Exhaustive prediction of microRNAs, snoRNAs and their targets

• Project/Area Number: 22240031
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: ASAI Kiyoshi 東京大学, 新領域創成科学研究科, 教授 (30356357)
• Co-Investigator(Kenkyū-buntansha): KIRYU Hisanori 東京大学, 大学院新領域創成科学研究科, 准教授 (80415778) ; HIROSE Tetsurou 北海道大学, 遺伝子病制御研究所, 教授 (30273220)
• Co-Investigator(Renkei-kenkyūsha): SATO Kengo 慶應義塾大学, 理工学部, 講師 (20365472)
• Project Period (FY): 2010-04-01 – 2013-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥46,410,000 (Direct Cost: ¥35,700,000、Indirect Cost: ¥10,710,000); Fiscal Year 2012: ¥15,340,000 (Direct Cost: ¥11,800,000、Indirect Cost: ¥3,540,000); Fiscal Year 2011: ¥14,430,000 (Direct Cost: ¥11,100,000、Indirect Cost: ¥3,330,000); Fiscal Year 2010: ¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
• Keywords: バイオインフォマティクス / 機能性RNA / RNA / snoRNA / マイクロRNA / 確率モデル / RNA-RNA相互作用

Research Abstract

The following is the main results of this project. (a) We developed a microRNA finding tool, which combines structural and evolutionary features of microRNAs. We showed that our tool outperforms previous methods with less false positives. (b) We developed an algorithm for computing secondary structural accessibilities of RNA sequences. We were able to detect the evolutionary constraints around the target sites of microRNAs. (c) We developed a tool to calculate the changes of free energies and entropies of RNA secondary structures in response to mutations. We applied our method to mitochondrial tRNAs and showed that the increase of structural fluctuation caused by mutations correlated with disease susceptibility. (d) We developed a tool to predict potential secondary structural contexts for each base of an RNA sequence. We applied our method to binding sites of RNA-binding proteins and detected the structural specificities of the proteins.

Research Products

• [Journal Article] CapR : revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data (2014)
  • Author(s): Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki and Hisanori Kiryu
  • Journal Title: Genome Biology Volume: 15 Issue: 1
  • DOI: 10.1186/gb-2014-15-1-r16
  • Peer Reviewed / Open Access
• [Journal Article] MixSIH : a mixture model for single individual haplotyping (2013)
  • Author(s): Hirotaka Matsumoto, and Hisanori Kiryu
  • Journal Title: BMC genomics Volume: 14 Issue: S2
  • DOI: 10.1186/1471-2164-14-s2-s5
  • Peer Reviewed
• [Journal Article] Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions (2013)
  • Author(s): Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
  • Journal Title: Bioinformatics Volume: 29 Issue: 20 Pages: 2524-2528
  • DOI: 10.1093/bioinformatics/btt453
  • Peer Reviewed
• [Journal Article] CentroidAlign-Web : A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs (2013)
  • Author(s): Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
  • Journal Title: International journal of molecular sciences Volume: 14 Issue: 3 Pages: 6144-6156
  • DOI: 10.3390/ijms14036144
  • Peer Reviewed
• [Journal Article] Rchange : Algorithms for computing the energy changes of RNA secondary structures in response to base mutations (2012)
  • Author(s): Hisanori Kiryu and Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 28(8) Issue: 8 Pages: 1093-1101
  • DOI: 10.1093/bioinformatics/bts097
  • Peer Reviewed
• [Journal Article] DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition (2012)
  • Author(s): Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
  • Journal Title: Bioinformatics Volume: 28 Issue: 24 Pages: 3218-3224
  • DOI: 10.1093/bioinformatics/bts612
  • Peer Reviewed
• [Journal Article] Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features (2012)
  • Author(s): Goro Terai, Hiroaki Okida, Kiyoshi Asai, Toutai Mituyama
  • Journal Title: PLoS One Volume: 7 Issue: 9 Pages: e44314-e44314
  • DOI: 10.1371/journal.pone.0044314
  • Peer Reviewed
• [Journal Article] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming (2012)
  • Author(s): Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
  • Journal Title: Nucleic Acids Res Volume: 40 Issue: W1 Pages: W29-W34
  • DOI: 10.1093/nar/gks412
  • Peer Reviewed
• [Journal Article] A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA) (2012)
  • Author(s): Michiaki Hamada, Kiyoshi Asai
  • Journal Title: J Comput Biol Volume: 19 Issue: 5 Pages: 532-549
  • DOI: 10.1089/cmb.2011.0197
  • Peer Reviewed
• [Journal Article] Sufficient statistics and expectation maximization algorithms in phylogenetic tree models (2011)
  • Author(s): Hisanori Kiryu
  • Journal Title: Bioinformatics Volume: 27 Issue: 17 Pages: 2346-2353
  • DOI: 10.1093/bioinformatics/btr420
  • Peer Reviewed
• [Journal Article] CentroidHomfold-LAST : accurate prediction of RNA secondary structure using automatically collected homologous sequences (2011)
  • Author(s): Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai
  • Journal Title: Nucleic Acids Res Volume: 39 Issue: suppl_2 Pages: W100-W106
  • DOI: 10.1093/nar/gkr290
  • Peer Reviewed
• [Journal Article] A detailed investigation of accessibilities around target sites of siRNAs and miRNAs (2011)
  • Author(s): Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, and Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 27 Pages: 1788-1797
  • Peer Reviewed
• [Journal Article] Generalized Centroid Estimators in Bioinformatics (2011)
  • Author(s): Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai
  • Journal Title: PLoS ONE Volume: 6(2) Issue: 2 Pages: e16450-e16450
  • DOI: 10.1371/journal.pone.0016450
  • Peer Reviewed
• [Journal Article] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming (2011)
  • Author(s): K.Sato, Y.Kato, M.Hamada, T.Akutsu, K.Asai
  • Journal Title: Bioinformatics Volume: 27 Issue: 13 Pages: i85-i93
  • DOI: 10.1093/bioinformatics/btr215
  • Peer Reviewed
• [Journal Article] Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F (2011)
  • Author(s): Hironori Adachi, Akira Ishiguro, Michiaki Hamada, Eri Sakota, Kiyoshi Asai, Yoshikazu Nakamura
  • Journal Title: Biochimie Volume: 93 Issue: 7 Pages: 1081-1088
  • DOI: 10.1016/j.biochi.2011.04.003
  • Peer Reviewed
• [Journal Article] Improving the accuracy of predicting secondary structure for aligned RNA sequences (2011)
  • Author(s): Michiaki Hamada, Kengo Sato, Kiyoshi Asai
  • Journal Title: Nucleic Acids Res Volume: 39 Issue: 2 Pages: 393-402
  • DOI: 10.1093/nar/gkq792
  • Peer Reviewed
• [Journal Article] On algorithms for computing thermodynamic entropy of RNA secondary structures (2011)
  • Author(s): Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 27 Pages: 1788-1797
  • Peer Reviewed
• [Journal Article] CentroidHomfold-LAST : accurateprediction of RNA secondary structure using automatically collected homologous sequences (2011)
  • Author(s): Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai
  • Journal Title: Nucleic Acids Research Volume: 39
  • Peer Reviewed
• [Journal Article] Prediction of RNA secondary structure by maximizing pseudo-expected accuracy (2010)
  • Author(s): Michiaki Hamada, Kengo Sato, Kiyoshi Asai
  • Journal Title: BMC Bioinformatics Volume: 11 Issue: 1 Pages: 586-586
  • DOI: 10.1186/1471-2105-11-586
  • Peer Reviewed
• [Journal Article] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming (2010)
  • Author(s): Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
  • Journal Title: Bioinformatics Volume: 26 Issue: 18 Pages: i460-i466
  • DOI: 10.1093/bioinformatics/btq372
  • Peer Reviewed
• [Journal Article] A non-parametric Bayesian approach for predicting RNA secondary structures (2010)
  • Author(s): Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasufumi Sakakibara
  • Journal Title: Journal of Bioinformatics and Computational Biology Volume: 8 Issue: 04 Pages: 727-742
  • DOI: 10.1142/s0219720010004926
  • Peer Reviewed
• [Journal Article] Discovery of short pseudogenes derived from messenger RNAs (2010)
  • Author(s): Goro Terai, Aya Yoshizawa, Hiroaki Okida, Kiyoshi Asai, Toutai Mituyama
  • Journal Title: Nucleic Acids Res Volume: 38 Issue: 4 Pages: 1163-1171
  • DOI: 10.1093/nar/gkp1098
  • Peer Reviewed
• [Presentation] MixSIH: a mixture model for single individual haplotyping (2012)
  • Author(s): 松本拡高
  • Organizer: ISCB-Asia/SCCG 2012
  • Place of Presentation: Shenzhen, China
  • Year and Date: 2012-12-17
• [Presentation] On algorithms for computing thermodynamic entropy of RNA secondary structures (2011)
  • Author(s): Hisanori Kiryu and Kiyoshi Asai
  • Organizer: 第34回日本分子生物学会年会
  • Year and Date: 2011-12-14
• [Presentation] On algorithms for computing thermodynamic entropy of RNA secondary structures (2011)
  • Author(s): Hisanori Kiryu
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 神奈川県横浜市パシフィコ横浜(招待講演)
  • Year and Date: 2011-12-14
• [Presentation] Recent advances in structure prediction of RNA (2011)
  • Author(s): Kiyoshi Asai
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 神奈川県横浜市パシフィコ横浜(口頭発表)
  • Year and Date: 2011-12-14
• [Presentation] Algorithms for RNA sequence analysis (2011)
  • Author(s): Kiyoshi Asai
  • Organizer: GIW2011
  • Place of Presentation: 韓国、釜山、Haeundae Grand Hotel(招待講演)
  • Year and Date: 2011-12-06
• [Presentation] On algorithms for computing thermodynamic entropy of RNA secondary structures (2011)
  • Author(s): Kiyoshi Asai
  • Organizer: CBI/JSBI2011合同大会
  • Place of Presentation: 兵庫県神戸市神戸国際会議場(ポスター発表)
  • Year and Date: 2011-11-09
• [Presentation] Prediction of conserved miRNA precursors and their mature forms by integrating position-specific structural features (2011)
  • Author(s): Goro Terai
  • Organizer: The 16Th Annual Meeting of the RNA Society
  • Place of Presentation: 京都府京都市国立京都国際会館
  • Year and Date: 2011-06-17
• [Presentation] Binary estimation problems in structural information analysis of RNA (2011)
  • Author(s): Kiyoshi Asai
  • Organizer: The 16Th Annual Meeting of the RNA Society
  • Place of Presentation: 京都府京都市国立京都国際会館
  • Year and Date: 2011-06-15
• [Remarks]
  • URL: http://www.ncrna.org/
• [Remarks]
  • URL: http://www.ncrna.org/software/dafs/
• [Remarks]
  • URL: http://www.ncrna.org/software/rchange/
• [Remarks]
  • URL: http://rna.naist.jp/
• [Remarks]
  • URL: http://mirrim2.ncrna.org/
• [Remarks]
  • URL: https://sites.google.com/site/hmatsu1226/software/mixsih
• [Remarks]
  • URL: http://rna.naist.jp/ipknot/
• [Remarks]
  • URL: http://www.ncrna.org/centroidhomfold/
• [Remarks]
  • URL: http://www.ncrna.org/software/Raccess/
• [Remarks]
  • URL: http://www.ncrna.org/software/fdur/