研究紹介

生命医科学研究センター

トランスクリプトーム研究チーム

チームリーダー CARNINCI Piero (Ph.D.)
CARNINCI Piero (Ph.D.)

細胞内の全DNAの塩基配列情報をさす「ゲノム」に対し、細胞内の全転写産物(全RNA)を「トランスクリプトーム」とよびます。トランスクリプトームの大半はタンパク質の情報を持たないノンコーディングRNA(ncRNA)であり、エピジェネティック制御やタンパク質合成制御、幹細胞性の制御など様々な機能に関わっています。当チームは、ncRNAを網羅的に検出する技術やその機能を網羅的に調べる技術を開発し、新たなバイオマーカーの同定や薬剤候補因子の発見、細胞制御、細胞変換に応用します。ncRNAクロマチン、レトロトランスポゾンのncRNAによる制御や、ncRNAのタンパク質合成における制御を調べます。また定量的な発現解析手法であるCAGE技術等のトランスクリプトーム技術の標準化を進めます。

研究主分野

総合生物

研究関連分野

生物学

キーワード

  • CAGE法
  • RNA
  • シングルセル
  • バイオインフォルマティクス
  • ゲノミクス

主要論文

  1. Hon Chung Chau, RAMILOWSKI Jordan, Harshbarger Jayson Mathew, Bertin Nicolas, Rackham Owen, Gough Julian, Denisenko Elena, Schmeier Sebastian, Poulsen Thomas M, Severin Jessica, Lizio Marina, Kawaji Hideya, Kasukawa Takeya, Itoh Masayoshi, Burroughs Alexander, Noma Shohei, Djebali Sarah, Tanvir Alam, Medvedeva Yulia A., Testa Alison C., Lipovich Leonard, Yip Chi Wai , Abugessaisa Imad, Mendez Mickaël, Hasegawa Akira, Tang Dave, Lassmann Timo, Heutink Peter, Babina Magda, Wells Christine, Kojima Soichi, Nakamura Yukio, Suzuki Harukazu, Daub Carsten O., de Hoon Michiel JL, Arner Erik, Hayashizaki Yoshihide, Carninci Piero, and Forrest Alistair Raymond Russel.
    "An atlas of human long non-coding RNAs with accurate 5’ends"
    Nature, 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374. Epub 2017 Mar 1.
  2. Schein Aleks, Zucchelli Silvia, Kauppinen Sakari, Gustincich Stefano, and Carninci Piero.
    "Identification of antisense long noncoding RNAs that function as SINEUPs in human cells"
    Sci Rep 2016 Sep 20;6:33605. doi: 10.1038/srep33605.
  3. Hashimoto K, Suzuki AM, Dos Santos A, Desterke C, Collino A, Ghisletti S, Braun E, Bonetti A, Fort A, Qin XY, Radaelli E, Kaczkowski B, Forrest AR, Kojima S, Samuel D, Natoli G, Buendia MA, Faivre J, Carninci P.:
    "CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors."
    Genome Res. 2015 Dec;25(12):1812-24. doi: 10.1101/gr.191031.115. Epub 2015 Oct 28.
  4. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.:
    "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells."
    Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.
  5. Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, Suzuki H, Wei CL, Koseki H; FANTOM Consortium, Hasegawa Y, Forrest AR, Carninci P.:
    "Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance."
    Nat Genet. 2014 Jun;46(6):558-66. doi: 10.1038/ng.2965. Epub 2014 Apr 28.
  6. Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.:
    "A promoter-level mammalian expression atlas."
    Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.
  7. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.:
    "An atlas of active enhancers across human cell types and tissues."
    Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038/nature12787.
  8. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S.:
    "Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat."
    Nature. 2012 Nov 15;491(7424):454-7. doi: 10.1038/nature11508. Epub 2012 Oct 14.
  9. ENCODE Project Consortium.:
    "An integrated encyclopedia of DNA elements in the human genome."
    Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.
  10. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P.:
    "The regulated retrotransposon transcriptome of mammalian cells."
    Nat Genet. 2009 May;41(5):563-71. doi: 10.1038/ng.368. Epub 2009 Apr 19.

メンバーリスト

主宰者

CARNINCI Piero
チームリーダー

メンバー

橋本 浩介
専任研究員
KRATZ Anton
研究員
PASCARELLA Giovanni
研究員
BONETTI Alessandro
研究員
THONGJUEA Supat
研究員
新田 和広
研究員
村田 光義
技師
末木 広美
技師
小島 美樹
技師
加藤 紗智
技師
SHARMA Harshita
特別研究員
高橋 葉月
リサーチアソシエイト
吉原 正仁
大学院生リサーチ・アソシエイト
BOETTCHER Michael
国際プログラム・アソシエイト
VALENTINE Matthew
テクニカルスタッフⅠ
NGUYEN Quan Hoang
客員研究員
BUDIC Maruska
訪問研究員
鎭西 真理子
研修生
KOZHUHAROVA Ana
研究支援パートタイマー