Destabilization of the Human Epigenome: Consequences of Foreign DNA Insertions

Abstract

Aim: We previously reported changes of DNA methylation and transcription patterns in mammalian cells that carry integrated foreign DNA. Experiments were now designed to assess the epigenetic consequences of inserting a 5.6 kbp plasmid into the human genome. Methods: Differential transcription and CpG methylation patterns were compared between transgenomic and nontransgenomic cell clones by using gene chip microarray systems. Results: In 4.7% of the 28.869 gene segments analyzed, transcriptional activities were up- or downregulated in the transgenomic cell clones. Genome-wide profiling revealed differential methylation in 3791 of > 480,000 CpG’s examined in transgenomic versus nontransgenomic clones. Conclusion: The data document genome-wide effects of foreign DNA insertions on the epigenetic stability of human cells. Many fields in experimental biology and medicine employ transgenomic or otherwise genome-manipulated cells or organisms without considering the epigenetic consequences for the recipient genomes.

Keywords::

• epigenetics
• foreign DNA
• destabilization
• transgenomes
• DNA methylation
• differential gene expression
• differential methylation

Acknowledgements

The transcriptional profiles (primary data) were determined by KFB in Regensburg, Germany. We are indebted to the Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg Medical School for their continued support of W Doerfler’s senior research group. S Weber performed most of the laboratory experiments and was involved in the planning and interpretation of the project. A Hofmann performed all statistical analyses, was involved in the interpretation of data and wrote part of the manuscript. S Weber and A Hofmann have contributed equally to this work. S Herms performed molecular karyotyping. P Hoffmann carried out methylation profiling, interpreted data and wrote part of the manuscript. W Doerfler initiated and planned the project, was involved in the interpretation of data and wrote the manuscript. KFB in Regensburg did the transcription analyses.

Financial & competing interests disclosure

This research was made possible by grants to W Doerfler from the Thyssen Foundation, Köln (Az. 10.07.2.138.) and from the Deutsche Forschungsgemeinschaft, Bonn (DO 165/28-1). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

This research was made possible by grants to W Doerfler from the Thyssen Foundation, Köln (Az. 10.07.2.138.) and from the Deutsche Forschungsgemeinschaft, Bonn (DO 165/28-1). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.No writing assistance was utilized in the production of this manuscript.