Abstract
BackgroundNumerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates.ResultsTo enable functional analysis of human transposase-derived genes, we combined forward chemical genetic hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1) screening with massively parallel paired-end DNA sequencing and structural variant genome assembly and analysis. Here, we report the HPRT1 mutational spectrum induced by the human transposase PGBD5, including PGBD5-specific signal sequences (PSS) that serve as potential genomic rearrangement substrates.ConclusionsThe discovered PSS motifs and high-throughput forward chemical genomic screening approach should prove useful for the elucidation of endogenous genome remodeling activities of PGBD5 and other domesticated human DNA transposases and recombinases.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2877-x) contains supplementary material, which is available to authorized users.
Highlights
Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates
The human hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1) gene contains 12 annotated DNA transposon copies (Additional file 1: Table S1). These transposons are only distantly related to piggyBac transposons that are evolutionarily related to the potential substrates of PGBD5 [4]
To eliminate HPRT1 variants induced by spontaneous gene mutations and enable the specific selection of those induced by PGBD5, we grew cells in the presence of HAT medium for 15 doublings [18]
Summary
Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. The human genome contains over 20 genes with similarity to DNA transposases [1]. Human THAP9 and PGBD5 have been found to mobilize transposons in human cells [3, 4]. This discovery raises the possibility that, similar to the RAG1 recombinase [5], these endogenous human transposases may catalyze human genome rearrangements during normal somatic cell development or in distinct disease states. The human genome contains thousands of genetic elements with apparent sequence similarity to transposons, but their evolutionary divergence hinders the identification of elements that may serve as substrates for endogenous human transposases in general [6], and PGBD5 in particular [4].
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