An Epigenetic CRISPR Editor That Can Turn Genes On and Off
A new study presents a programmable epigenetic memory writer that acts as an on-off switch for gene expression
Within our cells, we can find the complete DNA recipe to cook up a human being. Most of the DNA of the human genome is found in the cell’s nucleus, with some small DNA fragments floating around in the mitochondria.
Certain chunks of DNA are genes, sequences that code for a protein. Those DNA sequences are transcribed into messenger RNA which is then translated into a sequence of amino acids. Linked together, these amino acids make a protein. There are also genes that influence the activity of other genes, known as transcription factors.
That tweaking of gene activity, by transcription factors or via other means, is one of the reasons why different types of cells — despite having the same genome — look and behave differently.
As it goes in biology, things get even more complicated. Let’s add another level to all this by introducing epigenetics.
Epigenetics involves the study of tags that are added or removed from DNA. Epigenetic modifications — which can interact with transcription factors to add yet another layer of complexity — change the activity of specific genes, and thus protein production.
Of course, genes matter. But what matters too is how you use the genes you have. More specifically, we’re starting to unravel the importance of gene expression and regulation. As an example I’ve written about earlier: in aging brains, changes in gene activity lead to several manifestations of aging.
CRISPR, or clustered regularly interspaced short palindromic repeats, is the name for DNA sequences that were first identified in bacteria in 1987. As the name suggests, these DNA sequences are short, clustered together, the same if you read them from front to back or back to front (palindromic), repeated, and regularly interrupted by other DNA chunks.
Odd, funny, but little more than one of the genome’s many curiosities. Or so we thought.
Until 2007, when scientists figured out that these CRISPR sequences protect bacteria against repeated virus infections. By integrating bits of virus DNA into their genome, the bacteria are able to quickly recognize another infection by the same virus and cut the invader’s genome into pieces before it can do much harm.
Then, in 2012, the breakthrough came. Scientists thought: ‘hey, we have this thing that is good at recognizing specific DNA sequences. This could be useful.’ Indeed it is. Researchers (Jennifer Doudna, Emmanuelle Charpentier, and their colleagues, as well as Feng Zhang and his team) developed gene-editing tools based on CRISPR and the DNA-cutting protein Cas9.
These CRISPR tools give us a way to edit genes faster, cheaper, and more accurate than ever before. The system is not perfect, but improvements are being made all the time.
CRISPR is often likened to a cut-and-paste gene-editing tool. Steer it toward the gene you want to alter, cut out the part you want to replace, and paste an alternative in its place.
This means it changes the DNA sequence, and the only way to undo that is to cut and paste again.
What if we can make a CRISPR for the epigenome?
No more cutting, only tagging. After all, in many (but not all) cases what we hope to achieve is to turn certain genes on or off. Ideally, we’d also like to be able to do this reversibly, which is tricky with current CRISPRs.
Now, we can. A new study presents CRISPRoff, a:
…single fusion protein that programs heritable epigenetic memory
This epigenetic memory writer (or wiper) is based on the Cas9 protein used in normal CRISPR. Here, however, Cas9 is ‘dead’, meaning that its DNA-cutting ability has been turned off. Together, with single guide RNAs that identify the targets, this forms the CRISPRoff system. Guided by the RNAs, the dead Cas9 can tag the target genes with epigenetic methyl groups, changing gene activity.
Since the system does not alter the underlying DNA sequence, it's fully reversible. By using enzymes that can accurately target methyl groups, the tags can be removed — a method the scientist have dubbed CRISPRon.
To test their system, the researchers used pluripotent stem cells. They silenced a gene in these stem cells and then coaxed them to develop into neurons. The alteration remained throughout the differentiation process and cell divisions, suggesting that these epigenetic changes can persist.
As a second test, they dialed down the gene coding for Tau protein — implicated in Alzheimer’s disease. And indeed, the expression of Tau went down significantly (although it was not entirely shut down).
The authors see a lot of potential:
The broad ability of CRISPRoff to initiate heritable gene silencing… enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.
While this is an early, proof-of-concept study, it’s pretty epi(c).