In defense of deleterious retrotransposition of intracisternal A particle (IAP) elements, IAP loci are heavily methylated and silenced in mouse somatic cells. To determine whether IAP is also repressed in pluripotent stem cells by DNA methylation, we examined IAP expression in demethylated mouse embryonic stem cells (mESCs) and epiblast-derived stem cells. DNA methylation, an epigenetic modification where a methyl group is covalently added to the cytosine of CpG dinucleotides, is catalyzed by a family of DNA methyltransferases (Dnmts) 2 that include de novo (Dnmt3a and -3b) and maintenance methyltransferases (Dnmt1) (1, 2). DNA methylation is known to regulate developmental gene expression, genomic imprinting, X-inactivation, and genomic stability (3-6). Many retrotransposable repetitive elements are heavily methylated, and current evidence supports a causal relationship between DNA methylation and repression of retrotransposons (7-9). Intracisternal A particles (IAPs) are murine endogenous retroviral repetitive elements, with an estimation of over 1000 copies across the haploid murine genome (10 -12). Germ line mutations due to IAP retrotransposition most often occur at intronic sites, disrupting gene expression through premature termination, aberrant splicing, or viral LTR-driven transcription (13). Furthermore, insertional mutagenesis of IAP elements is noted in various murine cancer cell lines with subsequent activation of oncogenes or cytokine genes (14, 15).When expressed, IAP proteins are non-infectious viral particles that are retained in the cisternae of the endoplasmic reticulum (16). IAP proteins can be transiently detected in preimplantation embryos (17, 18), although DNA methylation of IAP elements is largely maintained throughout embryogenesis (19,20). In established lines of mouse embryonic stem cells (ESCs) derived from the inner cell mass, IAP elements are already heavily methylated with little detectable IAP expression (21).Here, we examine expression of IAP proteins in control and demethylated somatic cells, EpiSCs, and mESCs. Using a previously generated antibody against IAP protein (p73) (22) as well as our polyclonal antibody raised against recombinant IAP gag protein (9, 23), we mapped changes in IAP protein levels after Dnmt1 gene deletion in floxed (Dnmt1 2lox/2lox ) mouse embryonic fibroblasts (MEFs) using virus-mediated cre recombinase. Unexpectedly, we found that IAP mRNA and protein levels are not detected in Oct4
Dnmt1Ϫ/Ϫ ESCs but are dramatically increased in demethylated mESC cultures upon in vitro differentiation, suggestive of the presence of DNA methylation-independent repres-