Given that there are much fewer genes in metazoans than previously predicted, there are several mechanisms in biology to generate diversity at the transcriptional and translational level. One such mechanism is RNA editing, in which a base in RNA is modified by an enzyme to form a different base. The most common type of RNA editing is Adenosine-to-Inosine (A- to-I), catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes. ADAR binds to double-stranded RNA and de-aminates Adenosine to form Inosine, which is then read as Guanosine by the cellular machinery. Thus, RNA editing can contribute to the diversity of the transcriptome by changing the amino acid sequences of proteins, altering the locations of start or stop codons, influencing alternative splicing patterns, and affecting the ability of miRNAs to bind to their target sites. Tight regulation by RNA editing plays import roles as exemplified by a number of cases linked to diseases. Our recent results suggest that cis regulation plays a major role in RNA editing regulation. However, how RNA editing is regulated by cis regulatory elements remains largely unexplored. There is a lack of systematic, genome-wide studies to elucidate the cis regulation of RNA editing. In this work, we aim to develop systematic approaches to deciphering the regulatory code of RNA editing cis regulation. First, we will map cis quantitative trait loci (QTLs) that are associated with RNA editing levels across human individuals. Second, we will examine editing QTLs also involved in other cellular processes that may be functionally related to RNA editing. Third, we will apply synthetic biology approaches to introduce mutations in the dsRNA substrates to measure editing specificity and efficiency for variants at each base in vitro and in human cells, and experimentally determine ADAR binding affinity and RNA secondary structure in vitro. Taken together, the goals of this proposed project will provide an unprecedented understanding of primary sequence and secondary structure features that govern the cis regulation of A-to-I RNA editing, and reveal the functional relationship between RNA editing and other cellular processes.

Public Health Relevance

RNA editing has been linked to various human neurological diseases and cancers. The number of the editing events has greatly expanded in the past five years. We propose to apply cutting-edge experimental and computational techniques to understand how RNA editing is regulated by the local sequences and structures and how RNA editing may affect other cellular processes. This deep understanding will help us better interpret human genomes to identify genetic variants or mutations that lead to aberrant RNA editing changes.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM124215-01
Application #
9365748
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Bender, Michael T
Project Start
2017-09-01
Project End
2021-08-31
Budget Start
2017-09-01
Budget End
2018-08-31
Support Year
1
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Stanford University
Department
Genetics
Type
Schools of Medicine
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94304
Yablonovitch, Arielle L; Fu, Jeremy; Li, Kexin et al. (2017) Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates. Nat Commun 8:1570
Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran et al. (2017) Dynamic landscape and regulation of RNA editing in mammals. Nature 550:249-254