Poster abstracts
Poster number 148 submitted by Rachel Trebesch
Role of RNA Structure in Gene Regulation by sRNAs
Rachel Trebesch (Biochemistry and Molecular Biology Program - Gustavus Adolphus College), Kristen Martens (Chemistry Department - Gustavus Adolphus College), Dr. Janie Frandsen (Biology Department, Chemistry Department, Biochemistry and Molecular Biology Program - Gustavus Adolphus College)
Abstract:
Antibiotic resistance remains a public health problem because bacteria continue to overcome the effects of antibiotic treatments. These treatments primarily target a single cellular process; therefore, targeting alternative processes may provide a method to combat antibiotic resistance. Targeting small RNAs (sRNAs) may be a solution as they regulate bacterial homeostasis through direct binding with mRNAs. Each sRNA can bind to multiple mRNAs; however, it is unknown which features of these interactions dictate the order of binding. One feature that may affect binding order is the structure of the mRNA. This research focuses on Escherichia coli and its sRNA-mRNA interactions. Analysis of mRNA structure using RNA structure probing quantifies the structure of the mRNA by finding the frequency of chemical modifications at each position. The more modifications at a position, the less structured and more accessible it is for sRNA binding. For each binding site, a binding site accessibility score was calculated by dividing the average binding site reactivity by the average reactivity of the whole transcript for each mRNA target. The scores were first used to compare the accessibility of sRNA binding sites in different mRNA transcripts. Most mRNAs have binding sites that are more accessible than the rest of the transcript. Next, the scores were used to compare true target accessibility versus false target accessibility data. Most true targets have greater binding site accessibility than false targets. Lastly, the computational program RNAplfold, which calculates the probability of each nucleotide being unpaired, was used to compare computational versus experimental accessibility. The program's output was inconsistent with the reactivity data unless SHAPE files were put as a constraint. This analysis shows the importance of incorporating experimental data into computational pipelines Overall, it appears that mRNA structure plays an important role in mRNA-sRNA interactions.
Keywords: Small RNAs, Gene Regulation, Structure Probing