Centers & Labs

RIKEN Center for Integrative Medical Sciences

Laboratory for Transcriptome Technology

Team Leader: Piero Carninci (Ph.D.)
Piero  Carninci(Ph.D.)

We will develop technologies to comprehensively detect non-coding RNAs and comprehensively screen their functions. Using those technologies, we will explore regulatory interactions of ncRNAs within cells, with particular emphasis on the interaction of non-coding RNA with chromatin, retrotransposition and ncRNAs having a role in the regulation of protein synthesis. These technologies will be important for the development of cell conversion methods. Additional emphasis will be on standardization of transcriptome technologies like CAGE, to make a universal and finely quantitative transcriptome technology. Such standardization is essential for the identification of novel biomarkers and drug target candidates.

Main Research Field

Biological Sciences

Related Research Fields

Biology

Keywords

  • CAGE
  • RNA
  • Single Cell
  • Bioinformatics
  • Genomics

Selected Publications

  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.

Lab Members

Principal Investigator

Piero Carninci
Team Leader

Core Members

Kosuke Hashimoto
Senior Research Scientist
Anton Kratz
Research Scientist
Giovanni Pascarella
Research Scientist
Alessandro Bonetti
Research Scientist
Supat Thongjuea
Research Scientist
Kazuhiro Nitta
Research Scientist
Mitsuyoshi Murata
Technical Scientist
Hiromi Sueki
Technical Scientist
Miki Kojima
Technical Scientist
Sachi Kato
Technical Scientist
Harshita Sharma
Postdoctoral Researcher
Hazuki Takahashi
Research Associate
Masahito Yoshihara
Junior Research Associate
Michael Boettcher
International Program Associate
Matthew Valentine
Technical Staff I
Quan Hoang Nguyen
Visiting Scientist
Maruska Budic
Visiting Researcher
Mariko Chinzei
Student Trainee
Ana Kozhuharova
Part-time Worker