title: DNA methylation and transcription in HERV (K, W, E) and LINE sequences remain unchanged upon foreign DNA insertions.
abstract: OBJECTIVE
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institute of Clinical & Molecular Virology, University Erlangen-Nürnberg Medical School, 91054 Erlangen, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Weber
authors.affiliation: Pediatric Research Center, University Erlangen-Nürnberg, 91052 Erlangen, Germany.
authors.forename: Susan
authors.initials: S
authors.lastname: Jung
authors.affiliation: Institute of Clinical & Molecular Virology, University Erlangen-Nürnberg Medical School, 91054 Erlangen, Germany.|Institute of Genetics, University of Cologne, 50674 Cologne, Germany.
authors.forename: Walter
authors.initials: W
authors.lastname: Doerfler
mesh_terms: D045744:Cell Line, Tumor; D018899:CpG Islands; D019175:DNA Methylation; D020077:Endogenous Retroviruses / Q000235:genetics*; D020869:Gene Expression Profiling; D045325:HCT116 Cells; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D016254:Mutagenesis, Insertional; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D015533:Transcriptional Activation
keywords: CpG methylation in HERV and LINE-1.2 DNA; bisulfite genomic sequencing; comparisons of methylation and transcription between non-transgenomic and transgenomic cells; human cell line HCT116; human endogenous retroviral (HERV-K,-W,-E) and LINE-1.2 sequences; plasmid-transgenomic HCT116 cells; quantitative real-time PCR