Education | What is Genome Engineering?

Erin Nolan was active in the GWG 2017 inaugural meeting during her fellowship at Mayo Clinic and studies at Winona State University

Erin Nolan was active in the GWG 2017 inaugural meeting during her fellowship at Mayo Clinic and studies 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 just the coolest. 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 crop glow, or DNA from a bacteria and put it in a plant so it can make its own 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. When I heard about the synthetic base pair X,Y, I lost my mind. 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 when I’m 80 as  I am now.

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 more 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 more patents on crops and more mono-cultures. The rich getting into designer pets, more genetic therapies being created, more glowing organisms, and more vaccines. I see the debate on whether or not DNA can be considered intellectual property being settled. I hope the answer is no.

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 in knowledge for knowledge’s sake. 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 on the knowledge for knowledge’s sake mindset a bigger contribution to the scientific community as a whole than any discovery I could ever make. I see myself spreading the knowledge for knowledge’s sake mindset whenever possible for the rest of my life.

What do genome writers do?

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

What is genome engineering?

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

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 CRISPRCas9 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 through one of two main pathways, homologous recombination, or non-homologous end joining. Errors are common during the DNA repair process and base pairs can be added or deleted causing a frame shift mutation. Frame shift mutations cause a gene 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 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 CRISPERCas9 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 cleave domains come together pinching the DNA until both strands break. The cell then repairs the damage the same as described for CRISPER.

Zinc Fingers: Zink Finger Nucleases work very similarly to TALENs. Like TALENs, Zink finger nucleases (ZFNs) are used in pairs, are composed of a binding domain and a cleave domain, often use Fok I for their cleavage domain, and bind to each strand of the DNA around the cut site. Zink Fingers come from regulatory proteins (proteins that can regulate the function of certain genes) found in African-clawed frogs that require Zink ions to function. A chain of Zink 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 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 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 can be used to add in a new genes or knock out preexisting genes, depending on the paste-site. When the SB transponson is pasted into a non-coding region, the DNA in transposon will be expressed like a new gene and the other genes will not be affected. When the SB transposon is pasted into the middle of a pre-existing gene, then that gene will lose the ability to function. The transposon can contain preexisting or man-made DNA. In this way a new gene can be added to an organism or an old one can be taken out.

Sleeping Beauty is named such because the DNA that codes for the transposon had been mutated over time into an inactive state. When scientist reconstructed a functional transposon, it was like bringing it back from an evolutionary sleep.

 

Synthetic biology. What is it?

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin imperdiet gravida quam nec efficitur. Mauris sit amet viverra turpis. Suspendisse maximus mauris eget velit efficitur sodales. Aliquam placerat laoreet mi, eu hendrerit mauris semper et. Sed in tincidunt metus, non luctus augue. Maecenas sem erat, eleifend eget ex sed, porta laoreet erat.

Are you editing human genes? Can you fix mine?

Example of someone who has had their genes edited. That biotech company that screens embryos? Talk with your physician about your options. Gene editing in humans is very rare and requires a lot of justification. In very few and rare cases for medical reasons. Probably not.
 

What do genome writers do?

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

What is genome engineering?

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

What are some of the gene editing tools?

CRISPR: 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 CRISPRCas9 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 through one of two main pathways, homologous recombination, or non-homologous end joining. Errors are common during the DNA repair process and base pairs can be added or deleted causing a frame shift mutation. Frame shift mutations cause a gene 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 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.

Sleeping Beauty Transposon System: Mauris sit amet viverra turpis. Suspendisse maximus mauris eget velit efficitur sodales. Aliquam placerat laoreet mi, eu hendrerit mauris semper et.

TALENs: Mauris sit amet viverra turpis. Suspendisse maximus mauris eget velit efficitur sodales. Aliquam placerat laoreet mi, eu hendrerit mauris semper et.

Zinc Fingers: Mauris sit amet viverra turpis. Suspendisse maximus mauris eget velit efficitur sodales. Aliquam placerat laoreet mi, eu hendrerit mauris semper et.

Synthetic biology. What is it?

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin imperdiet gravida quam nec efficitur. Mauris sit amet viverra turpis. Suspendisse maximus mauris eget velit efficitur sodales. Aliquam placerat laoreet mi, eu hendrerit mauris semper et. Sed in tincidunt metus, non luctus augue. Maecenas sem erat, eleifend eget ex sed, porta laoreet erat.

Are you editing human genes? Can you fix mine?

Example of someone who has had their genes edited.

That biotech company that screens embryos?

Talk with your physician about your options. Gene editing in humans is very rare and requires a lot of justification.

In very few and rare cases for medical reasons. Probably not.