General transcription factors bind promoters repressed by Polycomb group proteins

To maintain cell identity during development and differentiation, mechanisms of cellular memory have evolved that preserve transcription patterns in an epigenetic manner. The proteins of the Polycomb group (PcG) are part of such a mechanism, maintaining gene silencing. They act as repressive multiprotein complexes that may render target genes inaccessible to the transcriptional machinery1,2, inhibit chromatin remodelling3,4, influence chromosome domain topology5 and recruit histone deacetylases (HDACs)6. PcG proteins have also been found to bind to core promoter regions7, but the mechanism by which they regulate transcription remains unknown. To address this, we used formaldehyde-crosslinked chromatin immunoprecipitation (X-ChIP) to map TATA-binding protein (TBP), transcription initiation factor IIB (TFIIB) and IIF (TFIIF), and dHDAC1 (RPD3) across several Drosophila promoter regions. Here we show that binding of PcG proteins to repressed promoters does not exclude general transcription factors (GTFs) and that depletion of PcG proteins by double-stranded RNA interference leads to de-repression of developmentally regulated genes. We further show that PcG proteins interact in vitro with GTFs. We suggest that PcG complexes maintain silencing by inhibiting GTF-mediated activation of transcription.