My research is primarily focused on exploring the evolution and molecular mechanisms that underlie gene regulation. Some key areas of my research include:

  • Investigating the formation of heterochromatin through the H3K9/K27 methylation pathway and the small RNA pathway.
  • Exploring the molecular mechanisms and evolutionary implications of transposons in mammals.
  • Unraveling the role of archaic-derived DNA in shaping human evolution.

I successfully completed my PhD studies under the guidance of Professor Hiroyuki Sasaki at Kyushu University in Japan. During this period, I developed a strong expertise in understanding the significance of DNA methylation in human evolution. Subsequently, I embarked on postdoctoral research from 2015 to 2022 with Dr. Yoichi Shinkai at RIKEN. This research phase resulted in the publication of several impactful papers on topics ranging from the evolution of transposon regulation in primates to unraveling the intricate molecular mechanisms governing transposon regulation in mammals.

In 2022, I was awarded a scholarship that allowed me to delve into the evolution of immune reactions in humans in Irene’s Lab. During my time in the lab, I focused on investigating specific archaic-derived DNA sequences prevalent in South East Asian populations, utilising induced pluripotent stem cells (iPS cells) as a research model.

In recognition of my groundbreaking contributions to the field of transposon evolution and regulation, I was honoured to receive the prestigious 2022 Japan Genetics Award.

Key achievements

2022  Japan Genetics Award



Selected publications

Fukuda K, Shimi T, Shimura C, Ono T, Suzuki T, Onoue K, Okayama S, Miura H, Hiratani I, Ikeda K, Okada Y, Dohmae N, Yonemura S, Inoue A, Kimura H, Shinkai Y. Epigenetic plasticity safeguards heterochromatin configuration in mammals. Nucleic Acids Res. 2023 Jul 7;51(12):6190-6207. doi: 10.1093/nar/gkad387. PMID: 37178005; PMCID: PMC10325917.


Fukuda K, Makino Y, Kaneko S, Shimura C, Okada Y, Ichiyanagi K, Shinkai Y. Potential role of KRAB-ZFP binding and transcriptional states on DNA methylation of retroelements in human male germ cells. Elife. 2022 Mar 22;11:e76822. doi: 10.7554/eLife.76822. PMID: 35315771; PMCID: PMC8967385.

Fukuda K, Okuda A, Yusa K, Shinkai Y. A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells. Genome Res. 2018 Jun;28(6):846-858. doi: 10.1101/gr.227280.117. Epub 2018 May 4. PMID: 29728365; PMCID: PMC5991520.

Fukuda K, Inoguchi Y, Ichiyanagi K, Ichiyanagi T, Go Y, Nagano M, Yanagawa Y, Takaesu N, Ohkawa Y, Imai H, Sasaki H. Evolution of the sperm methylome of primates is associated with retrotransposon insertions and genome instability. Hum Mol Genet. 2017 Sep 15;26(18):3508-3519. doi: 10.1093/hmg/ddx236. PMID: 28637190.