Illegitimate DNA integration in mammalian cells

Abstract

Foreign DNA integration is one of the most widely exploited cellular processes in molecular biology. Its technical use permits us to alter a cellular genome by incorporating a fragment of foreign DNA into the chromosomal DNA. This process employs the cell's own endogenous DNA modification and repair machinery. Two main classes of integration mechanisms exist: those that draw on sequence similarity between the foreign and genomic sequences to carry out homology-directed modifications, and the nonhomologous or 'illegitimate' insertion of foreign DNA into the genome. Gene therapy procedures can result in illegitimate integration of introduced sequences and thus pose a risk of unforeseeable genomic alterations. The choice of insertion site, the degree to which the foreign DNA and endogenous locus are modified before or during integration, and the resulting impact on structure, expression, and stability of the genome are all factors of illegitimate DNA integration that must be considered, in particular when designing genetic therapies.

The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair

“…Homology-dependent integration depends on homologous recombination (HR) repair proteins and the extent of homology between foreign and endogenous DNA (10)(11)(12). Illegitimate integration inserts exogenous DNA into nonhomologous genomic sequences and is far more efficient, probably in part because of the much larger number of potential illegitimate integration sites.…”

“…Exogenous DNA is usually integrated into the genome by two mechanisms: homology-dependent integration and illegitimate integration (10). Homology-dependent integration depends on homologous recombination (HR) repair proteins and the extent of homology between foreign and endogenous DNA (10)(11)(12).…”

“…Illegitimate integration inserts exogenous DNA into nonhomologous genomic sequences and is far more efficient, probably in part because of the much larger number of potential illegitimate integration sites. Illegitimate integration sites are not random but probably depend on open chromatin associated with transcription or repair, allowing access of foreign DNA and integration factors to the genomic DNA (10)(11)(12). Illegitimate integration resembles nonhomologous end-joining (NHEJ) repair, because it is enhanced by DNA damage, especially double-strand breaks (DSBs); it is homology-independent and involves end joining (12)(13)(14).…”

miRNA Control of Tissue Repair and Regeneration

“…58 Although adenovirus-derived vectors and Sendai virus were proclaimed as safe nonintegrating methods for production of iPSCs, the statement should be used with extreme caution. Harui et al 59 have reported that in established cell lines, adenoviral vectors do integrate into the genome.…”

Expanding Horizons of Cellular Plasticity in Regenerative Medicine

“…Genomic integration following viral transduction increases the risk of modifying recipient chromosomal locus making the recipient genomic loci unstable. 28 Although the integration frequency of adenovirus into chromosomal DNA in vitro was estimated to be in the order of 10 À3 to 10 À5 events per cell, 29 caution should be exercised while assessing in vivo risks based on such in vitro data. Do RNA viruses integrate into the host genome?…”