RIKEN Center for Life Science Technologies

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Labs & Technologies

Epigenome Technology Exploration Unit

Solving the epigenomic codes

Unit Leader
Aki Minoda  Ph.D.

W421, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 JAPAN
Tel: +81-(0)45-503-9309 (Ext. 8113)

2_8_minoda.png

Research Area

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 Publications List

1

Comparative analysis of metazoan chromatin organization.

Ho JW, Jung YL, Liu T, Alver BH*, Lee S, Ikegami K*, Sohn KA*, Minoda A*, Tolstorukov MY*, Appert A*, Parker SC*, Gu T*, Kundaje A*, Riddle NC*, Bishop E*, Egelhofer TA*, Hu SS*, Alekseyenko AA*, Rechtsteiner A*, Asker D*, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.
*Co-second authors
Nature, 512(7515), 449-452 (2014).
2

Impact of sequencing depth in ChIP-seq experiments

Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.
Nucleic Acids Res, 42(9), e74 (2014).
3

Nature and function of insulator protein binding sites in the Drosophila genome.

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.
Genome Res, 22(11), 2188-2198 (2012).
4

Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.

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.
PLoS Genet, 8(9), e1002954. (2012).
5

Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.

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.
PLoS Genet, 8(4), e1002646 (2012).
6

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

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.
Nature, 471(7339), 480-485 (2011).
7

Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair.

Chiolo I, Minoda A, Colmenares SU, Polyzos A, Costes SV, Karpen GH.
Cell, 144(5), 732-744 (2011).
8

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.

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.
*Co-first authors
Genome Res, 21(2), 147-163 (2011).
9

An assessment of histone-modification antibody quality.

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.
*Co-first authors
Nat Struct Mol Biol, 18(1), 91-93 (2011).
10

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

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.
Science, 330(6012), 1787-1797 (2010).

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