Using CRISPR/Cas9 to Epigenetically Activate or Deactivate Genes

Since the discovery of the CRISPR-Cas9 system, targeting DNA more precisely for genetic editing has become a lot easier. However, removing part of the genetic code may not be necessary in all cases, especially if there were a way to switch off a gene of interest instead. Thankfully, scientists have found that CRISPR/Cas9 can also be used to do just this – deactivate genes without altering the underlying DNA sequence.

When we refer to a cell’s DNA, we’re actually talking about the same genetic code that exists in every cell in the body, from hair follicles to all organs, skin…. everything. But DNA alone doesn’t determine what a specific cell is or how it functions. There’s another layer of information that is needed to give cells their unique identity – the epigenome. This layer consists of various chemical compounds attached to certain areas along the genetic code that determine which genes are activated, in other words, turned on or off.

The epigenome is also susceptible to environmental influences. Where DNA is static, epigenetic factors can change. If an abnormal epigenetic modification were to occur, then it’s likely that the cell would not function properly. Many diseases, like cancer and diabetes, are associated with unusual epigenetic changes. And, because these modifications are reversible, it is believed that therapies could be developed to counteract abnormal changes, reinstating proper functioning back to a cell.

Different types of epigenetic mechanisms affect gene expression, including DNA methylation, histone modifications, and non-coding RNA. The most well studied and abundant of these is DNA methylation, which includes the addition of a chemical group to DNA.

Prior studies have shown that genes that have more DNA methylation tend to be turned off, and those with less are turned on. Unfortunately, controlling the amount of DNA methylation at a specific gene is problematic. Plus, researchers are still unsure exactly what this epigenetic mechanism does for cell function and how it’s dysregulation ultimately leads to disease development.

To better understand how a particular DNA methylation state contributes to disease, scientists at McGill University set out to block DNA methylation at specific targets. To do so, they used the CRISPR Cas9 genome editing technology to precisely target methylation activity and “de-methylate” the DNA. The process they developed proved that a gene can be edited – or rather the gene activity can be adjusted – anywhere on the DNA without altering the genetic code and with no off-target activity in other locations on the DNA.

Their work, published as an open-access article in Nature Communications, explains the procedures needed to remove DNA methylation marks at any gene of interest. They hope that other scientists will use this new technique to determine if DNA methylation is incorrectly shutting off an important gene that should be on. Knowing this could help determine DNA methylation’s role, not only as a marker but as a contributor to a particular disease.

For instance, researchers could evaluate whether DNA methylation causes the insulin gene to fail to regulate blood sugar levels in diabetes. Moreover, further studies using the CRISPR/Cas9 editing technique on the epigenome could also lead to the development of new disease treatments or therapies.  

Source: Daniel M. Sapozhnikov, Moshe Szyf. (2021). Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9. Nature Communications.

Reference: How to turn specific genes on and off. McGill University. November 9, 2021.