All Things Stem Cell

While it is widely accepted that embryonic stem cells (ESCs) have the ability to become any type of cell, the molecular causes for this characteristic are still under much investigation, although one suspected player is chromatin. Recently, more evidence has been reported to support the important role of chromatin structure in maintaining an undifferentiated state in ESCs; the specific protein involved is called Chd1 (Gaspar-Maia et al., 2009).

DNA is condensed on histones, creating a structure called chromatin. (Left) A single DNA strand (formed by a sugar-phosphate backbone and nucleotide base-pairs). (Right) Chromatin is the complex formed by histones (green) and DNA (blue); the DNA can be tightly wrapped around the histones. (DNA bound to histones may be inaccessible to the transcription machinery, preventing the transcription of these genes, while unbound DNA allows space for the machinery and the genes may be transcribed.) Chd1 may function in ESCs to maintain chromatin in an open (euchromatin) state and potentially promote pluripotency in this way.

Chromatin structure plays an important role in regulating what genes are created, or expressed, in a given cell. In eukaryote organisms (almost all large organisms, such as animals, plants, and fungi, but not bacteria), DNA forms a complex with proteins that are called histones. This complex of DNA and histones is called chromatin (see figure). Histones act as spools for the DNA to be spun around, binding to DNA and packaging it into tightly coiled units (without histones, the long DNA strands would take up a very large amount of space). Whether the histones bind to the DNA or not can be regulated through chemical modification of the histones (they can be methylated or acetylated). When histones are bound to the DNA, the chromatin is in a condensed state (called heterochromatin) and the genes are not expressed because they cannot be accessed by the gene transcription machinery. However, when the histones are not bound to the DNA, the chromatin is extended (called euchromatin), and the DNA can be accessed and these genes can be expressed.

It was previously believed that embryonic stem cells had lots of open chromatin (euchromatin), but this was not a proven theory. A study on stem cells and gene expression (Efroni et al., 2008) reported that, globally but at low-levels, more genes in ESCs are actively turned into protein than are in differentiated cells. Additionally, proteins involved in changing chromatin structure and transcribing genes were expressed at relatively high levels in ESCs too. When the function of some proteins involved in chromatin-remodeling was changed, normal ESC proliferation and differentiation was also affected. Overall, Efroni et al. suggested that the differentiation of ESCs may correlate with a loss of active transcription of the cell genome.

Chd1 (chromodomain-helicase-DNA-binding protein 1) was suspected since its discovery in 1993 to play a role in gene regulation (Delmas et al., 1993). This protein was found to be in most, if not all, mammals. It has three key protein domains: a DNA-binding domain, a chromodomain (which may bind euchromatin), and a helicase domain (which is thought to activate transcription by acting against repressing transcription effects, such as heterochromatin structure).

A few months ago, research efforts led by Dr. Eran Meshorer (of Alexander Silberman Institute of Life Sciences at the Hebrew University) and Dr. Miguel Ramalho-Santos (of the University of California, San Francisco) published findings that suggest that Chd1 regulates euchromatin in mouse ESCs (Gaspar-Maia et al., 2009). Specifically, they found that Chd1 is highly expressed in ESCs (relative to differentiated cells) and that Chd1 binds to the promoters of genes actively being transcribed in mouse ESC euchromatin. When the mouse ESCs had decreased amounts of Chd1, heterochromatin (close chromatin) formed. When the ESCs had no Chd1 at all, the cells could not differentiate into all of the three germ layers (specifically, endoderm was not detected, and a preference was found for neuronal lineages). In other words, Chd1-deficient ESCs were no longer pluripotent; Chd1 appears to be necessary for this key trait of ESCs.

Interestingly, the authors also reported that Chd1 may play a key role in reprogramming cells into induced pluripotent stem cells (iPSCs); when Chd1 was downregulated in fibroblast cells and researchers tried to reprogram these cells into iPSCs, significantly fewer iPSCs resulted. These findings indicate that Chd1 may not only be important in maintaining pluripotency in ESCs, but also in creating pluripotency in cells that are not stem cells.

Overall, Chd1 definitely merits further investigation as a possible key regulator of stem cell potency and differentiation. Currently, although it is known that Chd1 binds to euchromatin, the exact mechanisms of how Chd1 counters heterochromatin formation are unclear; it may act to prevent the spread of heterochromatin areas to euchromatin. Additionally, it will be important to see whether this role of Chd1 as a regulator of stem cell potency is maintained in human ESCs and other stem cell types. With a better understanding of Chd1 function, it may be possible to improve the potency of some stem cells, such as in the creation of iPSCs, and it may also be possible to better direct desired stem cell differentiation for potential clinical applications downstream.

References

Gaspar-Maia, A., Alajem, A., Polesso, F., Sridharan, R., Mason, M. J., Heidersbach, A., Ramalho-Santos, J., McManus, M. T., Plath, K., Meshorer, E., Ramalho-Santos, M. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature. 2009. 460: 863-868.
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Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett-Jones, D. P., Grice, S. L., McKay, R. D. G., Buetow, K. H., Gingeras, T. R., Misteli, T., Meshorer, E. Global Transcription in Pluripotent Embryonic Stem Cells. Cell Stem Cell. 2008. 2(5): 437-447.
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Delmas, V., Stokes, D. G., Perry, R. P. A mammalian DNA-binding protein that contains a chromodomain and an SNF2/SWI2-like helicase domain. Proc. Natl. Acad. Sci. 1993. 90(6): 2414-2418.
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Image of “Chromatin” was taken from Wikipedia and redistributed freely as it is in the public domain.

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