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The Link Between Epigenetics and CRISPR-Cas9

Posted by Abdul Ally on Jun 29, 2016 11:00:00 AM

CRISPR-gene_editing.jpgWhen it was first released in 2012, the CRISPR-Cas system stunned scientists with its potential for revolutionizing biological research. Researchers initially noticed that bacterial genomes often contain “clustered regularly interspaced short palindromic repeats,” now dubbed CRISPR sequences. When scientists provide the Cas enzyme with a guide RNA sequence, they can tell it precisely where to slice the DNA. This allows unprecedented control over DNA slicing and insertion of new genetic code.

When we first covered the CRISPR-Cas system earlier this year, we -- like many biotech researchers -- were intrigued by the possibilities of this precise system for gene modification. Now, new evidence suggests that not only can CRISPR-Cas modify genes, but this technology may also be employed to shape epigenetic processes regulating gene expression.

Gene Editing with CRISPR-Cas

Animal models such as knockout mice have long been a staple of biomedical research, but these organisms have traditionally been challenging to create, requiring several generations to establish. The CRISPR-Cas9 system changes that, giving researchers unprecedented control over gene splicing. Simply by creating an RNA sequence to target the Cas9 enzyme to the appropriate part of the genome, researchers can splice out a given gene, yielding a knockout mouse in just one generation.

This technology has the potential to significantly decrease the amount of time spent editing an organism’s genetic code, letting scientists get down to the real work of biomedical research: determining how these genetic changes influence the organism’s phenotype. Until recently, CRISPR-Cas9 had been used to change the genetic itself. However, this technology may provide a dramatic new way to probe epigenetic processes that have been heretofore too technically challenging to characterize.

Modifying the CRISPR-Cas System for Use in Epigenetic Engineering

Over the past few decades, biomedical researchers have become increasingly interested in epigenetic processes that determine how and when certain genes are expressed. Epigenetic processes appear to be important for risk for cancer, heart disease, mental health problems, and even the foundations of aging. Thus, the ability to precisely characterize the epigenetic landscape has grown critical for solving major public health problems.

The difficulty with studying genetics is that this science has primarily been descriptive. Researchers have identified millions of epigenetic markers but have relied on statistical associations with gene expression. Although zinc finger proteins and transcription activator-like effectors (TALEs) can be used for histone methylation, demethylation, and deacetylation, there is no existing method that can effectively product targeted histone acetylation. Histone acetylation is strongly associated with gene enhancers and regulatory elements. To move science forward, we need a reliable, precise way to alter these epigenetic markers and note their downstream effects.

In a recent study published in Nature Biotechnology, researchers from Duke University laid out a path to use CRISPR-Cas to modulate the epigenetic landscape. By borrowing an enzyme from the CRISPR-Cas system, the Duke researchers were able to change its properties to engage in histone acetylation. Rather than chopping up DNA as it does in typical gene editing, the Cas9 nuclease was engineered to guide molecular machinery to the appropriate point in the genome. By pairing the enzyme with a histone acetyltransferase domain, the scientists were able to induce acetylation of the histone at a particular locus. This gives researchers unprecedented control over specific enhancers or gene promoters. By using this technology, biomedical scientists will be able to modify specific epigenetic sites and determine the downstream effects on gene expression.

Looking Toward the Future: What’s Next for CRISPR-Cas and Epigenetics

Adding this new tool to the CRISPR-Cas toolbox is an exciting advance for geneticists. As a proof of concept, the Duke University researchers also created fusions of the modified Cas enzyme to other epigenetic regulators, such as zinc finger proteins and TALEs. Together, these modified proteins will be able to alter epigenetic activity at specific sites, permitting precise and detailed investigations of the epigenome.

Collectively, these findings suggest that the CRISPR-Cas system has the potential to overhaul the face of genetics and epigenetics research. Not only will biomedical scientists be able to study the basic mechanisms of gene regulation, the epigenome, and gene regulatory elements, but they will be able to apply these findings to study the mechanisms of chronic disease. Furthermore, this use of the CRISPR-Cas system has potential therapeutic implications. By incorporating epigenetic alterations into gene therapy, researchers could silence genes that have been abnormally activated or control differentiation of stem cells. The future is bright for the CRISPR-Cas system and its applications in human health and disease.

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