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

• Published in: Nature communications 2021-07, Vol.12 (1), p.4280-14, Article 4280
• Main Authors: Tan, Shengjun, Ma, Huijing, Wang, Jinbo, Wang, Man, Wang, Mengxia, Yin, Haodong, Zhang, Yaqiong, Zhang, Xinying, Shen, Jieyu, Wang, Danyang, Banes, Graham L., Zhang, Zhihua, Wu, Jianmin, Huang, Xun, Chen, Hua, Ge, Siqin, Chen, Chun-Long, Zhang, Yong E.
• Format: Article
• Language: English
• Subjects: 38/1; 38/22; 38/23; 38/39; 38/43; 38/77; 45/91; 631/181/2474; 631/181/735; 631/208/212/748; 631/208/737/2007; 64/24; 82/58; 82/80; Animals; Biochemistry, Molecular Biology; Cancer; Catalysts; Cellular Biology; Chimeras; Deoxyribonucleic acid; DNA; DNA Transposable Elements - genetics; Gene sequencing; Genes; Genetics; Genome, Plant - genetics; Genomes; Genomics; Human genetics; Humanities and Social Sciences; Inverted repeat; Life Sciences; Molecular biology; multidisciplinary; Nucleotide sequence; Oryza - genetics; Positive selection; Proteomics; Reproduction (copying); Science; Science (multidisciplinary); Subcellular Processes; Terminal Repeat Sequences - genetics; Transposition; Transposons
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-24585-9

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. Transposons are accepted as evolutionary catalysts but how they do so remains less clear. Analyzing 100 animal genomes finds that terminal inverted repeat-type transposable elements catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.