DNA methylation directs polycomb-dependent 3D genome re- organisation in naive pluripotency

Abstract

The DNA hypomethylation that occurs when embryonic stem cells (ESCs) are directed to the ground state of naïve pluripotency by culturing in 2i conditions results in redistribution of polycomb (H3K27me3) away from its target loci. Here we demonstrate that 3D genome organisation is also altered in 2i. We found chromatin decompaction at polycomb target loci as well as loss of long-range polycomb interactions. By preventing DNA hypomethylation during the transition to the ground-state, we are able to restore the H3K27me3 distribution, and polycomb-mediated 3D genome organisation that is characteristic of primed ESCs grown in serum, to ESCs in 2i. However, these cells retain the functional characteristics of 2i ground state ESCs. Our findings demonstrate the central role of DNA methylation in shaping major aspects of 3D genome organisation but caution against assuming causal roles for the epigenome and 3D genome in gene regulation and function in ESCs.

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability

“…This redistribution may partially explain the derepression of HOXA9 [52] and the de novo bivalent promoters [53] observed in MM. H3K27me3 redistribution could also play an important role in chromatin decompaction, as has been shown in ESCs [54], and could explain the increase in open chromatin regions within the heterochromatin state of MM samples [55]. These data highlight that PMDs must be considered as a separate entity in genomic analyses.…”

Coolpup.py:versatile pile-up analysis of Hi-C data

“…TADs longer than 1,500 kbp were not used due to their likely artefactual nature (based on both visual inspection, and the fact that TAD sizes are reported to be on the order of a few hundred kbp in mammalian cells (Rao et al, 2014)). The same loop annotations for mouse embryonic stem (ES) cells were used as in our recent preprint (McLaughlin et al, 2019).…”

“…TADs have been reported to constrain enhancer-promoter communication in some cases (Lupiáñez et al, 2015;Franke et al, 2016;Williamson et al, 2019) and might be related to genome stability (Canela et al, 2017(Canela et al, , 2019, while some loops have been suggested to correspond to enhancerpromoter contacts (Rao et al, 2014). In addition, distal polycomb sites can be brought together in 'loops' (Joshi et al, 2015;McLaughlin et al, 2019).…”

“…Since its inception in the current form (Rao et al, 2014), originally termed APA ("Aggregate Peak Analysis"), pile-up analysis has been used in numerous publications, both to analyse single-cell Hi-C data (Flyamer et al, 2017;Gassler et al, 2017;Nagano et al, 2017) and as a general way of quantifying feature strength (Fudenberg et al, 2016;Schwarzer et al, 2017;Bonev et al, 2017;Nora et al, 2017;McLaughlin et al, 2019;Rao et al, 2017;Díaz et al, 2018;Kruse et al, 2019;Abdennur et al, 2018;Rowley et al, 2019;Krietenstein et al, 2019;Hsieh et al, 2019). A visual interactive tool to semi-manually classify and pile-up predefined regions has also been developed (Lekschas et al, 2018).…”

Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells

“…Nevertheless, it may be speculated that CpG demethylation is necessary albeit not sufficient for H3K27me3 hypermethylation and naive state. In fact, a recent bioRxiv preprint suggests that restoration of Serum-like DNA methylation in the naive state also reverts back the H3K27me3 landscape, albeit the cell maintains a naive transcriptome and phenotype 21 . Vice versa, H3K27me3-deficient EED -/-mESC have been shown to exhibit increased CpG methylation in 2i 22 , while also maintaining the naive transcriptome 5 .…”