2.4. Reprogramming of somatic cells to pluripotency: reversing the epigenetic landscape

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

It is a fundamental belief that pluripotent and multipotent cells differentiate into terminal irreversible states. However, in animals that are able to regenerate certain organs, differentiated cells can revert to more undifferentiated phenotypes, allowing proliferation and re-differentiation to repair or even rebuild the new organ. Mammals seem to have lost this property, raising the question of whether differentiated states could be reversed. Nuclear transfer experiments 2 decades ago showed for the first time that it is possible to revert the differentiated phenotype (Wilmut et al., 1997), and, more recently, it has been shown that it is possible to reprogramme somatic cells to pluripotency using the transcription factors Oct4, Sox2, Klf4 and Myc (Takahashi and Yamanaka, 2006).

The process of reprogramming using ectopic expression of factors is very inefficient, likely due to the impossibility of hitting condensed chromatin with these factors. The use of small molecules such as inhibitors of histone deacetylases and DNA methyltransferases to enhance preprogramming suggests that chromatin acts as a barrier in this process (Feng et al., 2009). Chromatin remodelling factors like CHD1 (Gaspar-Maia et al., 2009) and components of the BAF complex (Singhal et al., 2010) have also been shown to facilitate reprogramming, by contributing to the opening up of chromatin at genomic sites that are bound by the reprogramming factors (Figure 2.5).

Methylation of H3K27 needs to be properly regulated during reprogramming. While the H3K27me3 demethylase UTX is needed to remove the H3K27me3 mark at pluripotency-related genes (Mansour et al., 2013), cells that show defective PRC2 activity fail to silence developmental regulators and reprogramme into pluripotency (Fragola et al., 2013). Removal of DNA methylation at self-renewal genes is another critical step that requires the action of TET2 and TET1 (Doege et al., 2012; Costa et al., 2013; Gao et al., 2013) (Figure 2.5). Additionally, gain of H3K4me3/2 at self-renewal genes during reprogramming requires the action of MLL complexes (Ang et al., 2011).

In accordance with the role of H3K9 methylation in the establishment of heterochromatin, depletion of the H3K9 methyltransferases Ehmt1, Ehmt2 and Setdb1 and of the methyl H3K9-binding protein Cbx3 facilitates reprogramming (Sridharan et al., 2013), while the presence of H3K9 demethylases promotes reprogramming (Chen et al., 2013). These findings are in agreement with the discovery of megabase-sized blocks marked with H3K9me3 in differentiated cells that are refractory to binding by the reprogramming factors during the early stages of reprogramming (Soufi et al., 2012).

During the reprogramming process, the changes in gene expression appear ordered in time: the silencing of the cell-specific programmes occurs first, followed by activation of the pluripotency network (Sridharan et al., 2009). However, most early change in histone modification consist in the gain of H3K4me2 at pluripotency-related and developmentally regulated gene promoters and enhancers. This change, which precedes changes in H3K27me3, might act as a priming event, since it precedes transcriptional changes within the corresponding locus (Koche et al., 2011). Epigenetic barriers that prevent the gain of H3K4me2 at this locus, such as the presence of macroH2A (Barrero et al., 2013a), are likely to contribute to the low efficiency of the reprogramming process.

Principles of Stem Cell Biology and Cancer 2.5

Figure 2.5. Chromatin factors involved in the process of somatic cell reprogramming to pluripotency. Middle panel shows factors that have been shown to facilitate (green) or block (red) reprogramming to induced pluripotent stem cells (iPSC). These factors are involved in critical events such as DNA demethylation or H3K27me3 removal and gain of H3K4me2/3 at pluripotency genes and silencing of developmental genes through gain of H3K27me3.


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