Centers & Labs

RIKEN Center for Life Science Technologies

Genomics Algorithms Development Unit

Unit Leader: Michiel Jan Laurens De Hoon (Ph.D.)
Michiel Jan Laurens De Hoon(Ph.D.)

Genome-wide transcriptome studies such as FANTOM and ENCODE have shown that genomic loci generate a wide variety of transcript isoforms, many of which do not code for proteins. Though in most cases the specific biological function of such non-coding RNAs is unknown, their cell-type specific expression patterns suggest that they play essential roles in establishing cell type identity. The unit will develop and apply novel methodologies to analyze genome-wide data generated using next-generation sequencers for the purpose of categorizing and functionally understanding RNA molecules, their role in biological networks, as well as the relation between the function and the 3D structure of the non-coding RNA.

Research Subjects

  • Non-coding RNA
  • FANTOM6
  • RNA structure
  • Bioinformatics

Selected Publications

  1. De Hoon, M., Shin, J.W., Carninci, P.:
    "Paradigm shifts in genomics through the FANTOM projects"
    Mammalian Genome 26, 391-402 (2015).
  2. Arner, E.; Daub, C.O.; Vitting-Seerup, K.; Andersson, R.; Lilje, B.; Drabløs, F.; Lennartsson, A.; Rönnerblad, M.; Hrydziuszko, O.; Vitezic, M.; Freeman, T.C.; Alhendi, A.M.; Arner, P.; Axton, R.; Baillie, J.K.; Beckhouse, A.; Bodega, B.; Briggs, J.; Brombacher, F.; Davis, M.; Detmar, M.; Ehrlund, A.; Endoh, M.; Eslami, A.; Fagiolini, M.; Fairbairn, L.; Faulkner, G.J.; Ferrai, C.; Fisher, M.E.; Forrester, L.; Goldowitz, D.; Guler, R.; Ha, T.; Hara, M.; Herlyn, M.; Ikawa, T.; Kai, C.; Kawamoto, H.; Khachigian, L.M.; Klinken, S.P.; Kojima, S.; Koseki, H.; Klein, S.; Mejhert, N.; Miyaguchi, K.; Mizuno, Y.; Morimoto, M.; Morris, K.J.; Mummery, C.; Nakachi, Y.; Ogishima, S.; Okada-Hatakeyama, M.; Okazaki, Y.; Orlando, V.; Ovchinnikov, D.; Passier, R.; Patrikakis, M.; Pombo, A.; Qin, X.Y.; Roy, S.; Sato, H.; Savvi, S.; Saxena, A.; Schwegmann, A.; Sugiyama, D.; Swoboda, R.; Tanaka, H.; Tomoiu, A.; Winteringham, L.N.; Wolvetang, E.; Yanagi-Mizuochi, C.; Yoneda, M.; Zabierowski, S.; Zhang, P.; Abugessaisa, I.; Bertin, N.; Diehl, A.D.; 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, T.F.; Mungall, C.J.; Murata, M.; Nishiyori-Sueki, H.; Sahin, S.; Nagao-Sato, S.; Severin, J.; De Hoon, M.J.L.; Kawai, J.; Kasukawa, T.; Lassmann, T.; Suzuki, H.; Kawaji, H.; Summers, K.M.; Wells, C.; FANTOM Consortium; Hume, D.A.; Forrest, A.R.; Sandelin, A.; Carninci, P.; Hayashizaki, Y.:
    "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells"
    Science 347, 1010-1014 (2015).
  3. Boele, J., Persson, H., Shin, J.W., Ishizu, Y., Newie, I.S., Søkilde, R., Hawkins, S.M., Coarfa, C., Ikeda, K., Takayama, K.I., Horie-Inoue, K., Ando, Y., Burroughs, A.M., Sasaki, C,, Suzuki, C., Sakai, M., Aoki, S., Ogawa, A., Hasegawa, A., Lizio, M., Kaida, K., Teusink, B., Carninci, P., Suzuki, H., Inoue, S., Gunaratne, P.H., Rovira, C., Hayashizaki, Y., De Hoon, M.J.L.:
    "PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease"
    Proceedings of the National Academy of Sciences USA 111, 11467-11472 (2014).
  4. Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C.A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., Noro, Y., Wong, C.H., De Hoon, M.J.L., Andersson, R., Sandelin, A., Suzuki, H., Wei, C.L., Koseki, H., The FANTOM Consortium, Hasegawa, Y., Forrest, A.R.R., Carninci, P.:
    "Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance"
    Nature Genetics 46, 558-566 (2014).
  5. FANTOM Consortium and the RIKEN PMI and CLST (DGT).:
    "A promoter-level mammalian expression atlas"
    Nature 507, 462-470 (2014)
  6. Francia, S., Michelini, F., Saxena, A., Tang, D., De Hoon, M.J.L., Anelli, V., Mione, M., Carninci, P., d'Adda di Fagagna, F.:
    "Site-specific DICER and DROSHA RNA products control the DNA-damage response"
    Nature 488, 231-235 (2012)
  7. Burroughs, A.M., Ando, Y., De Hoon, M.J.L., Tomaru, Y., Nishibu, T., Ukekawa, R., Funakoshi, T., Kurokawa, T., Suzuki, H., Hayashizaki, Y., Daub, C.O.:
    "A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness"
    Genome Research 20, 1398-1410 (2010)
  8. De Hoon, M.J.L., Taft, R.J., Hashimoto, T., Kanamori-Katayama, M., Kawaji, H., Kawano, M., Kishima, M., Lassmann, T., Faulkner, G.J., Mattick, J.S., Daub, C.O., Carninci, P., Kawai, J., Suzuki, H., Hayashizaki, Y.:
    "Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries"
    Genome Research 20, 257-264 (2010)
  9. Cock, P.J., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., De Hoon, M.J.L.:
    "Biopython: freely available Python tools for computational molecular biology and bioinformatics"
    Bioinformatics 25, 1422-1423 (2009)
  10. The FANTOM Consortium & Riken Omics Science Center.:
    "The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line"
    Nature Genetics 41, 553-562 (2009)

Lab Members

Principal Investigator

Michiel Jan Laurens De Hoon
Unit Leader

Core Members

Saumya Agrawal
Postdoctoral Researcher
Timo Lassmann
Visiting Scientist

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan

Email: michiel.dehoon [at] riken.jp

Related links

Recent research results