Detection of translational signal in RNAs

• Project/Area Number: 25540129
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: Tohoku University
• Principal Investigator: YAMASHITA Riu 東北大学, 東北メディカル・メガバンク機構, 准教授 (10401259)
• Project Period (FY): 2013-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2013: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 翻訳制御 / non-coding RNA / データベース / 翻訳調節 / short peptide / 翻訳 / Ribosomal profiling / モチーフ / 国際情報交換

Outline of Final Research Achievements

There is not clear definition of non-coding RNAs so far. Here I detected potential coding RNA from non-coding RNAs. Some of them were detected as short peptides by Mass spectrometry analysis. Moreover, one of them shows cell-cycle accelation by overexpression of the smll peptide. I made the databse for potetial small peptide, and it is availble on web site.

Research Products

• [Journal Article] DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. (2015)
  • Author(s): Suzuki A, Wakaguri H, Yamashita R, Kawano S, Tsuchihara K, Sugano S, Suzuki Y, Nakai K.
  • Journal Title: Nucleic Acids Res. Volume: 43 Issue: D1 Pages: 1-5
  • DOI: 10.1093/nar/gku1080
  • Peer Reviewed / Open Access
• [Journal Article] The Babesia bovis gene and promoter model: an update from full-length EST analysis. (2014)
  • Author(s): Yamagishi J, Wakaguri H, Yokoyama N, Yamashita R, Suzuki Y, Xuan X, Igarashi I.
  • Journal Title: BMC Genomics Volume: 15 Issue: 1 Pages: 678-678
  • DOI: 10.1186/1471-2164-15-678
  • Peer Reviewed / Open Access
• [Journal Article] BioHackathon series in 2011 and 2012 : penetration of ontology and linked data in life science domains (2014)
  • Author(s): Katayama T, Komiyama Y, et al.
  • Journal Title: Journal of Biomedical Semantics Volume: 5 Issue: 1 Pages: 5-5
  • DOI: 10.1186/2041-1480-5-5
  • Peer Reviewed / Open Access
• [Journal Article] MicroRNA-126-mediated control of cell fate in B-cell myeloid progenitors as a potential alternative to transcriptional factors. (2013)
  • Author(s): Okuyama K, Ikawa T, Gentner B, Hozumi K, Harnprasopwat R, Lu J, Yamashita R, Ha D, Toyoshima T, Chanda B, Kawamata T, Yokoyama K, Wang S, Ando K, Lodish HF, Tojo A, Kawamoto H, Kotani A
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 110 Issue: 33 Pages: 13410-13415
  • DOI: 10.1073/pnas.1220710110
  • Peer Reviewed
• [Presentation] transcriptional research to translational research (2015)
  • Author(s): Riu Yamashita et al
  • Organizer: 第一回translational research meeting
  • Place of Presentation: 東京都港区 東京大学医科学研究所
  • Year and Date: 2015-03-13
• [Presentation] 潜在的に翻訳されるRNAとそのデータベース (2014)
  • Author(s): 山下理宇
  • Organizer: SIG-BIO研究会
  • Place of Presentation: 北陸先端大学
• [Presentation] Potential translation in RNA sequences (2013)
  • Author(s): Riu yamashita
  • Organizer: 生命医薬情報学連合大会
  • Place of Presentation: タワーホール船堀
• [Presentation] 翻訳に着目したnon-coding RNAとcoding RNA (2013)
  • Author(s): 山下理宇
  • Organizer: NGS現場の会
  • Place of Presentation: 神戸国際会議場
• [Remarks]
  • URL: http://dbtss.hgc.jp