RNA Variation: Mechanisms that Underlie RNA Editing and RNA-DNA Differences

Talk Overview

Variations in gene expression generate much of the biodiversity we observe in nature. Dr. Vivian Cheung employs a genetic approach to identify regulators that influence expression levels of genes. By treating gene expression levels as quantitative traits, her laboratory was able to correlate DNA variants with gene expression levels. This analysis revealed cis- and trans-acting gene regulators such as DNA demethylase KDM4C, a master regulator of a subset of genes that control growth and apoptosis.

By sequencing and systematically comparing the DNA and RNA of individuals, the Cheung laboratory discovered thousands of sites where the RNA was different from its corresponding DNA sequence. Although other forms of RNA editing have been reported before, this report showed RNA-DNA differences (RDDs) that couldn’t be explained by previous mechanisms. Cheung’s laboratory characterized these RDDs and showed that these changes in the RNA were permanent and could result in a different protein.

In her third talk, Cheung overviews the molecular mechanisms that lead to RNA editing and other forms of RDDs. Her laboratory showed that the deaminase ADAR binds to a specific motif of the RNA to mediate A- to G- editing. In the other hand, they showed that RDDs are formed 60-100 nucleotides outside the polymerase bubble, which perfectly time with the formation of R-loops, a hybrid between the template DNA and the nascent RNA during transcription. A mutation that results in an overactive senataxin, a helicase that resolves R-loops, causes a rare form of amyotrophic lateral sclerosis (ALS). Cheung’s group showed that the increased helicase activity that resulted from senataxin mutation correlates with a decrease in R-loops in these patients and therefore a decrease in RDDs.

Speaker Bio

Vivian Cheung

Dr. Vivian Cheung is a professor of genetics at the University of Michigan and a Howard Hughes Medical Institute investigator. Cheung obtained a bachelor’s degree in microbiology at the University of California, Los Angeles and graduated from Tufts School of Medicine.  She continued her medical training as a pediatric resident at UCLA, and completed a… Continue Reading