Epigenetic control of embryonic stem cell fate

Abstract

Embryonic stem (ES) cells are derived from the inner cell mass of the preimplantation embryo and are pluripotent, as they are able to differentiate into all cell types of the adult organism. Once established, the pluripotent ES cells can be maintained under defined culture conditions, but can also be induced rapidly to differentiate. Maintaining this balance of stability versus plasticity is a challenge, and extensive studies in recent years have focused on understanding the contributions of transcription factors and epigenetic enzymes to the "stemness" properties of these cells. Identifying the molecular switches that regulate ES cell self-renewal versus differentiation can provide insights into the nature of the pluripotent state and enhance the potential use of these cells in therapeutic applications. Here, we review the latest models for how changes in chromatin methylation can modulate ES cell fate, focusing on two major repressive pathways, Polycomb group (PcG) repressive complexes and promoter DNA methylation.

Figure 1.

ES cell self-renewal and differentiation. ES cells have the ability to self-renew or differentiate into cells of all three germ layers (endoderm, ectoderm, and mesoderm). In ES cells, OCT4, SOX2, and NANOG form a core transcriptional network influencing the stem cell self-renewal machinery. Several hundred target genes co-occupied by OCT4, SOX2, and NANOG can be classified into two groups of downstream genes exerting opposing functions. One group includes actively transcribed genes associated with proliferation and transcription factors necessary to maintain the ES cell state. The other group includes transcriptionally silent genes encoding developmental regulators that are only activated as cells differentiate and commit to particular lineages.

Figure 2.

Dynamic recruitment of PcG proteins to chromatin during lineage specification. In ES cells, differentiation and development-promoting genes (Dev. A, B, and C) are repressed by bivalent domains, whereas late differentiation genes are not marked by H3K27me3, but not expressed. Pluripotency genes such as OCT4 are methylated at H3K4 and expressed. Differentiation signals generate cells committed to various somatic lineages, and activate lineage-specific genes that lose the repressive H3K27me3 mark (Dev. A). However, many genes preserve the bivalent domains and are not expressed (Dev. B and C); a few of these genes (e.g., those that are selectively expressed in other somatic cell lineages) also gain promoter DNA methylation during lineage commitment to ensure silencing (Dev. C). Late differentiation genes become marked by H3K27 in a manner dependent on the particular committed cell type, resulting in the formation of new bivalent domains that may be resolved in more mature differentiated cells. Examples of the aforementioned dynamics during neuronal differentiation of ES cells are NEUROG1, encoding for a neurogenic transcription factor (Dev. A); GATA4, encoding for an endodermal marker (Dev. B); TPARP, encoding for a germline-specific polyadenylate polymerase (Dev. C); and SCN1B, encoding for a neuronal voltage-gated sodium channel (late diff. gene; Mohn et al., 2008). The population of de novo DNA-methylated genes is also enriched in pluripotency-specific genes such as OCT4, ensuring the stable repression of transcripts that are required for ES cell maintenance.

Figure 3.

Potential mechanisms of PRC2 recruitment to target genes. PRC2 is recruited to target genes by a combination of transcription factors and ncRNAs. A fraction of PRC2 associates with JARID2, which is required for PRC2 binding to its target genes in ES cells. JARID2 might therefore represent a core component of PRC2 in ES cells, although other PRC2 complexes exist; these contain MTF2, PHF1, and other uncharacterized factors that could represent alternative targeting mechanisms operative both during ES cell self-renewal and differentiation. Sequence-specific transcription factors (TF) and ncRNA might also recruit the PRC2 core complex to target genes during differentiation. Finally, PcG target genes are CpG-rich, and proteins binding to CpG elements such as TET1 or the histone demethylase FBXL10 might have a role in recruiting Polycomb to target genes. For additional information on the components of PRC1 and PRC2 complexes, see Morey and Helin (2010).