Silencing of episomal transgene expression in liver by plasmid bacterial backbone DNA is independent of CpG methylation.

Minicircle DNA vectors devoid of plasmid bacterial backbone, (BB) DNAs, are transcriptionally persistent, whereas their parent plasmid counterparts are silenced in the liver. In this study we establish that circular plasmid BB provided in trans did not silence a transgene expression cassette in vivo, further confirming our previous conclusions that the covalent attachment of the plasmid BB to the expression cassette is required for DNA silencing. Given the high concentration of CpG dinucleotides in the plasmid BB, we investigated the role of DNA methylation on transgene silencing in vivo. The presence or absence of methylation in CpG motifs in routine plasmid BBs had no significant effect on transcriptional silencing. Furthermore, the removal of the CpG motifs from the BB did not ameliorate transcriptional silencing. Transgene silencing was partially inhibited when two tandem copies of the chicken cHS4 insulator at each end of a routine plasmid vector were used. These results are consistent with the idea that the transcriptional repression observed with plasmid DNA vectors in the liver is caused by formation of repressive heterochromatin on the plasmid DNA backbone, which then spreads and inactivates the transgene in cis, and that CpG content or methylation has little or no influence in the process.

Histone modifications are associated with the persistence or silencing of vector-mediated transgene expression in vivo.

One of the major obstacles to success in non-viral gene therapy is transcriptional silencing of the DNA vector. The mechanisms underlying gene silencing/repression in mammalian cells are complex and remain unclear. Because changes in chromatin structure and, in particular, histone modifications are involved in transcriptional regulation of endogenous genes, we hypothesized that changes in the pattern of histone modifications were related to the observed transcriptional silencing of exogenous DNA vectors. We used antibodies against specific modified histones to perform chromatin immunoprecipitation (ChIP) analyses on liver lysates from mice transfected with two types of plasmids: (i) DNA minicircles (MCs) devoid of bacterial plasmid backbone DNA, which showed marked persistence of transgene expression, and (ii) their parental plasmids, which were silenced over time. Silencing of the transgene from the parental vectors was accompanied by an increase in heterochromatin-associated histone modifications and a decrease in modifications typically associated with euchromatin. Conversely, the pattern of histone modifications on the MC DNA was consistent with euchromatin. Our data indicates that (i) episomal vectors undergo chromatinization in vivo, and (ii) both persistence and silencing of transgene expression are associated with specific histone modifications.