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RIKEN Center for Integrative Medical Sciences Laboratory for Transcriptome Technology

Team Leader: Piero Carninci (Ph.D.)

Research Summary

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 Fields

  • Biological Sciences

Related Research Fields

  • Biology

Keywords

  • CAGE
  • RNA
  • Single Cell
  • Bioinformatics
  • Genomics

Selected Publications

  • 1.Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Noguchi S, Agirre E, Kashi K, Samudyata, Luginbuühl J, Cazzoli R, Agrawal S, Luscombe NM, Blanchette M, Kasukawa T, Hoon M, Arner E, Lenhard B, Plessy C, Castelo- Branco G, Orlando V, Carninci P.
    "RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions."
    Nat Commun. 2020 Feb 24;11(1):1018. doi: 10.1038/s41467-020-14337-6.
  • 2.Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima Y, Yabukami H, Terooatea T, Sasaki T, Suzuki T, Valentine M, Pascarella G, Okazaki Y, Suzuki H, Shin JW, Minoda A, Taniuchi I, Okano H, Arai Y, Hirose N, Carninci P.
    "Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians."
    Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):24242-24251. doi: 10.1073/pnas.1907883116.
  • 3.Hirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori- Kondo A, Takeuchi O, Carninci P, Katayama S, Hayashizaki Y, Kere J, Kawaji H, Murakawa Y.
    "NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements."
    Nat Genet. 2019 Sep;51(9):1369-1379. doi: 10.1038/s41588-019-0485-9.
  • 4.Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbuühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin JW.
    "C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution."
    Nat Commun. 2019 Jan 21;10(1):360. doi: 10.1038/s41467-018-08126-5.
  • 5.Nguyen Q, Aguado J, Iannelli F, Suzuki AM, Rossiello F, d'Adda di Fagagna F, Carninci P.
    "Target-enrichment sequencing for detailed characterization of small RNAs."
    Nat Protoc. 2018 Apr;13(4):768-786. doi: 10.1038/nprot.2018.001.
  • 6.Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR.
    "An atlas of human long non-coding RNAs with accurate 5' ends."
    Nature. 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374.
  • 7.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.
  • 8.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.
  • 9.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.
  • 10.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, Muüller F, Forrest ARR, Carninci P, Rehli M, Sandelin A.
    "An atlas of active enhancers across human cell types and tissues."
    Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787.

Recent Research Results

Events

Publications

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Lab Members

Principal investigator

Piero Carninci
Team Leader

Core members

Masaki Kato
Senior Scientist
Giovanni Pascarella
Research Scientist
Harshita Sharma
Research Scientist
Hazuki Takahashi
Special Fixed Term Contract Researcher
Pauline Robbe
Postdoctoral Researcher
Matthew Valentine
Postdoctoral Researcher
Diane Delobel
Research Associate
Mitsuyoshi Murata
Expert Technician
Hiromi Sueki
Expert Technician
Miki Kojima
Expert Technician
Sachi Kato
Expert Technician
Wing Hin Yip
Technical Staff I

Careers

Position Deadline
Seeking a Part timer (Y20004) Open until filled
Seeking a Postdoctoral Researcher or Technical Staff I (IMS101-2004) Open until filled
Seeking a Research Scientist, Postdoctoral Researcher or Technical Staff I (IMS101-2003) Open until filled

Contact Information

1-7-22 Suehiro-cho, Tsurumi-ku
Yokohama, Kanagawa
230-0045, Japan
Email: carninci [at] riken.jp

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