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Nat Genet. 2015 Oct;47(10):1179-1186. doi: 10.1038/ng.3393. Epub 2015 Aug 31.

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.

Author information

1
Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.
2
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
3
Cancer Research UK London Research Institute, London, UK.
4
Department of Genetics, Evolution & Environment, University College London, London, UK.
5
Department of Biochemistry, Oxford University, Oxford, UK.
6
present address: Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan.
7
Bioinformatics, The Babraham Institute, Cambridge, UK.
8
Agilent Technologies Inc., Santa Clara, California, USA.
9
Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
10
Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan.
#
Contributed equally

Abstract

The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.

PMID:
26323060
PMCID:
PMC4847639
DOI:
10.1038/ng.3393
[Indexed for MEDLINE]
Free PMC Article

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