Laboratory for Cellular Function Conversion Technology

Main Publications List

　　

1. Yoshino, T., Suzuki, T., Nagamatsu, G., Yabukami, H., Ikegaya, M., Kishima, M., Kita, H., Imamura, T., Nakashima, K., Nishinakamura, R., Tachibana, M., Inoue, M., Shima, Y., Morohashi, K., and Hayashi K.
   "Generation of ovarian follicles from mouse pluripotent stem cells
   Science 373(6552):eabe0237 (2021)
2. Suzuki T, Furuhata E, Maeda S, Kishima M, Miyajima Y, Tanaka Y, Lim J, Nishimura H, Nakanishi Y, Shojima A, Suzuki H.
   "Master Transcription Factors Regulate the DNA Methylation Landscape During Hepatocyte Differentiation."
   bioRxiv, (2020)
   10.1101/2020.12.16.423165
3. Nakano R, Kitanaka T, Namba S, Kitanaka N, Sato M, Shibukawa Y, Masuhiro Y, Kano K, Matsumoto T, Sugiya H.
   "All-trans retinoic acid induces reprogramming of canine dedifferentiated cells into neuron-like cells.
   PLOS ONE, 15, e0229892 (2020)
4. Pervolarakis N, Nguyen QH, Williams J, Gong Y, Gutierrez G, Sun P, Jhutty D, Zheng GXY, Nemec CM, Dai X, Watanabe K, Kessenbrock K."
   "Integrated Single-Cell Transcriptomics and Chromatin Accessibility Analysis Reveals Regulators of Mammary Epithelial Cell Identity."
   Cell Rep., 33, 108273 (2020)
5. Watanabe K, Panchy N, Noguchi S, Suzuki H, Hong T.
   "Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition."
   NPJ Syst Biol Appl. 2019 Jun 14;5:21.
6. Watanabe K, Liu Y, Noguchi S, Murray M, Chang JC, Kishima M, Nishimura H, Hashimoto K, Minoda A, Suzuki H.
   "OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages."
   Sci Rep. 2019 Apr 24;9(1):6490.
7. Guler R, Mpotje T, Ozturk M, Nono JK, Parihar SP, Chia JE, Abdel Aziz N, Hlaka L, Kumar S, Roy S, Penn-Nicholson A, Hanekom WA, Zak DE, Scriba TJ, Suzuki H, Brombacher F.
   "Batf2 differentially regulates tissue immunopathology in Type 1 and Type 2 diseases."
   Mucosal Immunol. 2019 Mar;12 (2):390-402.
8. Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Guler R, Bajic VB, Brombacher F, Suzuki H.
   "Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages."
   Sci Rep. 2018 Apr 30;8(1):6758
9. Suzuki T, Shimizu Y, Furuhata E, Maeda S, Kishima M, Nishimura H, Enomoto S, Hayashizaki Y, Suzuki H.
   "RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells."
   Blood Adv., 1(20):1699-1711. (2017)
10. Suzuki T, Maeda S, Furuhata E, Shimizu Y, Nishimura H, Kishima M, Suzuki H.
    A screening system to identify transcription factors that induce binding site-directed DNA demethylation.
    Epigenetics Chromatin., 10(1):60. (2017)
11. Goyal S, Suzuki T, Li JR, Maeda S, Kishima M, Nishimura H, Shimizu Y, Suzuki H.
    RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions.
    BMC Mol Biol., 8(1):9. (2017)
12. 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, 543(7644):199-204. (2017)
13. Li JR, Suzuki T, Nishimura H, Kishima M, Maeda S, Suzuki H.
    Asymmetric Regulation of Peripheral Genes by Two Transcriptional Regulatory Networks.
    PLoS One, 11(8):e0160459. (2016)
14. Murakawa Y, Yoshihara M, Kawaji H, Nishikawa M, Zayed H, Suzuki H, Fantom Consortium, Hayashizaki Y.
    Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases.
    Trends Genet., 32(2):76-88. (2016)
15. Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS, FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J.
    A predictive computational framework for direct reprogramming between human cell types.
    Nat Genet., 48(3):331-5. (2016)
16. Roy S, Guler R, Parihar SP, Schmeier S, Kaczkowski B, Nishimura H, Shin JW, Negishi Y, Ozturk M, Hurdayal R, Kubosaki A, Kimura Y, de Hoon MJ, Hayashizaki Y, Brombacher F, Suzuki H.
    Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.
    J Immunol., 194(12):6035-44. (2015)
17. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
    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.
    Science, 347(6225):1010-4. (2015)
18. Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.
    Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJ, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Bajic VB, Guler R; Fantom Consortium, Brombacher F, Suzuki H.
    Nucleic Acids Res., 43(14):6969-82. (2015)
19. A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.
    Tomaru Y, Hasegawa R, Suzuki T, Sato T, Kubosaki A, Suzuki M, Kawaji H, Forrest AR, Hayashizaki Y, FANTOM Consortium, Shin JW, Suzuki H.
    Nucleic Acids Res., 42(14):8905-13. (2014)
20. A promoter-level mammalian expression atlas.
    FANTOM Consortium and the RIKEN PMI and CLST (DGT), 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.
    Nature., 507(7493):462-70. (2014)
21. An atlas of active enhancers across human cell types and tissues.
    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, Forrest ARR, Carninci P, Rehli M, Sandelin A.
    Nature, 507(7493):455-461. (2014)
22. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.
    Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR; FANTOM Consortium, Suzuki H.
    Sci Rep., 4:5228 (2014)
23. Capturing drug responses by quantitative promoter activity profiling.
    Kajiyama K, Okada-Hatakeyama M, Hayashizaki Y, Kawaji H, Suzuki H.
    CPT Pharmacometrics Syst Pharmacol., 2:e77. (2013)
24. Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming.
    Shin JW, Suzuki T, Ninomiya N, Kishima M, Hasegawa Y, Kubosaki A, Yabukami H, Hayashizaki Y, Suzuki H.
    Nucleic Acids Res., 40(21):e165. (2012)
25. Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.
    Suzuki T, Nakano-Ikegaya M, Yabukami-Okuda H, de Hoon M, Severin J, Saga-Hatano S, Shin JW, Kubosaki A, Simon C, Hasegawa Y, Hayashizaki Y, Suzuki H.
    PLoS One, 7(3):e33474. (2012)
26. CC chemokine ligand 2 and leukemia inhibitory factor cooperatively promote pluripotency in mouse induced pluripotent cells.
    Hasegawa Y, Takahashi N, Forrest AR, Shin JW, Kinoshita Y, Suzuki H, Hayashizaki Y.
    Stem Cells, 29(8):1196-205. (2011)
27. An atlas of combinatorial transcriptional regulation in mouse and man.
    Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y.
    Cell, 140(5):744-52. (2010)
28. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
    FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.
    Nat Genet., 41(5):553-62. (2009)