Research Summary

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

• 1. *Kubo N, Uehara R, Uemura S, Ohishi H, Shirane S, and Sasaki H.:
  "Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells"
  Nat Commun, 15(1):3266, 2024.
• 2. *Kubo N, Chen PB, Hu R, Ye Z, and Ren B.:
  "H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation."
  Mol Cell, 84(9):1742-1752.e5, 2024.
• 3. *Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, and Ren B.:
  "The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes."
  Cell Rep, 8;41(6):111630, 2022.
• 4. *Li EY, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion O.B, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, & Ren B.:
  "An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum."
  Nature, 598(7879):129-136, 2021.
• 5. *Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker J, Conte M, Gorkin D, Yu M, Li B, Dixon J, Hu M, Nicodemi M, Zhao H, and Ren B.:
  "Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation."
  Nat Struct Mol Biol, 28(2):152-161, 2021.
• 6. *Pugacheva EM, Kubo N, Loukinov D, Tajmul M, Kang S, Kovalchuk AL, Strunnikov AV, Zentner GE, Ren B, and Lobanenkov VV.:
  "CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention."
  Proc. Natl. Acad. Sci., 117(4):2020-2031, 2020.
• 7. *Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, and Ren B.:
  "Joint profiling of DNA methylation and chromatin architecture in single cells."
  Nat Methods, 16(10):991-993, 2019.
• 8. *Kubo N, Harada T, Shiraishi Y, Nosaki K, Nakagaki N, Takeshita M, Ouchi H, Iwama E, Tanaka K, Okamoto I, Sasaki H, and Nakanishi Y.:
  "Identification of genomic alterations acquired during treatment with EGFR-TKIs in non-small cell lung cancer."
  Anticancer Res, 39(2):671-677, 2019.
• 9. *Shibahara D, Tanaka K, Iwama E, Kubo N, Ota K, Azuma K, Harada T, Fujita J, Nakanishi Y, and Okamoto I.:
  "Intrinsic and Extrinsic Regulation of PD-L2 Expression in Oncogene-Driven Non-Small Cell Lung Cancer."
  J Thorac Oncol, 13(7):926-937, 2018.
• 10. *Kubo N, Toh H, Shirane K, Shirakawa T, Kobayashi H, Sato T, Sone H, Sato Y, Tomizawa S, Tsurusaki Y, Shibata H, Saitsu H, Suzuki Y, Matsumoto N, Suyama M, Kono T, Ohbo K, and Sasaki H.:
  "DNA Methylation and Gene Expression Dynamics during Spermatogonial Stem Cell Differentiation in the Early Postnatal Mouse Testis."
  BMC Genomics, 624, 16, 2015.

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• Transcriptome-Epigenome Research and Development Team’s website

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