Analysis of the microRNA regulatory mechanisms based on the development of human microRNA expression vectors

• Project/Area Number: 20770133
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: The University of Tokyo
• Principal Investigator: NAITO Yuki The University of Tokyo, 大学院・理学系研究科, 特任助教 (60451829)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2010: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2009: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2008: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: マイクロRNA

Research Abstract

The human microRNA (miRNA) expression vectors and the miRNA sensors were developed in order to investigate the regulatory mechanisms of miRNAs. We present siDirect 2.0 webserver, which provides functional siRNA design with the reduction of the seed-dependent, miRNA-like off-target effects of an siRNA.

Research Products

• [Journal Article] Designing functional siRNA with reduced off-target effects. (2011)
  • Author(s): Naito Y, Ui-Tei K.
  • Journal Title: Methods in Molecular Biology in press.
  • Peer Reviewed
• [Journal Article] Designing functional siRNA with reduced off-target effects. (2011)
  • Author(s): Naito Y, Ui-Tei K
  • Journal Title: Methods in Molecular Biology Volume: (掲載確定)
  • Peer Reviewed
• [Journal Article] Genome-wide identification and analysis of miRNAs complementary to upstream sequences of mRNA transcription start sites. (2010)
  • Author(s): Narikawa K, Nishi K, Naito Y, Yonezawa S, Mazda M, Ui-Tei K.
  • Journal Title: Gene Silencing : Theory, Techniques and Applications Pages: 287-319
  • Peer Reviewed
• [Journal Article] Genome-wide identification and analysis of miRNAs complementary to upstream sequences of mRNA transcription start sites. (2010)
  • Author(s): Narikawa K, Nishi K, Naito Y, Yonezawa S, Mazda M, Ui-Tei K
  • Journal Title: Gene Silencing : Theory, Techniques and Applications Pages: 287-319
  • Peer Reviewed
• [Journal Article] siDirect 2.0 : updated software for designing functional siRNA with reduced seed-dependent off-target effect. (2009)
  • Author(s): Naito Y, Yoshimura J, Morishita S, Ui-Tei K.
  • Journal Title: BMC Bioinformatics 10 Pages: 392-392
  • Peer Reviewed
• [Journal Article] 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. (2009)
  • Author(s): Ui-Tei K, Nishi K, Naito Y, Zenno S, Juni A, Saigo K.
  • Journal Title: Proceedings of the 2009 Micro-Nano Mechatronics and Human Science(MHS2009) Pages: 298-304
  • Peer Reviewed
• [Journal Article] Functional shRNA expression system with reduced off-target effects. (2009)
  • Author(s): Naito Y, Nishi K, Juni A, Ui-Tei K.
  • Journal Title: Proceedings of the 2009 Micro-Nano Mechatronics and Human Science (MHS2009) Pages: 291-297
  • Peer Reviewed
• [Journal Article] Bipartite roles of the central region of the siRNA guide strand in RNA interference due to modified siRNA with a DNA seed arm. (2009)
  • Author(s): Ui-Tei K, Naito Y, Zenno S, Nishi K, Juni A, Tanaka A, Saigo K.
  • Journal Title: Research Advances in Nucleic Acids Research 3 Pages: 1-17
  • Peer Reviewed
• [Journal Article] siDirect 2.0 : updated software for designing functional siRNA with reduced seed-dependent off-target effect (2009)
  • Author(s): Naito, Y., ら
  • Journal Title: BMC Bioinformatics 10 Pages: 392-392
  • Peer Reviewed
• [Journal Article] Functional shRNA expression system with reduced off-target effects (2009)
  • Author(s): Naito, Y., ら
  • Journal Title: Proceedings of the 2009 Micro-Nano Mechatronics and Human Science Pages: 291-297
  • Peer Reviewed
• [Journal Article] 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 (2009)
  • Author(s): Ui-Tei K, Nishi K, Naito Y, Zenno S, Juni A, Saigo K
  • Journal Title: Proceedings of the 2009 Micro-Nano Mechatronics and Human Science Pages: 298-304
  • Peer Reviewed
• [Journal Article] Experimental validation of published siRNA design algorithms. (2009)
  • Author(s): Naito, Y. ら
  • Journal Title: Small Interfering RNA : New Research 印刷中(掲載確定)
  • Peer Reviewed
• [Journal Article] Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect. (2008)
  • Author(s): Ui-Tei K, Naito Y, Nishi K, Juni A, Saigo K.
  • Journal Title: Nucleic Acids Res. 36 Pages: 7100-7109
  • Peer Reviewed
• [Journal Article] DNA-modified siRNA-dependent gene silencing with reduced off-target effect is induced through a pathway parallel to that for siRNA-mediated RNA interference. (2008)
  • Author(s): Ui-Tei K, Zenno S, Naito Y, Takahashi F, Nishi K, Juni A, Tanaka A, Saigo K.
  • Journal Title: Proceedings of the 2008 Micro-Nano Mechatronics and Human Science (MHS2008) Pages: 339-345
  • Peer Reviewed
• [Journal Article] Evaluation of published rational iRNA design algorithms using firefly luciferase gene as a reporter. (2008)
  • Author(s): Naito Y, Saigo K, Ui-Tei K.
  • Journal Title: RNA interference research progress Pages: 3-11
  • Peer Reviewed
• [Journal Article] Evaluation of published rational siRNA design algorithms using firefly luciferase gene as a reporter. (2008)
  • Author(s): Naito, Y. ら
  • Journal Title: RNA interference research progress Pages: 3-11
  • Peer Reviewed
• [Journal Article] Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect. (2008)
  • Author(s): Ui-Tei, K. ら
  • Journal Title: Nucleic Acids Res. 36 Pages: 7100-7109
  • Peer Reviewed
• [Presentation] 高いゲノム多様性をもつHIV-1を標的とする至適siRNAの設計 (2010)
  • Author(s): 内藤雄樹
  • Organizer: 第20回日本数理生物学会年会
  • Place of Presentation: 札幌市北海道大学学術交流会館
  • Year and Date: 2010-09-16
• [Presentation] siDirect 2.0 : an Updated Website to Select Functional, Target-specific siRNA with Reduced Seed-dependent Off-target Effect for Mammalian Functional Genomics. (2010)
  • Author(s): Naito Y, Yoshimura J, Morishita S, Ui-Tei K.
  • Organizer: The 19th CDB Meeting "RNA Sciences in Cell and Developmental Biology"
  • Place of Presentation: Kobe.
  • Year and Date: 2010-05-10
• [Presentation] siDirect 2.0 : an Updated Website to Select Functional, Target-specific siRNA with Reduced Seed-dependent Off-target Effect for Mammalian Functional Genomics (2010)
  • Author(s): Naito Y, Yoshimura J, Morishita S, Ui-Tei K
  • Organizer: The 19th CDB Meeting "RNA Sciences in Cell and Developmental Biology"
  • Place of Presentation: 神戸市理化学研究所発生・再生科学総合研究センター
• [Presentation] siDirect2.0 : a website updated to select functional siRNA with reduced off-target effect for functional genomics. (2009)
  • Author(s): 内藤雄樹, 吉村淳, 森下真一, 程久美子
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-11
• [Presentation] siDrect2.0 : a website updated to select functional siRNA with reduced off-target effect for functional genomics (2009)
  • Author(s): 内藤雄樹, ら
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-11
• [Presentation] 高いゲノム多様性をもつHIV-1を標的とする至適siRNAの設計 (2009)
  • Author(s): 内藤雄樹
  • Organizer: 第20回日本数理生物学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2009-09-16
• [Book] Experimental validatio of published siRNA design algorithms(Small Interfering RNA : New Research) (2009)
  • Author(s): Naito Y, Saigo K, Ui-Tei K.
  • Publisher: Nova Science Publishers.
• [Book] Experimental validation of published siRNA design algorithms In : Small Interfering RNA : New Research (2009)
  • Author(s): Naito, Y., ら
  • Total Pages: 265
  • Publisher: Nova Science Publishers
• [Remarks] siDirect 2.0ウェブサーバ
  • URL: http://siDirect2.RNAi.jp/
• [Remarks]
  • URL: http://siDirect2.RNAi.jp/
• [Remarks]
  • URL: http://siDirect2.RNAi.jp/
• [Patent(Industrial Property Rights)] RNA干渉ポリヌクレオチド混合物の設計装置、RNA干渉ポリヌクレオチド混合物の作製方法、及びRNA (2010)
  • Inventor(s): 武部豊、内藤雄樹、西郷薫、名取幸和
  • Industrial Property Rights Holder: 国立感染症研究所長、国立大学法人東京大学、(株)アルファジェン
  • Filing Date: 2010-12-10