Publications

Research Papers & Reviews

 * Corresponding author

1. Ishibashi K, Shichino Y, Han P, Wakabayashi K, Mito M, Inada T, Kimura S, Iwasaki S, *Mishima Y. (2024) Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish. PLOS Biology https://doi.org/10.1371/journal.pbio.3002887

2. Zhao X, Ma D, Ishiguro K, Saito H, Akichika S, Matsuzawa I, Mito M, Irie T, Ishibashi K, Wakabayashi K, Sakaguchi Y, Yokoyama T, Mishima Y, Shirouzu M, Iwasaki S, *Suzuki T, *Suzuki T. (2023) Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell doi: https://doi.org/10.1016/j.cell.2023.10.026

3. Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, *Mishima Y. (2023) Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA 29: 1910-1927. 2023 RNA Journal Prize

4. Uchiyama J, Roy R, Wang DO, Morikawa K, Kawahara Y, Iwasaki M, Yoshino C, Mishima Y, *Ishihama Y, *Imami K. (2022) pSNAP: Proteome-wide analysis of elongating nascent polypeptide chains. iScience. doi: https://doi.org/10.1016/j.isci.2022.104516

5. *Mishima Y, Han P, Ishibashi K, Kimura S, Iwasaki S. (2022) Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control. The EMBO Journal e109256

6. *Mishima Y and Inoue K. (2021) Tethered function assay to study RNA regulatory proteins in zebrafish embryos. Methods in Molecular Biology 2218:347-354.

7. Mito M, Mishima Y, *Iwasaki S. (2020) Protocol for Disome Profiling to Survey Ribosome Collision in Humans and Zebrafish. STAR Protocols 1:100168 

8. Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Tanaka M, Mishima Y, Inada T, *Iwasaki S. (2020) Genome-wide survey of ribosome collision. Cell Reports 31(5): 107610. 

9. Fujino Y, Yamada K, Sugaya C, Ooka Y, Ovara H, Ban H, Akama K, Otosaka S, Kinoshita H, Yamasu K, Mishima Y and *Kawamura A. (2018) Deadenylation by the CCR4-NOT complex contributes to the turnover of hairy-related mRNAs in the zebrafish segmentation clock. FEBS Letters  592(20):3388-3398. 

10. *Mishima Y (2018) PAINTing translation. Nature Chemical Biology 14(9):832–833. News & View

11. *Mishima Y and Tomari Y. (2017) Pervasive yet nonuniform contributions of Dcp2 and Cnot7 to maternal mRNA clearance in zebrafish. Genes to Cells 22(7):670-678

12. *Mishima Y and Tomari Y. (2016) Codon usage and 3' UTR length determine maternal mRNA stability in zebrafish. Molecular Cell 61(6):874-885. 

13. Makino S, *Mishima Y, Inoue K, *Inada T. (2015) Roles of mRNA-fate modulators Dhh1 and Pat1 in TNRC6-dependent gene silencing recapitulated in yeast. The Journal of Biological Chemistry 290(13):8331-47.

14. Fukao A, Mishima Y, Takizawa N, Oka S, Imataka H, Pelletier J, Sonenberg N, Thoma C, *Fujiwara T. (2014) microRNAs trigger dissociation of eIF4AI and II from target mRNAs in humans. Molecular Cell 56(1):79-89.

15. Hirose T, Mishima Y, *Tomari Y. (2014) Elements and machinery of non-coding RNAs: toward their taxonomy. EMBO Reports 15(5):489-507 Review

16. Stahlhut C, Lu J, Suarez C, *Mishima Y, *Giraldez AJ. (2012) miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression. Development 139(23):4356-65 

17. *Mishima Y, Fukao A, Kishimoto T, Sakamoto H, Fujiwara T, *Inoue K. (2012) Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish. Proceedings of the National Academy of Sciences U.S.A. 109 (4):1104-9

18. *Mishima Y. (2012) Widespread roles of microRNAs during zebrafish development and beyond. Development Growth and Differentiation 54(1):55-65. Review

19. Cifuentes D, Xue H, Taylor D.W, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson N, Wolfe S, *Giraldez AJ. (2010) A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 328(5986): 1694-8

20. Takeda Y, Mishima Y, Fujiwara T, Sakamoto H, *Inoue K. (2009) DAZL relieves miRNA-mediated repression of germline mRNAs by controlling poly(A) tail length in zebrafish. PLoS ONE 4: e7513

21. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, *Giraldez AJ. (2009) Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes & Development 23(5):619-32. 

22. Mishima Y, Stahlhut C, *Giraldez AJ. (2007) miR-1-2 gets to the heart of the matter. Cell 129(2):247-9. Review

23. Mishima Y, Giraldez AJ, Takeda Y, Fujiwara T, Sakamoto H, *Schier A.F, *Inoue K. (2006) Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR-430. Current Biology 16(21):2135-42. 

24. *Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright A.J, *Schier AF. (2006) Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312(5770):75-9

25. Yamakita S, Mishima Y, *Ikenishi K. (2004) A novel gene the protein product of which is mainly expressed in germline cells and in the dorsal structures of Xenopus. Development Genes and Evolution 214(2):89-95.