Gene editing refers to the process of inserting, deleting or replacing bases in a DNA sequence of an organism. There are many techniques and technologies that enable gene editing and some newer ones like CRISPR have become very popular in the media. In this article i will describe of all the technologies used to edit genes.
First of all i will have to assume you know some of the basics of genetics, like that DNA makes RNA and RNA proteins with a mechanism that involves other proteins, that DNA is made up of four bases (A, T, C, G) and that DNA is double stranded with A going opposite to T and C opposite to G. I will also be providing links to videos and illustrations, so if you feel like you don’t understand something, this article will probably have an alternative explanation for you to understand the concepts described.
Why do we edit genes.
Gene editing for now is mostly used for research purposes. It is used to modify organisms in the lab, including various microorganisms and mice. Some common reasons for gene editing on an organism, include, determining the cause of a disease, determining the function of a gene and whether editing this gene will result in an improved health condition.
If a genome is sequenced, and you realize through that xperiment that a particular gene causes issues you can then use gene editing on model organisms to perform further tests. A common use of gene editing in such a scenario is to add the dysfunctional gene to an animal and create a transgenic animal. If the animal expresses the same symptoms as the human, then you know that this gene is the one to blame for that disease. Then you can attempt to treat the animal with drugs and treatments to determine their effectiveness and safety before trying them on actual human patients.
You can also edit genes to determine their function. If you suspect that a gene has a particular purpose, then you can alter or remove it and see if that function gets better, worse or stays unaffected.
Another thing that is now gaining momentum is gene therapy. This has been showing no promise for many years. Experts thought it had too many risks and that it wasn’t worth using. But some of the latest studies show that gene therapy does have potential in many diseases. Gene therapy is basically gene editing on an organism to directly replace, add or remove a gene that causes a disease.
Some organisms are easier to work with than others. Humans for example are very complex compared to microorganisms like yeast. Therefore some techniques work best on some animal models but can fail in clinical trials. Recent studies have shown that this can be avoided but we still have work to do for gene editing on humans to become possible, safe and even ethical.
How does it work.
Most organisms have many enzymes and processes to repair DNA damage. Simpler ones have less, thus are easier to work with. Bacteria and yeast can be editing by site-directed mutagenesis and basic PCR methods. Basically breaking the DNA in a specific site and then adding more DNA hoping it sticks in a certain way within that area. For simpler organisms it may work but it is not really efficient and no modern lab would use such techniques.
Then there are organisms like bacteria, with plasmids that have the ability to jump between cells and multiply. Such plasmids can be easily engineered and used to edit bacteria.
Bacteria also have enzymes that cut DNA in specific sections. Geneticists have taken advantage of such enzymes called restriction endonucleases (or enzymes). The way those enzymes cut DNA, leaves specific ends. Because they cut in specific sequences too, you end up with all the cut DNA having compatible tails. Like legos they like to stick together. So you cut both the plasmid and the DNA you want to add to the plasmid with the same restriction enzyme and you make them stick to each other perfectly. Hopefully the video below helps you imagine this process.
Next, there is Zinc finger nuclease-based engineering.
Zinc finger nucleases can bind to several protein-DNA interaction sites. Those sites are specific, 3 nucleotide sites on the DNA sequence. By combining various ZFNs that bind to varying 3 nucleotide sites, you can end up with enzymes that bind to targeted 20 nucleotide long sequences. Those can be as specific as you want. They are also bound with proteins called Fokl. This Fokl is actually an endonuclease that cuts DNA around it, in a nonspecific manner. But because it is bound to the Zinc finger assembly, it is directed by it, to make cuts in sequences you specify. Imagine Zinc fingers acting as detectors and Fokl endonucleases acting as scissors. Of course there are limitations to this technology, and one of them is in manufacturing. It is hard to make such sequences. Another one is in its specificity. Other technologies like CRISPR are more precise and accurate in their cuts and can work with larger DNA fragments. But Zinc finger nucleases have helped researchers for a long time to edit genomes. The following video explains this concept with drawings, unfortunately there are not many high quality animations for it.
Another technique is called TALEN.
TALENs, transcription activator-like effector nucleases, are proteins that, like Zinc fingers, bind to specific sequences. Again, in the same way Zinc fingers work, TALENs are bound to a Fokl protein that cuts the DNA in a sequence specified by the TALENs used. They tend to be more precise than Zinc fingers and easier to work with.
Along with Zinc finger nucleases, TALENs have been the best methods for gene editing for a long time. Restriction enzymes while simple, aren’t as powerful for editing more complex genomes. Overall TALENs, still remain very precise tools for gene editing even compared to newer ones like CRISPR.
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a mechanism that microorganisms use to find viral DNA in their genome and remove it. It works like an immune system for them. The Cas9 protein does most of the work with this technology along with its associated RNAs. The bacteria that use it as an immune system, have a guide RNA on the Cas9 that is the same as the one that a virus would insert. Thus when a virus does indeed insert its DNA, the Cas9 can find it and if similar to the guide RNA, will remove it. We have manipulated in the lab this Cas9 protein, to do many things. One of the most popular Cas9 variants is used to replace specific sequences. How you specify a sequence for it to replace, cut or modify? You just add it to the guide RNA. It works surprisingly well in many cells. So well in fact that companies are trying to use it for gene therapy in humans. The following video will give you a better idea for how this technology works, and if you would like to learn more, there is an article here on Qul Mind you should read on CRISPR.
Multiplex Automated Genomic Engineering (MAGE)
This is a relatively new and more complex technique. It starts with an two lab-made sequences that are complementary to the target gene and have the area that we want to change in the middle. Changes though can only be up to 60 bases long. The cells used have to lack mismatch repair mechanisms. Through electroporation, the fragments are introduced to the cell, and then during replication the fragments “trick” the cells replication mechanisms into making a daughter cell with the desired change. Though the change is only on the one copy of the genome. After a second replication, the daughter cell will indeed have the edit fully incorporated in its DNA. Thus after replication you end with one cell being edited and one being normal. The benefit of this technique, is that edits can occur simultaneously at many sites in a genome, can be introduced to all cells after some division cycles and can be automated in MAGE devices. There are many potential benefits to this technology and seems very promising but i haven’t found many studies using it in the past. After searching though i did found a lot of them, although most of them used this techniques in microorganisms. It seems like CRISPR is prefered when working with humans.
At this moment most researchers studying human genes seem to prefer CRISPR. It is a great technology although it’s alternatives are good too. Although compared to TALENs and ZFNs, CRISPR appears to be cheaper. In general all those technologies still remain valid and used in different scenarios.
There are risks when editing genes and creating transgenic organisms, but for now those seem to be limited. Overall gene editing has proven to be safe, but as always, more testing will be required to say that with greater confidence.
Then there is gene therapy, that has recently shown great potential. It’s safety is debated, but i am optimistic, since i would really like to see gene therapy succeed. It would result in curing most diseases we face today.
Then there is gene editing for personal reasons. An example for that would be to become smarter or stronger. But this is a completely different topic to discuss. Of course the ethics of it are huge. Especially if you consider editing our children. Let me know if you would like me to do an article on this topic though, or your opinion, or anything in the comments. I always appreciate opinions, discussions and feedback.
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