Epigenetic regulation of pluripotency and differentiation

Abstract

The precise, temporal order of gene expression during development is critical to ensure proper lineage commitment, cell fate determination, and ultimately, organogenesis. Epigenetic regulation of chromatin structure is fundamental to the activation or repression of genes during embryonic development. In recent years, there has been an explosion of research relating to various modes of epigenetic regulation, such as DNA methylation, post-translational histone tail modifications, noncoding RNA control of chromatin structure, and nucleosome remodeling. Technological advances in genome-wide epigenetic profiling and pluripotent stem cell differentiation have been primary drivers for elucidating the epigenetic control of cellular identity during development and nuclear reprogramming. Not only do epigenetic mechanisms regulate transcriptional states in a cell-type-specific manner but also they establish higher order genomic topology and nuclear architecture. Here, we review the epigenetic control of pluripotency and changes associated with pluripotent stem cell differentiation. We focus on DNA methylation, DNA demethylation, and common histone tail modifications. Finally, we briefly discuss epigenetic heterogeneity among pluripotent stem cell lines and the influence of epigenetic patterns on genome topology.

Keywords: epigenomics; methylation; stem cell, pluripotent.

Figure 1

Proteins involved in the regulation of common epigenetic modifications. “Writer” refers to the enzyme(s) that catalyze and establish a particular modification. “Readers” are proteins or multiprotein complexes that recognize and bind the modification, and “Erasers” are a group of enzymes that catalyze removal of the mark. The coordinated action of these three groups not only ensures the faithful maintenance of epigenetic heritability but also determines the dynamic nature of epigenetic regulation during development. The list of histone modification writers, readers and erasers is exceedingly long. Therefore, we have listed only a few well-studied examples for each modification. New nomenclature guidelines have been proposed for many of these proteins; however, we have used the old nomenclature because it is more widely used in the literature. Proteins denoted in blue text exhibit heart defects when mutated. See also. DPF3B – Tetralogy of Fallot, MLL2- Kabuki Syndrome, CHD7 - CHARGE Syndrome, WHSC1 - Wolf-Hirschhorn Syndrome.

Figure 2

DNA methylation dynamics. Cytosine is methylated at carbon 5 of the pyrimidine ring by DNA methyltransferases (DNMT) to generate 5-methylcytosine (5mC), which can be hydroxylated to 5-hydroxymethylcytosine (5hmC) by TET dioxygenases. 5hmC can be deaminated by the cytidine deaminase, AID, to generate 5-hydroxymethyluracil (5hmU), or further oxidized by TETs to 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC). 5hmU, 5fC and 5caC are all substrates for thymine DNA glycosylase (TDG); the primary glycosylase that initiates base excision repair-mediated DNA demethylation.

Figure 3

Epigenetic control and remodeling of regulatory elements during development. (A) Poised enhancers/promoters are typically found in pluripotent stem cells. They possess epigenetic modifications indicative of both transcriptionally active (green marks) and repressed (red mark) chromatin. For instance, the Trithorax Group (TrxG) proteins and Polycomb Group (PcG) proteins, which catalyze H3K4me3 and H3K27me3 respectively, localize to poised promoters. Poised regulatory elements are also generally devoid of 5mC and enriched for 5hmC. Poised enhancers can be distinguished from poised promoters by the presence of the enhancer-specific mark, H3K4me1, and bound Mediator complex. Chromatin loops organized by CTCF binding localizes distal poised (or active) enhancers and promoters within close physical proximity to facilitate transcription. (B) The transition from poised to active regulatory elements involves loss of PcG localization, and demethylation and concomitant acetylation of H3K27. Gains of H3K36me3 within gene bodies are also observed upon gene activation. (C) Heterochromatin formation is associated with gene repression. This is mediated in part by erasure of activating histone modifications (H3K4me1, H3K27ac, 5hmC), establishment of repressive marks such as H3K27me3 and 5mC, and nucleosomal compaction. MBD, methyl-DNA binding domain protein; DNMT, DNA methyltransferase; TET, ten eleven translocation dioxygenase; HAT, histone acetyltransferase; HDAC, histone deacetylase; PcG, polycomb group complex; TrxG, trithorax group complex; TF, transcription factor; MED, Mediator complex; POL II, RNA polymerase II.

Figure 4

Schematic of cell type-specific genome topology. Genetic loci (depicted as colored circles) cluster together making both intra- (Chr A: Chr A) and inter- (Chr A: Chr B) chromosomal interactions in a cell type-specific manner. This establishes coregulated transcription of multigene networks that confer cellular identity. Differing topological interaction patterns are expected to be associated with different cell types such as ESCs (Cell type 1) and progenitor cells (Cell type 2).