• Figure 1.
    Download figureOpen in new tabFigure 1. Human PGBD5 is a distinct piggyBac-like transposase.

    Sequence alignment of piggyBac-like transposases frog Uribo 2, bat piggyBat, lepidopteran piggyBac, and human PGBD5. Catalytic residues conserved among piggyBac transposases are highlighted in red. Human PGBD5 D168, D194, and D386 residues, identified in our study (Figure 7), are marked in yellow.

    DOI: http://dx.doi.org/10.7554/eLife.10565.003

    Figure 2.
    Download figureOpen in new tabFigure 2. Human piggyBac-like transposable elements have intact inverted terminal repeat sequences similar to the T. ni piggyBac transposon.

    (A) Chromosome ideogram representing the distribution of annotated piggyBac-like elements in the human genome (version hg19). (B) Multiple sequence alignment of the piggybac inverted terminal repeat (ITR) sequence with the consensus ITR sequences of the MER75 and MER85 families of piggyBac-like elements. (C) Chromosome ideogram representing the distribution of piggyBac-like elements annotated in the human genome (version hg19) with TTAA target site duplication as well as ITR sequences aligning with the consensus (intact ITRs).

    DOI: http://dx.doi.org/10.7554/eLife.10565.005

    Figure 5.
    Download figureOpen in new tabFigure 5. Schematic of transposon-specific flanking sequence exponential anchored–polymerase chain reaction amplification (FLEA-PCR) and massively parallel single molecule sequencing assay for mapping and sequencing transposon insertions.

    DOI: http://dx.doi.org/10.7554/eLife.10565.015

  • Table 1.

    Summary of annotated human piggyBac-like elements

    DOI: http://dx.doi.org/10.7554/eLife.10565.004

    Total piggyBac-like elementsIntact elements*
    MER75475144
    MER75A9362
    MER75B11427
    MER8590595
    UCON292400
    Looper5310
    • Denotes elements with intact ITR sequences that align with the consensus without gaps and contain a TTAA target site duplication.

    • ITR, inverted terminal repeat.

  • Table 2.

    Sequence identity matrix of the piggyBac inverted terminal repeat sequences and consensus sequences of the MER75 and MER85 human piggyBac-like elements

    DOI: http://dx.doi.org/10.7554/eLife.10565.006

    piggyBacMER75MER85
    piggyBac100%
    MER7553%100%
    MER8556%63%100%
  • Table 3.

    Analysis of transposon integration sequences in human genomes induced by PGBD5

    DOI: http://dx.doi.org/10.7554/eLife.10565.018

    Intact transposonMutant transposon
    TTAA ITRNon-ITRTTAA ITRNon-ITR
    Transposase
     GFP-PGBD582% (65)18% (14)11% (4)89% (33)
     GFP Control17% (2)83% (10)40% (27)60% (40)
    • Cells expressing GFP-PGBD5 and intact transposons exhibit significantly higher frequency of genomic integration as compared to either GFP control, or GFP-PGBD5 with mutant transposons, with 82% (65 out of 79) of sequences demonstrating DNA transposition of ITR transposons into TTAA sites (†p = 1.8 × 10-5). Mutation of the transposon ITR significantly reduces ITR-mediated integration, with only 11% (4 out of 37) of sequences (‡p = 0.0016). Numbers in parentheses denote absolute numbers of identified insertion sites.

    • GFP, green fluorescent protein; ITR, inverted terminal repeat.

  • The following datasets were generated:

    Henssen A, Henaff E, Jiang E, Eisenberg AR, Carson JR, Villasante CM, Ray M, Still E, Burns M, Gandara J, Feschotte C, Mason CE, Kentsis A, 2015, DNA sequencing, http://www.ncbi.nlm.nih.gov/sra/SRP061649, Publicly available at the NCBI Short Read Archive (Accession no: SRP061649).

    Henssen A, Henaff E, Jiang E, Eisenberg AR, Carson JR, Villasante C, Ray M, Still E, Burns M, Gandara J, Feschotte C, Mason CE, Kentsis A, 2015, Data from: Genomic DNA transposition induced by human PGBD5, http://datadryad.org/resource/doi:10.5061/dryad.b2hc1, Available at Dryad Digital Repository under a CC0 Public Domain Dedication.

    Henaff E, Henssen A, Mason CE, Kentsis A, 2015, Genomic DNA transposition induced by human PGBD5 (Accompanying Scripts for Computational Analyses), http://dx.doi.org/10.5281/zenodo.22206, Publicly available at the Zenodo (Accession no: 10.5281/zenodo.22206).