Epigenetic alterations upon the insertion of foreign DNA into mammalian Genomes: Oncogenesis and evolution

Abstract

The fate of foreign DNA in mammalian systems has been a long-term interest in our laboratory [Doerfler (Foreign DNA in mammalian systems. Wiley-VCH, 2000)]. The current overview summarizes an update of the data presented at the Fifth Weissenburg Symposium 2014 (Weissenburg Symposia, 2001–2014). In earlier studies on integrated adenovirus type 12 (Ad12) DNA in Ad12-transformed hamster cells, we discovered that the CpG methylation profiles in some of their ubiquitous endogenous retrotransposon sequences and in several cellular genes were markedly increased. This hypermethylation persisted in revertants of the transformed cells which had lost all Ad12 genomes. Alterations of cellular methylation and transcription profiles were also observed in hamster cells transgenomic for bacteriophage lambda DNA. We have now investigated human HCT116 cells which were transgenomic for a 5.6 kbp bacterial plasmid. In five non-transgenomic HCT116 control clones, transcription and methylation patterns proved similar, if not identical. This finding opened the possibility to compare these patterns between non-transgenomic and transgenomic cell clones. In 4.7 % of the 28,869 gene segments analyzed, the transcriptional activities were upregulated (907 genes) or downregulated (436 genes) in plasmid-transgenomic cell clones in comparison to control clones. Genome-wide methylation profiling was performed for >480,000.CpG sites. In comparisons to methylation levels in five transgenomic versus four non-transgenomic cell clones, 3791.CpGs were differentially methylated, 1504.CpGs were hypermethylated, and 2287 were hypomethylated. The mechanisms underlying the observed epigenetic alterations are unknown. Extent and location of alterations in genome activities and CpG methylation might depend on the site(s) of foreign DNA insertion. Genome manipulations have been an everyday practice in many laboratories. With further refinement of epigenetic technologies, hitherto unsuspected complications in the evaluation of experiments with genome manipulated cells and organisms will become apparent.