Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity

Yu H. Sun, Hongxiao Cui, Chi Song, Jiafei Teng Shen, Xiaoyu Zhuo, Ruoqiao Huiyi Wang, Xiaohui Yu, Rudo Ndamba, Qian Mu, Hanwen Gu, Duolin Wang, Gayathri Guru Murthy, Pidong Li, Fan Liang, Lei Liu, Qing Tao, Ying Wang, Sara Orlowski, Qi Xu, Huaijun Zhou, Jarra Jagne, Omer Gokcumen, Nick Anthony, Xin Zhao () and Xin Zhiguo Li ()
Additional contact information
Yu H. Sun: University of Rochester Medical Center
Hongxiao Cui: Northwest A&F University
Chi Song: The Ohio State University
Jiafei Teng Shen: Zhejiang University School of Medicine
Xiaoyu Zhuo: Washington University School of Medicine
Ruoqiao Huiyi Wang: University of Rochester Medical Center
Xiaohui Yu: Northwest A&F University
Rudo Ndamba: University of Rochester Medical Center
Qian Mu: University of Rochester Medical Center
Hanwen Gu: University of Rochester Medical Center
Duolin Wang: University of Rochester Medical Center
Gayathri Guru Murthy: University of Rochester Medical Center
Pidong Li: Grandomics Biosciences Co., Ltd
Fan Liang: Grandomics Biosciences Co., Ltd
Lei Liu: Grandomics Biosciences Co., Ltd
Qing Tao: Grandomics Biosciences Co., Ltd
Ying Wang: University of California
Sara Orlowski: University of Arkansas
Qi Xu: McGill University
Huaijun Zhou: University of California
Jarra Jagne: Cornell University College of Veterinary Medicine
Omer Gokcumen: University at Buffalo, State University of New York
Nick Anthony: University of Arkansas
Xin Zhao: McGill University
Xin Zhiguo Li: University of Rochester Medical Center

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.

Date: 2023
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DOI: 10.1038/s41467-023-36354-x

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