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CRISPR: Gene Editing

CRISPR (otherwise known as “Clustered Regularly Interspaced Short Palindromic Repeat”) is a gene editing system, but it is not a human invention. It was originally part of the antiviral ‘immune system’ of a particular form of bacteria. Unlike our immune system, which destroys cells infected with viruses, CRISPR seeks to destroy the actual virus itself, sparing the cell.

Viruses are parasites at the molecular level; they are essentially ‘glitches’ in DNA, which have evolved mechanisms to spread from cell to cell via small particles emitted by their infected host cells.

The DNA-based nature of viruses is what makes CRISPR so useful to us; it’s essentially a naturally produced gene editing tool that’s capable of removing specific sequences of DNA (or specific genes).

These sequences can be recovered by scientists before being packaged into any number of different ‘vehicles’ (such as a virus programmed to insert itself into the DNA but not to self-replicate), which can then be delivered to any cell in the body, thus giving that cell the gene removed by CRISPR.

How can we control CRISPR?

The way we control and ‘program’ CRISPR is by playing tricks with its ‘vision’; normally, CRISPR ‘sees’ by sending small strings of guide RNA (gRNA) into the area surrounding the DNA.

This gRNA is programmed to stick to a very specific string of DNA – in nature, this string is part of a virus’s DNA. In the lab, however, we can produce our own gRNA that sticks to useful DNA.

Once a part of the CRISPR system, called “Cas9”, brushes against a sequence of gRNA which is bound to DNA, it latches onto the gene and cuts it off for us to use in the future.

It is worth noting that there are a number of variants of CRISPR, including the well-known Cas9 and the Cpf1 form, which has a better affinity with mammalian cells and is therefore of interest to researchers hoping to translate their work to humans.

What are the concerns with CRISPR?

As with all science, there are always bumps in the road. Recently, a research team found that CRISPR can cause unintentional mutations throughout the DNA of targeted cells [1].

However, the system is constantly being refined and improved and progress has recently been made in this area using the CRISPR-Cpf1 form [2]. Researchers have found a way to make edits more accurate, and the hope is to reduce off target mutations to improve safety.

How CRISPR might help us to treat age-related diseases

Aging is comprised of a number of distinct processes as described in the Hallmarks of Aging [3]. We have covered the hallmarks of aging in plain language here. Dr. Oliver Medvedik from LEAF has also given a talk about CRISPR and aging, which may be of interest.

Through the use of CRISPR, we can modify the genes present in a cell as well as modify which genes are switched on or off. This has a number of potential applications relevant to addressing the aging processes, and thus it could potentially be used to prevent or reverse various age-related diseases.


Overall, CRISPR is an exciting technology in the battle against age-related diseases and ill health. While it has limitations, like all technologies, it is being refined and improved constantly.

Indeed, while CRISPR isn’t a magic bullet that will solve all things relating to aging, there are plenty of reasons for us to be enthusiastic about it. It is a tremendously powerful tool that a mere half a decade or so ago we could only dream of.

Often, in science, hype is usually not warranted; in the case of CRISPR, we feel that perhaps it is.

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[1] Schaefer, K. A., Wu, W. H., Colgan, D. F., Tsang, S. H., Bassuk, A. G., & Mahajan, V. B. (2017). Unexpected mutations after CRISPR-Cas9 editing in vivo. Nature methods, 14(6), 547-548.

[2] Zhong, G., Wang. H., Li, Y., Mai, H., Farzan, M. (2017) Cpf1 proteins excise CRISPR RNAs from mRNA transcripts in mammalian cells. Nature chemical biology, doi:10.1038/nchembio.2410.

About the author
Patrick Deane

Patrick Deane

As an undergraduate of Human Biosciences at Plymouth University, aging research has been Patrick’s passion for a long time now. While he has aspirations to later directly join the research effort, for now, he provides the community with educational articles, spreading knowledge of the biology behind the aging process while he himself learns.
  1. jimofoz
    July 9, 2017

    I thought the main problem with CRISPR-Cas9 use in humans was its low rate of cutting and then inserting a desired gene via HDR, much preferring the NHEJ pathway? See Michael Rae’s April 2016 comment on the Fightaging! blog:

    “But your (Barbara’s) implicit premise seems to be that the CRISPR/Cas9 system could easily be used for somatic gene therapy — ie, introducing therapeutic genes into existing tissue in situ. And if you didn’t mean that, such is certainly the explicit premise of others in the comments to this thread, and in previous comments in FA! to which I’ve not previously responded. In fact, using the CRISPR/Cas9 system for this purpose would require a great deal of innovation, including the emergence of strategies that no one has yet identified, even in principle.

    For one thing, CRISPR/Cas9 does not come with any kind of vector system to deliver both components of it, and we don’t have a sufficiently safe and effective delivery vector for it, although people are certainly working on delivery systems all the time. And whereas most delivery systems for gene therapy currently in use are for a single active component, it’s actually at the moment very difficult even in cell culture to assure the coincident presence (and expression, as relevant), in the same cell at once, of all of the components of the system (the Cas9 exonuclease, the guide RNA, and the exogenous repair template) — let alone to do this in vivo across an entire somatic tissue. Additionally, the payload size that the system can handle is as of yet far too limited to be used for any kind of gene therapy useful to us, although people are working on that, too.

    There are much larger problems, however, that are more central to the genome-editing mechanism of the system itself. The system works because the Cas9 endonuclease makes double-strand breaks in the host cell genome (or, using the trickier, engineered “dual nickase” system, you use two modified Cas9s that each make its own single-strand breaks at one end of the desired insertion site) at a site determined by the guide RNA, and the cell’s DNA repair machinery “repairs” the break with new genetic material introduced in a separate repair template. The cell can use one of two DNA repair mechanisms to do this: the Non-Homologous End Joining (NHEJ) pathway or the Homology Directed Repair (HDR) pathway.

    NHEJ is more or less OK for making decent-sized loss-of-function mutations (which scientists often want to do), but is too sloppy to be used for insertion of therapeutic genes, whether in mice or in humans: it often leaves small insertions or deletions that bridge over the site of the break in the strand, resulting in either frameshift mutations or premature stop codons within the open reading frame of the gene, resulting in either a protein that is prematurely truncated and useless or producing useless mRNA that just gets degraded by nonsense-mediated decay (or, theoretically, even a gene with a deleterious gain-of-function mutation, though I’ve never heard this raised as a serious prospect).

    HDR is very precise, but it has a very low (<10% of modified alleles) efficiency, and it is only active in cells that are actively in the process of dividing, making it useless for introducing therapeutic genes into mature neurons or heart and skeletal muscle cells, and for substantial numbers of cells in organs like the liver and the skin at any given time."

  2. July 9, 2017

    Hi Jim,

    The low level of Homology Mediated Repair vs NHEJ is definitely a problem that needs to be overcome. Labs are working on a number of different approaches to solving thus, including but not limited to, inhibiting NHEJ.

    The second problem in situ would be delivery of the system to specific cells using modified viral vectors. specificity and limits to payload size are also problems to be overcome.

    In vitro thats not as much of a problem. as far as low cutting efficiency is concerned when the CRISPR system enters the cell, im not aware of that problem. Can you send me a reference?

  3. jimofoz
    July 11, 2017

    Sorry I meant cutting and inserting as one phrase which wasn’t the best way to word things. CRISPR is very efficient at cutting as far as I know, it is just the HDR insertions that are low efficiency.

    Here is a good Nature piece from last year on the current gene editing race. It would be cool to see some layperson friendly articles on integrases and recombinases:

  4. jimofoz
    July 11, 2017

    This frame of a video has George Church’s summary of the current editing approaches, with the approached that avoid NHEJ on the right:

    Unfortunately “despite 13 years of study in Church’s lab, lambda Red works only in bacteria.”

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