Transposon-host arms race: a saga of genome evolution

Yuka W Iwasaki; Keisuke Shoji; Shinichi Nakagwa; Tomoichiro Miyoshi; Yukihide Tomari

doi:10.1016/j.tig.2025.01.009

Transposon-host arms race: a saga of genome evolution

Trends Genet. 2025 May;41(5):369-389. doi: 10.1016/j.tig.2025.01.009. Epub 2025 Feb 20.

Authors

Yuka W Iwasaki¹, Keisuke Shoji², Shinichi Nakagwa³, Tomoichiro Miyoshi⁴, Yukihide Tomari⁵

Affiliations

¹ Laboratory for Functional Non-coding Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
² Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan; Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
³ RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan.
⁴ Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
⁵ Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: tomari@iqb.u-tokyo.ac.jp.

PMID: 39979178
DOI: 10.1016/j.tig.2025.01.009

Abstract

Once considered 'junk DNA,' transposons or transposable elements (TEs) are now recognized as key drivers of genome evolution, contributing to genetic diversity, gene regulation, and species diversification. However, their ability to move within the genome poses a potential threat to genome integrity, promoting the evolution of robust host defense systems such as Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KRAB-ZFPs), the human silencing hub (HUSH) complex, 4.5SH RNAs, and PIWI-interacting RNAs (piRNAs). This ongoing evolutionary arms race between TEs and host defenses continuously reshapes genome architecture and function. This review outlines various host defense mechanisms and explores the dynamic coevolution of TEs and host defenses in animals, highlighting how the defense mechanisms not only safeguard the host genomes but also drive genetic innovation through the arms race.

Keywords: evolutionary arms race; genetic conflicts; genome evolution; host defense mechanisms; transposable elements (TEs).

Publication types

Review

MeSH terms

Animals
DNA Transposable Elements* / genetics
Evolution, Molecular*
Genome* / genetics
Humans
RNA, Small Interfering / genetics

Substances

DNA Transposable Elements
RNA, Small Interfering