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Nucleic Acids Research Advance Access originally published online on July 7, 2007
Nucleic Acids Research 2007 35(14):4743-4754; doi:10.1093/nar/gkm455
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Nucleic Acids Research, 2007, Vol. 35, No. 14 4743-4754
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Widely variable endogenous retroviral methylation levels in human placenta

Daphne Reiss1,2, Ying Zhang1,2 and Dixie L. Mager1,2,*

1Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC and 2Department of Medical Genetics, University of British Columbia, Canada

*To whom correspondence should be addressed. Tel: +1-604-675-8139; Fax: +1-604-877-0712; Email: dmager{at}bccrc.ca

Received January 22, 2007. Revised May 1, 2007. Accepted May 22, 2007.

It is generally assumed that transposable elements, including endogenous retroviruses (ERVs), are silenced by DNA methylation/chromatin structure in mammalian cells. However, there have been very few experimental studies to examine the methylation status of human ERVs. In this study, we determined and compared the methylation status of the 5' long terminal repeats (LTRs) of different copies of the human endogenous retrovirus (HERV) family HERV-E, which are inserted in various genomic contexts. We found that three HERV-E LTRs which function as alternative gene promoters in placenta are unmethylated in that tissue but heavily methylated in blood cells, where these LTRs are not active promoters. This difference is not solely due to global hypomethylation in placenta, since two general measures of methylation levels of HERV-E and HERV-K LTRs suggest only 10–15% lower overall HERV methylation in placenta compared to blood. Comparisons between methylation levels of the LTR-derived gene promoters and six random HERV-E LTRs in placenta showed that the former display significantly lower methylation levels than random LTRs. Moreover, the differences in methylation between LTRs cannot always be explained by their genomic environment, since methylation of flanking sequences can be very different from methylation of the LTR itself.


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