DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans

Shengjun Tan, Huijing Ma, Jinbo Wang, Man Wang, Mengxia Wang, Haodong Yin, Yaqiong Zhang, Xinying Zhang, Jieyu Shen, Danyang Wang, Graham L. Banes, Zhihua Zhang, Jianmin Wu, Xun Huang, Hua Chen, Siqin Ge, Chun-Long Chen () and Yong E. Zhang ()
Additional contact information
Shengjun Tan: Chinese Academy of Sciences
Huijing Ma: Chinese Academy of Sciences
Jinbo Wang: Chinese Academy of Sciences
Man Wang: Peking University Cancer Hospital & Institute
Mengxia Wang: Chinese Academy of Sciences
Haodong Yin: Chinese Academy of Sciences
Yaqiong Zhang: Chinese Academy of Sciences
Xinying Zhang: Chinese Academy of Sciences
Jieyu Shen: Chinese Academy of Sciences
Danyang Wang: University of Chinese Academy of Sciences
Graham L. Banes: University of Wisconsin–Madison
Zhihua Zhang: University of Chinese Academy of Sciences
Jianmin Wu: Peking University Cancer Hospital & Institute
Xun Huang: University of Chinese Academy of Sciences
Hua Chen: University of Chinese Academy of Sciences
Siqin Ge: Chinese Academy of Sciences
Chun-Long Chen: PSL Research University, CNRS UMR 3244
Yong E. Zhang: Chinese Academy of Sciences

Nature Communications, 2021, vol. 12, issue 1, 1-14

Abstract: Abstract Despite long being considered as “junk”, transposable elements (TEs) are now accepted as catalysts of evolution. One example is Mutator-like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate duplication in animals is almost unexplored. Here we identify 370 Pack-TIRs in 100 animal reference genomes and one Pack-TIR (Ssk-FB4) family in fly populations. We find that single-copy Pack-TIRs are mostly generated via transposition-independent gap filling, and multicopy Pack-TIRs are likely generated by transposition after replication fork switching. We show that a proportion of Pack-TIRs are transcribed and often form chimeras with hosts. We also find that Ssk-FB4s represent a young protein family, as supported by proteomics and signatures of positive selection. Thus, TIR TEs catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.

Date: 2021
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DOI: 10.1038/s41467-021-24585-9

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