ZFIN ID: ZDB-LAB-121016-1
Laboratory of RNA regulation
PI/Director: Mishima, Yuichiro
Contact Person: Mishima, Yuichiro
Email: mishima@cc.kyoto-su.ac.jp
URL: http://www.mishima-lab.com
Address: Faculty of Lifesciences Kyoto Sangyo University Bldg.15, Room 15B15 Kamigamo Motoyama, Kita-ku Kyoto 603-8555
Country: Japan
Phone:
Fax:
Line Designation: ksu


GENOMIC FEATURES ORIGINATING FROM THIS LAB
Show all 3 genomic features


STATEMENT OF RESEARCH INTERESTS
Translation of mRNA by the ribosome converts an array of codons into protein and therefore lies at the core of the central dogma. We discovered from zebrafish embryos that mRNA stability just after fertilization is determined by codon composition (Mishima et al., Mol Cell. 2016). This discovery indicates that translating ribosome senses the unknown difference of codons and modulates mRNA stability. However, the molecular mechanism underlying codon-mediated mRNA decay by the ribosome remains largely unknown. We aim to elucidate the molecular mechanism of codon-mediated control of mRNA stability by combining our knowledge and unique approaches established in zebrafish embryos.


LAB MEMBERS


ZEBRAFISH PUBLICATIONS OF LAB MEMBERS
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. 186(25):5517-5535.e24
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 (New York, N.Y.). 29(12):1910-1927
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. 41(5):e109256
Mishima, Y., Inoue, K. (2021) Tethered Function Assay to Study RNA-Regulatory Proteins in Zebrafish Embryos. Methods in molecular biology (Clifton, N.J.). 2218:347-354
Mito, M., Mishima, Y., Iwasaki, S. (2020) Protocol for Disome Profiling to Survey Ribosome Collision in Humans and Zebrafish. STAR protocols. 1:100168
Han, P., Shichino, Y., Schneider-Poetsch, T., Mito, M., Hashimoto, S., Udagawa, T., Kohno, K., Yoshida, M., Mishima, Y., Inada, T., Iwasaki, S. (2020) Genome-wide Survey of Ribosome Collision. Cell Reports. 31:107610
Fujino, Y., Yamada, K., Sugaya, C., Ooka, Y., Ovara, H., Ban, H., Akama, K., Otosaka, S., Kinoshita, H., Yamasu, K., Mishima, Y., 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
Mishima, Y., Tomari, Y. (2017) Pervasive yet nonuniform contributions of Dcp2 and Cnot7 to maternal mRNA clearance in zebrafish. Genes to cells : devoted to molecular & cellular mechanisms. 22(7):670-678
Mishima, Y., Tomari, Y. (2016) Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish. Molecular Cell. 61:874-885
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
Stahlhut, C., Suárez, Y., Lu, J., Mishima, Y., and Giraldez, A.J. (2012) miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish. Development (Cambridge, England). 139(23):4356-4365
Mishima, Y., Fukao, A., Kishimoto, T., Sakamoto, H., Fujiwara, T., and Inoue, K. (2012) Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 109(4):1104-1109
Mishima, Y. (2012) Widespread roles of microRNAs during zebrafish development and beyond. Development, growth & differentiation. 54(1):55-65
Cifuentes, D., Xue, H., Taylor, D.W., Patnode, H., Mishima, Y., Cheloufim, S., Ma, E., Mane, S., Hannon, G.J., Lawson, N.D., Wolfe, S.A., and Giraldez, A.J. (2010) A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science (New York, N.Y.). 328(5986):1694-1698
Takeda, Y., Mishima, Y., Fujiwara, T., Sakamoto, H., and Inoue, K. (2009) DAZL relieves miRNA-mediated repression of germline mRNAs by controlling poly(A) tail length in zebrafish. PLoS One. 4(10):e7513
Mishima, Y., Abreu-Goodger, C., Staton, A.A., Stahlhut, C., Shou, C., Cheng, C., Gerstein, M., Enright, A.J., and Giraldez, A.J. (2009) Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes & Development. 23(5):619-632
Mishima, Y., Giraldez, A.J., Takeda, Y., Fujiwara, T., Sakamoto, H., Schier, A.F., and Inoue, K. (2006) Differential Regulation of Germline mRNAs in Soma and Germ Cells by Zebrafish miR-430. Current biology : CB. 16(21):2135-2142
Giraldez, A.J., Mishima, Y., Rihel, J., Grocock, R.J., Van Dongen, S., Inoue, K., Enright, A.J., and Schier, A.F. (2006) Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs. Science (New York, N.Y.). 312(5770):75-79
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