Publications

2017

  • Wang Q, Ui-Tei K (2017)
    Computational prediction of CRISPR/Cas9 target sites reveals potential off-target risks in human and mouse.
    "Genome Editing in Animals: Methods and Protocols" (Ed.Hatada I) Methods Mol. Biol.), in press
  • Galipon J, Ishii R, Suzuki Y, Tomita M, Ui-Tei K (2017)
    Differential binding of three major human ADAR isoforms to coding and long non-coding transcripts.
    Genes , 8, 68. [PDF]
    doi:10.3390/genes8020068
  • Ui-Tei K, Maruyama S, Nakano Y. (2017)
    Enhancement of single guide RNA transcription for efficient CRISPR/Cas-based genomic engineering.
    Genome , in press 

2016

  • Kato M, Huang Y-Y, Matsuo M, Takashina Y, Sasaki K, Horai Y, Juni A, Kamijo S, Saigo K, Ui-Tei K, Tei H. (2016)
    RNAi-Mediated Knockdown of Mouse Melanocortin-4 Receptor in vitro and in vivo, using an siRNA expression Construct Based on the mir-187 Precursor.
    Experimental Animals, 66, 41-50. [PDF]
    doi: 10.1538/expanim.16-0065.
  • Ui-Tei K. (2016)
    Is the efficiency of RNA silencing evolutionarily regulated ?
    Int. J. Mol. Sci. 17, 719. [PDF]
    doi: 10.3390/ijms17050719.

2015

  • Kamola PJ, Nakano Y, Takahashi T, Wilson PA, Ui-Tei K. (2015)
    The siRNA Non-Seed Region and its Target Sequences are Auxiliary Determinants of Off-Target Effects.
    PLoS Comput. Biol. 11, e1004656.[PDF]
    doi: 10.1371/journal.pcbi.1004656.
  • Nishi K, Takahashi T, Suzawa M, Miyakawa T, Nagasawa T, Ming Y, Tanokura M, Ui-Tei K, (2015)
    Control of the localization and function of a miRNA silencing component TNRC6A by Argonaute protein.
    Nucleic Acids Res. 43, 9856-9873. [PDF]
    doi: 10.1093/nar/gkv1026.
  • Ishikawa T, Takizawa T, Iwaki J, Mishima T, Ui-Tei K, Takeshita T, Matsubara S, Takizawa T. (2015)
    Fc gamma receptor IIb participates in maternal IgG trafficking of human placental endothelial cells.
    Int. J. Mol. Med. 35,1273-1789. [PDF]
    doi: 10.3892/ijmm.2015.2141.
  • Naito Y, Hino K, Bono H, UI-Tei K. (2015)
    CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.
    Bioinformatics 31,1120-1123. [PDF]
    doi: 10.1093/bioinformatics/btu743.

2014

  • Kume H, Hino K, Galipon J, Ui-Tei K. (2014)
    A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency.
    Nucleic Acids Res. 42, 10050-10060.[PDF]
    doi: 10.1093/nar/gku662
  • Takahashi T, Zenno S, Ishibashi O, Takizawa T, Saigo K, Ui-Tei K. (2014)
    Interactions between the non-seed region of siRNA and RNA-binding RLC/RISC proteins, Ago and TRBP, in mammalian cells.
    Nucleic Acids Res. 42, 5256-5269.[PDF]
    doi: 10.1093/nar/gku153
  • Yukinaga H, Shionyu C, Hirata E, Ui-Tei K, Nagashima T, Kondo S, Okada-Hatakeyama M, Naoki H, Matsuda M. (2014)
    Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells.
    J. Cell Sci. 127, 1805-1815.[PDF]
    doi:10.1242/jcs.139733

2013

  • Nagata Y, Shimizu E, Hibio N, Ui-Tei K. (2013)
    Fluctuation of global gene expression by endogenous miRNAs response to the introduction of an exogenous miRNA.
    Int. J. Mol. Sci. 14, 11171-11189.[PDF]
    doi:10.3390/ijms140611171
  • Ui-Tei K. (2013)
    Optimal choice of functional and off-target effect-reduced siRNAs for RNAi therapeutics.
    Front. Genet. 4, 107.[PDF]
    doi:10.3389/fgene.2013.00107
  • Takahashi T, Miyakawa T, Zenno S, Nishi K, Tanokura M, Ui-Tei K.(2013)
    Distinguishable In Vitro Binding Mode of Monomeric TRBP and Dimeric PACT with siRNA.
    PLoS ONE 8, e63434.[PDF]
    doi:10.1371/journal.pone.0063434
  • Nishi K, Nishi A, Nagasawa T, Ui-Tei K.(2013)
    Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus.
    RNA 19, 17-35. [PDF]
    doi:10.1261/rna.034769.112
  • Naito Y, Ui-Tei K. (2013)
    Designing functional siRNA with reduced off-target effects.
    "siRNA Design"
    Methods Mol. Biol. 942, 57-68.
    doi: 10.1007/978-1-62703-119-6_3
  • Ackerman WE 4th, Carter AM, De Mestre AM, Golos TG, Jeschke U, Kusakabe K, Laurent LC, Parast MM, Roberts RM, Robinson JM, Rutherford J, Soma H, Takizawa T, Ui-Tei K, Las GE. (2013)
    IFPA meeting 2012 workshop report I: Comparative placentation and animal models, advanced techniques in placental histopathology, human pluripotent stem cells as a model for trophoblast differentiation
    Placenta, 34, S3-5.

2012

  • Hibio N, Hino K, Shimizu E, Nagata Y, Ui-Tei K. (2012)
    Stability of miRNA 5’ terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy.
    Sci. Rep. 2, 996. [PubMed]
    doi:10.1038/srep00996, 2012.
  • Ui-Tei K.(2012)
    sdRNA: siRNA with a DNA seed for an efficient and target-gene specific RNA interference.
    Gene Technology. 1, 102. [PDF]
  • Naito Y, Ui-Tei K (2012)
    siRNA design software for a target gene-specific RNA interference.
    Front. Genet. 3, 102. [PDF]
    doi: 10.3389/fgene.2012.00102
  • Ui-Tei K, Nishi K, Takahashi T, Nagasawa T. (2012)
    Thermodynamic control of small RNA-mediated gene silencing.
    Front. Genet. 3, 101. [PDF]
    doi: 10.3389/fgene.2012.00101

2011

  • Mazda M, Nishi K, Naito Y,Ui-Tei K. (2011)
    E-cadherin is transcriptionally activated via suppression of ZEB1 transcriptional repressor by small RNA-mediated gene silencing.
    PLoS ONE. 6, e28688.[PDF]
  • Yamato K, Egawa K, Endo S, Ui-Tei K, Yamada T, Saigo K, Hyodo I, Kiyano T, Nakagawa I. (2011)
    Enhanced specificity of HPV16 E6E7 siRNA by RNA-DNA chimera modification.
    Cancer Gene Ther. 18, 587-597.[PDF]
  • Naito Y, Ui-Tei K. (2011)
    Designing functional siRNA with reduced off-target effects.
    Methods Mol. Biol. In press.
  • Sasaki N, Shinomi M, Hirano K, Ui-Tei K, Nishihara S. (2011)
    Lacdinac (Galnacβ1-4glcnac) Contributes to Self-Renewal of Mouse Embryonic Stem Cells by Regulating LIF/STAT3 Signaling.
    Stem Cells. 29, 641-650. [PDF]

2010

  • Tanaka F, Mochizuki T, Liang X, Asanuma H, Tanaka S, Suzuki K, Kitamura SI, Nishikawa A, Ui-Tei K, Hagiya M. (2010)
    Robust and Photocontrollable DNA Capsules Using Azobenzenes.
    Nano Lett. 10, 3560-3565. [PDF]
  • Takizawa T, Gemma A, Ui-Tei K, Aizawa Y, Sadovsky Y, Robinson JM, Seike M, Miyake K. (2010)
    Basic and clinical studies on functional RNA molecules for advanced medical technologies.
    J. Nippon Med. Sch. 77, 71-79. [PDF]
  • Taniue K, Nishida A, Hamada F, Sugie A, Oda T, Ui-Tei K, Tabata T, Akiyama T. (2010)
    Sunspot, a link between Wingless signaling and endoreplication in Drosophila.
    Development 137, 1755-1764.[PubMed]
  • Hamada T, Teraoka M, Imaki J, Ui-Tei K, Ladherc R.K, Asahara T. (2010)
    Gene expression of Spag6 in chick central nervous system.
    Anat. Histol. Embryol. 39, 227-32. [PDF]
  • Narikawa K, Nishi K, Naito Y, Mazda M, Ui-Tei K. (2010)
    Genome-wide identification and analysis of miRNAs complementary to upstream of mRNA transcription start sites.
    Gene Silencing: Theory Techniques and Applications, Nova Science Publishers,287-319. [PDF]

2009

  • Naito Y, Yoshimura J, Morishita S, Ui-Tei K. (2009)
    siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect.
    BMC Bioinformatics 10, 392. [PDF]
  • Ui-Tei K, Nishi K, Naito Y, Zenno S, Juni A, Saigo K. (2009)
    Reduced base-base interactions between the DNA seed and RNA target are the major determinants of a significant reduction in the off-target effect due to DNA-seed-containing siRNA.
    Proceedings of the 2009 Micro-NanoMechatronics and Human Science (MHS2009), 298-304. [PDF]
  • Naito Y, Nishi K, Juni A, Ui-Tei K. (2009)
    Functional shRNA expression system with reduced off-target effects.
    Proceedings of the 2009 Micro-NanoMechatronics and Human Science (MHS2009), 291-297. [PDF]
  • Naito Y, Saigo K, Ui-Tei K. (2009)
    Experimental validation of published siRNA design algorithms.
    Small Interfering RNA: New Research, 185-194.
  • Ui-Tei K, Naito Y, Zenno S, Nishi K, Juni A, Tanaka A, Saigo K. (2009)
    Bipartite roles of the central region of the siRNA guide strand in RNA interference due to modified siRNA with a DNA seed arm.
    Research Advances in Nucleic Acids Research, 3, 1-17.

2008

  • Ui-Tei K, Naito Y, Nishi K, Juni A, Saigo K. (2008)
    Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.
    Nucleic Acids Res. 36, 7100-7109. [PDF]
  • Ui-Tei K, Zenno S, Naito Y, Takahashi F, Nishi K, Juni A, Tanaka A, Saigo K. (2008)
    DNA-modified siRNA-dependent gene silencing with reduced off-target effect is induced through a pathway parallel to that for siRNA-mediated RNA interference.
    Proceedings of the 2008 Micro-NanoMechatronics and Human Science (MHS2008), 339-345. [PDF]
  • Piao Z-F, Takahashi F, Saigo K, Ui-Tei K. (2008)
    RNAi microarray by reverse transfection of siRNA and shRNA for functional genomics.
    Proceedings of the 2008 Micro-NanoMechatronics and Human Science (MHS2008), 346-351. [PDF]
  • Naito Y, Saigo K, Ui-Tei K. (2008)
    Evaluation of published rational siRNA design algorithms using firefly luciferase gene as a reporter.
    RNA interference research progress, 3-11. [PDF]
  • Okamoto M, Tomonari S, Naito Y, Saigo K, Noji S, Ui-Tei K, Ohuchi H. (2008)
    Introduction of silencing-inducing transgene against Fgf19 does not affect expression of Tbx5 and β3-tubulin in the developing chicken retina.
    Dev. Growth Differ. 50, 159-168. [PubMed]
  • Ui-Tei K, Naito Y, Zenno S, Nishi K, Yamato K, Takahashi F, Juni A, Saigo K. (2008)
    Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.
    Nucleic Acids Res. 36, 2136-2151. [PDF]
  • Yamato K, Yamada T, Kizaki M, Ui-Tei K, Natori Y, Fujino M, Nishihara T, Ikeda Y, Nasu Y, Saigo K, Yoshinouchi M. (2008)
    New highly potent and specific E6 and E7 siRNAs for treatment of HPV16 positive cervical cancer.
    Cancer Gene Ther. 15, 140-153. [PDF]
  • Sasaki N, Okishio K, Ui-Tei K, Saigo K, Kinoshita-Toyoda A, Toyoda H, Nishimura T, Suda Y, Hayasaka M, Hanaoka K, Hitoshi S, Ikenaka K, Nishihara S. (2008)
    Heparan sulfate regulates self-renewal and pluripotency of embryonic stem cells.
    J. Biol. Chem. 283, 3594-3606. [PDF]

2007

  • Nishi K, Saigo K. (2007)
    Cellular internalization of green fluorescence protein fused with herpes simplex virus protein VP22 via a lipid-raft-mediated endocytic pathway independent of caveolae and Rho family GTPases but dependent on dynamin and Arf6.
    J. Biol. Chem. 282, 27503-27517. [PDF]
  • Nishimura I, Ui-Tei K, Saigo K, Ishii H, Sakuma Y, Kato M. (2007)
    17β-estradiol at physiological concentrations augments Ca2+-activated K+ currents via estrogen receptor β in the GnRH neuronal cell line GT1-7.
    Endocrinology 149, 774-782. [PDF]
  • Ui-Tei K, Zenno S, Saigo K. (2007)
    Sequence requirements for effective mammalian RNAi induced by short double-stranded RNAs equal to or more than 22bp in length.
    Antisense Elements (Genetics) Research Focus. 141-160.[PDF]
  • Naito Y, Nohtomi K, Onogi T, Uenishi R, Ui-Tei K, Saigo K, Takebe Y. (2007)
    Optimal design and validation of antiviral siRNA for targeting HIV-1.
    Retrovirology 6, 80.[PDF]
  • Kojima S, Matsumoto K, Hirose M, Shimada M, Nagano M, Shigeyoshi Y, Hoshino SI, Ui-Tei K, Saigo K, Green CB, Sakaki Y, Tei H. (2007)
    LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1.
    Proc. Natl. Acad. Sci. USA 104, 1859-1864. [PDF]
  • Ui-Tei K, Naito Y, Saigo K. (2007)
    Guidelines for the selection of effective short-interfering RNA sequences for functional genomics.
    Methods Mol. Biol. 361, 201-216. [PubMed]

2006

  • Ui-Tei K, Naito Y, Saigo K. (2006)
    Essential notes regarding the design of functional siRNAs for efficient mammalian RNAi.
    J. Biomed. Biotechnol. 2006, 65052. [PDF]
  • siVirus web server at http://siVirus.RNAi.jp/
    Naito Y, Ui-Tei K, Nishikawa T, Takebe Y, Saigo K. (2006)
    siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.
    Nucleic Acids Res. 34, W448-W450. [PDF]
  • Kamiyama S, Sasaki N, Goda E, Ui-Tei K, Saigo K, Narimatsu H, Jigami Y, Kannagi R, Irimura T, Nishihara S. (2006)
    Molecular cloning and characterization of a novel 3′-phosphoadenosine 5′-phosphosulfate transporter, PAPST2.
    J. Biol. Chem. 281, 10945-10953. [PDF]

2005

  • Ui-Tei K, Zenno S, Juni A, Saigo K. (2005)
    RNAi induced in mammalian and Drosophila cells via transfection of dimers and trimers of short interfering RNA.
    J. RNAi Gene Silencing 1, 79-87. [PDF]
  • dsCheck web server at http://dsCheck.RNAi.jp/
    Naito Y, Yamada T, Matsumiya T, Ui-Tei K, Saigo K, Morishita S. (2005)
    dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference.
    Nucleic Acids Res. 33, W589-W591. [PDF]
  • Takahashi M, Takahashi F, Ui-Tei K, Kojima T, Saigo K. (2005)
    Requirements of genetic interactions between Src42A, armadillo and shotgun, a gene encoding E-cadherin, for normal development in Drosophila.
    Development 132, 2547-2559. [PDF]
  • Niimura M, Isoo N, Takasugi N, Tsuruoka M, Ui-Tei K, Saigo K, Morohashi Y, Tomita T, Iwatsubo T. (2005)
    Aph-1 contributes to the stabilization and trafficking of the gamma-secretase complex through mechanisms involving intermolecular and intramolecular interactions.
    J. Biol. Chem. 280, 12967-12975. [PDF]

2004

  • Takagi Y, Nomizu M, Ui-Tei K, Tokushige N, Hirohashi S. (2004)
    Active sites in the carboxyl-terminal region of the laminin alpha chain in Drosophila neuronal cell spreading.
    Arch. Insect. Biochem. Physiol. 56, 162-169. [PubMed]
  • siDirect web server at http://design.RNAi.jp/
    Naito Y, Yamada T, Ui-Tei K, Morishita S, Saigo K. (2004)
    siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.
    Nucleic Acids Res. 32, W124-W129. [PDF]
  • Ui-Tei K, Ueda R, Zenno S, Takahashi F, Doi N, Naito Y, Yamamoto M, Hashimoto N, Takahashi K, Hamada T, Tokunaga T, Saigo K. (2004)
    RNA-interference, induced by transient and continuous expression of hairpin RNA in cells from Drosophila and mammals.
    Mol. Biol. 38, 276-287. [PubMed]
  • Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K. (2004)
    Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference.
    Nucleic Acids Res. 32, 936-948. [PDF]
  • Mishima T, Hamada T, Ui-Tei K, Takahashi F, Miyata Y, Imaki J, Suzuki H, Yamashita K. (2004)
    Expression of DDAH1 in chick and rat embryos.
    Dev. Brain Res. 148, 223-232. [PDF]

2003

  • Kato M, Ui-Tei K, Watanabe M, Sakuma Y. (2003)
    Characterization of voltage-gated calcium currents in gonadotropin-releasing hormone neurons tagged with green fluorescent protein in rats.
    Endocrinology 144, 5118-5125. [PDF]
  • Iwabuchi M, Ui-Tei K, Yamada K, Matsuda Y, Sakai Y, Tanaka K, Ohki-Hamazaki H. (2003)
    Molecular cloning and characterization of avian bombesin-like peptide receptors: new tools for investigating molecular basis for ligand selectivity.
    Br. J. Pharmacol. 139, 555-566. [PDF]
  • Doi N, Zenno S, Ueda R, Ohki-Hamazaki H, Ui-Tei K, Saigo K. (2003)
    Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors.
    Curr. Biol. 13, 41-46. [PDF]

2002

  • Hamada T, Ui-Tei K, Imaki J, Takahashi F, Onodera H, Mishima T, Miyata Y. (2002)
    The expression of SCDGF/PDGF-C/fallotein and SCDGF-B/PDGF-D in the rat central nervous system.
    Mech. Dev. 112, 161-164. [PDF]
  • Seike M, Gemma A, Hosoya Y, Hosomi Y, Okano T, Kurimoto F, Uematsu K, Tekenaka K, Yoshimura A, Shibuya M, Ui-Tei K, Kudoh S. (2002)
    The pomoter region of the human BUBR1 gene and its expression analysis in lung cancer.
    Lung Cancer 38, 229-234. [PDF]
  • Uwo MF, Ui-Tei K, Park P, Takeda M. (2002)
    Replacement of midgut epithelium in the greater wax moth, Galleria mellonela, during larval-pupal moult.
    Cell Tissue Res. 308, 319-331. [PDF]

2001

  • Piao ZF, Ui-Tei K, Nagano M, Miyata Y. (2001)
    Participation of Intracellular Ca2+/calmodulin and Protein Kinase(s) in the Pathway of Apoptosis Induced by a Drosophila Cell Death Gene, reaper.
    Mol. Cell. Biol. Res. Commun. 4, 307-312. [PDF]
  • Hamada T, Ui-Tei K, Imaki J, Miyata Y. (2001)
    Molecular Cloning of SCDGF-B, a Novel Growth Factor Homologous to SCDGF/PDGF-C/fallotein.
    Biochem. Biophys. Res. Commun. 280, 733-737. [PDF]

2000

  • Ui-Tei K, Zenno S, Miyata Y, Saigo K. (2000)
    Sensitive assay of RNA interference in Drosophila and chinese hamster cultured cells using firefly luciferase gene as target.
    FEBS Lett. 479, 79-82. [PDF]
  • Ui-Tei K, Nagano M, Miyata Y. (2000)
    Calmodulin-dependent and -independent apoptosis in cells of a Drosophila neuronal cell line.
    Apoptosis 5, 133-140. [PDF]
  • Nagano M, Ui-Tei K, Suzuki H, Piao Z, Miyata Y. (2000)
    CDK inhibitors suppress apoptosis induced by chemicals and by excessive expression of a cell death gene, reaper, in Drosophila cell.
    Apoptosis 5, 543-550. [PDF]
  • Usui-Aoki K, Ito, H, Ui-Tei K, Takahashi K, Lukacsovich T, Awano W, Nakata H, Piao ZF, Nilsson EE, Tomida J, Yamamoto D.(2000)
    Formation of the male-specific muscle in female Drosophila by ectopic fruitless expression.
    Nat. Cell Biol. 2, 500-506. [PDF]
  • Hamada T, Ui-Tei K, Miyata Y. (2000)
    A novel gene derived from developing spinal cords, SCDGF, is a unique member of the PDGF/VEGF family.
    FEBS Lett. 475, 97-102. [PDF]
  • Takagi Y, Ui-Tei K, Hirohashi Y. (2000)
    Adhesion-dependent tyrosine phosphorylation of Enabled in Drosophila neuronal cell line.
    Biochem. Biophys. Res. Commun. 270, 482-487. [PDF]
  • Ui-Tei K, Miyata Y.(2000)
    Cell lines derived from Drosophila larval central nervous system and their practical applications.
    Drosophila Information Service 83, 188-189. [PDF]