Centers & Labs

RIKEN Center for Life Science Technologies

Epigenome Technology Exploration Unit

Unit Leader: Aki Minoda (Ph.D.)
Aki  Minoda(Ph.D.)

Our mission is to understand the very complex regulations of cellular functions and regulations at the epigenetic level, with focus on histone modifications. In recent years, a lot of data on the genome-wide localisation of histone modifications (the “Epigenome”) have been obtained and analysed. There are hundreds of possible combinations of modifications and there are in fact many modifications found at any given locus, which reflects the complex regulations it may be responsible for. However, whether a different combination of these modifications mean different things is still unclear, mainly due to the lack of technologies that can analyse them in such way.

One of the main focuses of our lab is to develop novel epigenomic technologies to study combinations of histone modifications that are present on each histone and nucleosome. By applying such methods to disease cells, including cancer, we aim to identify epigenomic signatures that may exist, which may lead to identification of novel diagnostic and therapeutic targets.

Main Research Field

Biological Sciences

Related Research Fields


Research Subjects

  • Development of Single Cell Epigenome sequencing technology
  • Application of the Single Cell Epigenome sequencing technology in disease cells, including cancer stem cells
  • Identification of therapeutic targets based on the Single Cell Epigenome

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
  1. *Kharchenko, PV., Alekseyenko, AA., Schwartz, YB., Minoda, A., Riddle, NC., Ernst, J., Sabo, PJ., Larschan, E., Gorchakov, AA., Gu, T., Linder-Basso, D., Plachetka, A., Shanower, G., Tolstorukov, MY., Luquette, LJ., Xi, R., Jung, YL., Park, RW., Bishop, EP., Canfield, TK., Sandstrom, R., Thurman, RE., MacAlpine, DM., Stamatoyannopoulos, JA., Kellis, M., Elgin, SC., Kuroda, MI., Pirrotta, V., Karpen, GH., Park, PJ.
    "Comprehensive analysis of the chromatin landscape in Drosophila melanogaster"
    Nature 471, 480-5 (2011)
  2. *Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH.
    "Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin"
    Genome Res. 21(2), 147-63 (2011)
  3. *Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD.
    "An assessment of histone-modification antibody quality"
    Nat Struct Mol Biol. 18(1), 91-3 (2011)
  4. *modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.
    "Identification of functional elements and regulatory circuits by Drosophila modENCODE"
    Science 330(6012), 1787-97 (2010)
  5. *Chiolo I, Minoda A, Colmenares SU, Polyzos A, Costes SV, Karpen GH.
    "Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair"
    Cell 144(5), 732-44, (2011)
  6. *Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Elgin SC.
    "Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain"
    PLoS Genet. 8(9):e1002954 (2012)
  7. *Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA,Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V.
    "Nature and function of insulator protein binding sites in the Drosophila genome"
    Genome Res. 22(11), 2188-98 (2012)
  8. *Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Karpen GH, Pirrotta V, Kuroda MI, Park PJ.
    "Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context"
    PLoS Genet. 8(4), e1002646 (2012)
  9. *Minoda A, Saitoh S, Takahashi K, Toda T.
    "BAF53/Arp4 homolog Alp5 in fission yeast is required for histone H4 acetylation, kinetochore-spindle attachment, and gene silencing at centromere"
    Mol Biol Cell. 16(1), 316-27 (2005)

Lab Members

Principal Investigator

Aki Minoda
Unit Leader

Core Members

Lusy Handoko
Research Scientist
Jen-Chien Chang
Postdoctoral Researcher
Jitsutaro Mac Master
Part-time Worker

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Tel: +81-(0)45-503-9309

Email: akiko.minoda [at]