SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells

The self-renewal and pluripotency of ES cells are regulated by both genetic and epigenetic mechanisms (Boyer etal. 2005; Surani etal. 2007; Chen and Daley 2008; Chen etal. 2008; Kim etal. 2008). Epigenetic silencing represses developmental programs, guiding ES cell differentiation into distinct lineages (Surani etal. 2007; Hong etal. 2011). SETDB1, also known as ESET or KMT1E, was identified as a key chromatin modifier required for ES cell maintenance through the suppression of developmental regulators (Bilodeau etal. 2009). Consistently, we have shown previously that Setdb1 is essential for embryogenesis (Dodge etal. 2004). In coordination with POU5F1, SETDB1 suppresses the trophectoderm cell lineage (Yuan etal. 2009; Lohmann etal. 2010). SETDB1 was also shown to be involved in various developmental processes (Wang etal. 2011; Mysliwiec etal. 2012) as well as silencing of endogenous retrovirus(Matsui etal. 2010; Karimi etal. 2011). Although SETDB1 is a major histone methyltransferase(HMT) responsible for transcription repression mainly via H3K9me3 (Schultz etal. 2002), deletion of Setdb1 has little or no effect on global H3K9me3 level in ES cells (Dodge etal. 2004). Brain-specific deletion of Setdb1 leads to impaired brain development accompanying the suppressed expression of neuronal genes (Tan etal. 2012). Since SETDB1 is a transcription suppressor, it is unlikely that the suppression of neuronal genes upon Setdb1 deletion is directly resulted from the change of H3K9me3 mediated by SETDB1. These observations indicated that there may be H3K9me3 independent roles of SETDB1 in gene expression and development regulation. Consistent with the roles of SETDB1 in early development, searching genome-wide SETDB1 binding sites in mouse ES cells has indicated that SETDB1 is associated with developmental regulators which are often poised as bivalent genes that are manifested by the co-occupancy of the repressive H3K27me3 and the active H3K4me3methyl marks (Bilodeau etal. 2009; Yuan etal. 2009). Moreover, SETDB1 bindings are found to overlap with the Polycomb proteins (Bilodeau etal. 2009). There is also evidence indicating that SETDB1 could interact with JARID2, an interacting protein of the PRC2complex (Mysliwiec etal. 2012). Since PRC2is thought to maintain ES cell pluripotency by silencing developmental regulators (Margueron and Reinberg 2011), it is of importance to determine whether SETDB1 can act in coordination with the PRC complex to regulate stem cell pluripotency and differentiation; and if so, whether such coordination will require H3K9 trimethylation mediated by SETDB1.