Yukihide Tomari

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. ncbi request reprint Perspective: machines for RNAi
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 19:517-29. 2005
  2. pmc miRNA-like duplexes as RNAi triggers with improved specificity
    Juan G Betancur
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
    Front Genet 3:127. 2012
  3. pmc Sorting of Drosophila small silencing RNAs
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell 130:299-308. 2007
  4. ncbi request reprint Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes
    Christian Matranga
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Cell 123:607-20. 2005
  5. ncbi request reprint A protein sensor for siRNA asymmetry
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Science 306:1377-80. 2004
  6. ncbi request reprint Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes
    Shintaro Iwasaki
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    Mol Cell 39:292-9. 2010
  7. pmc Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein
    Klaus Forstemann
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    PLoS Biol 3:e236. 2005
  8. doi request reprint Structural determinants of miRNAs for RISC loading and slicer-independent unwinding
    Tomoko Kawamata
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan
    Nat Struct Mol Biol 16:953-60. 2009
  9. pmc ATP-dependent human RISC assembly pathways
    Mayuko Yoda
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Nat Struct Mol Biol 17:17-23. 2010
  10. pmc Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins
    Natsuko Izumi
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    RNA 19:896-901. 2013

Collaborators

Detail Information

Publications36

  1. ncbi request reprint Perspective: machines for RNAi
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 19:517-29. 2005
    ..Here, we review our current understanding of how small RNAs are produced, how they are loaded into protein complexes, and how they repress gene expression...
  2. pmc miRNA-like duplexes as RNAi triggers with improved specificity
    Juan G Betancur
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
    Front Genet 3:127. 2012
    ....
  3. pmc Sorting of Drosophila small silencing RNAs
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell 130:299-308. 2007
    ..Thus, in flies small-RNA duplexes are actively sorted into Argonaute-containing complexes according to their intrinsic structures...
  4. ncbi request reprint Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes
    Christian Matranga
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Cell 123:607-20. 2005
    ..For siRNAs, virtually all RISC is assembled through this cleavage-assisted mechanism. In contrast, passenger-strand cleavage is not important for the incorporation of miRNAs that derive from mismatched duplexes...
  5. ncbi request reprint A protein sensor for siRNA asymmetry
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Science 306:1377-80. 2004
    ..Thus, R2D2 is both a protein sensor for siRNA thermodynamic asymmetry and a licensing factor for entry of authentic siRNAs into the RNAi pathway...
  6. ncbi request reprint Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes
    Shintaro Iwasaki
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    Mol Cell 39:292-9. 2010
    ..Our data suggest that the chaperone machinery may serve as the driving force for the RISC assembly pathway...
  7. pmc Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein
    Klaus Forstemann
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    PLoS Biol 3:e236. 2005
    ..Thus, every known Drosophila RNase-III endonuclease is paired with a dsRBD protein that facilitates its function in small RNA biogenesis...
  8. doi request reprint Structural determinants of miRNAs for RISC loading and slicer-independent unwinding
    Tomoko Kawamata
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan
    Nat Struct Mol Biol 16:953-60. 2009
    ..Our findings show that unwinding of miRNAs is a precise mirror-image process of target recognition, and both processes reflect the unique geometry of RNAs in Ago proteins...
  9. pmc ATP-dependent human RISC assembly pathways
    Mayuko Yoda
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Nat Struct Mol Biol 17:17-23. 2010
    ..All these features of human AGO proteins are highly reminiscent of fly Ago1 but not fly Ago2...
  10. pmc Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins
    Natsuko Izumi
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    RNA 19:896-901. 2013
    ..Our data highlight a role of Hsp90 in accurate loading of precursor piRNAs into PIWI proteins...
  11. doi request reprint Drosophila argonaute1 and argonaute2 employ distinct mechanisms for translational repression
    Shintaro Iwasaki
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
    Mol Cell 34:58-67. 2009
    ..Our finding that the two Ago proteins in flies regulate translation by different mechanisms may reconcile previous, contradictory explanations for how miRNAs repress protein synthesis...
  12. doi request reprint Recognition of the pre-miRNA structure by Drosophila Dicer-1
    Akihisa Tsutsumi
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Nat Struct Mol Biol 18:1153-8. 2011
    ..This unique mechanism allows fly Dicer-1 to strictly inspect the authenticity of pre-miRNA structures...
  13. pmc A role for transcription from a piRNA cluster in de novo piRNA production
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo, Japan
    RNA 18:265-73. 2012
    ..Bioinformatic analyses suggest that the fusion transcript is a source of GFP primary piRNAs. Our data implicate a role for transcription from a piRNA cluster in initiating de novo piRNA production against a new insertion...
  14. ncbi request reprint Argonaute-mediated translational repression (and activation)
    Shintaro Iwasaki
    Institute of Molecular and Cellular Biosciences and Department of Medical Genome Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Fly (Austin) 3:204-6. 2009
    ..This review focuses on how miRNAs regulate translation in light of these new findings...
  15. pmc The comprehensive epigenome map of piRNA clusters
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi, Tokyo, Japan
    Nucleic Acids Res 41:1581-90. 2013
    ..Collectively, we envision that the euchromatic, opened nature of unique piRNA clusters or piRNA cluster-associated TSSs allows piRNA clusters to capture new insertions efficiently...
  16. pmc The silkworm W chromosome is a source of female-enriched piRNAs
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
    RNA 17:2144-51. 2011
    ..Collectively, we revealed the nature of the silkworm W chromosome as a source of piRNAs...
  17. doi request reprint Molecular insights into microRNA-mediated translational repression in plants
    Hiro Oki Iwakawa
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Mol Cell 52:591-601. 2013
    ..These silencing effects require more extensive base pairing to the target site in comparison to typical animal miRNAs. Our data provide mechanistic insights into miRNA-mediated translational repression in plants...
  18. ncbi request reprint RISC assembly defects in the Drosophila RNAi mutant armitage
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell 116:831-41. 2004
    ..Our results suggest that armi is required for RISC maturation...
  19. doi request reprint MicroRNAs mediate gene silencing via multiple different pathways in drosophila
    Takashi Fukaya
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    Mol Cell 48:825-36. 2012
    ..Differential contribution from these multiple pathways may explain previous, apparently contradictory observations of how microRNAs inhibit protein synthesis...
  20. doi request reprint Native gel analysis for RISC assembly
    Tomoko Kawamata
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
    Methods Mol Biol 725:91-105. 2011
    ..We developed a native agarose gel system to directly detect Ago1-RISC, Ago2-RISC, and their precursor complexes. Methods presented here will provide powerful tools to biochemically dissect the RISC assembly pathways...
  21. pmc Zygotic amplification of secondary piRNAs during silkworm embryogenesis
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    RNA 17:1401-7. 2011
    ..These results provide on-site evidence for the ping-pong cycle...
  22. pmc PABP is not essential for microRNA-mediated translational repression and deadenylation in vitro
    Takashi Fukaya
    Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo ku, Tokyo, Japan
    EMBO J 30:4998-5009. 2011
    ..Instead, we propose that each of the multiple functional domains within GW182 has a potential for silencing, and yet they need to act together in the context of full-length GW182 to exert maximal silencing...
  23. ncbi request reprint The RNA-induced silencing complex is a Mg2+-dependent endonuclease
    Dianne S Schwarz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 USA
    Curr Biol 14:787-91. 2004
    ..Thus, the RISC-component that mediates endonucleolytic cleavage of the target RNA remains to be identified...
  24. doi request reprint The microRNA pathway and cancer
    Pieter Bas Kwak
    Institute of Molecular and Cellular Biosciences Department of Medical Genome Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Cancer Sci 101:2309-15. 2010
    ..In this review, we summarize how miRNAs are produced, assembled into RISC, and regulate target mRNAs, and discuss how the miRNA pathway is involved in cancer...
  25. pmc Multilayer checkpoints for microRNA authenticity during RISC assembly
    Tomoko Kawamata
    Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan
    EMBO Rep 12:944-9. 2011
    ..Consequently, the miRNA authenticity is inspected at multiple steps during RISC assembly...
  26. doi request reprint 3' end formation of PIWI-interacting RNAs in vitro
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    Mol Cell 43:1015-22. 2011
    ..Importantly, 3' end methylation is tightly coupled with trimming and yet is not a prerequisite for determining the mature piRNA length. Our system provides a biochemical framework for dissecting piRNA biogenesis...
  27. pmc Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs
    Mayuko Yoda
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan Department of Medical Genome Sciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    Cell Rep 5:715-26. 2013
    ..Our findings define the maturation step in the miRNA biogenesis pathway that depends on Ago2-mediated cleavage...
  28. pmc The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113 8657, Japan
    RNA 15:1258-64. 2009
    ..Taken together, BmN4 is a unique cell line in which both primary and secondary steps of piRNA biogenesis pathways are active. This cell line would provide useful tools for analysis of piRNA biogenesis and function...
  29. ncbi request reprint MicroRNA biogenesis: drosha can't cut it without a partner
    Yukihide Tomari
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Curr Biol 15:R61-4. 2005
    ....
  30. pmc Dicer is dispensable for asymmetric RISC loading in mammals
    Juan G Betancur
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    RNA 18:24-30. 2012
    ..Our data show that, unlike the well-characterized fly Ago2-RISC assembly pathway, mammalian Dicer is dispensable for asymmetric RISC loading in vivo and in vitro...
  31. pmc Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly
    Yayoi Endo
    Institute of Molecular and Cellular Biosciences, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 1 1 1, Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    EMBO Rep 14:652-8. 2013
    ..These findings suggest that AGO7 uses multiple checkpoints to select miR390, thereby circumventing promiscuous tasiRNA production. ..
  32. doi request reprint The N domain of Argonaute drives duplex unwinding during RISC assembly
    Pieter Bas Kwak
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Nat Struct Mol Biol 19:145-51. 2012
    ....
  33. doi request reprint Making RISC
    Tomoko Kawamata
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    Trends Biochem Sci 35:368-76. 2010
    ....
  34. pmc Diversity of the piRNA pathway for nonself silencing: worm-specific piRNA biogenesis factors
    Natsuko Izumi
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo ku, Tokyo 113 0032, Japan
    Genes Dev 28:665-71. 2014
    ..These works greatly expand our understanding of the piRNA pathway in worms, highlighting both its shared and its unique properties. ..
  35. pmc Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1
    Klaus Forstemann
    Gene Center and Munich Center for Integrated Protein Science CiPS M, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, D 81377 Munich, Germany
    Cell 130:287-97. 2007
    ..Thus, the two members of the Drosophila Ago subclade of Argonaute proteins are functionally specialized, but specific small RNA classes are not restricted to associate with Ago1 or Ago2...
  36. ncbi request reprint piRNAs--the ancient hunters of genome invaders
    Julia Verena Hartig
    Gene Center of the Ludwig Maximilians University, D 81377 Munchen, Germany
    Genes Dev 21:1707-13. 2007
    ..We summarize the recent literature on piRNA biogenesis and function with an emphasis on work in Drosophila, where genetics and biochemistry have met very successfully...