Research Activities

Research Activities

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Principal Investigators

Dept. of Life Science Frontiers 
Hirohide Saito (Professor)


Kawasaki S, Ono H, Hirosawa M, Kuwabara T, Sumi S, Lee S, Woltjen K, Saito H

Programmable mammalian translational modulators by CRISPR-associated proteins Nature Communications, 2023 Apr 19;14(1):2243.

Ohno H*, Akamine S, Mochizuki M, Hayashi K, Akichika S, Suzuki T, and Saito H*.

Versatile strategy using vaccinia virus-capping enzyme to synthesize functional 5' cap-modified mRNAs Nucleic Acids Res., 2023 Feb 3 gkad019

Kameda S, Ohno H, and Saito H*.

Synthetic circular RNA switches and circuits that control protein expression in mammalian cells Nucleic Acids Res., 2023 Jan 16;51(4):e24

Miyashita E, Komatsu KR, Saito H*.

Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST Methods Mol Biol., 2022 Jul 8;2509:279-290

Saito H*.

The RNA world "hypothesis" Nat Rev Mol Cell Biol., 2022 July 6;23(9):582

Nakanishi H*, Yoshii T, Tsukiji S, Saito H*.

A protocol to construct RNA-protein devices for photochemical translational regulation of synthetic mRNAs in mammalian cells. STAR Protocols, 2022 Jun 10;3(2):101451. doi: 10.1016/j.xpro.2022.101451.

Tsujisaka Y, Hatani T, Okubo C, Ito R, Kimura A, Narita M, Chonabayashi K, Funakoshi S, Lucena-Cacace A, Toyoda T, Osafune K, Kimura T, Saito H*, Yoshida Y*.

Purification of human iPSC-derived cells at large scale using microRNA switch and magnetic-activated cell sorting. Stem Cell Reports, 2022 May 30:S2213-6711(22)00255-7.

Fujita Y, Kameda T, Singh CR, Pepper W, Cecil A, Hilgers M, Thornton M, Asano I, Moravek C, Togashi Y*, Saito H*, Asano K*.

Translational recoding by chemical modification of non-AUG start codon ribonucleotide bases. Sci Adv., 2022 Apr 8;8(14): eabm8501.

Pardi ML, Wu J, Kawasaki S, Saito H*.

Synthetic RNA-based post-transcriptional expression control methods and genetic circuits. Advanced Drug Delivery Reviews, 2022 Mar 184:114196. (Review)

Nakanishi H, Saito H, Itaka K*.

Versatile Design of Intracellular Protein-Responsive Translational Regulation System for Synthetic mRNA. ACS Synth Biol., 2022 Mar 18;11(3):1077-1085.

Fujita Y*, Hirosawa M, Hayashi K, Hatani T, Yoshida Y, Yamamoto T, Saito H*.

A versatile and robust cell purification system with an RNA-only circuit composed of microRNA-responsive ON and OFF switches. Sci Adv., 2022 Jan 7;8(1):eabj1793.

Nakanishi H, Saito H*.

Purification of Specific Cell Populations Differentiated from Stem Cells Using MicroRNA-Responsive Synthetic Messenger RNAs. Methods Mol Biol., 2021 2312:73-86.

Minegishi K, Rothé B, Komatsu KR, Ono H, Ikawa Y, Nishimura H, Katoh TA, Kajikawa E, Sai X, Miyashita E, Takaoka K, Bando K, Kiyonari H, Yamamoto T, Saito H*, Constam DB*, Hamada H*.

Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex. Nat Commun., 2021 Jul 1;12(1):4071.

Nakanishi H, Yoshii T, Kawasaki S, Hayashi K, Tsutsui K, Oki C, Tsukiji S, Saito H*.

Light-controllable RNA-protein devices for translational regulation of synthetic mRNAs in mammalian cells. Cell Chem Biol, 2021 Jan 20:S2451-9456(21)00002-7. doi: 10.1016/j.chembiol.2021.01.002.

Komatsu K. R., Taya T., Matsumoto S., Miyashita E., Kashida S.*, & Saito H*.

RNA structure-wide discovery of functional interactions with multiplexed RNA motif library Nature Communications, 2020 Dec 8;11(1):6275. doi: 10.1038/s41467-020-19699-5

Ohno H, Akamine S, Saito H*.

Synthetic mRNA-Based Systems in Mammalian Cells. Adv Biosyst. 2020 May;4(5):e1900247. (Review)

Nakanishi H, Saito H*.

Caliciviral protein-based artificial translational activator for mammalian gene circuits with RNA-only delivery. Nat Commun. 2020 Mar 10;11(1):1297.

Parr CJC, Wada S, Kotake K, Kameda S, Matsuura S, Sakashita S, Park S, Sugiyama H, Kuang Y*,
Saito H*.

N1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells. Nucleic Acids Res. 2020 Apr 6;48(6):e35.

Kawasaki S, Ono H, Hirosawa M, Saito H*.

RNA and protein-based nanodevices for mammalian post-transcriptional circuits. Curr Opin Biotechnol. 2020 Jun;63:99-110. (Review)

Ono H, Kawasaki S, Saito H*.

Orthogonal Protein-Responsive mRNA Switches for Mammalian Synthetic Biology. ACS Synth Biol. 2020 Jan 17;9(1):169-174. (Selected as a front cover)

Endo K, Hayashi K, Saito H*.

Numerical operations in living cells by programmable RNA devices Science Advances 2019 Aug 21;5(8):eaax0835. doi: 10.1126/sciadv.aax0835.

Sunohara T, Morizane A, Matsuura S, Miyamoto S, Saito H, Takahashi J

MicroRNA-Based Separation of Cortico-Fugal Projection Neuron-Like Cells Derived From Embryonic Stem Cells. Front Neurosci. 2019 Oct 23;13:1141. doi: 10.3389/fnins.2019.01141. eCollection 2019.

Hirosawa M, Fujita Y, Saito H*.

Cell-Type-Specific CRISPR Activation with MicroRNA-Responsive AcrllA4 Switch ACS Synthetic Biology 2019 8(7): 1575-1582

Saito H*, Yokobayashi Y*

Editorial overview: Mammalian synthetic biology: from devices to multicellular systems. Curr Opin Chem Biol. 2019 Oct;52:A1-A2. doi: 10.1016/j.cbpa.2019.07.010

Nakanishi H and Saito H*.

Mammalian gene circuits with biomolecule-responsive RNA devices. Curr Opin Chem Biol. 2019 Oct;52:16-22. doi: 10.1016/j.cbpa.2019.04.013 (Review)

Kashida S, Wang DO, Saito H, Gueroui Z.

Nanoparticle-based local translation reveals mRNA as a translation-coupled scaffold with anchoring function. Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13346-13351. doi: 10.1073/pnas.1900310116

Ohno H, Akamine S, and Saito H*.

RNA nanostructures and scaffolds for biotechnology applications. Curr Opin Biotechnol. 2019 Aug;58:53-61. doi: 10.1016/j.copbio.2018.11.006 (Review)

Matsuura S, Ono H, Kuang Y, Kawasaki S, Fujita Y, Saito H*.

Synthetic RNA-based logic computation in mammalian cells Nature Communications. 9(1):4847, doi: 10.1038/s41467-018-07181-2. (2018)

Zhitnyuk Y, Gee P, Lung MSY, Sasakawa N, Xu H, Saito H, Hotta A

Efficient mRNA delivery system utilizing chimeric VSVG-L7Ae virus-like particles. Biochem Biophys Res Commun. 2018 Nov 10;505(4):1097-1102. doi: 10.1016/j.bbrc.2018.09.113.

Endo Kei, and Hirohide Saito*.

mRNA Engineering for the Control of Mammalian Cells in Medical Applications. Applied RNA Bioscience. Springer. Singapore, 2018. 95-114.

Kashida Shunnichi, and Hirohide Saito.

Design of Ligand‐Controlled Genetic Switches Based on RNA Interference. Synthetic Biology: Parts, Devices and Applications. 8 (2018).

Yamada GT, Hori Y, Suzuki S, Kawasaki S, Hiroi N, Saito H, Funahashi A.

Mathematical modeling identifies the conditions required for RNA- based oscillator SICE 2018 Annual Conference, Position Paper (2018)

Shibata T, Fujita Y, Ohno H, Suzuki Y, Hayashi K, Komatsu K.R., Kawasaki S, Hidaka K, Yonehara S, Sugiyama H, Endo M, Saito H*.

Protein-Driven RNA Nanostructured Devices That Function in Vitro and Control Mammalian Cell Fate. Nature Communications. 2017 Sep 14;8(1):540. doi: 10.1038/s41467-017-00459-x.

Hirosawa M, Fujita Y, Parr C.J.C., Hayashi K, Kashida S, Hotta A, Woltjen K, Saito H*.

Cell-Type-Specific Genome Editing with a microRNA-Responsive CRISPR-Cas9 Switch. Nucleic Acids Research. 2017 Jul 27;45(13):e118. doi: 10.1093/nar/gkx309.

Kawasaki S, Fujita Y, Nagaike T, Tomita K, Saito H*.

Synthetic mRNA Devices That Detect Endogenous Proteins and Distinguish Mammalian Cells. Nucleic Acids Research. 2017 Jul 7;45(12):e117. doi: 10.1093/nar/gkx298.

Nakanishi H, Miki K, Komatsu KR, Umeda M, Mochizuki M, Inagaki A, Yoshida Y, Saito H*.

Monitoring and visualizing microRNA dynamics during live cell differentiation using microRNA-responsive non-viral reporter vectors. Biomaterials. 2017 Jun;128:121-135. doi: 10.1016/j.biomaterials.2017.02.033. PMID:28325684

Parr Callum, Shinya Yamanaka, Hirohide Saito*.

An update on stem cell biology and engineering for brain development. Molecular Psychiatry. volume 22, pages 808-819 (2017), doi:10.1038/mp.2017.66. (Review)

Tang L, Morris J, Wan J, Moore C, Fujita Y, Gillaspie S, Aube E, Nanda J, Marques M, Jangal M, Anderson A, Cox C, Hiraishi H, Dong L, Saito H, Singh CR, Witcher M, Topisirovic I, Qian SB, Asano K.

Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide. Nucleic Acids Research. 2017 Nov 16;45(20):11941-11953. doi: 10.1093/nar/gkx808.

Kuang Y, Miki K, Parr CJC, Hayashi K, Takei I, Li J, Iwasaki M, Nakagawa M, Yoshida Y, Saito H*.

Efficient, Selective Removal of Human Pluripotent Stem Cells via Ecto-Alkaline Phosphatase-Mediated Aggregation of Synthetic Peptides. Cell Chem Biol. 2017 Jun 22;24(6):685-694.e4. doi: 10.1016/j.chembiol.2017.04.010.

Karagiannis P, Fujita Y, Saito H*.

RNA-based gene circuits for cell regulation. Proc Jpn Acad Ser B Phys Biol Sci. 2016;92(9):412-422. PMID: 27840389

Parr CJ, Katayama S, Miki K, Kuang Y, Yoshida Y, Morizane A, Takahashi J, Yamanaka S, Saito H*.

MicroRNA-302 switch to identify and eliminate undifferentiated human pluripotent stem cells. Scientific Reports. 2016 Sep 9;6:32532. doi: 10.1038/srep32532.PMID: 27608814

Ohno H, Saito H*.

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology. Prog Mol Biol Transl Sci. 2016;139:165-85. doi: 10.1016/bs.pmbts.2015.12.004. Review. PMID: 26970194

Endo K, Hayashi K, Saito H*.

High-resolution Identification and Separation of Living Cell Types by Multiple microRNA-responsive Synthetic mRNAs Scientific Reports. 2016 Feb 23;6:21991. PMID: 26902536

Liliana Wroblewska, Tasuku Kitada, Kei Endo, Velia Siciliano, Breanna Stillo, Hirohide Saito*, and Ron Weiss*.

Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery. Nature Biotechnology, 2015, 33(8):839-41. doi: 10.1038/nbt.3301. PMID: 26237515

Miki K, Endo K, Takahashi S, Funakoshi S, Takei I, Katayama S, Toyoda T, Kotaka M, Takaki T, Umeda M, Okubo C, Nishikawa M, Oishi A, Narita M, Miyashita I, Asano K, Hayashi K, Osafune K, Yamanaka S, Saito H*, Yoshida Y*.

Efficient Detection and Purification of Cell Populations Using Synthetic MicroRNA Switches. Cell Stem Cell. 2015 May 20. pii: S1934-5909(15)00163-0. doi: 10.1016/j.stem.2015.04.005. [Epub ahead of print] PMID: 26004781

Shibata T, Suzuki Y, Sugiyama H, Endo M, Saito H*.

Folding RNA-Protein Complex into Designed Nanostructures. Methods Mol Biol. 2015;1316:169-79. doi: 10.1007/978-1-4939-2730-2_14. PMID: 25967061

Ohno H, Osada E, Saito H*.

Design, Assembly, and Evaluation of RNA-Protein Nanostructures. Methods Mol Biol. 2015;1297:197-211. doi: 10.1007/978-1-4939-2562-9_14. PMID: 25896005

Morita M, Onoe H, Yanagisawa M, Ito H, Ichikawa M, Fujiwara K, Saito H, Takinoue M.

Droplet-Shooting and Size-Filtration (DSSF) Method for Synthesis of Cell-Sized Liposomes with Controlled Lipid Compositions. Chembiochem. 2015 Sep 21;16(14):2029-35. doi: 10.1002/cbic.201500354

Saito H*.

Synthetic RNA technologies to control functions of mammalian cells. Yakugaku Zasshi. 2015;135(3):399-404. doi: 10.1248/yakushi.14-00240-4. Japanese. PMID: 25759049

Kei Endo, Parr Callum, Hirohide Saito*.

Expanding the synthetic ribonucleoprotein world in cells. Nature Methods. News and Views, 11:1105-06 (2014)

Eriko Osada, Yuki Suzuki, Kumi Hidaka, Hirohisa Ohno, Hiroshi Sugiyama, Masayuki Endo, Hirohide Saito*.

Engineering RNA-Protein Complexes with Different Shapes for Imaging and Therapeutic Applications. ACS Nano. 2014 Aug 5. [Epub ahead of print] PMID: 25058166.

Masami Hagiya*, Akihiko Konagaya, Satoshi Kobayashi, Hirohide Saito, Satoshi Murata.

Molecular robots with sensors and intelligence. Acc Chem Res. 2014 Jun 17;47(6):1681-90. doi:10.1021/ar400318d. Epub 2014 Jun 6. PMID: 24905779.

Shunnichi Kashida, Hirohide Saito*.

A three-dimensional design strategy for a protein-responsive shRNA switch. Methods Mol Biol. 2014;1111:269-86. doi: 10.1007/978-1-62703-755-6_20.PMID: 24549627

Kei Endo, Hirohide Saito*.

Engineering protein-responsive mRNA switch in mammalian cells. Methods Mol Biol. 2014;1111:183-96. doi: 10.1007/978-1-62703-755-6_13.PMID: 24549620

Kei Endo, Karin Hayashi, Tan Inoue*, and Hirohide Saito*.

A versatile cis-acting inverter module for synthetic translational switches. Nature Communications, 4:2393, DOI: 10.1038/ncomms3393 (2013)

Kei Endo, James A. Stapleton, Karin Hayashi, Hirohide Saito*, and Tan Inoue*.

Quantitative and stimulataneous translational control of distinct mammalian mRNAs. Nucleic Acid Res., 41(13):e135 (2013)

Tomoaki Hara, Hirohide Saito*, and Tan Inoue*.

Directed evolution of a synthetic RNA-protein module to create a new translational switch. Chemical Communications (Camb). 2013 Feb 4. [Epub ahead of print], (Selected as the front cover image)

Hirohisa Ohno, Eriko Osada, Tan Inoue, and Hirohide Saito*.

Synthetic RNA-Protein Nanostructures and Their Potential Applications. Review: RNA Nanotechnology and Therapeutics, (ed. Guo, P., CRC press), in press (2013)

Shunnichi Kashida, Tan Inoue*, and Hirohide Saito*.

Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation. Nucleic Acids Research, 40(18):9369-9378 (Selected as Featured Articles represent the top 5% of papers) (2012)

James A. Stapleton, Kei Endo, Yoshihiko Fujita, Karin Hayashi, Masahiro Takinoue, Hirohide Saito*, and Tan Inoue*.

Feedback Control of Protein Expression in Mammalian Cells by Tunable Synthetic Translational Inhibition. ACS Synthetic Biology, 1(3): 83-88 (2012)

Hirohide Saito*, Yoshihiko Fujita, Shunnichi Kashida, Karin Hayashi, and *Tan Inoue.

Synthetic human cell fate regulation by protein-driven RNA swiches Nature Communications, 2, 160 (2011)

Hirohisa Ohno, Tetsuhiro Kobayashi, Rinko Kabata, Kei Endo, Takuma Iwasa, Shige Yoshimura, Kunio Takeyasu, Tan Inoue*, and Hirohide Saito*.

Synthetic RNA-protein complex shaped like an equilateral triangle. Nature Nanotechnology, 6: 116-120 (2011)

Rei Ohmori, Hirohide Saito, Yoshiya Ikawa, Yoshihiko Fujita, Tan Inoue.

Self-Replication Reactions Dependent on Tertiary Interaction Motifs in an RNA Ligase Ribozyme. J Mol Evol., 73:221-9 (2011)

Sergii Rudiuk, Hirohide Saito, Tomoaki Hara, Tan Inoue, Kenichi Yoshikawa, Damien Baigl.

Light-Regulated mRNA Condensation by a Photosensitive Surfactant Works as a Series Photoswitch of Translation Activity in the Presence of Small RNAs. Biomacromolecules, 12(11):3945-51 (2011)

Hirohide Saito*, Tetsuhiro Kobayashi, Tomoaki Hara, Yoshihiko Fujita, Karin Hayashi, Rie Furushima, and Tan Inoue*.

Synthetic Translational Regulation by an L7Ae-Kink-turn RNP Switch. Nature Chemical Biology, 6: 71-78 (2010)

Shigeyoshi Matsumura, Rei Ohmori, Hirohide Saito, Yoshiya Ikawa, Tan Inoue.

Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction. loop-receptor interaction FEBS Letters, 583 (17): 2819-26 (2009)

André Estévez-Torres, Cécile Crozatier, Antoine Diguet, Tomoaki Hara, Hirohide Saito, Kenichi Yoshikawa, Damien Baigl.

Sequence-independent and reversible photocontrol of transcription/expression systems using a photosensitive nucleic acid binder. PNAS, 106 (30): 12219-23 (2009)

Hirohide Saito*, Yusho Kato, MAel Le Berre, Ayako Yamada, Tan Inoue, Kenichi Yoshikawa, and Damien Baigl.

Time-resolved tracking of a minimum gene expression system reconstituted in giant liposomes. ChemBioChem. 10 (10): 1640-3 (2009)

Hirohide Saito* and Tan Inoue*.

Synthetic Biology with RNA motifs. Int. J. Biochem. Cell Biol., 41(2):398-404 (2009).

Tomoaki Shiohara, *Hirohide Saito and Tan Inoue.

A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions. Nucleic Acids Res. 37(3):e23 (2009).

Hirohide Saito, Tamiko Minamisawa, Takao Yamori, Kiyotaka Shiba.

Motif-programmed artificial protein induces apoptosis in several cancer cells by disrupting mitochondria. Cancer Science, 99 (2): 398-406. (2008)

Hirohide Saito*, Shunichi Kashida, Tan Inoue, Kiyotaka Shiba.

The role of peptide motifs in the evolution of a protein network. Nucleic Acid. Res., 35 (19): 6357-6366. (2007)

Hirohide Saito*, Tan Inoue.

RNA and RNP as new molecular parts in synthetic biology. J. Biotechnol., 132 (1): 1-7. (2007)

Hirohide Saito, Tamiko Minamisawa, Kiyotaka Shiba.

Motif programming: a microgene-based method for creating synthetic proteins containing multiple functional motifs. Nucleic Acid. Res., 35(6):e38 (2007)

Hirohide Saito, Takako Honma,, Tamiko Minamisawa, Kanami Yamazaki, Tetsuo Noda, Takao Yamori, Kiyotaka Shiba.

Synthesis of functional proteins by mixing peptide motifs. Chemistry & Biology 11(6): 765-773 (2004)

Krishna Ramaswamy, Hirohide Saito, Hiroshi Murakami, Kiyotaka Shiba, Hiroaki Suga.

Designer Ribozymes: Programming the tRNA Specificity into Flexizyme. J. Am. Chem. Soc., 126 (37) 11454 –11455 (2004)

Hiroshi Murakami, Hirohide Saito, Hiroaki Suga.

A versatile tRNA aminoacylation catalyst based on RNA. Chemistry & Biology 10(7): 655-662 (2003)

Hirohide Saito, Hiroaki Suga.

Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme. Nucleic Acid. Res., 30 (23): 5151-5159 (2002)

Hirohide Saito, Hiroaki Suga.

A ribozyme exclusively aminoacylates the 3´- hydroxyl group of the tRNA terminal adenosine. J. Am. Chem. Soc., 123 (29): 7178-7179 (2001)

Hirohide Saito, Kimitsuna Watanabe, Hiroaki Suga.

Concurrent molecular recognition of both the amino acid and tRNA by a ribozyme. RNA, 7 (12): 1867-1878 (2001)

Hirohide Saito, Dimitrios Kourouklis, Hiroaki Suga.

An in vitro evolved precursor tRNA with aminoacylation activity. The EMBO Journal, 20 (7): 1797-1806 (2001)
Authored Book Chapters

Hiroaki Suga, Hirohide Saito, Hodgson David

RNA–catalyzed tRNA aminoacylation The Aminoacyl–tRNA Synthetases, Landes Bioscience, 364–373 (2004)
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