DNA Methylation and Transcription in HERV (K, W, E) and LINE Sequences Remain Unchanged Upon Foreign DNA Insertions

Abstract

Aim: DNA methylation and transcriptional profiles were determined in the regulatory sequences of the human endogenous retroviral (HERV-K, -W, -E) and LINE-1.2 elements and were compared between non-transgenomic and plasmid-transgenomic cells. Methods: DNA methylation profiles in the HERV (K, W, E) and LINE sequences were determined by bisulfite genomic sequencing. The transcription of these genome segments was assessed by quantitative real-time PCR. Results: In HERV-K, HERV-W and LINE-1.2 the levels of DNA methylation ranged between 75 and 98%, while in HERV-E they were around 60%. Nevertheless, the HERV and LINE-1.2 sequences were actively transcribed. No differences were found in comparisons of HERV and LINE-1.2 CpG methylation and transcription patterns between non-transgenomic and plasmid-transgenomic HCT116 cells. Conclusion: The insertion of a 5.6 kbp plasmid into the HCT116 genome had no effect on the HERV and LINE-1.2 methylation and transcription profiles, although other parts of the HCT116 genome had shown marked changes. These repetitive sequences are transcribed, probably because the large number of HERV and LINE-1.2 elements harbor copies with non- or hypo-methylated long terminal repeat sequences.

Keywords::

• bisulfite genomic sequencing
• comparisons of methylation and transcription between non-transgenomic and transgenomic cells
• CpG methylation in HERV and LINE-1.2 DNA
• human cell line HCT116
• human endogenous retroviral (HERV-K,-W,-E) and LINE-1.2 sequences
• plasmid-transgenomic HCT116 cells
• quantitative real-time PCR

Acknowledgements

The authors are indebted to the Institute for Virology Erlangen University Medical School for their continued support of W Doerfler’s senior research group. The authors are grateful to the staff of the sequencing facility of the Institute of Human Genetics, Universitätsklinikum Erlangen for nucleotide sequence determinations.

Author contributions

S Weber performed all laboratory experiments, was involved in the planning of the project and interpretation of the data. S Jung planned and analyzed the real-time PCR data. W Doerfler initiated and designed the project, was involved in the interpretation of data and wrote the manuscript.

Financial & competing interests disclosure

This research was made possible by grants to W Doerfler from the Thyssen Foundation, Köln (Az. 10.07.2.138), from the Deutsche Forschungsgemeinschaft, Bonn (DO 165/28-1) and by support from the Rotary Club Weissenburg to S Weber. 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), from the Deutsche Forschungsgemeinschaft, Bonn (DO 165/28-1) and by support from the Rotary Club Weissenburg to S Weber. 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.