The ability of embryonic stem cells to give rise to any cell type relies on a remodelling protein that maintains open chromatin. But the chromatin landscape of these cells may be more complex than previously thought.
Embryonic stem (ES) cells are ideal models for studying the molecular principles that dictate cell fate. ES cells can self-renew and form every type of cell in an organism — a property called pluripotency. It is well established that DNA-binding proteins set the stage for determining cell-type specificity by orchestrating complex patterns of gene expression1. However, DNA is tightly assembled with accessory proteins into a structure called chromatin, which limits its accessibility to regulatory proteins. Chromatin can be loosely packed, or 'open', allowing DNA-binding proteins ready access to the genome. Alternatively, it can be densely compacted, or 'closed', making the DNA relatively inaccessible2. On page 863 of this issue, Gaspar-Maia et al.3 provide evidence that chromatin structure is intimately connected with cell fate by showing that highly accessible chromatin is essential for the unique properties of stem cells.
ES cells have to achieve a delicate balance of gene regulation: they must suppress genes that result in premature differentiation, while maintaining expression of genes that allow self-renewal. Previous work4,5 has shown that ES cells maintain an open chromatin structure and express a large proportion of their genes. Differentiation of ES cells into mature cell types, such as neural cells, is accompanied by closing of chromatin4 and by widespread gene silencing5. As chromatin structure strongly dictates whether or not genes can be expressed, Gaspar-Maia and colleagues3 examined the role of enzymes that can modify this structure in keeping ES cells pluripotent.
The authors found that decreasing the amounts of a chromatin-remodelling protein called Chd1 impaired ES-cell proliferation and reduced expression of the DNA-binding transcription factor Oct4, which is a master regulator of ES-cell function. Chd1 has previously been shown to facilitate gene expression6, consistent with its role in Oct4 regulation. However, in this case3 its depletion did not result in a global decrease in gene activity, as would be expected for a factor widely associated with active gene transcription. Instead, ES cells lacking Chd1 upregulated the expression of genes involved in nervous-system development, and they tended to differentiate into cells of the neuronal lineage3.
Whether chromatin structure is accessible or compact is determined in part by chemical modification of its core protein components, histones. For example, trimethylation of lysine 4 on histone H3 (H3K4me3) is a marker of open chromatin. Chd1 contains a motif that recognizes H3K4me3 (refs 7, 8) and indeed, when Gaspar-Maia and colleagues performed genome-wide studies of Chd1 localization on chromatin in normal ES cells, they found that Chd1 co-localizes with H3K4me3. When the authors depleted ES cells of Chd1, they observed an increase in the proportion of condensed chromatin in these cells. On the basis of their results, they surmise that Chd1 maintains an open chromatin structure in ES cells, which is required for their pluripotency.
The interplay between Chd1, H3K4me3 and open chromatin (Fig. 1) highlighted by Gaspar-Maia and colleagues3 is reinforced by findings from other studies9,10,11,12,13. H3K4me3 is incorporated into chromatin during active transcription9; therefore, promotion of gene expression by Chd1 might ensure that chromatin is rich in H3K4me3 and maintained in an open conformation. Chd1 has also been shown10 to regulate DNA-replication-independent deposition of chromatin enriched in H3K4me3. Moreover, binding of Chd1 to chromatin may protect H3K4me3 from turnover through histone demethylation. This histone mark also prevents the binding of factors that mediate gene silencing, such as the NuRD histone-modifying complex11,12 and the DNA methyltransferase subunit DNMT3L13. Loss of H3K4me3 would therefore allow increased chromatin compaction induced by NuRD and DNA methylation, highlighting the need to maintain a correct balance of H3K4me3. In addition, the histone methyltransferase Suv39H1 facilitates the formation of silent chromatin domains by methylating lysine 9 on histone H3. Suv39H1 is known to act on histones that lack methylated H3K4 (Fig. 1); thus, open chromatin would serve to counteract this repressive activity.
What Gaspar-Maia and colleagues' work3 does not explain is how, despite depletion of Chd1, global ES-cell gene activation is largely unaffected while genes that drive differentiation towards the neuronal cell fate are upregulated. It is possible, though, to reconcile these findings by taking into account Chd1-mediated regulation of the distribution of H3K4me3. For instance, the p400/TIP60 complex, which turns genes on or off by changing the composition of chromatin, also seems to bind H3K4me3 (ref. 14). When the amount of H3K4me3 is reduced in ES cells, binding of p400/TIP60 to its chromatin targets is impaired14. In this way, the perturbation of H3K4me3 in the absence of Chd1 could impair gene silencing through its effects on factors such as p400/TIP60. Although unusual for somatic cells (non-gametes), in ES cells, H3K4me3 may be associated with silencing of genes at focal locations throughout chromatin15. Alternatively, widespread gene reactivation could be a consequence of indirect effects of the downregulation of ES-cell master regulatory factors such as Oct4.
Studying differentiated cells undergoing reprogramming to a pluripotent state16 allows insight into the core properties of stem-cell chromatin. Cells that fail reprogramming reactivate subsets of stem-cell-related genes, but simultaneously fail to repress lineage-specific transcription factors16. Thus, the correct mix of gene expression to achieve stem-cell properties may depend more on local alterations in chromatin structure than on global chromatin reorganization. Gaspar-Maia et al.3 show that Chd1 loss prevents the reprogramming of somatic cells to a pluripotent state. A small imbalance in chromatin structure, induced by loss of Chd1, might reorganize boundaries between open and closed chromatin states; this could result in failure to maintain the appropriate mix of specific gene expression and gene silencing, sending the ES cell down a path of differentiation.
Could the increased amount of closed chromatin observed in ES cells lacking Chd1 (ref. 3) stem from focal changes in chromatin at genes encoding cell-lineage-specifying factors, rather than representing a genome-wide alteration in chromatin structure? Current assays do not accurately measure the physical properties of chromatin structure in cells, and novel techniques to analyse higher-order chromatin structure in vivo are needed to answer such complex questions. It is clear, however, that the careful maintenance of an open chromatin structure, whether global or local, by factors such as Chd1, is crucial for the preservation of pluripotency.
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Proceedings of the National Academy of Sciences (2018)
PLoS ONE (2014)
Identification of novel CHD1-associated collaborative alterations of genomic structure and functional assessment of CHD1 in prostate cancer