Non-gonadal somatic piRNA pathways ensure sexual differentiation, larval growth, and wing development in silkworms.
*Kiuchi T, Shoji K, Izumi N, Tomari Y, *Katsuma S.
PLoS Genet. 2023 Sep 21;19(9):e1010912. [PubMed]
Nondomain biopolymers: Flexible molecular strategies to acquire biological functions.
Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomari Y, Yoda T, *Nakagawa S.
Genes Cells. 2023 Aug;28(8):539-552. [PubMed]
The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells.
*Shoji K, Umemura Y, Katsuma S, *Tomari Y.
PLoS Genet. 2023 Feb 9;19(2):e1010632. [PubMed]
The mechanisms of siRNA selection by plant Argonaute proteins triggering DNA methylation.
Liu W, Shoji K, Naganuma M, *Tomari Y, *Iwakawa HO.
Nucleic Acids Res. 2022 Dec 7. [PubMed]
The two Gtsf paralogs in silkworms orthogonally activate their partner PIWI proteins for target cleavage.
Izumi N, Shoji K, Kiuchi T, Katsuma S, *Tomari Y.
RNA. 2022 Nov 1. [PubMed]
Revisiting the Glass Treatment for Single-Molecule Analysis of ncRNA Function.
Shen S, Naganuma M, Tomari Y, *Tadakuma H.
Methods Mol Biol. 2022;2509:209-231. [PubMed]
GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins.
Arif A, Bailey S, Izumi N, Anzelon TA, Ozata DM, Andersson C, Gainetdinov I, MacRae IJ, Tomari Y, *Zamore PD.
Nature. 2022 Jun 30. [PubMed]
Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex.
Yamaguchi S, Naganuma M, Nishizawa T, Kusakizako T, *Tomari Y, *Nishimasu H, *Nureki O.
Nature. 2022 Jun 29. [PubMed] [Press Release]
Fusion with heat-resistant obscure (Hero) proteins have the potential to improve the molecular property of recombinant proteins.
Morimoto E, Tsuboyama K, *Tomari Y.
PLoS One. 2022 Jun 17;17(6):e0270097. [PubMed]
Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain.
Chen S, Liu W, Naganuma M, *Tomari Y, *Iwakawa HO.
Nucleic Acids Res. 2022 Apr 5:gkac223. [PubMed]
Life of RISC: Formation, action, and degradation of RNA-induced silencing complex.
*Iwakawa HO., *Tomari Y.
Mol Cell. 2022 Jan 6;82(1):30-43. [PubMed]
Cell-free reconstitution reveals the molecular mechanisms for the initiation of secondary siRNA biogenesis in plants.
Sakurai Y, Baeg K, Lam AYW, Shoji K, *Tomari Y, *Iwakawa HO.
Proc Natl Acad Sci U S A. 2021 Aug 3;118(31):e2102889118. [PubMed] [Press Release]
RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors.
Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, *Kirino Y.
Nat Commun. 2021 Jul 23;12(1):4498. [PubMed]
Single-molecule analysis of processive double-stranded RNA cleavage by Drosophila Dicer-2.
Naganuma M, *Tadakuma H, *Tomari Y.
Nat Commun. 2021 Jul 13;12(1):4268. [PubMed] [Press Release]
Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants.
*Iwakawa HO, Lam AYW, Mine A, Fujita T, Kiyokawa K, Yoshikawa M, Takeda A, Iwasaki S, Tomari Y.
Cell Rep. 2021 Jun 29;35(13):109300. [PubMed] [Press Release]
Dynamic subcellular compartmentalization ensures fidelity of piRNA biogenesis in silkworms.
Chung PY, Shoji K, Izumi N, *Tomari Y.
EMBO Rep. 2021 May 11:e51342. [PubMed] [Press Release]
Mechanistic analysis of the enhanced RNAi activity by 6-mCEPh-purine at the 5ʹ end of the siRNA guide strand.
Brechin V, Shinohara F, Saito JI, Seitz H, *Tomari Y.
RNA 2021 Feb;27(2):151-162. [PubMed]
siRNA potency enhancement via chemical modifications of nucleotide bases at the 5ʹ-end of the siRNA guide strand.
Shinohara F, Oashi T, Harumoto T, Nishikawa T, Takayama Y, Miyagi H, Takahashi Y, Nakajima Y, Sawada Y, Koda Y, Makino A, Sato A, Hamaguchi K, Suzuki M, Yamamoto J, Tomari Y, *Saito JI.
RNA 2021 Feb;27(2):163-173. [PubMed]
A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation.
*Tsuboyama K, Osaki T, Matsuura-Suzuki E, Kozuka-Hata H, Okada Y, Oyama M, Ikeuchi Y, Iwasaki S, *Tomari Y.
PLoS Biol. 2020 Mar 12;18(3):e3000632. [PubMed] [Press Release] [UTokyo FOCUS]
Zucchini consensus motifs determine the mechanism of pre-piRNA production.
Izumi N, Shoji K (equal contribution), Suzuki Y, Katsuma S, *Tomari Y.
Nature. 2020 Feb;578(7794):311-316. [PubMed] [Press Release] [UTokyo FOCUS]
Identification of an AGO (Argonaute) protein as a prey of TER94/VCP.
*Kobayashi H, *Tomari Y.
Autophagy. 2020 Jan;16(1):190-192. [PubMed]
VCP machinery mediates autophagic degradation of empty Argonaute.
*Kobayashi H, Shoji K, Kiyokawa K, Negishi L, *Tomari Y.
Cell Rep. 2019 July 30;28(5):1144-1153.e4. [PubMed] [Press Release] [UTokyo FOCUS]
Iruka eliminates dysfunctional Argonaute by selective ubiquitination of its empty state.
*Kobayashi H, Shoji K, Kiyokawa K, Negishi L, *Tomari Y.
Mol Cell. 2019 Jan 3;73(1):119-129.e5. [PubMed] [Press Release] [UTokyo FOCUS]
Conformational activation of Argonaute by distinct yet coordinated actions of the Hsp70 and Hsp90 chaperone systems.
Tsuboyama K, *Tadakuma H, *Tomari Y.
Mol Cell. 2018 May 17;70(4):722-729.e4. [PubMed] [Press Release] [UTokyo FOCUS] [新着論文レビュー]
PNLDC1, mouse pre‐piRNA Trimmer, is required for meiotic and post‐meiotic male germ cell development.
Nishimura T, Nagamori I, Nakatani T, Izumi N, Tomari Y, *Kuramochi‐Miyagawa S, *Nakano T.
EMBO Rep. 2018 Mar;19(3). [PubMed]
In vitro reconstitution of chaperone-mediated human RISC assembly
Naruse K, Matsuura SE (equal contribution), Watanabe M, *Iwasaki S, *Tomari Y.
RNA. 2018 Jan;24(1):6-11. [PubMed]
Transcriptome profiling reveals infection strategy of an insect maculavirus.
*Katsuma S, Kawamoto M, Shoji K, Aizawa T, Kiuchi T, Izumi N, Ogawa M, Mashiko T, Kawasaki H, Sugano S, Tomari Y, Suzuki Y, *Iwanaga M.
DNA Res. 2018 Jan 17;25(3):277-286. [PubMed]
In vitro RNA-dependent RNA Polymerase Assay Using Arabidopsis RDR6.
Baeg K, Tomari Y, *Iwakawa HO.
Bio Protoc. 2018 Jan 5;8(1):e2673. [PubMed]
Single-molecule analysis for RISC assembly and target cleavage.
Sasaki HM, Tadakuma H, Tomari Y.
Methods Mol Biol. 2018;1680:145-164. [PubMed]
Reconstitution of RNA interference machinery.
Iwasaki S, Tomari Y.
Methods Mol Biol. 2018;1680:131-143. [PubMed]
Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2.
Zhang H, Liu K, Izumi N (equal contribution), Huang H, Ding D, Ni Z, Sidhu SS, Chen C, *Tomari Y, *Min J.
Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):12483-12488. [PubMed]
Biochemical and single-molecule analyses of the RNA silencing suppressing activity of CrPV-1A.
Watanabe M, Iwakawa HO, Tadakuma H, *Tomari Y
Nucleic Acids Res. 2017 Oct 13;45(18):10837-10844. [PubMed]
Silencing messages in a unique way.
*Iwakawa HO, *Tomari Y
Nat Plants. 2017 Oct;3(10):769-770. [PubMed]
In vitro analysis of ARGONAUTE-mediated target cleavage and translational repression in plants.
Tomari Y, *Iwakawa HO
Methods Mol Biol. 2017;1640:55-71. [PubMed]
Pervasive yet nonuniform contributions of Dcp2 and Cnot7 to maternal mRNA clearance in zebrafish.
*Mishima Y, Tomari Y
Genes Cells. 2017 Jul;22(7):670-678. [PubMed]
The poly(A) tail blocks RDR6 from converting self mRNAs into substrates for gene silencing.
Baeg K, *Iwakawa HO, *Tomari Y.
Nat Plants. 2017 Mar 20;3:17036. [PubMed] [Press Release] [UTokyo Research]
ATP is dispensable for both miRNA- and Smaug-mediated deadenylation reactions.
Niinuma S, *Tomari Y.
RNA. 2017 Jun;23(6):866-871. [PubMed]
CCR4 and CAF1 deadenylases have an intrinsic activity to remove the post-poly(A) sequence
Niinuma S, Fukaya T, *Tomari Y.
RNA. 2016 Oct;22(10):1550-9. [PubMed]
Codon usage and 3′ UTR length determine maternal mRNA stability in zebrafish
*Mishima Y, Tomari Y.
Mol Cell. 2016 Mar 17;61(6):874-85. [PubMed] [UTokyo Research]
Identification and functional analysis of the pre-piRNA 3′ Trimmer in silkworms.
Izumi N, Shoji K, Sakaguchi Y, Honda S, Kirino Y, Suzuki T, Katsuma S, *Tomari Y.
Cell. 2016 Feb 25;164(5):962-73. [PubMed] [UTokyo Research] [新着論文レビュー]
RISC assembly: Coordination between small RNAs and Argonaute proteins.
Kobayashi H, *Tomari Y.
Biochim Biophys Acta. 2016 Jan;1859(1):71-81. [PubMed]
The functions of microRNAs: mRNA Decay and translational repression.
Iwakawa HO, *Tomari Y.
Trends Cell Biol. 2015 Nov;25(11):651-65. [PubMed]
Cryptic RNA-binding by PRC2 components EZH2 and SUZ12.
Betancur JG, *Tomari Y.
RNA Biol. 2015;12(9):959-65. [PubMed]
Single-molecule analysis of the target cleavage reaction by the Drosophila RNAi enzyme complex.
Yao C, Sasaki HM, Ueda T, *Tomari Y, *Tadakuma H.
Mol Cell. 2015 July 2;59(1):125-32. [PubMed] [UTokyo Research]
Defining fundamental steps in the assembly of the Drosophila RNAi enzyme complex.
Iwasaki S, Sasaki HM (equal contribution), Sakaguchi Y, Suzuki T, *Tadakuma H, *Tomari Y.
Nature. 2015 May 28;521(7553):533-6. [PubMed] [UTokyo Research] [新着論文レビュー]
My encounter with RNA.
*Tomari Y.
RNA. 2015 Apr;21(4):747-8. [PubMed]
The initial uridine of primary piRNAs does not create the tenth adenine that is the hallmark of secondary piRNAs.
Wang W, Yoshikawa M (equal contribution), Han BW, Izumi N, *Tomari Y, *Weng Z, *Zamore PD.
Mol Cell. 2014 Dec 4;56(5):708-16. [PubMed]
MicroRNAs Block Assembly of eIF4F Translation Initiation Complex in Drosophila.
Fukaya T, Iwakawa HO (equal contribution), *Tomari Y.
Mol Cell. 2014 Oct 2;56(1):67-78. [PubMed] [Press Release] [新着論文レビュー]
Elements and machinery of non-coding RNAs: toward their taxonomy.
Hirose T, Mishima Y, *Tomari Y.
EMBO Rep. 2014 Jul;14(7):652-8. [PubMed]
Diversity of the piRNA pathway for nonself silencing: worm-specific piRNA biogenesis factors.
Izumi N, *Tomari Y.
Genes Dev. 2014 Apr 1;28(7):665-71. [PubMed]
Molecular Insights into microRNA-Mediated Translational Repression in Plants.
Iwakawa HO, *Tomari Y.
Mol Cell. 2013 Nov 21;52(4):591-601. [PubMed] [Press Release] [新着論文レビュー]
Poly(A)-Specific Ribonuclease Mediates 3'-End Trimming of Argonaute2-Cleaved Precursor MicroRNAs.
Yoda M, Cifuentes D (equal contribution), Izumi N, Sakaguchi Y, Suzuki T, *Giraldez AJ, *Tomari Y.
Cell Rep. 2013 Nov 14;5(3):715-26. [PubMed]
Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly.
Endo Y, *Iwakawa HO, *Tomari Y.
EMBO Rep. 2013 Jul;14(7):652-8. [PubMed]
Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins.
Izumi N, Kawaoka S (equal contribution), Yasuhara S, Suzuki Y, Sugano S, *Katsuma S, *Tomari Y.
RNA. 2013 Jul;19(7):896-901. [PubMed] [Corrigendum]
The comprehensive epigenome map of piRNA clusters.
*Kawaoka S, Hara K, Shoji K, Kobayashi M, Shimada T, Sugano S, Tomari Y, Suzuki Y, *Katsuma S.
Nucleic Acids Res. 2013 Feb 1;41(3):1581-90. [PubMed] [Press Release]
microRNAs mediate gene silencing via multiple different pathways in Drosophila.
Fukaya T, *Tomari Y.
Mol Cell. 2012 Dec 28;48(6):825-36. [PubMed] [Press Release] [新着論文レビュー]
miRNA-like duplexes as RNAi triggers with improved specificity.
Betancur JG, Yoda M (equal contribution), *Tomari Y.
Front Genet. 2012;3:127. [PubMed]
The true core of RNA silencing revealed.
Sasaki HM, *Tomari Y.
Nat Struct Mol Biol. 2012 Jul 5;19(7):657-60. [PubMed]
Poly(A)-binding protein facilitates translation of an uncapped/nonpolyadenylated viral RNA by binding to the 3' untranslated region.
Iwakawa HO, Tajima Y, Taniguchi T, Kaido M, Mise K, Tomari Y, Taniguchi H, *Okuno T.
J Virol. 2012 Aug;86(15):7836-49. [PubMed]
The N domain of Argonaute drives duplex unwinding during RISC assembly.
Kwak PB, *Tomari Y.
Nat Struct Mol Biol. 2012 Jan 10;19(2):145-51. [PubMed] [Press Release]
A role for transcription from a piRNA cluster in de novo piRNA production.
Kawaoka S, Mitsutake H, Kiuchi T, Kobayashi M, Yoshikawa M, Suzuki Y, Sugano S, Shimada T, *Kobayashi J, *Tomari Y,* Katsuma S
RNA 2012 Feb;18(2):265-73. [PubMed]
PABP is not essential for microRNA-mediated translational repression and deadenylation in vitro.
Fukaya T, *Tomari Y.
EMBO J. 2011 Nov 25;30(24):4998-5009. [PubMed]
Dicer is dispensable for asymmetric RISC loading in mammals.
Betancur JG, *Tomari Y.
RNA. 2012 Jan;18(1):24-30. [PubMed]
The silkworm W chromosome is a source of female-enriched piRNAs.
Kawaoka S, Kadota K, Arai Y, Suzuki Y, Fujii T, Abe H, Yasukochi Y, Mita K, Sugano S, Shimizu K, Tomari Y, Shimada T, *Katsuma S.
RNA. 2011 Dec;17(12):2144-51. [PubMed]
Recognition of the pre-miRNA structure by Drosophila Dicer-1.
Tsutsumi A, Kawamata T, Izumi N, Seitz H, *Tomari Y.
Nat Struct Mol Biol. 2011 Sep 18;18(10):1153-8. [PubMed] [Press Release] [新着論文レビュー]
3' end formation of PIWI-interacting RNAs in vitro.
Kawaoka S, Izumi N, *Katsuma S, *Tomari Y.
Mol Cell. 2011 Sep 16;43(6):1015-22. [PubMed] [Press Release] [新着論文レビュー]
Multilayer checkpoints for microRNA authenticity during RISC assembly.
*Kawamata T, Yoda M, *Tomari Y.
EMBO Rep. 2011 Sep 1;12(9):944-9. [PubMed]
Zygotic amplification of secondary piRNAs during silkworm embryogenesis.
Kawaoka S, Arai Y, Kadota K, Suzuki Y, Hara K, Sugano S, Shimizu K, Tomari Y, Shimada T, *Katsuma S.
RNA. 2011 Jul;17(7):1401-7. [PubMed]
Native gel analysis for RISC assembly.
Kawamata T, *Tomari Y.
Methods Mol Biol. 2011;725:91-105. [PubMed]
Diazirine-containing RNA photocrosslinking probes for the study of siRNA-protein interactions.
Kuboe S, Yoda M (equal contribution), Ogata A, Kitade Y, *Tomari Y, *Ueno Y.
Chem Commun. 2010 Oct 21;46(39):7367-9. [PubMed]
The microRNA pathway and cancer.
Kwak PB, Iwasaki S (equal contribution), *Tomari Y.
Cancer Sci. 2010 Nov;101(11):2309-15. [PubMed]
Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes.
Iwasaki S, Kobayashi M (equal contribution), Yoda M, Sakaguchi Y, Katsuma S, Suzuki T, *Tomari Y.
Mol Cell. 2010 Jul 30;39(2):292-299. [PubMed] [Press Release] [新着論文レビュー]
Making RISC.
Kawamata T, *Tomari Y.
Trends Biochem Sci. 2010 Jul;35(7):368-76. [PubMed]
ATP-dependent human RISC assembly pathways.
Yoda M, Kawamata T, Paroo Z, Ye X, Iwasaki S, Liu Q, *Tomari Y.
Nat Struct Mol Biol. 2010 Jan;17(1):17-23. [PubMed] [Press Release]
Structural requirement of miRNAs for RISC-loading and slicer-independent unwinding.
Kawamata T, Seitz H, *Tomari Y.
Nat Struct Mol Biol. 2009 Sep;16(9):953-60. [PubMed] [Press Release]
Argonaute-mediated translational repression (and activation).
Iwasaki S, *Tomari Y.
Fly. 2009 Jul 14;3(3). [PubMed]
The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes.
Kawaoka S, Hayashi N, Suzuki Y, Abe H, Sugano S, Tomari Y, Shimada T, Katsuma S.
RNA. 2009 Jul;15(7):1258-64. [PubMed]
Drosophila Argonaute1 and Argonaute2 employ distinct mechanisms for translational repression.
Iwasaki S, Kawamata T, *Tomari Y.
Mol Cell. 2009 Apr 10;34(1):58-67. [PubMed]
Sorting of Drosophila small silencing RNA.
*Tomari Y, Du T, *Zamore PD.
Cell. 2007 Jul 27;130(2):299-308. [PubMed]
Drosophila microRNAs are sorted into functionally distinct Argonaute
protein complexes after their production by Dicer-1.
Forstemann K, Horwich MD, Wee L, Tomari Y, Zamore PD.
Cell. 2007 Jul 27;130(2):287-297. [PubMed]
piRNAs―the ancient hunters of genome invaders.
Hartig JV, *Tomari Y, *Forstemann K.
Genes Dev. 2007 Jul 15;21(14):1707-1713. [PubMed]
Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes.
Matranga C, Tomari Y, Shin C, Bartel DP, Zamore PD.
Cell. 2005 Nov 18;123(4):607-20. [PubMed]
Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein.
Forstemann K, Tomari Y, Du T, Vagin VV, Denli AM, Bratu DP, Klattenhoff C, Theurkauf WE, Zamore PD.
PLoS Biol. 2005 Jul;3(7):e236. [PubMed]
Perspective: machines for RNAi.
Tomari Y, Zamore PD.
Genes Dev. 2005 Mar 1;19(5):517-29. [PubMed]
MicroRNA biogenesis: Drosha can't cut it without a partner.
Tomari Y, Zamore PD.
Curr Biol. 2005 Jan 26;15(2):R61-4. [PubMed]
A protein sensor for siRNA asymmetry.
Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD.
Science. 2004 Nov 19;306(5700):1377-80. [PubMed]
The RNA-induced silencing complex is a Mg2+-dependent endonuclease.
Schwarz DS, Tomari Y, Zamore PD.
Curr Biol. 2004 May 4;14(9):787-91. [PubMed]
RISC assembly defects in the Drosophila RNAi mutant armitage.
Tomari Y, Du T, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE, Zamore PD.
Cell. 2004 Mar 19;116(6):831-41. [PubMed]
Decreased CCA-addition in human mitochondrial tRNAs bearing a pathogenic A4317G or A10044G mutation.
Tomari Y, Hino N, Nagaike T, Suzuki T, Ueda T.
J Biol Chem. 2003 May 9;278(19):16828-33. [PubMed]
tRNA recognition by CCA-adding enzyme.
Tomari Y, Suzuki T, Ueda T.
Nucleic Acids Res Suppl. 2002;(2):77-8. [PubMed]
Identification and characterization of mammalian mitochondrial tRNA nucleotidyltransferases.
Nagaike T, Suzuki T, Tomari Y, Takemoto-Hori C, Negayama F, Watanabe K, Ueda T.
J Biol Chem. 2001 Oct 26;276(43):40041-9. [PubMed]
Cell-free translation reconstituted with purified components.
Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T.
Nature Biotechnology. 2001 Aug;19(8):751-5. [PubMed]
The role of tightly bound ATP in Escherichia coli tRNA nucleotidyltransferase.
Tomari Y, Suzuki T, Watanabe K, Ueda T.
Genes Cells. 2000 Sep;5(9):689-98. [PubMed]
