The ability of short interfering RNAs (siRNAs) to recognize mRNA is widely appreciated. siRNAs are entering Phase I trials, but their ultimate potential to impact human health is unclear. Like any drug candidate, many options will need to be explored to make duplex RNAs more potent and more versatile. We have observed that 21-base antigene RNAs (agRNAs) complementary to promoter sequences within duplex chromosomal DNA act as potent inhibitors of gene expression. Nuclear run-on assays demonstrate agRNAs block gene expression at the level of transcription. Most recently, we have discovered agRNAs that activate gene expression, opening up new avenues for using duplex RNAs in the laboratory and the clinic. Objectives: The objective of this proposal is to understand the properties of agRNAs, elucidate their mechanism of action, and characterize their potential for gene silencing or activation.
In Aim 1, we investigate involvement of argonaute proteins in gene activation.
In Aim 2, we examine the mechanism of RNA-mediated recognition of chromosomal DNA and develop chemically modified RNAs with improved potencies and specificites.
In Aim 3, we develop rules for predicting agRNA activity by building a database correlating RNA sequence with silencing potency.
For Aim 4, we propose computational and experimental strategies to identify microRNAs that share identity with transcription start sites for human or viral genes. Rationale: Our proposed research will characterize the mechanism of agRNAs. Our experiments will have a substantial impact on biomedical research because they will 1) expand the reach of RNA-mediated therapy to targets within chromosomal DNA, 2) develop rules for using agRNAs to control gene expression, and 3) examine the role of agRNAs in normal pathways for cellular regulation of gene expression. Our studies will significantly expand the potential for developing RNA drugs. Relevance to Public Health: Agents that increase or decrease gene expression have the potential to be developed as agents for treating most diseases. Our work is relevant becauses it describes a new strategy for increasing or decreasing the levels of proteins involved in disease. Specifically, our work will expand the options available for designing RNA drugs to reduce gene expression and fills an unmet need by providing a new strategy for designing RNAs to increase gene expression.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM077253-04
Application #
7893811
Study Section
Special Emphasis Panel (ZRG1-GGG-J (10))
Program Officer
Tompkins, Laurie
Project Start
2007-08-15
Project End
2011-07-31
Budget Start
2010-08-01
Budget End
2011-07-31
Support Year
4
Fiscal Year
2010
Total Cost
$295,317
Indirect Cost
Name
University of Texas Sw Medical Center Dallas
Department
Pharmacology
Type
Schools of Medicine
DUNS #
800771545
City
Dallas
State
TX
Country
United States
Zip Code
75390
Chu, Yongjun; Kalantari, Roya; Dodd, David W et al. (2012) Transcriptional silencing by hairpin RNAs complementary to a gene promoter. Nucleic Acid Ther 22:147-51
Gagnon, Keith T; Corey, David R (2012) Argonaute and the nuclear RNAs: new pathways for RNA-mediated control of gene expression. Nucleic Acid Ther 22:3-16
Younger, Scott T; Corey, David R (2011) Transcriptional regulation by miRNA mimics that target sequences downstream of gene termini. Mol Biosyst 7:2383-8
Schwartz, Jacob C; Corey, David R (2011) Practical considerations for analyzing antigene RNAs (agRNAs): RNA immunoprecipitation of argonaute protein. Methods Mol Biol 764:301-15
Yu, Dongbo; Sakurai, Fuminori; Corey, David R (2011) Clonal Rett Syndrome cell lines to test compounds for activation of wild-type MeCP2 expression. Bioorg Med Chem Lett 21:5202-5
Watts, Jonathan K; Corey, David R (2010) Clinical status of duplex RNA. Bioorg Med Chem Lett 20:3203-7
Matsui, Masayuki; Sakurai, Fuminori; Elbashir, Sayda et al. (2010) Activation of LDL receptor expression by small RNAs complementary to a noncoding transcript that overlaps the LDLR promoter. Chem Biol 17:1344-55
Janowski, Bethany A; Corey, David R (2010) Minireview: Switching on progesterone receptor expression with duplex RNA. Mol Endocrinol 24:2243-52
Yue, Xuan; Schwartz, Jacob C; Chu, Yongjun et al. (2010) Transcriptional regulation by small RNAs at sequences downstream from 3' gene termini. Nat Chem Biol 6:621-9
Younger, Scott T; Corey, David R (2009) The puzzle of RNAs that target gene promoters. Chembiochem 10:1135-9

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