Studying RNA Editing Regulation and Consequences on Gene Expression from C. elegans to humans
Gene Expression and RNA modification
All cells of the body contain the same genetic material (DNA), but have distinct functions and phenotypes due to variations in the messenger RNAs (mRNAs) and in turn the proteins they express. Sequence alterations that change the genome-encoded information present in RNAs provide a powerful way to diversify the transcripts expressed in an organism’s cells over time. In addition to splicing, a major means to create diversity in RNA sequences is through enzymatic modification. RNA modifications are programmed in all organisms and influence many biological processes including metabolism, cognition and immunity.
(Image from Kahn Academy website)
ADARs: The RNA binding proteins we love!
Diverse classes of enzymes catalyze more than 100 different types of modifications in RNA. High-throughput sequencing has allowed cataloging of these modifications and indicates RNA modification plays a critical role in many disease processes. However, a fundamental understanding of the molecular determinants that dictate when, where, and to what extent RNA editing occurs is lacking. In the Hundley lab, we are trying to address these fundamental questions and specifically focus on the ADAR family of enzymes.
ADARs are essential in mammals and required for proper neuronal function in all animals. Consistent with this, ADARs are highly expressed in the nervous system of both C. elegans (worms) and humans. ADARs bind to double-stranded RNA, including small RNA precursors, long non-coding RNAs and double-stranded regions of mRNA, and convert adenosine (A) to inosine (I), a process commonly referred to as RNA editing.
Impacts of A-to-I Editing on Gene Expression
Deamination of adenosine (A) results in inosine (I), which has similar base-pairing properties as guanosine. Due to these differences in base-pairing, A-to-I editing can alter the amino acid encoded by a codon, modify splice sites and affect the interaction of the RNA molecule with itself or other RNAs, such as miRNAs and siRNAs. Thus, A-to-I editing in both coding and noncoding regions of mRNA can be biologically significant.
(Image from Deffit and Hundley, WIREs RNA, 2016)
A-to-I Editing during Development and Disease
Rather than serving as a static control of gene expression, A-to-I RNA editing provides a means to dynamically re-wire the genetic code during development and in a cell-type specific manner. In addition, alterations in A-to-I editing occur in a spectrum of central nervous system disorders (autism, stroke, epilepsy), neuropsychiatric diseases (chronic depression, bipolar disorder) neurodegenerative diseases (amyotrophic lateral sclerosis (ALS) and Alzheimer’s disease), and many types of cancer, including brain tumors (glioblastomas).
(Image from Farajollahi and Maas, Trends in Genetics, 2001)
Regulation of A-to-I Editing
Modulating editing may serve as an efficient therapeutic to treat both cancers and many neuopathological diseases. However, as two editing enzymes are responsible for editing thousands of human genes, overexpression of ADARs could result in unwanted effects. Therefore, developing approaches that enhance editing of specific targets are likely better therapeutic strategies. However, it is not known how to affect such editing modulation. One long-term goal of the Hundley lab is to understand how the activity of ADARs can be modulated at specific places in RNA. In this regards, a major focus of the lab is to identify cellular factors and molecular mechanisms that regulate RNA editing.
(Image from Washburn and Hundley, Advances in Experimental Medicine and Biology, 2016)
Understanding C. elegans ADAR function
As ADARs are not essential in the model organism, Caenorhabditis elegans, our lab uses this system to explore effects of editing on gene expression and organismal biology. In particular, we are asking how the presence or absence of ADARs in specific tissues (ex. nervous system) affects gene expression directly in those tissues and in other tissues (autonomous versus non-autonomous gene regulation). We are also asking how these gene expression changes impact processes such as pathogen resistance and reproduction.
(Image of C. elegans tree ornament made by P. Vadlamani)
Human ADARs in normal brain and glioblastoma
Our published studies of human ADAR function have been focused on how RNA editing is regulated in glioblastoma. We are interested in how the different human ADARs regulate oncogenic gene expression and what oncogenic phenotypes are driven by specific ADAR substrates. In addition, as all diseases are due to gene expression of normal cells gone awry, we are interested in understanding the role that ADARs play in neural stem cells and other cells of the human brain.
(Image from Oakes, JBC, 2017)