All cells in a multicellular organism contain the exact same DNA. However, to create the different cell types (neurons, blood cells, etc), each cell uses or expresses different pieces of DNA, creating mRNAs that encode for proteins needed in different cell types. I spent this semester researching the role eRNAs (a type of non-protein-coding RNAs) play in regulating mRNA expression. To test this I’m inhibiting eRNA expression and testing whether mRNA expression is affected. Beginning this semester, my goals were firstly to make progress in creating cell lines with an eRNA inhibited. This semester, I have successfully finished creating and confirming cell lines for one eRNA location and made progress with several of the other eRNA locations. Secondly, I aimed to optimize a new method, termed nascent RTqPCR, to accurately measure levels of eRNA and mRNA expression in these cells.
No one in my lab had previously done nascent RTqPCR in the way I hope to use it. I have worked on research prior to this semester, but this was my first time working with a protocol others in the lab were not familiar with. In the past, I have only worked with protocols that have already been optimized. My understanding of research progress and the trial/error aspect of research evolved a lot from this experience. For example, I was able to find the best amount of sample input that would allow for the most accurate results while also making sure there is enough sample left for replications. This cost/benefit analysis taught me the importance and time that goes into considering different variables. I gained an appreciation and perseverance for the research process of making sure experiments are effective.
Going forward in Dr. Hainer’s lab, I plan to continue my research into the role of eRNAs. I will be working to create more cell lines where an eRNA is inhibited. I will also be using the nascent RTqPCR protocol I have optimized to collect data from these cell lines, hopefully demonstrating a decrease in eRNA expression and possibly a change in mRNA expression as a result. Further in the future, I will pursue a graduate degree and career in biological research. I am grateful for the role this semester with the CURF had in helping me improve as a researcher.
Here is a picture of the mice embryonic stem cells I am using as a model in my experiments.