Mechanisms underpinning Polycomb mediated gene repression in stem cell self-renewal and differentiation

Polycomb complexes mediate long-range intra-chromosomal contacts between the Drosophila Antennapedia and Bithorax gene clusters. Emerging 4C chromosome conformation capture and DNA FISH data also suggest a role for Polycomb complexes in regulating gene expression in mammalian cells by mediating spatial genome organisation.

Using Promoter Capture Hi-C (CHi-C), an unbiased, genome-wide assay which maps spatial contacts for all mouse gene promoters at high resolution, we showed that PRC1 acts as a master regulator of ES cell genome architecture by organising genes in intra and inter-chromosomal three-dimensional interaction networks.

The strongest network (Hox spatial network) includes the four Hox clusters and promoters of key transcription factor genes essential for cell fate specification during early development (Figure 3).
Network map Figure 3: (Click to enlarge) Network map of 22,000 mouse promoters from WT (left) and Ring1A/B-dKO (Right) mouse ES cells. Inlay left the strongest network in ES cells centred on the Hox clusters and enriched for PRC1 bound key early developmental regulators. Inlay right, Hox network is completely disrupted on PRC1 knockout. Red: Hox Clusters; Blue: PRC1 bound; Grey: all other promoters


Proposed model for regulation Figure 3: (Click to enlarge) Proposed model for regulation of the Hox network during differentiation
The majority of these Hox spatial network members make contacts with ‘poised’ enhancers which harbour both H3K27me3 and H3K4me1. Induced PRC1 knockout leads to complete disruption of the promoter-promoter contacts comprising the Hox spatial network (Figure 3).

In contrast, promoter-poised enhancer contacts are maintained and this is accompanied by widespread acquisition of active chromatin signatures at these enhancers, as well as pronounced transcriptional up-regulation of genes in the network.

Our results show that PRC1 physically constrains promoters and regulatory elements of key transcription factor genes in a silenced but poised spatial network. We propose that selective release of genes from the Hox network drives lineage specification during early development (Figure 4).

Check out our paper in Nature Genetics.


Our lab is now focused on understanding how the different mechanisms contribute to Polycomb mediated gene regulation, how Polycomb spatial networks are regulated in vivo and how these mechanisms regulate stem cell self-renewal and differentiation.
mechanisms regulating stem cell self-renewal and differentiation