Dissection of epigenome dynamics of germ cel specification pathway through establishement of a ChIP-seq method from small number of cells

• Project/Area Number: 24681039
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Genome biology
• Research Institution: Kyoto University
• Principal Investigator: KURIMOTO Kazuki 京都大学, 医学(系)研究科(研究院), 助教 (20415152)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥23,010,000 (Direct Cost: ¥17,700,000、Indirect Cost: ¥5,310,000); Fiscal Year 2014: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000); Fiscal Year 2013: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2012: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
• Keywords: ChIP-seq / BLIMP1 / primordial germ cell / 始原生殖細胞 / 微量 / 次世代シークエンサー / 生殖細胞 / エピゲノム / PGC / Blimp1 / Blimpl

Outline of Final Research Achievements

The identity of all of the cells that comprise induviduals are defined by the cellular epigenom in the nuclei. Due to technical limitation,genome-wide analysis of binding sites of transcriptional regulators are almost limited to cell types for which many cells are abvailable, including hematopoietic cells and cultured cells. I established a method for ChIP-seq of transcriptiopn factors from small number of cells and enabled identification of the genome-wide binding sites of transcription factor at 1/100 ~ 1/1000 time previous scale. Using thise method, Using this method, I determined binding sites of two key transcription factors for germ cell specificatin pathway, BLIMP1 and T (Brachyury), in vitro. In addition, I determined representative histone modifications associated to active transcription and repression, and revealed landscape of chromatin dynamics during the PGC specifciation in vitro.

Research Products

• [Journal Article] Quantitative Dynamics of Chromatin Remodeling during Germ Cell Specification from Mouse Embryonic Stem Cells (2015)
  • Author(s): Kurimoto, K., Yabuta, Y., Hayashi, K., Ohta, H., Kiyonari, H., Mitani, T., Moritoki, Y., Kohri, K., Kimura, H., Yamamoto, T., Katou, Y., Shirahige, K., Saitou, M.
  • Journal Title: Cell Stem Cell Volume: 16 Issue: 5 Pages: 517-532
  • DOI: 10.1016/j.stem.2015.03.002
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression (2015)
  • Author(s): Nakamura, T., Yabuta, Y., Okamoto, I., Aramaki, S., Yokobayashi, S., Kurimoto, K., Sekiguchi, K., Nakagawa, M., Yamamoto, T., Saitou, M.
  • Journal Title: Nucleic Acids Res Volume: - Issue: 9 Pages: e60-e60
  • DOI: 10.1093/nar/gkv134
  • NAID: 120005825922
  • Peer Reviewed / Open Access
• [Journal Article] Paternal nucleosomes: are they retained in developmental promoters or gene deserts? (2014)
  • Author(s): Saitou, M., Kurimoto, K.
  • Journal Title: Dev Cell Volume: 30 Issue: 1 Pages: 6-8
  • DOI: 10.1016/j.devcel.2014.06.025
• [Journal Article] Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages (2014)
  • Author(s): Ohnishi, Y., Huber, W., Tsumura, A., Kang, M., Xenopoulos, P., Kurimoto, K., Oles, A. K., Arauzo-Bravo, M. J., Saitou, M., Hadjantonakis, A. K., Hiiragi, T.
  • Journal Title: Nat Cell Biol Volume: 16 Issue: 1 Pages: 27-37
  • DOI: 10.1038/ncb2881
  • Peer Reviewed
• [Journal Article] CCR1-mediated accumulation of myeloid cells in the liver microenvironment promoting mouse colon cancer metastasis (2014)
  • Author(s): Hirai H, Fujishita T, Kurimoto K, Miyachi H, Kitano S, Inamoto S, Itatani Y, Saitou M, Maekawa T, Taketo MM
  • Journal Title: Clin Exp Metastasis Volume: 31 Issue: 8 Pages: 977-989
  • DOI: 10.1007/s10585-014-9684-z
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] A mesodermal factor, T, specifies mouse germ cell fate by directly activating germline determinants (2013)
  • Author(s): Aramaki, S., Hayashi, K., Kurimoto, K., Ohta, H., Yabuta, Y., Iwanari, H., Mochizuki, Y., Hamakubo, T., Kato, Y., Shirahige, K., and Saitou, M
  • Journal Title: Developmental Cell Volume: 27 Issue: 5 Pages: 516-529
  • DOI: 10.1016/j.devcel.2013.11.001
  • Peer Reviewed / Open Access
• [Journal Article] Induction of mouse germ-cell fate by transcription factors in vitro. (2013)
  • Author(s): Nakaki F, Hayashi K, Ohta H, Kurimoto K, Yabuta Y, Saitou M.
  • Journal Title: Nature Volume: 501 Issue: 7466 Pages: 222-226
  • DOI: 10.1038/nature12417
  • Peer Reviewed
• [Journal Article] Replication-coupled passive DNA demethylation for the erasure of genome imprints in mice (2013)
  • Author(s): Kagiwada, S., Kurimoto, K., Hirota, T., Yamaji, M., and Saitou, M
  • Journal Title: The EMBO Journal Volume: 32 Issue: 3 Pages: 340-353
  • DOI: 10.1038/emboj.2012.331
  • Peer Reviewed
• [Journal Article] PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells (2013)
  • Author(s): Yamaji, M., Ueda, J., Hayashi, K., Ohta, H., Yabuta, Y., Kurimoto, K., Nakato, R., Shirahige, K., and Saitou, M
  • Journal Title: Cell Stem Cell Volume: 12 Issue: 3 Pages: 368-382
  • DOI: 10.1016/j.stem.2012.12.012
  • Peer Reviewed
• [Journal Article] Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice (2012)
  • Author(s): Hayashi, K., Ogushi, S., Kurimoto, K., Shimamoto, S., Ohta, H., Saitou, M
  • Journal Title: Science Volume: 338 Issue: 6109 Pages: 971-975
  • DOI: 10.1126/science.1226889
  • Peer Reviewed
• [Presentation] A method for ChlP-seq of transcription factors in small cell numbers (2012)
  • Author(s): tazuki Kurimoto. Mitinori Saitou
  • Organizer: nternational Joint Symposium on Single-Cell Analysis
  • Place of Presentation: Kyoto Research Park