Principles of stem cell biology and cancer: future applications and therapeutics. Edited by T. Regad, T. J. Sayers and R. C. Rees. John Wiley & Sons (2015)
Part I. Stem Cells
‘Epigenetics’ refers to particular features that can be inherited from cell to cell that are not part of the DNA sequence and that, unlike mutations, are reversible. These most commonly consist of chemical modifications of histones or DNA that have profound effects on the regulation of gene expression and are critical for establishing and maintaining cell identity. Establishment of aberrant epigenetic marks during the in vitro differentiation of embryonic stem cells (ESCs) can result in cells that are different from their in vivo counterparts, compromising their use for clinical applications, since they may be prone to reverting to more proliferative phenotypes once implanted into the body.
It has been known for some decades that DNA is wrapped around histones to form the nucleosome; however, the tremendous impact that the organization of DNA into chromatin has on the regulation of gene expression was not fully realized until recently. In general terms, areas of the genome immersed in compact chromatin will have a low chance of being accessed by transcription factors and RNA polymerase II (Pol II). However, genes located in less condensed areas will be more likely to recruit Pol II and be actively transcribed.
Levels of chromatin condensation and gene expression have been correlated with the presence of certain histone or DNA modifications. DNA can be methylated at cytosine residues located at CpG and non-CpG sites by the action of DNA methyltransferases (DNMTs). In both cases, methylation is associated with transcriptional repression, but methylation at non-CpG sites seems far less frequent than CpG methylation (Guo et al., 2013) and remains less explored. Additionally, 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC) by the action of the 2-oxoglutarate(2-OG) and Fe(II)-dependant dioxygenase Tet proteins (Tahiliani et al., 2009). While hydroxymethylation has been proposed to be an intermediary in the pathway of demethylation (Guo et al., 2011), it might also have other specific functions, since several proteins can specifically bind to hydroxymethylated DNA (Spruijt et al., 2013).
Histones can suffer virtually any described post-translational modification, including acetylation, methylation, phosphorylation and others. It is more likely that these modifications will take place at the N-terminal tails, since they tend to protrude out of the nucleosome and are more available to modifying enzymes. Histone modifications can be correlated with either transcriptional activation or transcriptional repression, depending on the modification and the residue that becomes modified, and are dynamically regulated by enzymes capable of writing and erasing the marks. The collection of large amounts of data concerning levels of gene expression and genome-wide maps of histone modifications has allowed the establishment of clear correlations between certain modifications and gene expression. Among others, acetylation usually correlates with transcriptional activation, likely because this modification introduces a positive charge in the nucleosome believed to render chromatin less condensed. Trimethylation of histone H3 at lysine 4 (H3K4me3) is usually present at the transcription start site (TSS) of actively transcribed genes. Trimethylation of histone H3 at lysine 27 (H3K27me3) is commonly located at repressed genes. Certain modifications, such as H3K4me3 and H3K9me3, seem to be mutually exclusive and rarely mark the same genomic locations. Others, such as H3K4me1 and H3K27 acetylation, co-localize at certain genomic elements, such as enhancers, and allow the prediction of genetic elements according to their co-presence.
DNA and histone modifications, with the exception of acetylation, do not change the structural properties of chromatin. Instead, modified residues can serve as docking sites for other factors, which are referred to as ‘readers’. In many cases, readers are subunits of remodelling complexes that use ATP to mediate the condensation or relaxation of chromatin and therefore prevent or facilitate the expression of genes.
The environment is believed to have a deep impact on the cell epigenome, although how the complexity of the signal transduction pathways converge on histone and DNA modifications remains poorly understood. Among other effects, environmental cues can impact on the balance of writers, erasers and readers, and therefore have important consequences for the expression of critical genes.