What is Genome Engineering?

Erin Nolan attended the GWG 2017  inaugural meeting during her fellowship at Mayo Clinic and studies Cell and Molecular Biology at Winona State University.

Erin Nolan attended the GWG 2017 inaugural meeting during her fellowship at Mayo Clinic and studies Cell and Molecular Biology at Winona State University.

Scientist Erin Nolan on being a student of genetics.

Why are you interested in genome engineering?

I think genetic engineering is amazing. First of all, I love DNA; There are four basic building blocks to every living thing on the planet. That means you can take DNA from something neat like a glowworm and put it in a crop to make that plant glow, or DNA from a bacteria and put it in a plant so it can make its own non-toxic herbicide. What if the DNA of an octopus or a salamander holds the key to regeneration? DNA makes every organism at least somewhat applicable to every other organism on earth. It connects us all. Without fail, every time I learn about a new method or tool in genetic engineering I get excited. I remember the exact moment I heard about the synthetic base pair X,Y; I felt suddenly energized and had an intense desire to know more. Less than five minutes after that conversation, I was looking for articles. There are so many amazing technologies out there and more to be discovered; the shear potential of genetics is awe-inspiring. I am convinced that I can spend my whole life learning about genetics and genome engineering and be just as engaged years from now as I was in my first genetics class.

What is more interesting- developing new applications or basic research?

Can I answer both? New applications make me the most excited when I hear about them but basic research teaches me the most. Reading and painting are two of my favorite hobbies. Basic research is like adding books to the library. Developing new applications is like adding new paint brushes and paints to my art kit. There is also the added benefit that new applications can be used for more research.

Where do you see the field going?

I see more personalized health care for patients with serious diseases and more efficient agriculture in the future. I see new stronger, healthier, crops, more genetic therapies being created, more organisms like the GloFish, and more vaccines. I see new tools being developed, and old tools used in ways previously unimaginable.

How do you want to fit in?

Honestly, my goal in life is very simple: I don’t want to be bored. My pursuit of genetics is based on that. I find genetics and genome engineering fascinating. I want to spend the rest of my life learning and I think genome engineering is a field with enough depth and a fast enough pace that I will never run out of interesting things.

I love sharing knowledge, and I’m a strong believer that the general pursuit of knowledge is worthwhile because knowledge, of all kinds, is inherently valuable. I want to share what I’m learning and learn from like-minded people. In other words, I want to be contributing to the knowledge pool and surround myself with others who do so. Additionally, I consider convincing others to join the pursuit of knowledge a bigger contribution to the scientific community as a whole than any discovery I could ever make. I see myself spreading the mindset that knowledge is inherently valuable, whenever possible for the rest of my life.

What do genome writers do?

Genome writers create genetically modified organisms for research, medicine, agriculture, or the pet industry.

What is genome engineering?

Genome engineering is the act of modifying or manipulating an organism’s genome or genetic makeup through the use of biotechnology.  

Are you editing human genes? Can you fix mine?

Editing human genes it a topic of much ethical debate and the practice is still relatively uncommon. Up until November of 2017, all human gene editing was done outside the body. Cells are taken, the genome edited, and then those cells are returned to the body. In 2017, a biotech company was able to inject a specialized vector carrying a gene insert and zinc fingers into the blood stream of a patient to edit cells without removing them from the body. Currently, gene editing in humans is only used in adult cells to create personalized, targeted, therapies. Edits are not made to patients’ germline cells (sperm and egg), so any changes from genetic therapy one would receive are not passed down to offspring. If you are concerned about a genetic disease/disorder, talk with your physician about your options. Gene editing in humans is rare, highly regulated, and requires strong justification, but if the conditions are met, maybe we can fix some of your genes.

Read about the research done by GWG member Dr. Scott McIvor and his colleague Dr. Chet Whitley, that enabled the first case of gene editing in the body: University of Minnesota research was pivotal in landmark gene editing trial

What are some of the gene editing tools?

CRISPR: is like a programmable search and destroy. The CRISPR/Cas9 system is led by a guide length of RNA that reads and matches with a specified sequence of DNA. Once the CRISPR/Cas9 system is bound to the specified sequence of DNA, Cas9 cuts through both strands of DNA, creating a double stranded break. The cell then recognizes the break and repairs the DNA. Errors are common during the DNA repair process and base pairs can be added or deleted causing a frame shift mutation. Frame shift mutations inside a gene cause it to be unreadable, resulting in a loss of function of the gene, creating what is known as a knock-out. To create a knock-in, researchers can engineer and insert a segment of DNA with a new gene sandwiched between two specialized segments of DNA known as homology arms. The cell will recognize the homology arms during the repair process and copy the whole sandwich, adding  in the new gene to the space created by the double stranded break, effectively adding a gene to that cell and all of its daughter cells.

TALENs: TALEN stands for transcription activator-like effector nuclease. TALENs are similar to the CRISPER/Cas9 system in that they are programed to recognize a specified sequence of DNA, bind to it, and cut both strands at a designated site. TALENs are comprised of TAL effectors bound to DNA cleavage domains (often Fok I). TAL effectors are proteins that are secreted from bacteria that commonly infects many plant species. TAL effectors read the DNA and bind the TALEN to its designated spot, then Fok I cuts the DNA. TALENs are used in pairs, one for each strand of DNA. The TAL effectors bind to either side of the cut site and the cleavage domains come together pinching the DNA until both strands break. The cell then repairs the damage the same as described for CRISPER.

Zinc Fingers: Zinc Finger Nucleases work very similarly to TALENs. Like TALENs, Zinc finger nucleases (ZFNs) are used in pairs, are composed of a binding domain and a cleavage domain, often use Fok I for their cleavage domain, and bind to each strand of the DNA around the cut site. Zinc Fingers come from regulatory proteins (proteins that can regulate the function of certain genes) found in African-clawed frogs that require Zinc ions to function. A chain of Zinc fingers leads the ZFN to the binding site and Fok I comes together cutting the DNA. The cell then repairs the DNA like described for CRISPR.

Sleeping Beauty Transposon System: The Sleeping Beauty transposon system received its fanciful name from scientists who developed the system while working under Dr. Perry Hackett, GWG Patron and founder, at the University of Minnesota. Over time, the DNA that encodes for the system had been mutated into an inactive state. When scientists reconstructed a functional transposon millions of years later, it was brought back, or “awakened” from an evolutionary sleep.

The Sleeping Beauty transposon systems is comprised of two pieces: the Sleeping Beauty transposon and transposase. A transposon is a transposable element, or a segment of DNA that can be moved from one position to another. Transposase is an enzyme that cuts DNA at a specified site and guides the transposon into place. The Sleeping Beauty transposon system is like a cut and paste mechanism for genes. Transposase does the cutting and the transposon is what gets pasted in.

The Sleeping Beauty transposon system can be used to add in a new genes or knock out preexisting genes, depending on the paste-site. When the SB transposon is pasted into a non-coding region, the DNA in the transposon will be expressed like a new gene and the other genes will remain unaffected. When the SB transposon is pasted into the middle of a pre-existing gene, then that gene will lose the ability to function. In this way a new gene can be added to an organism or an old one can be taken out.

Synthetic biology. What is it?

Synthetic biology is the union of biology and engineering, typically for research, engineering, or medical applications. Synthetic biology has no official definition and if you ask a professional, you will get slightly different answers depending on whether that person is a biologist or an engineer. Qualified biologist and engineers can both do work in synthetic biology, creating and redesigning features of biological systems. This can be the design of new molecules, biological pathways, tissues, or organisms.

Synthetic biology and genetic engineering do have significant cross over but in relation to genome modification, genetic engineers tends to focus on adding, removing, or modifying a single or small number of traits of an organism. Whereas synthetic biology uses genome modification to redesign a system for a new purpose.

Written by Erin Nolan