Passer, a highly active transposon from a fish genome, as a potential new robust genetic manipulation tool

Abstract

The discovery of new, active DNA transposons can expand the range of genetic tools and provide more options for genomic manipulation. In this study, a bioinformatics analysis suggested that Passer (PS) transposons, which are members of the pogo superfamily, show signs of recent and current activity in animals and may be active in some species. Cell-based transposition assays revealed that the native PS transposases from Gasterosteus aculeatus and Danio rerio displayed very high activity in human cells relative to the Sleeping Beauty transposon. A typical overproduction inhibition phenomenon was observed for PS, and transposition capacity was decreased by ∼12% with each kilobase increase in the insertion size. Furthermore, PS exhibited a pronounced integration preference for genes and their transcriptional regulatory regions. We further show that two domesticated human proteins derived from PS transposases have lost their transposition activity. Overall, PS may represent an alternative with a potentially efficient genetic manipulation tool for transgenesis and mutagenesis applications.

Mage transposon: a novel gene delivery system for mammalian cells

“…In comparison, OPI of SB was slightly more sensitive and reached peak activity at lower transposase concentrations whereas the MG did not reach peak activity until the transposase concentration reached 500 ng (Figure 2 ). OPI demonstrated by SB is extensively documented in the literature ( 13 , 14 , 69 , 79 , 80 ). Our in vitro assessments, spanning various transposon-to-transposase plasmid ratios, spotlighted 5:1 as the most effective ratio.…”

“…Within mammalian cells, three prominent DNA transposons are commonly employed: Sleeping Beauty ( SB ) from the Tcl/mariner superfamily ( 8 ), piggyBac ( PB ) from the piggyBac superfamily ( 9 ), and Tol2 from the hAT superfamily ( 10 ). Moreover, numerous active transposons from various superfamilies have been recently discovered, including TcBuster ( 11 ) and Tgf2 ( 12 ) from the hAT superfamily, ZB ( 13 ) from the Tcl/mariner superfamily, and Passer from the pogo superfamily ( 14 ), among others. These DNA transposons have proven invaluable in various genetic studies, providing insights into genome engineering, gene therapy, and understanding the mechanisms underlying transposition events.…”

Advances in transposable elements: from mechanisms to applications in mammalian genomics

“…These systems have been used for genome manipulations in vertebrates, such as integrating foreign genes into tissue culture cells, generating transgenic animals, conducting forward genetic screens for functional gene annotation, and serving as therapeutic carriers to introduce beneficial genes into individuals with genetic disorders. Other novel transposons discovered in fish also exhibit similar behaviors as a genetic editing tool ( Shen et al, 2021 ; Wang et al, 2023 ). SB has high activity in all vertebrates, but Tol2 only presents high activity in zebrafish germline cells ( Kawakami et al, 2004 ; Parinov et al, 2004 ; Rafferty and Quinn, 2018 ).…”

FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research

“…However, as research has progressed, studies have found that TEs actually play important roles in organisms, including participating in gene regulation ( 3 ), mediating the formation of new genes ( 4 ), affecting methylation levels ( 5 ), maintaining and shaping 3D genome structure ( 6 ), promoting environmental adaptation ( 7 ) and participating in species differentiation ( 8 ). Moreover, besides their important contributions to organisms, TEs are also important targets for the development of genetic tools, from the early Sleeping Beauty, PiggyBac and Tol2 to Tn5 used by ATAC-seq technology ( 9 , 10 ) to newly developed TE genetic manipulation tools ( 11 , 12 ). The significance of TEs in biological research is increasingly emphasized, with recent research findings on the mechanism of TE transposition garnering significant attention ( 13 , 14 ), effectively illustrating this point.…”