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RIKEN Center for Biosystems Dynamics Research Laboratory for Quantitative Biology of Cell Fate Decision

Team Leader: Yumi Konagaya (Ph.D.)

Research Summary

Yumi Konagaya

Tissue homeostasis relies on constant tissue renewal, notably within the rapidly regenerating intestinal epithelium. Precise control of cell proliferation during differentiation is critical for maintaining tissue homeostasis, as its disruptions lead to atrophy or cancer. Our research focuses on elucidating how cell proliferation and differentiation are orchestrated in the intestinal epithelium. In particular, we aim to uncover the molecular mechanisms underlying the cell fate decision of intestinal epithelial stem cells by live imaging of mouse intestinal organoids, multiplexed tissue imaging, and quantitative analyses.

Main Research Fields

  • Biology

Related Research Fields

  • Biological Sciences
  • Molecular biology
  • Cell biology
  • Developmental biology-related


  • Quantitative biology
  • Live-cell imaging
  • Intestinal organoids
  • Cell cycle
  • Cell signaling

Selected Publications

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

  • 1.Konagaya, Y., Rosenthal, D., Ratnayeke, N., Fan, Y., & Meyer, T.
    "An intermediate Rb-E2F activity state safeguards proliferation commitment."
    Nature, 631, 424-431. (2024).
  • 2. *He, J., Yamamoto, M., Sumiyama, K., Konagaya, Y., Terai, K., Matsuda, M., & Sato, S.
    "Two‐photon AMPK and ATP imaging reveals the bias between rods and cones in glycolysis utility."
    The FASEB Journal, 35(9), e21880. (2021).
  • 3. *Konagaya, Y., Takakura, K., Sogabe, M., Bisaria, A., Liu, C., Meyer, T., Sehara-Fujisawa, A., Matsuda, M. & Terai, K.
    "Intravital imaging reveals cell cycle-dependent myogenic cell migration during muscle regeneration."
    Cell Cycle, 19(22), 3167-3181. (2020).
  • 4. *Liu, C., Konagaya, Y., Chung, M., Daigh, L.H., Fan, Y., Yang, H.W., Terai, K., Matsuda, M. & Meyer, T.
    "Altered G1 signaling order and commitment point in cells proliferating without CDK4/6 activity."
    Nature Communications, 11(1), 5305. (2020).
  • 5. *Konagaya, Y., Terai, K., Hirao, Y., Takakura, K., Imajo, M., Kamioka, Y., Sasaoka, N., Kakizuka, A., Sumiyama, K., Asano, T. & Matsuda, M.
    "A highly sensitive FRET biosensor for AMPK exhibits heterogeneous AMPK responses among cells and organs."
    Cell Reports, 21(9), 2628-2638. (2017).
  • 6. *Isoe, Y., Konagaya, Y., Yokoi, S., Kubo, T. & Takeuchi, H.
    "Ontogeny and sexual differences in swimming proximity to conspecifics in response to visual cues in medaka fish."
    Zoological Science, 33(3), 246-254. (2016).

Related Links

Lab Members

Principal investigator

Yumi Konagaya
Team Leader

Core members

Shuji Matsuguchi
Postdoctoral Researcher
Ayaka Omori
Technical Staff II
Miki Fujiwara


Position Deadline
Seeking a few Postdoctoral Researcher or Research Associate (BDR-23-038) Open until filled

Contact Information

Developmental Biology Bldg. A, Fl. 3, S301-303
2-2-3 Minatojima-minamimachi, Chuou-ku,
Kobe, Hyogo
650-0047, Japan
Email: yumi.konagaya [at] riken.jp