Data from: Genomic DNA transposition induced by human PGBD5

Henssen, Anton G.1; Henaff, Elizabeth2; Jiang, Eileen3; Eisenberg, Amy R.1; Carson, Julianne R.1; Villasante, Camila M.1; Ray, Mondira1; Still, Eric4; Burns, Melissa3; Gandara, Jorge2; Feschotte, Cedric4; Mason, Christopher E.2; Kentsis, Alex1, 5

Published Sep 28, 2015 on Dryad. https://doi.org/10.5061/dryad.b2hc1

Data files

Sep 28, 2015 version files 894.71 MB

pb-ef1-neo_seq.fa

7.05 KB
pcr1_HEK293-GFP-PBwt.vs.hg19_pbneo.mem.bam

100.43 MB
pcr2_HEK293-GFP-PBmut.vs.hg19_pbneo.mem.bam

213.01 MB
pcr3_HEK293-PGBD5-PBwt.vs.hg19_pbneo.mem.bam

143.45 MB
pcr4_HEK293-PGBD5-PBmut.vs.hg19_pbneo.mem.bam

437.74 MB
summary_insertion_sites_pub.xlsx

70.51 KB

Abstract

Transposons are mobile genetic elements that are found in nearly all organisms, including humans. Mobilization of DNA transposons by transposase enzymes can cause genomic rearrangements, but our knowledge of human genes derived from transposases is limited. In this study, we find that the protein encoded by human PGBD5, the most evolutionarily conserved transposable element-derived gene in vertebrates, can induce stereotypical cut-and-paste DNA transposition in human cells. Genomic integration activity of PGBD5 requires distinct aspartic acid residues in its transposase domain, and specific DNA sequences containing inverted terminal repeats with similarity to piggyBac transposons. DNA transposition catalyzed by PGBD5 in human cells occurs genome-wide, with precise transposon excision and preference for insertion at TTAA sites. The apparent conservation of DNA transposition activity by PGBD5 suggests that genomic remodeling contributes to its biological function.

Usage notes

Reads from HEK293-GFP-PBwt mapped to hg19+pb-ef1_neo.

Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-GFP-PBwt, mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.

pcr1_HEK293-GFP-PBwt.vs.hg19_pbneo.mem.bam

Reads from HEK293-GFP-PBmut mapped to hg19+pb-ef1-neo

Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-GFP-PBmut, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.

pcr2_HEK293-GFP-PBmut.vs.hg19_pbneo.mem.bam

Reads from HEK293-PGBD5-PBwt mapped to hg19+pb-ef1-neo

Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-PGBD5-PBwt, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.

pcr3_HEK293-PGBD5-PBwt.vs.hg19_pbneo.mem.bam

Reads from HEK293-PGBD5-PBmut mapped to hg19+pb-ef1-neo

Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-PGBD5-PBmut, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.

pcr4_HEK293-PGBD5-PBmut.vs.hg19_pbneo.mem.bam

Summary table of DNA transposon integration loci

Spreadsheet listing human genome and transposon coordinate positions of transposon integrations, integration type (ITR transposition vs non-ITR transposition), and DNA sequences surrounding the genomic integration sites.

summary_insertion_sites_pub.xlsx

Transposon reporter plasmid sequence: pb-ef1-neo

Plasmid sequence of NEO reporter flanked by PiggyBac ITRs. Reads from FLEA PCR were mapped to a hybrid genome consisting of this sequence and the hg19 human genome reference.

pb-ef1-neo_seq.fa