ADARs are RNA editing enzymes that convert adenosine to inosine in cellular and viral double- stranded RNA (dsRNA). One function of ADARs is to target codons in mRNA to allow multiple protein isoforms from the information in a single gene. Codon editing is found in many neuronally important mRNAs, and aberrant levels of editing have been linked to neurological disease. Fundamental to determining how ADARs contribute to human health, and sometimes disease, is a complete understanding of their catalytic mechanism. Experiments are proposed to determine the amino acids in the human ADAR2 catalytic domain that control its catalytic efficiency and lead to targeting of precise adenosines. A screen has identified mutations that affect these proceses, and these wil be characterized using a variety of biochemical assays. Despite its importance, editing in codons is rare, and there are far more inosines in noncoding RNA sequences. Yet, the function of inosines in noncoding sequences is unclear. Since ADARs target any dsRNA sequence, one posibility is that they affect dsRNA-mediated gene silencing pathways. High- throughput sequencing will be performed to compare the small RNAs of wildtype C. elegans with those in strains lacking ADARs. The focus will be on small RNAs that are processed from a dsRNA precursor, namely, microRNAs and endogenous siRNAs. Altered levels of small RNAs as well as their editing sites will be tabulated, and the latter will be distinguished from sequencing errors by their absence in animals lacking ADAR editing. Effects of ADARs on small RNAs will be correlated with predicted changes in mRNA levels using microarray analyses. While C. elegans lacking ADARs are viable, they have chemotaxis defects, and it is anticipated they have other subtle defects that have not been recognized. After validation of observations made with bioinformatics studies, phenotypes suggested by molecular defects will be tested.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM044073-20
Application #
8448658
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Bender, Michael T
Project Start
1990-04-01
Project End
2015-04-30
Budget Start
2013-05-01
Budget End
2014-04-30
Support Year
20
Fiscal Year
2013
Total Cost
$215,798
Indirect Cost
$71,048
Name
University of Utah
Department
Biochemistry
Type
Schools of Medicine
DUNS #
009095365
City
Salt Lake City
State
UT
Country
United States
Zip Code
84112
Blango, Matthew G; Bass, Brenda L (2016) Identification of the long, edited dsRNAome of LPS-stimulated immune cells. Genome Res 26:852-62
Whipple, Joseph M; Youssef, Osama A; Aruscavage, P Joseph et al. (2015) Genome-wide profiling of the C. elegans dsRNAome. RNA 21:786-800
Kuttan, Ashani; Bass, Brenda L (2012) Mechanistic insights into editing-site specificity of ADARs. Proc Natl Acad Sci U S A 109:E3295-304
Warf, M Bryan; Shepherd, Brent A; Johnson, W Evan et al. (2012) Effects of ADARs on small RNA processing pathways in C. elegans. Genome Res 22:1488-98
Bass, Brenda; Hundley, Heather; Li, Jin Billy et al. (2012) The difficult calls in RNA editing. Interviewed by H Craig Mak. Nat Biotechnol 30:1207-9
Warf, M Bryan; Johnson, W Evan; Bass, Brenda L (2011) Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. RNA 17:563-77
Eggington, Julie M; Greene, Tom; Bass, Brenda L (2011) Predicting sites of ADAR editing in double-stranded RNA. Nat Commun 2:319
Evan Johnson, W; Welker, Noah C; Bass, Brenda L (2011) Dynamic linear model for the identification of miRNAs in next-generation sequencing data. Biometrics 67:1206-14
Hundley, Heather A; Bass, Brenda L (2010) ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends Biochem Sci 35:377-83
Hellwig, Sabine; Bass, Brenda L (2008) A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes. Proc Natl Acad Sci U S A 105:12897-902

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