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The interplay of epigenetic marks during stem cell differentiation and development

Key Points

  • Repressive epigenetic marks (such as DNA methylation, dimethylation of histone H3 at lysine 9 (H3K9me2) and H3K27me3) are dispensable for pre-implantation embryonic development and naive pluripotency.

  • DNA methylation patterns change through development: naive pluripotency, pre-implantation epiblasts and primordial germ cells are associated with global DNA demethylation, whereas post-implantation epiblasts and epiblast-derived stem cells (EpiSCs) have high levels of DNA methylation.

  • Dynamic chromatin interactions occur during development and stem cell differentiation. Topologically associated domains (TADs) are largely stable during stem cell differentiation but sub-TAD interactions might change.

  • Enhancer activation is initiated by pioneer transcription factors and is often followed by H3K4me1 deposition (enhancer priming) and H3K27 acetylation (enhancer activation).

  • H3K27me3 and H3K4me3 promoter bivalency is observed in stem cells and in differentiated cells. Bivalency has a prominent role in post-implantation embryonic development.

  • DNA methylation and H3K27me3 are mutually exclusive at CpG-rich promoters: DNA methylation prevents deposition of the H3K27me3 mark.

  • Exit from naive pluripotency and embryonic stem cell differentiation is accompanied by progressive restriction of chromatin accessibility and histone acetylation.

Abstract

Chromatin, the template for epigenetic regulation, is a highly dynamic entity that is constantly reshaped during early development and differentiation. Epigenetic modification of chromatin provides the necessary plasticity for cells to respond to environmental and positional cues, and enables the maintenance of acquired information without changing the DNA sequence. The mechanisms involve, among others, chemical modifications of chromatin, changes in chromatin constituents and reconfiguration of chromatin interactions and 3D structure. New advances in genome-wide technologies have paved the way towards an integrative view of epigenome dynamics during cell state transitions, and recent findings in embryonic stem cells highlight how the interplay between different epigenetic layers reshapes the transcriptional landscape.

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Figure 1: Dynamics of epigenetic modifications during early mouse development and ESC differentiation.
Figure 2: 3D organization of the genome.
Figure 3: Sequence of events during enhancer activation and decommissioning.
Figure 4: The interplay between DNA methylation and histone modifications in different pluripotency states.

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Acknowledgements

The authors thank C. Logie for reading the manuscript and for feedback. This work was supported and funded by the European Union grant ERC-2013-ADG-339431 “SysStemCell”.

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Glossary

Genomic imprints

Epigenetic markings that regulate allelic gene expression according to the parent of origin.

Epigenome

Instructive chromatin information that is not stored in the genetic code (DNA) and can be inherited by cell progeny.

Primordial germ cells

(PGCs). Embryonic cells in the gonads that give rise to gametes.

Pluripotency

The potential of self-renewing stem cells to give rise to all cell types of all three germ layers (but not to extra-embryonic trophoblast cells). This state is detected in early embryos and in in vitro-cultured mouse and human embryonic stem cells (ESCs) as well as mouse epiblast-derived stem cells (EpiSCs) and epiblast-derived stem cell-like cells (EpiSCLCs).

2i medium

A serum-free and defined culture medium that is supplemented with MAPK/ERK kinase (MEK) and glycogen synthase kinase 3 (GSK3) inhibitors.

Epiblast-derived stem cells

(EpiSCs). In vitro-cultured stem cells that are derived from the post-implantation epiblast.

Tetraploid complementation assays

A technique that combines diploid embryonic stem cells (ESCs) and tetraploid embryos to examine the pluripotency potential of ESCs to generate a viable organism.

COMPASS-like complexes

Complex proteins associated with SET1 complexes are multisubunit protein complexes that are involved in mono-, di- and tri-methylation of histone H3 at lysine 4 (H3K4) and include many enzymatic proteins such as mixed lineage leukaemia protein 1 (MLL1), MLL2, MML3 and MLL4.

Writers

Enzyme (complexes) depositing chemical modifications in chromatin. These proteins include, among others, histone modifiers (for example, histone acetyltransferase or histone methylases) and DNA modifiers (such DNA methyltransferases).

Eraser

An enzyme that removes chemical modifications from chromatin, such as histone deacetylases or histone demethylases.

Readers

Proteins that recognize and bind to chemical modifications on chromatin, such as bromodomain-containing proteins that recognize acetylated histones or other proteins.

Inner cell mass

(ICM). Cells in the pre-implantation embryo (blastocyst) that will eventually give rise to different cell types in the embryo.

Polycomb repressive complex 2

(PRC2). Polycomb repressive complexes are multisubunit protein complexes that are writers of histone marks. These include PRC1, which is responsible for mono-ubiquitylation of histone H2A at lysine 119 (H2AK119Ub1), and PRC2, which is responsible for trimethylation of histone H3 at lysine 27 (H3K27me3).

5-Methylcytosine

(5mC). Methylated form of cytosine that is found in DNA and RNA molecules. DNA methyltransferase 3A (DNMT3A), DNMT3B, DNMT3C and DNMT1 are the writers of 5mC on DNA.

5-Hydroxymethylcytosine

(5hmC). Oxidized form of 5-methylcytosine that is generated by the action of TET proteins. 5hmC can be further converted into formyl and carboxyl methylcytosine, which can be removed from DNA to generate unmethylated cytosine.

Topologically associated domains

(TADs). TADs are densely interacting regions of the genome that represent the structural units of 3D chromatin organization in interphase cells.

CTCF

An 11-zinc-finger protein that functions as an insulator of genomic loci; it interacts as a homodimer with two CTCF motifs to mediate chromatin looping.

Cohesin complex

A multisubunit complex that holds sister chromatids together after replication. Together with CTCF, it mediates the formation of chromatin interaction loops (such as enhancer–promoter interactions). Subunits of the cohesin complex include structural maintenance of chromosomes protein 1 (SMC1), SMC3 and RAD21 proteins.

Primed-state pluripotency

A restricted state of pluripotency that exists in early post-implantation epiblasts and their in vitro-derived cells.

Enhancer priming

Pre-marking of enhancers with monomethylation of histone H3 at lysine 4 (H3K4me1) in progenitor cells for later activation (for example, with H3K27 acetylation (H3K27ac)) in differentiated cells.

Pioneer transcription factor

A transcription factor that recognizes closed chromatin regions and makes these regions more accessible to binding of other transcription factors.

Super-enhancers

Densely clustered enhancers that control genes involved in regulating the cell identity.

Hi-C

A chromosome conformation capture technique that maps all the chromatin interactions in the genome.

Extreme long-range interactions

(ELRI). Promoter–promoter interactions that occur over megabase distances and are associated with trimethylation of histone H3 at lysine 27 (H3K27me3) marks in embryonic stem cells (ESCs).

Ground-state pluripotency

A state of pluripotency detected in pre-implantation epiblast cells and in 2i-cultured embryonic stem cells (ESCs) that is independent of many repressive epigenetic marks.

CRISPR–Cas9 editing technology

A targeted genome-editing tool that has been engineered from components of a prokaryotic immune system.

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Atlasi, Y., Stunnenberg, H. The interplay of epigenetic marks during stem cell differentiation and development. Nat Rev Genet 18, 643–658 (2017). https://doi.org/10.1038/nrg.2017.57

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