Kyle Swing ’23 Investigates the Efficiency of CRISPR/Cas9 System at the University of Minnesota Medical School’s Lab

My name is Kyle Swing, and I am a rising senior majoring in BBMB (Biophysics, Biochemistry, and Molecular Biology). This summer, I’ve had the privilege of working in Professor Eric Hendrickson’s lab at the University of Minnesota Medical School.

During this internship experience, I’ve been working on a project that looks at different genes that affect the editing efficiency of one method of CRISPR/Cas9 use. The CRISPR/Cas9 system is a ground-breaking and relatively simple method for making precise genome edits in organisms. More specifically, the pathway our project is looking at is called single-stranded DNA incorporation (ssDI). At the start of this project, Brian (my boss and the project manager) found that two enzymes, SETDBI and ATF7IP, could possibly restrict the efficiency of ssDI. SETDBI is a known histone methyltransferase, meaning that it helps to wrap up DNA so that it can’t be transcribed and expressed, while ATF7IP is known to be important for SETDBI to carry out that function. To study their effect, we have done “knock outs” among other things to these two genes and to other known histone methyltransferases and then studied the effects of these changes on editing efficiency through looking at the resulting expressions of green fluorescent protein (GFP) as an indicator. The changes in fluorescence can be seen using a special microscope and quantified using a flow cytometer.

Today, I ran a PCR (polymerase chain reaction), which basically makes a ton of copies of a small fragment of DNA, and then I put samples of that amplified fragment onto a gel to image it so that we can confirm we had that piece. Next, I sent that piece to be sequenced. Later, I went through eight 96-well plates (768 well populations in total!) using the fluorescent microscope to find good clone populations to continue growing and expanding. In the first picture, you can see me looking at the clone population in one well using the microscope. I then went into the cell culture room to move the selected clonal populations into bigger wells so they can grow nicely. In the second picture, you can see me doing just that in the cell culture room, where I spend a lot of my time. This is also where we perform the CRISPR/Cas9 edits by zapping the cells with electricity.

This project has been huge to me in a number of different ways. As a BBMB major, I have spent a lot of time taking lab classes where we learn different techniques and methodologies, but these are most often isolated lessons/experiments that don’t have any new implications. As a part of a real laboratory project, I have been able to help in doing things that have never been done and that produce new knowledge with implications for the field of genome editing and other areas such as epigenetics. This opportunity has also shown me what a real research project looks and feels like on such a large scale. Brian and I have each put thousands of hours of work into this and are just recently starting to gather data that can tell us something. A lot of work, time, and patience go into a research project, which you can’t really appreciate in a lab class or by reading research papers. Furthermore, this experience has given me insight and more to think about in terms of what I would like to do after Whitman.

Experiences like Kyle Swing’s are made possible by the Whitman Internship Grant, which provides funding for students to participate in unpaid internships at nonprofit, some for-profit, and government organizations. We are happy to be sharing blog posts from students who were supported by either a summer, fall, spring, or year-long grants at organizations, businesses, and research labs all around the world. To learn how you could secure a Whitman Internship Grant or host a Whitman intern at your organization, contact us at ccec_info@whitman.edu.