DNA methylation site loss for plasticity-led novel trait genetic fixation

• 成果类型: Article
• 署名作者: Katsumura, Takafumi; Sato, Suguru; Yamashita, Kana; Oda, Shoji; Gakuhari, Takashi; Tanaka, Shodai; Fujitani, Kazuko; Nishimaki, Toshiyuki; Imai, Tadashi; Yoshiura, Yasutoshi; Takeshima, Hirohiko; Hashiguchi, Yasuyuki; Sekita, Yoichi; Mitani, Hiroshi; Ogawa, Motoyuki; Takeuchi, Hideaki; Oota, Hiroki
• 署名单位: Kitasato University; Okayama University; Kyushu University; Kitasato University; University of Tokyo; Kanazawa University; Kitasato University; Japan Fisheries Research & Education Agency (FRA); Fukui Prefectural University; Tokai University; Osaka Medical & Pharmaceutical University; Kitasato University; Tohoku University; University of Tokyo
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2534817123
• 发表日期: 2026-03-31
• 页码: e2534817123
• 关键词: dna methylation; phenotypic plasticity; genetic fixation; medaka fish; association; EVOLUTION; DISCOVERY; cells; fish; tool; set

摘要

Phenotypic plasticity allows organisms to adapt traits in response to environmental changes, yet the molecular basis by which such plastic traits become genetically fixed remains unclear. Here, we investigated gut-length plasticity in medaka fish (Oryzias latipes) through genome-wide methylation profiling, CRISPR/Cas9-mediated deletion, and population genomic analyses. We found that seasonal methylation of CpG sites upstream of the Plxnb3 is correlated with gut-length plasticity, and deletion of this region abolishes plasticity. Additionally, standing variation in Ppp3r1 is associated with genetically fixed longer gut length in populations lacking plasticity. These results suggest that loss of epigenetic regulation via CpG site reduction triggers the genetic fixation of novel traits. Our findings provide molecular evidence linking epigenetic plasticity and genetic assimilation, advancing understanding of plasticity-led evolution in natural populations.