RIKEN BioResource Research Center (BRC®) Developmental Genome Plasticity Research Team
Team Director: Akihiko Sakashita (Ph.D.)
Research Summary
Our long-term research goal is to decipher the molecular mechanisms underlying epigenetic and genetic events during mammalian development and reproduction, as well as their evolutionary divergence. As a first step toward this goal, we focus on dissecting the dynamics of epigenetic remodeling and transcriptional network activation that drive development and lineage commitment. Additionally, we aim to uncover the functionalities of multi-copy genetic reservoirs—including transposable elements, duplicated gene and pseudogene clusters, and non-coding DNA segments—in shaping developmental genome plasticity in germline cells. In parallel, we explore species diversity in developmental programs through a cross-species comparative approach.
Main Research Fields
- Biology
Related Research Fields
- Agricultural Sciences
- Informatics
- Biological Sciences
- Medicine, Dentistry & Pharmacy
- Developmental Biology
- Molecular Biology
- Genome Biology
Keywords
- Totipotency Regulation
- Early Embryonic Development
- Epigenetic Reprogramming
- Transposable Elements
- Comparative Genomics
Selected Publications
Papers with an asterisk(*) are based on research conducted outside of RIKEN.
- 1.
*Otsuka K., Sakashita A., Maezawa S., Schultz RM., Namekawa SH.
"KRAB-zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptome and genome evolution."
Genome Res. In press (2025) - 2.
*Guo Y., Kitano T., Inoue K., Murano K., Hirose M., Li TD., Sakashita A., Ishizu H., Ogonuki N., Matoba S., Sato M., Ogura A., Siomi H.
"Obox4 promote zygotic genome activation upon loss of Dux."
Elife Jun10:13:e95856. (2024) - 3.
*Sakashita A, Ooga M, Otsuka K, Maezawa S, Takeuchi C, Wakayama S, Wakayama T, Namekawa SH.
"Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin."
Nucleic Acids Res. Jul 21;51(13):6668-6683. (2023) - 4.
*Sakashita A, Kitano T, Ishizu H, Guo Y, Masuda H, Ariura M, Murano K, Siomi H.
"Transcription of MERVL retrotransposons is required for preimplantation embryo development."
Nat Genet. Mar;55(3):484-495. (2023) - 5.
*Sakashita A, Takeuchi C, Maezawa S, Namekawa SH.
"Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts."
Methods Mol Biol. : 2577:123-146. (2023) - 6.
*Sakashita A., Ariura M., Namekawa SH.
"CRISPR-mediated activation of transposable elements in embryonic stem cell."
Methods Mol Biol. ;2509:171-194. (2022) - 7.
*Sakashita A, Maezawa S, Takahashi K, Alavattam KG, Yukawa M, Hu YC, Kojima S, Parrish NF, Barski A, Pavlicev M, Namekawa SH.
"Endogenous retroviruses drive species-specific germline transcriptomes in mammals."
Nat Struct Mol Biol.; 27(10):967-977. (2020) - 8.
*Maezawa S, Sakashita A (Co-first), Yukawa M, Chen X, Takahashi K, Alavattam KG, Nakata I, Weirauch MT, Barski A, Namekawa SH.
"Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition."
Nat Struct Mol Biol.; 27(10):978-988. (2020) - 9.
*Sakashita A, T Wakai, Y Kawabata, C Nishimura, Y Sotomaru, KG Alavattam, Namekawa SH, Kono T.
"XY oocytes of sex-reversed females with a Sry mutation deviate from the normal developmental process beyond the mitotic stage."
Biol Reprod.; 100(3):697-710. (2019) - 10.
*Alavattam KG, Maezawa S, Sakashita A, Khoury H, Barski A, Kaplan N, Namekawa SH.
"Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development."
Nat Struct Mol Biol.; 26(3):175-184. (2019)
Related Links
Lab Members
Principal investigator
- Akihiko Sakashita
- Team Director
Contact Information
3-1-1 Koyadai
Tsukuba, Ibaraki
305-0074 Japan
Email: akihiko.sakashita@riken.jp