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 Nature

Lucas BA, Lavi E, Shiue L, Cho H, Katzman S, Miyoshi K, Siomi MC, Carmel L, Ares M Jr, Maquat LE.
Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.
Proc Natl Acad Sci U S A. 2018 PNAS
doi: 10.1073/pnas.1715531115

Sakakibara K, Siomi MC.
The PIWI-Interacting RNA Molecular Pathway: Insights From Cultured Silkworm Germline Cells.
Bioessays 2018 Bioessays
doi: 10.1002/bies.201700068

Yamashiro H, Siomi MC.
PIWI-Interacting RNA in Drosophila: Biogenesis, Transposon Regulation, and Beyond.
Chem Rev. 2017 Chem Rev.
doi: 10.1021/acs.chemrev.7b00393

Ishizu H, Sumiyoshi T, Siomi MC.
Use of the CRISPR-Cas9 system for genome editing in cultured Drosophila ovarian somatic cells.
Methods 2017 ScienceDirect
doi: 10.1016/j.ymeth.2017.05.021

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. Cell
doi: 10.1016/j.cell.2016.09.002.

Guida V, Cernilogar FM, Filograna A, De Gregorio R, Ishizu H, Siomi MC, Schotta G, Bellenchi GC, Andrenacci D.
Production of Small Non-coding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster.
Genetics 2016; Genetics
doi: 10.1534/genetics.116.187922

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. Genes Dev.
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: 1-12. [PDF]
doi: 10.1016/j.molcel.2016.06.008

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 May 9; 37: 226-37. Dev. Cell
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 (Austin) 2015; Fly

Shibata S, Murota Y, Nishimoto Y, Yoshimura M, Nagai T, Okano H, Siomi MC.
Immuno-Electron Microscopy and Electron Microscopic In Situ Hybridization for Visualizing piRNA Biogenesis Bodies in Drosophila Ovaries.
Methods Mol Biol. 2015; 1328:163-78. [PDF]
doi: 10.1007/978-1-4939-2851-4_12.

Hirakata H, Siomi MC.
piRNA biogenesis in the germline: From transcription of piRNA genomic sources to piRNA maturation
BBA. 2015; [ScienceDirect]
doi: 10.1016/j.bbagrm.2015.09.002

Liang C, Wang Y, Murota Y, Liu X, Smith D, Siomi MC, Liu Q,
TAF11 Assembles the RISC Loading Complex to Enhance RNAi Efficiency
Mol Cell. 2015; 59: 807-18.[PDF]
doi: 10.1016/j.molcel.2015.07.006

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: 553-63.[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: 429-40.[PDF]
doi: 10.1016/j.celrep.2015.06.035

Siomi H, Siomi MC.
RNA. Phased piRNAs tackle transposons.
Science. 2015; 348: 756-7.[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 Reports. 2015 11:366-75.[PDF]
doi: 10.1016/j.celrep.2015.03.030

Sato K, Siomi MC.
Functional and structural insights into the piRNA factor Maelstrom.
FEBS Lett. 2015 589:1688-93.[PDF]
doi: 10.1016/j.febslet.2015.03.023.

Iwasaki YW, Siomi MC, Siomi H.
PIWI-Interacting RNA: Its Biogenesis and Functions.
Annu Rev Biochem. 2015 Mar 5.[PDF]

Yu-Ching Lin Z, 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.2015.01.014.

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 Reports. 2015. 10:193-203.[PDF]

Yamanaka S, Siomi MC, Siomi H.
piRNA clusters and open chromatin structure
Mobile DNA. 2014.5:22[PDF]

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 Reports. 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]

Siomi MC. (Ed.)
PIWI-interacting RNAs
Methods in Molecular Biology 2014, XI, 249p [website]
ISBN 978-1-62703-694-8

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: 1693-1705[PDF]

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

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]

Sato K, Siomi MC.
Piwi-interacting RNAs: biological functions and biogenesis
Essays Biochem 2013. 54: 39-52[website]

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.[ElsevierLink]

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]

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]

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]

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]

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]

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]

Siomi H, Siomi MC.
Stress signaling etches heritable marks on chromatin
Cell 2011. 145: 1005-1007.[PDF]

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]

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]

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]

Saito K, Siomi MC.
Small RNA-mediated quiescence of transposable elements in animals
Dev. Cell 2010. 19: 687-697. [PDF]

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]

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]

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]

Siomi H, Siomi MC.
Posttranscriptional regulation of microRNA biogenesis in animals
Mol. Cell 2010. 38: 323-332.[PDF]

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]

Sato K, Siomi H.
Is canalization more than just a beautiful idea?
Genome Biology 2010. 11: 109-111. [PDF]

Miyoshi K, Miyoshi T, Hartig JV, Siomi H, Siomi MC.
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]

Siomi MC, Miyoshi T, Siomi H.
piRNA-mediated silencing in Drosophila germlines
Seminars-Cell and Developmental Biology. 2010. 21: 754-759[PDF]

Siomi MC.
piRNAs (PIWI-interacting RNA)
McGraw Hill 2010 Yearbook of Sience & Technology.
ISBN-13: 978-0071639286[McGraw-hill]

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]

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]

Siomi MC.
JOURNAL CLUB: A biologist praises a mouse model of autism inheritance
Nature 2009. 461: 451.[PDF]

Siomi H, Siomi MC.
RISC hitches onto endosome trafficking
Nat. Cell Biol. 2009. 11: 1049-1051.[PDF]

Siomi MC.
Short interfering RNA-mediated gene silencing; towards successful application in human patients
Adv. Drug Deliv. Rev. 2009. 61: 668-671.[PDF]

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]

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]

Kim VN, Han J, Siomi MC.
Biogenesis of small RNAs in animals
Nat. Rev. Mol. Cell. Biol. 2009. 10: 126-139.[PDF] [Poster]

Siomi H, Siomi MC.
On the road to reading the RNA-interference code
Nature 2009. 457: 396-404. [PDF]

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]

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

Siomi MC, Saito K, Siomi H.
How selfish retorotransposons are silenced in Drosophila germline and somatic cells
FEBS Lett. 2008. 582: 2473-2478.[PDF]

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]

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]

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]

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]

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: 1911-22. [PDF] [S-Fig.1] [S-Fig.2] [S-Fig.3] [S-Fig.4] [S-Fig.5] [S-Table 1] [S-Table 2] [S-Table 3] [S-Table 4] [S-Table 5]

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: 1603-8.[PDF]

Siomi H, Siomi MC.
Perspective: Expanding RNA physiology: microRNAs in a unicellular organism
Genes Dev. 2007; 21: 1153-6.[PDF]

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
2007; 315: 1587-90.[PDF]

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: 2214-22.[PDF]

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; 342: 277-86. [PubMed]

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: 2837-48. [PDF]

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: 1004-11.[PDF]

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: e235.[PDF]

Siomi MC, Siomi H.
Identification of components of RNAi pathways using the Tandem Affinity Purification (TAP) method.
Methods in Molecular Biology 2005; 309:1-9. [PDF]

Taura T, Siomi MC, Siomi H.
The molecular mechanisms of mRNA export.
Nuclear Import and Export in Plants and Animals 2005; 161-74. 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; 18:1655-66.[PDF]

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: 68-74. Review.[PDF]

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: 8438-47.[PDF]

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: 2497-508.[PDF]

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: 1331-5.[PDF]

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: 861-71.[PDF]

Siomi MC.
The molecular mechanisms of messenger RNA nuclear export.
Cell Struct Funct. 2000 Aug; 25: 227-35. Review.[PDF]

Inoue SB, Siomi MC, Siomi H.
Molecular mechanisms of fragile X syndrome.
J Med Invest. 2000 Aug; 47: 101-7. Review.[PDF]