Publications

Selected publications

 

  1. Tetsuya Yamamoto, Tomohiro Yamazaki, Kensuke Ninomiya, Shinichi Nakagawa, Tetsuro Hirose.Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA.Journal of Molecular Biology.437(9):169016(2025）
  2. Manisha Yadav, Rachel J Harding, Tiantian Li, Xin Xu, Terence Gall-Duncan, Mahreen Khan, Costanza Ferrari Bardile, Glen L Sequiera, Shili Duan, Renu Chandrasekaran, Anni Pan, Jiachuan Bu, Tomohiro Yamazaki, Tetsuro Hirose, Panagiotis Prinos, Lynette Tippett, Clinton Turner, Maurice A Curtis, Richard L M Faull, Mahmoud A Pouladi, Christopher E Pearson, Housheng Hansen He, Cheryl H Arrowsmith.Huntingtin is an RNA binding protein and participates in NEAT1-mediated paraspeckles.Science Advances.Jul 19;10(29):eado5264.（2024）
  3. Ichiro Taniguchi , Tetsuro Hirose , Mutsuhito Ohno.The RNA helicase DDX39 contributes to the nuclear export of spliceosomal U snRNA by loading of PHAX onto RNA.Nucleic Acids Research.52(17):10668-10682 (2024）
  4. Takakuwa H, Yamazaki T, Souquere S, Adachi S, Yoshino H, Fujiwara N, Yamamoto T, Natsume T, Nakagawa S, Pierron G, Hirose T. Shell protein composition specified by NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles. Nat. Cell Biol.  25:1664–1675 (2023)
  5. Ninomiya K, Yamazaki T, Hirose T. Satellite RNAs: emerging players in subnuclear architecture and gene regulation. EMBO J. 42:e114331 (2023)
  6. Hirose T, Ninomiya K, Nakagawa S, Yamazaki T. A guide to membraneless organelles and their various roles in gene regulation. Nat Rev Mol Cell Biol. 24(4):288-304. (2023).
  7. Ninomiya K, Iwakiri J, Aly MK, Sakaguchi Y, Adachi S, Natsume T, Terai G, Asai K, Suzuki T, Hirose T. m6A-modification of HSATIII lncRNAs regulates temperature-dependent splicing. EMBO J. 40(15):e107976 (2021).
  8. Yamazaki T, Yamamoto T, Yoshino H, Souquere S, Nakagawa S, Pierron G, Hirose T. Paraspeckles are constructed as block copolymer micelles. EMBO J. 40(12): e107270 (2021).
  9. Yamazaki T, Nakagawa S, Hirose T. Architectural RNAs for Membraneless Nuclear Body Formation. Cold Spring Harb Symp Quant Biol. 039404 (2020).
  10. Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J. 39: e102729 (2020).
  11. Yamazaki T, Souquere S, Chujo T, Kobelke S, Chong YS, Fox AH, Bond CS, Nakagawa S, Pierron G, Hirose T. Functional domains of NEAT1 architectural lncRNA induce paraspeckle assembly through phase separation. Mol Cell. 70: 1038-1053 (2018).
  12. Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S, Hirose T. Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. EMBO J. 36: 1447-1462 (2017).
  13. Mannen T, Yamashita S, Tomita K, Goshima N, Hirose T. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL. J Cell Biol. 214: 45-59 (2016).
  14. Hennig S, Kong G, Mannen T, Sadowska A, Kobelke S, Blythe A, Knott GJ, Iyer KS, Ho D, Newcombe EA, Hosoki K, Goshima N, Kawaguchi T, Hatters D, Trinkle-Mulcahy L, Hirose T, Bond CS, Fox AH. Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. J Cell Biol. 210: 529-539 (2015)
  15. Kawaguchi T, Tanigawa A, Naganuma T, Ohkawa Y, Souquere S, Pierron G, Hirose T. SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies. Proc Natl Acad Sci USA. 112: 4304-4309 (2015).
  16. Hirose T, Virnicchi G, Tanigawa A, Naganuma T, Li R, Kimura H, Yokoi T, Nakagawa S, Bénard M, Fox A, Pierron G NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol. Biol. Cell. 25: 169-183 (2014).
  17. Naganuma T, Nakagawa S, Tanigawa A, Sasaki YF, Goshima N, Hirose T. Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J. 31: 4020-4034 (2012).
  18. Sasaki, Y.T., Ideue, T., Sano, M., Mitsuyama, T., Hirose T. MENɛ/β noncoding RNAs are structural integrator of the nuclear body, paraspeckle. Proc Natl Acad Sci USA. 106: 2525-2530 (2009).
  19. Ideue, T., Sasaki, Y.T., Hagiwara, M., Hirose T. Introns play an essential role in splicing-dependent formation of the exon junction complex. Genes & Dev. 21: 1993-1998 (2007).
  20. Hirose T, Ideue T, Nagai M, Hagiwara M, Shu M-D, Steitz JA A spliceosomal intron binding protein, IBP160, links position-dependent assembly of intron-encoded box C/D snoRNP to pre-mRNA splicing. Mol Cell. 23: 673-684. (2006)
  21. Hirose T, Shu M-D, Steitz JA Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay. Proc Natl Acad Sci USA. 101: 17976-17981 (2004).
  22. Hirose T, Shu M-D., Steitz JA Splicing-dependent and independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell. 12: 113-123 (2003)
  23. Hirose T, Steitz JA Positions within host intron is critical for efficient processing of box C/D snoRNAs in mammalian cell. Proc Natl Acad Sci USA. 98: 12914-12919 (2001)
  24. Hirose T, Sugiura M Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system. EMBO J. 20: 1144-1152 (2001).
  25. Hirose T, Sugiura M Both RNA editing and RNA cleavage are required for translation of tobacco chloroplast ndhD mRNA: a possible regulatory mechanism for the expression of a chloroplast operon consisting of functionally unrelated gene. EMBO J. 16: 6804-6811 (1997)
  26. Hirose T, Sugiura M Cis-acting elements and trans-acting factor(s) for accurate translation of tobacco psbA mRNA in chloroplasts; development of a chloroplast in vitro translation system. EMBO J. 15: 1687-1695 (1996).

Complete publication list

Complete publication list