Molecular basis of the noncoding RNA function that underlies species specificity

• Project/Area Number: 26650001
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Molecular biology
• Research Institution: Hokkaido University
• Principal Investigator: Hirose Tetsuro 北海道大学, 遺伝子病制御研究所, 教授 (30273220)
• Research Collaborator: CHUJO Takeshi
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 核酸 / 細胞・組織 / 発現制御 / 遺伝子 / 蛋白質 / ノンコーディングRNA / 核内構造体 / 種特異性 / エンハンサー

Outline of Final Research Achievements

The human-specific NBPF ncRNA, which is localized in nuclear bodies, is derived from the intronic regions of the human specific NBPF repeat cluster. By the experiment using a splicing inhibitor, we showed that NBPF ncRNAs are the excised introns which were created upon splicing of the precursor transcripts. Next generation RNA sequencing of the RNAs prepared from the cells in which NBPF ncRNA was specifically knocked down revealed that the expression of NOTCH2NL gene which is located adjacent to the NBPF cluster is activated by NBPF ncRNA. We also discovered that NBPF ncRNA exhibits semi-extractable feature in the process of the standard RNA preparation method, which is common to that of NEAT1 ncRNA localized in another nuclear body.

Research Products

• [Int'l Joint Research] 西オーストラリア大学(オーストラリア)
• [Journal Article] Architectural RNAs (arcRNAs): A class of long noncoding RNAs that functions as the scaffold of nuclear bodies (2016)
  • Author(s): Takeshi Chujo, Tomohiro Yamazaki, Tetsuro Hirose
  • Journal Title: Biochim Biophys Acta Volume: 1859 Issue: 1 Pages: 139-146
  • DOI: 10.1016/j.bbagrm.2015.05.007
  • Peer Reviewed
• [Journal Article] Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. (2015)
  • Author(s): Hennig S, Kong G, Mannen T, Sadowska A, Kobelke S, Blythe A, Knott G, Iyer S, Ho D, Newcombe EA, Hosoki K, Goshima N, Hatters D, Trinkle-Mulcahy L, Hirose T*, Bond CS*, Fox AH* (*co-corresponding)
  • Journal Title: J. Cell Biol. Volume: 210 Issue: 4 Pages: 3529-539
  • DOI: 10.1083/jcb.201504117
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Clues to long noncoding RNA taxonomy. (2015)
  • Author(s): Hirose T, Nakagawa S.
  • Journal Title: Biochim. Biophys. Acta. Volume: 1859 Issue: 1 Pages: 1-2
  • DOI: 10.1016/j.bbagrm.2015.11.011
  • Peer Reviewed
• [Journal Article] Rapid and Efficient Elimination of Specific Nuclear Noncoding RNAs in Mammalian Cells with Antisense Oligonucleotides. (2015)
  • Author(s): Hirose, T., Mannen, T.
  • Journal Title: Methods Mol. Biol. Volume: 1206 Pages: 149-156
  • DOI: 10.1007/978-1-4939-1369-5_13
  • ISBN: 9781493913688, 9781493913695
  • Peer Reviewed
• [Journal Article] Elements and machinery of non-coding RNAs: toward their taxonomy (2014)
  • Author(s): Tetsuro Hirose, Yuichiro Mishima, Yukihide Tomari
  • Journal Title: EMBO Reports Volume: 印刷中 Issue: 5 Pages: 489-507
  • DOI: 10.1002/embr.201338390
  • Peer Reviewed / Open Access
• [Presentation] Re-quantification of paraspeckle architectural components and an exploratory search for novel nuclear RNA bodies by using an improved RNA extraction method (2016)
  • Author(s): Takeshi Chujo, Tomohiro Yamazaki, Shinichi Nakagawa, Tetsuya Kawaguchi, Chikako Fujikawa, Ayaka Kubota, Toru Takumi, Tetsuro Hirose
  • Organizer: Keystone symposia
  • Place of Presentation: Santa Fe,USA
  • Year and Date: 2016-02-21
  • Int'l Joint Research
• [Presentation] NEAT1 lncRNAの難溶性を考慮したパラスペックル構造因子の再定量と構造構築原理の探究 (2015)
  • Author(s): 中條 岳志、中川 真一、川口哲哉、内匠 透、廣瀬 哲郎
  • Organizer: 日本分子生物学会
  • Place of Presentation: 神戸ポートアイランド（兵庫県神戸市）
  • Year and Date: 2015-12-01
• [Presentation] ノンコーディングRNAによる核内アーキテクチュア (2015)
  • Author(s): 廣瀬哲郎
  • Organizer: Aging, Bone and Cnacer Frontline Forum
  • Place of Presentation: 庭のホテル（東京都千代田区）
  • Year and Date: 2015-05-25
  • Invited
• [Presentation] RNA機能と神経変性 (2015)
  • Author(s): 廣瀬哲郎
  • Organizer: 日本神経学会北海道支部会
  • Place of Presentation: 北海道大学（北海道・札幌市）
  • Year and Date: 2015-03-08
  • Invited
• [Presentation] Subnuclear architecture by long noncoding RNAs (2014)
  • Author(s): Tetsuro Hirose
  • Organizer: 理研セミナー
  • Place of Presentation: 理化学研究所横浜キャンパス（神奈川県・横浜市）
  • Year and Date: 2014-12-08
  • Invited
• [Presentation] 難溶性RNAの解析：NEAT1 ncRNAの細胞内再定量と新しいRNA群の探索 (2014)
  • Author(s): 中條岳志、廣瀬哲郎
  • Organizer: 日本RNA学会年会
  • Place of Presentation: ウィンクあいち（愛知県・名古屋市）
  • Year and Date: 2014-07-23 – 2014-07-25
• [Book] Long Noncoding RNAs: Structures and Functions (2015)
  • Author(s): Mannen, T., Chujo, T., Hirose, T
  • Total Pages: 22
  • Publisher: Springer