Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency

Abstract

Serum-to-2i interconversion of mouse embryonic stem cells (mESCs) is a valuable in vitro model for early embryonic development. To assess whether 3D chromatin organization changes during this transition, we established Capture Hi-C with target-sequence enrichment of DNase I hypersensitive sites. We detected extremely long-range intra- and inter-chromosomal interactions between a small subset of H3K27me3 marked bivalent promoters involving the Hox clusters in serum-grown cells. Notably, these promoter-mediated interactions are not present in 2i ground-state pluripotent mESCs but appear upon their further development into primed-like serum mESCs. Reverting serum mESCs to ground-state 2i mESCs removes these promoter-promoter interactions in a spatiotemporal manner. H3K27me3, which is largely absent at bivalent promoters in ground-state 2i mESCs, is necessary, but not sufficient, to establish these interactions, as confirmed by Capture Hi-C on Eed(-/-) serum mESCs. Our results implicate H3K27me3 and PRC2 as critical players in chromatin alteration during priming of ESCs for differentiation.

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

“…At active/enhancer regions, the Mediator complex is thought to sustain long-range interactions with associated promoters and could account for part of these CTCF-independent interactions (Phillips-Cremins et al 2013). At repressed regions, the PRC1 and PRC2 complex were shown to mediate long-range interactions and could account for the homotypic bridging of H3K27me3-rich chromatin regions (Denholtz et al 2013;Joshi et al 2015;Schoenfelder et al 2015). The controlled spatial clustering of repressed or active regions, analogous to the domain-wide clustering of A and B compartments on a larger scale (Lieberman-Aiden et al 2009), could be seen as another layer of gene regulation.…”

Switch-Like Roles for Polycomb Proteins from Neurodevelopment to Neurodegeneration

“…In this respect, the loss of PRC2 function disrupts long range interactions [53,54], but does not affect mammalian TAD formation.…”

Dynamic chromatin organization: Role in development and disease

“…Klf1 and pluripotency factor networks (7,9). Similarly, loci associated with Polycomb proteins and the repressive chromatin modification H3K27me3 tend to cluster together (10). Artificial tethering of TFs via the lac integration cassette has further corroborated this observation.…”