Murine Chd1 (chromodomain helicase DNA-binding protein 1), a 
chromodomain-containing chromatin remodeling protein, is necessary for embryonic 
stem (ES) cell pluripotency. Chd1 binds to nucleosomes trimethylated at histone 
3 Lys 4 (H3K4me3) near the beginning of active genes but not to bivalent domains 
also containing H3K27me3. To address the mechanism of this specificity, we 
reproduced H3K4me3- and CHD1-stimulated gene activation in HeLa extracts. 
Multidimensional protein identification technology (MuDPIT) and immunoblot 
analyses of purified preinitiation complexes (PICs) revealed the recruitment of 
CHD1 to naive chromatin but enhancement on H3K4me3 chromatin. Studies in 
depleted extracts showed that the Mediator coactivator complex, which controls 
PIC assembly, is also necessary for CHD1 recruitment. MuDPIT analyses of 
CHD1-associated proteins support the recruitment data and reveal numerous 
components of the PIC, including Mediator. In vivo, CHD1 and Mediator are 
recruited to an inducible gene, and genome-wide binding of the two proteins 
correlates well with active gene transcription in mouse ES cells. Finally, 
coimmunoprecipitation of CHD1 and Mediator from cell extracts can be ablated by 
shRNA knockdown of a specific Mediator subunit. Our data support a model in 
which the Mediator coordinates PIC assembly along with the recruitment of CHD1. 
The combined action of the PIC and H3K4me3 provides specificity in targeting 
CHD1 to active genes.