Epigenetic Regulation of Stem Cells

Our DNA is what makes us who we are. It determines our hair texture, skin colour, eye colour, and everything else within our bodies. Would you be surprised if you knew that our DNA can change? Changes in the physical structure of our DNA are attributed to epigenetics. Epigenetics also play an important role during development and are responsible for regulating stem cells to form the vast amount of cell types that make up our body. Each cell has the same DNA sequence, so we need epigenetic regulation (changes to the accessibility of the DNA for transcription) to allow different expression patterns in each type of cell, which are the cause for the specialization and differentiation of each cell type.

Epigenetic regulation of stem cell differentiation

During fetal development, stem cells are capable of extensive self-renewal and can differentiate into many cells. For a stem cell to commit to one lineage, long-lasting changes in gene expression must be made to prevent these stem cells from self-dividing into more stem cells. This is done through epigenetic changes. Epigenetic mechanisms such as DNA methylation and histone modification are vital for controlling stem cell differentiation during development.

Stem cells have two essential properties: the ability to self-divide and the ability to differentiate into many cell lineages. A single embryonic stem cell can divide into more stem cells and these can differentiate into any specific cell within the body. For example, a stem cell can turn into a skin cell, a cardiomyocyte, or even a natural killer cell depending on the epigenetic changes that it goes through.

Epigenetic regulation controls access to the DNA before DNA transcription is initiated. The primary epigenetic mechanisms that we will be discussing in this article are: DNA cytosine methylation and histone modification. Let's take a closer look at both these mechanisms.

Epigenetic regulation example

Histone modification

As DNA is organized within a chromosome, it is wounded around strands of histone proteins.¹ These histone proteins package the DNA into structural units called nucleosome complexes, which are responsible for regulating which enzymes have access to certain DNA regions.¹

If a specific gene needs to be transcribed, the nucleosome surrounding the DNA region carrying the gene can slide down the DNA to give the transcriptional machinery access to that given region.

Nucleosomes uncover DNA segments by unrolling the specific DNA segment with the gene that needs to be expressed. Nucleosomes can move to expose a segment of DNA; however, they do so in an extremely controlled manner. When nucleosomes are close to one another, they cover up a large segment of DNA, and the genes within that segment cannot be expressed since the transcriptional machinery cannot access them.

The way histone molecules (the components of the nucleosome) move to expose DNA segments is dependent on signals found both on the histone proteins and on the DNA.¹ These signals are special tags that are added to the histone and the DNA that tell the histones if a chromosomal segment should be exposed or not. The special tags can be added or deleted as needed based on which genes need to be transcribed. A tag can be phosphate, methyl, or acetyl groups that attach to amino acids within the histone protein or to nucleotides within DNA. These tags alter how tightly wound the DNA is around the histone protein.¹

DNA has a negative charge which means that changes in the charge of the histone will change how tightly wound the DNA molecule will be. Without the tags, histone proteins are positive which attracts the negative DNA resulting in a tightly wound nucleosome. When tags like phosphate groups are added to the histone protein, it becomes negatively charged which repels the DNA molecule resulting in a loosely wound nucleosome.¹

DNA methylation

DNA methylation is the addition of a methyl (-CH₃) group to the DNA strand at the 5^th carbon atom of a cytosine ring.¹ Once the methyl group attaches to the 5^th cytosine carbon, they create 5-methylcytosine which is catalyzed by enzymes called DNA methyltransferases (DNMTs).¹

In mammals, DNA methylation occurs mainly at the CpG dinucleotides which are stretches of DNA with a high number of cytosine and guanine dinucleotide pairs.¹ At these CpG dinucleotides, DNMTs called DNMT3a and DNMT3b establish methylation patterns by working together to create de novo methylation. On the other hand, methylation has to also be maintained: there also exist maintenance DNMTs, which copy the established methylation patterns onto newly replicated DNA strands.¹

DNA methylation changes how DNA interacts with histone proteins. Highly methylated DNA regions are tightly coiled and do not participate in transcription.¹ Epigenetic changes to DNA and histones do not alter the codons within the DNA so each DNA codon remains intact. Also, epigenetic changes are not permanent. Instead, they simply control which segment of DNA can be transcribed. A gene can be turned on or off depending on the epigenetic modifications discussed above.¹

RNA-mediated epigenetic regulation of gene expression

A wide array of RNA classes ranging from small RNAs to long non-coding RNAs have been identified as key regulators of gene expression.⁴ From the previous section, we understand that histone modification and DNA methylation drive the regulation of gene expression by controlling what genes are transcribed. Small RNAs control gene expression by recruiting epigenetic factors such as the ones mentioned above. The RNAi pathway is the primary pathway for RNA-mediated epigenetic regulation of stem cells.⁴ RNAi is a group of mechanisms that utilize small RNA molecules to facilitate gene silencing.⁴

We know from the regulation of gene expression article that most eukaryotic genes are transcribed by RNA polymerase II. Once transcribed, the RNA transcript is spliced and then exported into the cell's cytoplasm.⁴ Within the cytoplasm, ribosomes catalyze the translation of RNA into proteins.⁴ During this process, small RNA molecules are able to exert their silencing effects.

Epigenetic regulation of ageing stem cells

Epigenetics play a crucial role in cell differentiation by regulating which genes are expressed. The regulation of gene expression determines the cell lineage that a stem cell divides into. Stem cells are capable of asymmetrical cell division, which means that they can divide into two different types of cells. In other words, a multipotent stem cell can divide to create two daughter cells with different lineages: for example, one can be a neural precursor cell and the other a muscle precursor cell.

As a cell receives a signal, genes within that differentiating cell turn on and drive that cell toward a specific lineage. If a stem cell receives a signal telling it to differentiate into a nervous system cell, this stem cell will only express genes needed to form a nervous system cell. Another way that cell differentiation can be controlled is through environmental stimuli.

Now let's look at a specific example of how a cell responds to internal, external, and environmental signals to establish cell specialization.

Regulation of neurogenesis

The adult brain has two main regions where neurogenesis occurs: the subventricular zone (SVZ) and the dentate gyrus, located in the hippocampus. Within the SVZ, astrocytic stem cells differentiate into early neurons, called neuroblasts, and glial cells. When an astrocytic stem cell divides, it can produce either a neuroblast, transient amplifying cell, or another astrocytic stem cell in any combination. If the astrocytic stem cell divides into a neuroblast, a neuron will be produced.

Once the neuron is produced, internal and external signals will drive it toward a specific specialization. In the case of the subventricular zone, the neuron will be an olfactory neuron that specializes in transmitting chemical stimuli to the brain. On the other hand, if the astrocytic stem cell divides into a transient amplifying cell, a glial cell will be produced. Specific signals will drive that cell to either produce an astrocyte or an oligodendrocyte.

The level of specificity of a differentiating cell depends on which internal and external signals are present, as well as the location of the cell. The cell's location and signal stimuli determine what transcription factors are activated, which will determine what genes are expressed in that particular cell. A cell's gene expression is what determines its specialization.

Epigenetic regulation of cancer stem cells

Cancer is, simply put, uncontrolled cell division. Uncontrolled cell division may seem great at first since it could possibly lead to immortality; however, each new cell needs space and sustenance, causing a grievance to the other cells in the organism.

When a cancer cell divides, there is no control over what type of cell will be produced. For example, people with lung cancer can have teeth cells and bone cells develop in their lungs which hurts the lungs as blood flow interruptions and structural damage to the lungs can occur. The primary treatment for cancer is chemotherapy which is the introduction of harmful chemicals into the affected organism in an extremely controlled way in order to only kill the target cancer cells.

Chemotherapy is not effective in stopping all cancers which is why researchers are looking for new options. One of these treatment options is using epigenetics to regulate cancer cells. Researchers at the Northwestern University of Medicine discovered an epigenetic complex that works to allow widespread cell division in cancer cells.³ This complex is called the polycomb repressive complex 2 (PRC2).³

This complex is a methyltransferase like the ones we discussed above in the DNA methylation section.³ Usually, this complex is inhibited by DNA methylation. The methylated gene that inhibits PRC2 is called CATACOMB (Catalytic Antagonist of Polycomb). Usually, this gene is silenced in our genome due to DNA methylation.³ However, when the level of methylation is very low, the CATACOMB gene can be expressed and can bind to the PRC2 complex and inhibit its activity.³ This CATACOMB gene has the potential to utilize epigenetics to inhibit cancer cell activity and regulate cancer cells.³