Functional machinery for non-coding RNAs

2013 Fiscal Year Final Research Report

• Project Area: Functional machinery for non-coding RNAs
• Project/Area Number: 21115001
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: TOMARI Yukihide 東京大学, 分子細胞生物学研究所, 教授 (90447368)
• Co-Investigator(Kenkyū-buntansha): SUZUKI Takeo 東京大学, 大学院工学系研究科, 講師 (90533125) ; TEI Kumiko 東京大学, 大学院理学系研究科, 准教授 (50213327) ; NAKAZAWA Takanobu 大阪大学, 大学院薬学研究科, 特任准教授 (00447335) ; WADA Takeshi 東京理科大学, 薬学部, 教授 (90240548) ; SADO Takashi 近畿大学, 農学部, 教授 (70321601) ; KAGEYAMA Yuji 神戸大学, 遺伝子実験センター, 准教授 (90335480)
• Co-Investigator(Renkei-kenkyūsha): SIOMI Mikiko 東京大学, 大学院理学系研究科, 教授 (20322745) ; MIYAGAWA Satomi 大阪大学, 大学院医学系研究科, 特任講師 (90291153) ; NAKAGAWA Shinichi 独立行政法人理化学研究所, 中川RNA 生物学研究室, 准主任研究員 (50324679) ; TAKESHITA Fumitaka 独立行政法人国立がんセンター, 分子細胞治療研究分野, 主任研究員 (40466199) ; ODA Takeaki 東京大学, 分子細胞生物学研究所, 研究員 (00608523) ; YAMASHITA Akio 横浜市立大学, 医学部, 講師 (20405020) ; NISHIMURA Yukiko 東京大学, 分子細胞生物学研究所, 特任助教 (30514567)
• Project Period (FY): 2009-07-23 – 2014-03-31
• Keywords: 遺伝子 / 発現制御 / 核酸 / 蛋白質 / ゲノム

Research Abstract

To effectively promote research in our group, we openly exchanged our new findings and ideas at annual meetings. Workshops were also held to help our members to become familiar with new methods including bioinformatics. To enhance collaboration, publication fees for co-authored papers within our group were supported by the general group grant. As a result, so many important papers have been published from our group. We also hold a series of domestic and international symposiums and workshops to exchange ideas and communicate with world-class scientists in the non-coding RNA field. We have been continuously transmitting the outcome of our research to the public by actively running our website and blog as well as editing feature articles in general magazines. We made our special effort to support young students to grow them into leading scientists in the next generation.

Research Products

• [Journal Article] Elements and machinery of non-coding RNAs : toward their taxonomy (2014)
  • Author(s): Hirose T, Mishima Y, Tomari Y.
  • Journal Title: EMBO Rep Volume: 15(5) Pages: 489-507
  • Peer Reviewed
• [Journal Article] Nuclear lncRNAs as epigenetic regulators-beyond skepticism (2014)
  • Author(s): Nakagawa S, Kageyama Y.
  • Journal Title: Biochim Biophys Acta Volume: 39(3) Pages: 215-222
  • Peer Reviewed
• [Journal Article] Making piRNAs in vitro (2014)
  • Author(s): Kawaoka S, Katsuma S, Tomari Y.
  • Journal Title: Methods Mol Biol Volume: 1093 Pages: 35-46
  • Peer Reviewed
• [Journal Article] Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins (2013)
  • Author(s): Izumi N, Kawaoka S, Yasuhara S, Suzuki Y, Sugano S, Katsuma S, Tomari Y.
  • Journal Title: RNA Volume: 19(7) Pages: 896-901
  • Peer Reviewed
• [Journal Article] The comprehensive epigenome map of piRNA clusters (2013)
  • Author(s): Kawaoka S, Hara K, Shoji K, Kobayashi M, Shimada T, Sugano S, Tomari Y, Suzuki Y, Katsuma S
  • Journal Title: Nucleic Acids Res Volume: 41(3) Pages: 1581-1590
  • Peer Reviewed
• [Journal Article] Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus (2013)
  • Author(s): Yamamoto Y, Watanabe T, Hoki Y, Shirane K, Li Y, Ichiiyanagi K, Kuramochi-Miyagawa S, Toyoda A, Fujiyama A, Oginuma M, Suzuki H, Sado T, Nakano T, Sasaki H
  • Journal Title: Genome Res Volume: 23(2) Pages: 292-299
  • Peer Reviewed
• [Journal Article] Structure and function of Zucchini endoribonuclease in piRNA biogenesis (2012)
  • Author(s): Nishimasu H, Ishizu H, Saito K, Fukuhara S, Kamatani MK, Bonnefond L, Matsumoto N, Nishizawa T, Nakanaga K, Aoki J, Ishitani R, Siomi H, Siomi MC, Nureki O
  • Journal Title: Nature Volume: 491(7423) Pages: 284-287
  • Peer Reviewed
• [Journal Article] A role for transcription from a piRNA cluster in de novo piRNA production (2012)
  • Author(s): Kawaoka S, Mitsutake H, Kiuchi T, Kobayashi M, Yoshikawa M, Suzuki Y, Sugano S, Shimada T, Kobayashi J, Tomari Y, Katsuma S
  • Journal Title: RNA Volume: 18(2) Pages: 265-273
  • Peer Reviewed
• [Journal Article] Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish (2012)
  • Author(s): Mishima Y, Fukao A, Kishimoto T, Sakamoto H, Fujiwara T, Inoue K
  • Journal Title: Proc Natl Acad Sci USA Volume: 109(4) Pages: 1104-1109
  • Peer Reviewed
• [Journal Article] RNA and epigenetic silencing : insight from fission yeast (2012)
  • Author(s): Goto DB, Nakayama J.
  • Journal Title: Dev Growth Differ Volume: 54(1) Pages: 129-141
  • Peer Reviewed
• [Journal Article] The silkworm W chromosome is a source of female-enriched piRNAs (2011)
  • Author(s): Kawaoka S, Kadota K, Arai Y, Suzuki Y, Fujii T, Abe H, Yasukochi Y, Mita K, Sugano S, Shimizu K, Tomari Y, Shimada T, Katsuma S
  • Journal Title: RNA Volume: 17(12) Pages: 2144-2151
  • Peer Reviewed
• [Journal Article] 3' end formation of PIWI-interacting RNAs in vitro (2011)
  • Author(s): Kawaoka S, Izumi N, Katsuma S, Tomari Y
  • Journal Title: Mol Cell Volume: 43(6) Pages: 1015-1022
  • Peer Reviewed
• [Journal Article] Zygotic amplification of secondary piRNAs during silkworm embryogenesis (2011)
  • Author(s): Kawaoka S, Arai Y, Kadota K, Suzuki Y, Hara K, Sugano S, Shimizu K, Tomari Y, Shimada T, Katsuma S
  • Journal Title: RNA Volume: 17(7) Pages: 1401-1407
  • Peer Reviewed
• [Journal Article] Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus (2011)
  • Author(s): Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H
  • Journal Title: Science Volume: 332 Pages: 848-852
  • Peer Reviewed
• [Journal Article] MITOPLD is a mitochondrial protein essential for nuage nuage formation and piRNA buigenesis in the mouse germline (2011)
  • Author(s): Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, Hoki Y, Fujiyama A, Shibata T, Sado T, Noce T, Nakano T, Nakatsuji N, Lin H, Sasaki H
  • Journal Title: Dev Cell Volume: 23 Pages: 364-375
  • Peer Reviewed
• [Journal Article] Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes (2010)
  • Author(s): Iwasaki S, Kobayashi M, Yoda M, Sakaguchi Y, Katsuma S, Suzuki T, Tomari Y
  • Journal Title: Mol Cell Volume: 39(2) Pages: 292-299
  • Peer Reviewed
• [Journal Article] Sunspot, a link between Wingless signaling and endoreplication in Drosophila (2010)
  • Author(s): Taniue K, Nishida A, Hamada F, Sugie A, Oda T, Ui-Tei K, Tabata T, Akiyama T
  • Journal Title: Development Volume: 137(10) Pages: 1755-1764
  • Peer Reviewed
• [Journal Article] Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea (2010)
  • Author(s): Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T
  • Journal Title: Nat Chem Biol Volume: 6(4) Pages: 277-282
  • Peer Reviewed
• [Journal Article] RNA silencing in germlines--exquisite collaboration of Argonaute proteins with small RNAs for germline survival (2009)
  • Author(s): Siomi MC, Kuramochi-Miyagawa S
  • Journal Title: Curr. Opin. Cell. Biol Volume: 21(3) Pages: 426-434
  • Peer Reviewed
• [Journal Article] Yb integrates piRNA intermediates and processing factors into perinuclear bodies to enhance piRISC assembly
  • Author(s): Murota Y, Ishizu H, Nakagawa, S, Iwasaki YW, Shibata S, Kamatani, MK, Saito K, Okano H, Siomi H and Siomi MC
  • Journal Title: Cell Reports Volume: (in press)
  • Peer Reviewed