Methods. 2017. 126:66-75 [PDF]
DOI 10.1016/j.ymeth.2017.05.020
Hasuwa H, Siomi H.
Mobile elements control stem cell potency
Science. 2017. 355:581-582 [PDF]
DOI 10.1126/science.aam6589
Hirano T, Hasuwa H, Siomi H.
Identification of Mouse piRNA Pathway Components Using Anti-MIWI2 Antibodies
Germline Stem Cells (Methods in Molecluar Biology). 2017. 1463:205-216 [website]
DOI 10.1007/978-1-4939-4017-2_15
Matsumoto N, Nishimasu H, Sakakibara K, Nishida KM, Hirano T, Ishitani R, Siomi H, Siomi MC, Nureki O.
Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA
Cell. 2016. 167:484–497 [PDF]
DOI 10.1016/j.cell.2016.09.002
Sumiyoshi T, Sato K, Yamamoto H, Iwasaki YW, Siomi H, Siomi MC.
Loss of l(3)mbt leads to acquisition of the ping-pong cycle in Drosophila ovarian somatic cells
Genes Dev. 2016. 30:1617-1622 [PDF]
DOI 10.1101/gad.283929.116
Iwasaki YW, Murano K, Ishizu H, Shibuya A, Iyoda Y, Siomi MC, Siomi H, Saito K.
Piwi Modulates Chromatin Accessibility by Regulating Multiple Factors Including Histone H1 to Repress Transposons
Mol Cell. 2016. 63:408–419 [PDF]
DOI 10.1016/j.molcel.2016.06.008
Lin ZY-C, Hikabe O, Suzuki S, Hirano T, Siomi H, Sasaki E, Imamura M, Okano H.
Sphere-formation culture of testicular germ cells in the common marmoset, a small New World monkey
Primates. 2016. 57:129-135 [PDF]
DOI 10.1007/s10329-015-0500-4
Shibata N, Kashima M, Ishiko T, Nishimura O, Rouhana L, Misaki K, Yonemura S, Saito K, Siomi H, Siomi MC, Agata K.
Inheritance of a Nuclear PIWI from Pluripotent Stem Cells by Somatic Descendants Ensures Differentiation by Silencing Transposons in Planarian
Dev Cell. 2016. 37:226–237 [PDF]
DOI 10.1016/j.devcel.2016.04.009
Sato K, Iwasaki YW, Siomi H, Siomi MC.
Tudor-domain containing proteins act to make the piRNA pathways more robust in Drosophila
Fly. 2015. 9:86-90 [website]
DOI 10.1080/19336934.2015.1128599
Yamanaka S, Siomi H.
Misprocessed tRNA response targets piRNA clusters
EMBO J. 2015. 34: 2988-2989 [PDF]
DOI 10.15252/embj.201593322
Parrish NF, Fujimoto K, Shiromoto Y, Iwasaki YW, Ha H, Xing J, Makino A, Kuramochi-Miyagawa S, Nakano T, Siomi H, Honda T, Tominaga K.
piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals
RNA. 2015. 21: 1–13 [PDF]
DOI 10.1261/rna.052092.115
Sato K, Iwasaki YW, Shibuya A, Carninci P, Tsuchizawa Y, Ishizu H, Siomi MC, Siomi H.
Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline
Mol Cell. 2015. 59: 553–563 [PDF]
DOI 10.1016/j.molcel.2015.06.024
Ishizu H, Iwasaki YW, Hirakata S, Ozaki H, Iwasaki W, Siomi H, Siomi MC.
Somatic Primary piRNA Biogenesis Driven by cis-Acting RNA Elements and trans-Acting Yb
Cell Rep. 2015. 12: 429–440 [PDF]
DOI 10.1016/j.celrep.2015.06.035
Iwasaki YW, Siomi MC, Siomi H.
PIWI-Interacting RNA: Its Biogenesis and Functions
Annu Rev Biochem. 2015. 84: 405-433 [e-print]
DOI 10.1146/annurev-biochem-060614-034258
Siomi H, Siomi MC.
Phased piRNAs tackle transposons
Science. 2015. 348: 756–757 [PDF]
DOI 10.1126/science.aab3004
Matsumoto N, Sato K, Nishimasu H, Namba Y, Miyakubi K, Dohmae N, Ishitani R, Siomi H, Siomi MC, Nureki O.
Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom
Cell Rep. 2015. 11: 366–375 [PDF]
DOI 10.1016/j.celrep.2015.03.030
Hirano T, Siomi H.
Small RNAs: Artificial piRNAs for Transcriptional Silencing
Curr Biol. 2015. 25: R269–R293 [PDF]
DOI 10.1016/j.cub.2015.02.009
Lin ZY-C, Hirano T, Shibata S, Seki NM, Kitajima R, Sedohara A, Siomi MC, Sasaki E, Siomi H, Imamura M, Okano H.
Gene expression ontogeny of spermatogenesis in the marmoset uncovers primate characteristics during testicular development
Dev Biol. 2015. 400: 43-58 [PDF]
DOI 10.1016/j.ydbio.2015.01.014i
Nishida KM, Iwasaki YW, Murota Y, Nagao A, Mannen T, Kato Y, Siomi H, Siomi MC.
Respective Functions of Two Distinct Siwi Complexes Assembled during PIWI-Interacting RNA Biogenesis in Bombyx Germ Cells
Cell Rep. 2015. 10: 193-203 [PDF]
DOI 10.1016/j.celrep.2014.12.013
Iwasaki YW, Siomi H.
miRNA regulatory ecosystem in early development
Mol Cell. 2014. 56: 615-616 [PDF]
DOI 10.1016/j.molcel.2014.11.010
Yamanaka S, Siomi MC, Siomi H.
piRNA clusters and open chromatin structure
Mobile DNA. 2014. 5: 22 [PDF]
DOI 10.1186/1759-8753-5-22
Murota Y, Ishizu H, Nakagawa S, Iwasaki YW, Shibata S, Kamatani MK, Saito K, Okano H, Siomi H, Siomi MC.
Yb Integrates piRNA Intermediates and Processing Factors into Perinuclear Bodies to Enhance piRISC Assembly
Cell Rep. 2014. 8: 103–113 [PDF]
DOI 10.1016/j.celrep.2014.05.043
Hirano T, Iwasaki YW, Lin ZY, Imamura M, Seki NM, Sasaki E, Saito K, Okano H, Siomi MC, Siomi H.
Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate
RNA. 2014. 20: 1223-1237[PDF]
DOI 10.1261/rna.045310.114
Siomi H.
It’s time to exploit your favorite quirky organism with new technologies
EMBO Rep. 2014 May 12. [Epub ahead of print] [PDF]
DOI 10.15252/embr.201438955
Yamanaka S, Siomi H.
diRNA-Ago2-RAD51 complexes at double-strand break sites
Cell Res. 2014 April 11, advance online publication [PDF]
doi:10.1038/cr.2014.45
Saito K.
RNAi and Overexpression of Genes in Ovarian Somatic Cells
PIWI-Interacting RNAs: Methods and Protocols (Methods in Molecluar Biology). 2013. 1093:25-33 [website]
doi: 10.1007/978-1-62703-694-8_3
Ohtani H, Iwasaki YW, Shibuya A, Siomi H, Siomi MC, Saito K.
DmGTSF1 is necessary for Piwi–piRISC-mediated transcriptional transposon silencing in the Drosophila ovary
Genes Dev. 2013. 27: 1656-1661 [PDF]
doi:10.1101/gad.221150.113
Miyoshi K, Ogino A, Siomi MC, Siomi H.
Purification of dFMR1-Containing Complexes Using Tandem Affinity Purification
Trinucleotide Repeat Protocols (Methods in Molecular Biology). 2013. 1010: 111-121[website]
doi:10.1007/978-1-62703-411-1_8
Saito K.
The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila
Genes Genet. Syst. 2013. 88: 9-17 [PDF]
Nishida KM, Miyoshi K, Ogino A, Miyoshi T, Siomi H, Siomi MC.
Roles of R2D2, a Cytoplasmic D2 Body Component, in the Endogenous siRNA Pathway in Drosophila
Mol Cell. 2013. 49: 680–691 [PDF]
doi:10.1016/j.molcel.2012.12.024
Sato K, Siomi H.
PIWI proteins and their Slicer activity in piRNA biogenesis and transposon silencing
The Enzymes Vol. 32: Part B: RNA endonucleases in RNAi and microRNA metabolism and their partners 2012. 137-162. [Link]
Ishizu H, Siomi H, Siomi MC.
Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines
Genes Dev. 2012. 26: 2361-2373 [PDF]
doi:10.1101/gad.203786.112
Nishimasu H, Ishizu H, Saito K, Fukuhara S, Kamatani MK, Bonnefond L, Matsumoto N, Nishizawa T, Nakanaga K, Aoki J, Ishitani R, Siomi H, Siomi MC, Nureki O.
Structure and function of Zucchini endoribonuclease in piRNA biogenesis
Nature 2012. 491: 284-289 [PDF] [supplemental_PDF]
doi:10.1038/nature11509
Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Sardo FL, Saxena A, Miyoshi K, Siomi H, Siomi MC, Carninci P, Gilmour DS, Corona DFV, Orlando V.
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila
Nature 2011. 480: 391-395 [PDF] [supplemental_PDF]
doi:10.1038/nature.10492
Sato K, Nishida KM, Shibuya A, Siomi MC, Siomi H.
Maelstrom coordinates microtubule organization during Drosophila oogenesis through interaction with components of the MTOC
Genes Dev. 2011. 25: 2361-2373 [PDF][supplemental_PDF]
doi:10.1101/gad.174110.111
Nagao A, Sato K, Nishida KM, Siomi H, Siomi MC.
Gender-specific hierarchy in nuage localization of PIWI-interacting RNA factors in Drosophila
Front. Gene. 2011, 2:55 [PDF][PubMed]
doi:10.3389/fgene.2011.00055
Ishizu H, Nagao A, Siomi H.
Gatekeepers for Piwi－piRNA complexes to enter the nucleus
Curr. Opin. Genet. Dev. 2011, 21: 484-490 [PDF][PubMed]
doi:10.1016/j.gde.2011.05.001
Siomi H, Siomi MC.
Stress signaling etches heritable marks on chromatin
Cell 2011. 145: 1005-1007. [PDF]
doi:10.1016/j.cell.2011.06.009
Miyoshi K, Okada TN, Siomi H, Siomi MC.
Biological analyzes of endogenous Argonaute complexes immunopurified with anti-Argonaute monoclonal antibodies.
Methods in Molecular Biology. 2011. 725: 29-43. [PubMed]
doi:10.1007/978-1-61779-046-1_3
Siomi MC, Sato K, Pezic C, Aravin AA.
PIWI-interacting small RNAs: the vanguard of genome defence
Nat. Rev. Mol. Cell. Biol. 2011. 12: 246-258. [PDF]
doi:10.1038/nrm3089
Nagao A, Mitsuyama T, Huang H, Chen D, Siomi MC, Siomi H.
Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis
RNA 2010. 16: 2503-2515. [PDF] [supplemental_PDF]
doi:10.1261/rna.2270710
Saito K, Siomi MC.
Small RNA-mediated quiescence of transposable elements in animals
Dev. Cell 2010. 19: 687-697. [PDF]
doi:10.1016/j.devcel.2010.10.011
Saito K, Ishizu H, Komai M, Kotani H, Kawamura Y, Nishida KM, Siomi H, Siomi MC.
Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila
Genes Dev. 2010. 24: 2493-2498. [PDF] [supplemental_PDF]
doi:10.1101/gad.1989510
Saito K, Miyoshi K, Siomi MC, Siomi H.
The key features of RNA silencing
RNA Technologies and Their Applications 2010. 1-28. [SpringerLink]
doi: 10.1007/978-3-642-12168-5_1
Miyoshi T, Takeuchi A, Siomi H, Siomi MC.
A direct role for Hsp90 in pre-RISC formation in Drosophila
Nat. Struct. Mol. Biol. 2010. 17: 1024-1026. [PDF] [supplemental_PDF]
doi:10.1038/nsmb.1875
Miyoshi K, Miyoshi T, Siomi H.
Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production
Mol. Genet. Genomics 2010. 284: 95-103. [PDF]
doi:10.1007/s00438-010-0556-1
Siomi H, Siomi MC.
Posttranscriptional regulation of microRNA biogenesis in animals
Mol. Cell 2010. 38: 323-332. [PDF]
doi:10.1016/j.molcel.2010.03.013
Siomi MC, Mannen T, Siomi H.
How does the Royal Family of Tudor rule the PIWI-interacting RNA pathway?
Genes Dev. 2010. 24: 636-646. [PDF]
doi:10.1101/gad.1899210
Sato K, Siomi H
Is canalization more than just a beautiful idea?
Genome Biology 2010. 11: 109-111. [PDF]
doi:10.1186/gb-2010-11-3-109
Miyoshi K, Miyoshi T, Hartig JV, Siomi H, Siomi MC.
Functional Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and micro RNA biogenesis pathways in Drosophila
RNA 2010. 16: 506-515. [PDF] [supplemental_PDF]
doi:10.1261/rna.1952110
Siomi MC, Miyoshi T, Siomi H.
piRNA-mediated silencing in Drosophila germlines
Seminars-Cell and Developmental Biology. 2010. 21: 754-759 [PDF]
doi:10.1016/j.semcdb.2010.01.011
Siomi MC
piRNAs (PIWI-interacting RNA)
McGraw Hill 2010 Yearbook of Sience & Technology.
ISBN-13: 978-0071639286
Nishida KM, Okada TN, Kawamura T, Mituyama T, Kawamura Y, Inagaki S, Huang H, Chen D, Kodama T, Siomi H, Siomi MC.
Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines
EMBO J. 2009. 28: 3820-3831. [PDF] [supplemental_PDF]
doi:10.1038/emboj.2009.365
Saito K, Inagaki S, Mituyama T, Kawamura Y, Ono Y, Sakota E, Kotani H, Asai K, Siomi H, Siomi MC.
A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila
Nature 2009. 461: 1296-1301. [PDF] [supplemental_PDF]
doi:10.1038/nature.08501
Siomi MC.
JOURNAL CLUB: A biologist praises a mouse model of autism inheritance
Nature 2009. 461: 451. [PDF]
doi:10.1038/461451f
Siomi H, Siomi MC.
RISC hitches onto endosome trafficking
Nat. Cell Biol. 2009. 11: 1049-1051. [PDF]
doi:10.1038/ncb0909-1049
Siomi MC
Short interfering RNA-mediated gene silencing; towards successful application in human patients
Adv. Drug Deliv. Rev. 2009. 61: 668-671. [PDF]
doi:10.1016/addr.2009.04.008
Miyoshi K, Okada TN, Siomi H, Siomi MC.
Characterization of miRNA-RISC loading complex and miRNA-RISC formed in Drosophila miRNA pathway
RNA 2009. 15: 1282-1291. [PDF]
doi:10.1261/rna.1541209
Siomi MC, Kuramochi-Miyagawa S.
RNA silencing in germlines – exquisite collaboration of Argonaute proteins with small RNAs for germline survival
Curr. Opin. Cell Biol. 2009. 3: 426-34. [PDF]
doi:10.1016/j.ceb.2009.02.003
Kim VN, Han J, Siomi MC.
Biogenesis of small RNAs in animals
Nat. Rev. Mol. Cell. Biol. 2009. 10: 126-139. [PDF] [Poster]
doi:10.1038/nrm2632
Siomi H, Siomi MC.
On the road to reading the RNA-interference code
Nature 2009. 457: 396-404. [PDF]
doi:10.1038/nature07754
Qian ZR, Asa SL, Siomi H, Siomi MC, Yoshimoto K, Yamada S, Wang EL, Rahman MM, Inoue H, Itakura M, Sano T.
Overexpression of HMGA2 relates to reduction of the let-7 and its relationship to clinicopathological features in pituitary adenomas
Mod. Pathol. 2009. 22: 431-441. [PubMed]
doi:10.1038/modpathol.2008.202
Siomi MC, Nishida KM, Siomi H.
How to define targets for small guide RNAs in RNA silencing: a biochemical approach
Methods in Enzymology 2008. 449: 345-355. [PDF]
vol. 449; RNA turnover in Eukaryotes: Analysis of Specialized and Quality Control RNA Decay Pathways
doi:10.1016/S0076-6879(08)02416-6
Siomi MC, Saito K, Siomi H.
How selfish retorotransposons are silenced in Drosophila germline and somatic cells
FEBS Lett. 2008. 582: 2473-2478. [PDF]
doi:10.1016/febslet.2008.06.018
Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC, Siomi H.
Drosophila endogeneous small RNAs bind to Argonaute 2 in somatic cells
Nature 2008. 453: 793-797. [PDF]
doi:10.1038/nature.06938
Azuma-Mukai A, Oguri H, Mitsuyama T, Qian ZR, Asai K, Siomi H, Siomi MC.
Characterization of endogeneous human Argonautes and their miRNA partners in RNA silencing
Proc. Natl. Acad. Sci. USA. 2008. 105: 7964-7969.[PDF] [supplemental_PDF]
doi:10.1073/pnas.0800334105
Siomi H, Siomi MC
Interactions between transposable elements and Argonautes have (probably) been shaping the Drosophila genome throughout evolution.
Curr. Opin. Genet. Dev. 2008. 18: 181-187. [PDF]
doi:10.1016/j.gde.2008.01.002
Miyoshi K, Uejima H, Okada TN, Siomi H, Siomi MC.
In vitro RNA Cleavage Assay for Argonaute-Family Proteins.
Methods in Molecular Biology. 2008. 442: 29-43. [PubMed]
doi:10.1007/978-1-59745-191-8_3
Nishida KM, Saito K, Mori T, Kawamura Y, Nagami-Okada T, Inagaki S, Siomi H, Siomi MC.
Gene silencing mechanisms mediated by Aubergine-piRNA complexes in Drosophila male gonad
RNA 2007.13: 1911-1922. [PDF]
doi:10.1261/rna.744307
Saito K, Sakaguchi Y, Suzuki T, Suzuki T, Siomi H, Siomi MC.
Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi-interacting RNAs at their 3′ ends.
Genes Dev. 2007. 21: 1603-1608. [PDF]
doi:10.1101/gad.1563607
Siomi H, Siomi MC
Perspective: Expanding RNA physiology: microRNAs in a unicellular organism
Genes Dev. 2007. 21: 1153-1156. [PDF]
doi:10.1101/gad.1559707
Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC.
A Slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila
Science 2007. 315: 1587-1590. [PDF]
doi:10.1126/science.1140494
Saito K, Nishida KM, Mori T, Kawamura Y, Miyoshi K, Nagami T, Siomi H, Siomi MC.
Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome
Genes Dev. 2006. 20: 2214-2222. [PDF]
doi:10.1101/gad.1454806
Ishizuka A, Saito K, Siomi MC, Siomi H.
In vitro precursor microRNA processing assays using Drosophila Schneider-2 cell lysate
Methods in Molecular Biology 2006. vol. 342: MicroRNA Protocols, 277-286. Edited by: S. Ying. [PubMed]
doi:10.1385/1-59745-123-1:277
Miyoshi K, Tsukumo H, Nagami T, Siomi H, Siomi MC.
Slicer function of Drosophila Argonautes and its involvement in RISC formation
Genes Dev. 2005. 19:2837-2848. [PDF]
doi:10.1101/gad.1370605
Nelson D. Siomi MC
Chapter 56; Fragile X Syndrome.
Pediatric Nutrition in Chronic Diseases and Developmental Disorders -Prevention, Assessment, and Treatment- 2nd Edition (ed., Shirley Walberg Ekvall and Valli K. Ekvall)
ISBN: 0195165640. Oxford University Press, New York. 2005
Siomi MC, Tsukumo H, Ishizuka A, Nagami T, Siomi H.
A potential link between transgene silencing and poly(A) tails.
RNA 2005. 11:1004-1011. [PDF]
doi:10.1261/rna.2280105
Saito K, Ishizuka A, Siomi H, Siomi MC.
Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells.
PLoS Biol. 2005. 3(7): e235. [PDF]
doi:10.1371/journal.pbio.0030235
Siomi MC, Siomi H.
Identification of components of RNAi pathways using the Tandem Affinity Purification (TAP) method.
Methods in Molecular Biology 2005. vol. 309: RNA Silencing, pp1-9. (ed., Carmichael, Gordon)
(ISBN: 1-59259-935-4). [PDF]
doi:10.1385/1-59259-935-4:001
Taura T, Siomi MC, Siomi H.
The molecular mechanisms of mRNA export.
Nuclear Import and Export in Plants and Animals (ed., Tzfira, T and Citovsky, V.), 161-174.
Landes Bioscience, New York. 2005. Review. [PDF]
Okamura K, Ishizuka A, Siomi H, Siomi MC
Distinct roles for Argonate proteins in small RNA-directed RNA cleavage pathways
Genes Dev. 2004 Jul 15;18(14):1655-66. [PDF]
doi:10.1101/gad.1210204
Siomi H, Ishizuka A, Siomi MC.
RNA interference: a new mechanism by which FMRP acts in the normal brain? What can Drosophila teach us?
Ment Retard Dev Disabil Res Rev. 2004;10(1):68-74. Review. [PDF]
doi:10.1002/mrdd.10089
Siomi MC, Higashijima K, Ishizuka A, Siomi H.
Casein kinase II phosphorylates the fragile X mental retardation protein and modulates its biological properties.
Mol Cell Biol. 2002 Dec;22(24):8438-47. [PDF]
doi:10.1128/MCB.22.24.8438-8447.2002
Ishizuka A, Siomi MC, Siomi H.
A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins.
Genes Dev. 2002 Oct 1;16(19):2497-508. [PDF]
doi:10.1101/gad.1022002
Inoue S, Shimoda M, Nishinokubi I, Siomi MC, Okamura M, Nakamura A, Kobayashi S, Ishida N, Siomi H.
A role for the Drosophila fragile X-related gene in circadian output.
Curr Biol. 2002 Aug 6;12(15):1331-5. [PDF]
doi:10.1016/S0960-9822(02)01039-9
Tabara H, Yigit E, Siomi H, Mello CC.
The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans.
Cell. 2002 Jun 28;109(7):861-71. [PDF]
doi:10.1016/S0092-8674(02)00793-6
Siomi MC.
The molecular mechanisms of messenger RNA nuclear export.
Cell Struct Funct. 2000 Aug;25(4):227-35. Review. [PDF]
doi:10.1247/csf.25.227
Inoue SB, Siomi MC, Siomi H.
Molecular mechanisms of fragile X syndrome.
J Med Invest. 2000 Aug;47(3-4):101-7. Review. [PDF]