Polycomb repressive complex 1 regulates the nucleosome landscape but not accessibility at target genes [RNA-seq]. Mus musculus

Polycomb repressive complexes 1 and 2 (PRC1/2) act to limit transcriptional activity at gene promoters. One of the mechanisms by which they are proposed to achieve this is through the compaction of nucleosomal chromatin. However, this model is based largely upon in vitro studies and has yet to be explored sufficiently in living cells. We therefore characterised the chromatin accessibility of Polycomb-occupied gene promoters using assay for transposase accessible chromatin (ATAC-seq). Although Polycomb-occupied promoters exist in a less accessible state compared to Polycomb-free promoters, we were surprised to observe that deletion of either PRC1, PRC2 or both PRC1/2 did not result in any increases in chromatin accessibility. This was in contrast to widespread increases in the transcriptional activity of Polycomb target genes. Together with experiments examining chromatin accessibility in the context of RNA polymerase II inhibition, we therefore demonstrate an apparent uncoupling of the chromatin accessibility and transcriptional activity of gene promoters. Overall design: Mouse embryonic stem cells with conditional (RING1Bfl/fl) or constitutive mutations (RING1Bfl/fl;EED-/-) for PRC1 and/or PRC2 were profiled for gene expression using nuclear RNA-seq.