Retrovirus vector silencing is de novo methylase independent and marked bya repressive histone code

Retrovirus vectors are de novo methylated and transcriptionally silent in m ammalian stem cells. Here, we identify epigenetic modifications that mark r etrovirus-silenced transgenes, We show that murine stem cell virus (MSCV) a nd human immunodeficiency virus type 1 (HIV-1) vectors dominantly silence a linked locus control region (LCR) beta -globin reporter gene in transgenic mice. MSCV silencing blocks LCR hypersensitive site formation, and silent transgene chromatin is marked differentially by a histone code composed of abundant linker histone H1, deacetylated H3 and acetylated H3, Retrovirus-t ransduced embryonic stem (ES) cells are silenced predominanely 3 days post- infection, with a small subset expressing enhanced green fluorescent protei n to low levels, and silencing is not relieved in de novo methylase-null [d nmt3a-/-;dnmt3b-/-] ES cells. MSCV and HIV-1 sequences also repress reporte r transgene expression in Drosophila, demonstrating establishment of silenc ing in the absence of de novo and maintenance methylases. These findings pr ovide mechanistic insight into a conserved gene silencing mechanism that is de novo methylase independent and that epigenetically marks retrovirus chr omatin with a repressive histone code.