The goal of this application is to establish a new paradigm of gene regulation mediated by small RNA. Until recently, small RNAs have been thought to function mainly as the mediators of an evolutionally conserved gene silencing mechanism known as RNAi. We and others discovered that small double stranded RNA (dsRNA) targeting gene promoter sequence can induce potent and prolonged gene activation at the transcriptional level and in a sequence-specific manner, a phenomenon we termed RNAa. Despite the enormous potential for reprogramming gene expression in living cells, the molecular mechanism of RNAa is largely unknown and the rules for target selection are still quite obscure. We propose to use a combination of genomic, bioinformatic, and molecular biology approaches to address the following questions: How is transcriptional activation by promoter-targeted dsRNA achieved? What are the molecular machines involved? Is RNAa naturally exploited by cells for physiological function? What are the general rules governing the sensitivity and specificity of dsRNA-promoter targeting? Understanding the molecular mechanism of RNAa and establishing it as a new paradigm are likely to transform the way gene function is studied and diseases such as cancer are treated.

Public Health Relevance

RNAa is potentially a biological mechanism of fundamental importance. Understand this mechanism will have enormous potential for improving public health. First, RNAa may provide new insight to many physiological and diseases processes;second, RNAa can be used as a tool to interrogate gene function and study their involvement in diseases;lastly, RNAa may serve as a promising surrogate for traditional gene therapy for many diseases especially cancer.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZRG1-BCMB-A (51))
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Tompkins, Laurie
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University of California San Francisco
Schools of Medicine
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Portnoy, Victoria; Lin, Szu Hua Sharon; Li, Kathy H et al. (2016) saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res 26:320-35
Wang, Ji; Place, Robert F; Portnoy, Victoria et al. (2015) Inducing gene expression by targeting promoter sequences using small activating RNAs. J Biol Methods 2:
Wang, Ji; Huang, Vera; Ye, Lin et al. (2015) Identification of small activating RNAs that enhance endogenous OCT4 expression in human mesenchymal stem cells. Stem Cells Dev 24:345-53
Li, Long-Cheng (2014) Chromatin remodeling by the small RNA machinery in mammalian cells. Epigenetics 9:45-52
Huang, Vera; Li, Long-Cheng (2014) Demystifying the nuclear function of Argonaute proteins. RNA Biol 11:18-24
Guo, Dan; Barry, Liam; Lin, Sharon Szu Hua et al. (2014) RNAa in action: from the exception to the norm. RNA Biol 11:1221-5
Ren, Shancheng; Kang, Moo Rim; Wang, Ji et al. (2013) Targeted induction of endogenous NKX3-1 by small activating RNA inhibits prostate tumor growth. Prostate 73:1591-601
Ahmed, Muhammed; Li, Long-Cheng (2013) Adaptation and clonal selection models of castration-resistant prostate cancer: current perspective. Int J Urol 20:362-71
Huang, Vera; Zheng, Jiashun; Qi, Zhongxia et al. (2013) Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet 9:e1003821
Wang, Xiaoling; Wang, Ji; Huang, Vera et al. (2012) Induction of NANOG expression by targeting promoter sequence with small activating RNA antagonizes retinoic acid-induced differentiation. Biochem J 443:821-8

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