Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET.
Endogenous retroviruses (ERVs), retrovirus-like elements with long terminal repeats, are widely dispersed in the euchromatic compartment in mammalian cells, comprising approximately 10% of the mouse genome. These parasitic elements are responsible for >10% of spontaneous mutations. Whereas DNA methylation has an important role in proviral silencing in somatic and germ-lineage cells, an additional DNA-methylation-independent pathway also functions in embryonal carcinoma and embryonic stem (ES) cells to inhibit transcription of the exogenous gammaretrovirus murine leukaemia virus (MLV). Notably, a recent genome-wide study revealed that ERVs are also marked by histone H3 lysine 9 trimethylation (H3K9me3) and H4K20me3 in ES cells but not in mouse embryonic fibroblasts. However, the role that these marks have in proviral silencing remains unexplored. Here we show that the H3K9 methyltransferase ESET (also called SETDB1 or KMT1E) and the Krüppel-associated box (KRAB)-associated protein 1 (KAP1, also called TRIM28) are required for H3K9me3 and silencing of endogenous and introduced retroviruses specifically in mouse ES cells. Furthermore, whereas ESET enzymatic activity is crucial for HP1 binding and efficient proviral silencing, the H4K20 methyltransferases Suv420h1 and Suv420h2 are dispensable for silencing. Notably, in DNA methyltransferase triple knockout (Dnmt1(-/-)Dnmt3a(-/-)Dnmt3b(-/-)) mouse ES cells, ESET and KAP1 binding and ESET-mediated H3K9me3 are maintained and ERVs are minimally derepressed. We propose that a DNA-methylation-independent pathway involving KAP1 and ESET/ESET-mediated H3K9me3 is required for proviral silencing during the period early in embryogenesis when DNA methylation is dynamically reprogrammed.
Matsui
Toshiyuki
T
Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
Leung
Danny
D
Miyashita
Hiroki
H
Maksakova
Irina A
IA
Miyachi
Hitoshi
H
Kimura
Hiroshi
H
Tachibana
Makoto
M
Lorincz
Matthew C
MC
Shinkai
Yoichi
Y
D000818:Animals; D002460:Cell Line; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000172:deficiency / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D000090205:DNA Methyltransferase 3A; D053595:Embryonic Stem Cells / Q000201:enzymology* / Q000378:metabolism / Q000821:virology*; D020077:Endogenous Retroviruses / Q000235:genetics*; D005347:Fibroblasts; D017353:Gene Deletion; D020868:Gene Silencing; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D009687:Nuclear Proteins / Q000378:metabolism; D011496:Protein Methyltransferases / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D011533:Proviruses / Q000235:genetics*; D012097:Repressor Proteins / Q000378:metabolism; D000076183:Tripartite Motif-Containing Protein 28; D000097584:DNA Methyltransferase 3B
D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D009687:Nuclear Proteins; D011496:Protein Methyltransferases; D012097:Repressor Proteins; D000076183:Tripartite Motif-Containing Protein 28; D000097584:DNA Methyltransferase 3B; C000715535:Dnmt3a protein, mouse; C000619381:Dnmt1 protein, mouse; C516239:SETDB1 protein, mouse; C103190:Trim28 protein, mouse