RNA activation (RNAa) is a small RNA-guided and Argonaute-dependent gene regulation phenomenon in which promoter-targeted short double-stranded RNAs (dsRNAs) induce target gene expression at the transcriptional/epigenetic level. RNAa was first reported in a 2006 PNAS paper by Li et al. who also coined the term "RNAa" as a contrast to RNA interference (RNAi) to describe such gene activation phenomenon. Soon after, several groups made similar observation in different mammalian species including human, non-human primates, rat and mice, suggesting that RNAa is a general gene regulation mechanism conserved at least in mammals. In these studies, upregulation of gene expression is achieved by targeting selected promoter regions using either synthetic 21-nucleotide dsRNAs or vector expressed small hairpin RNAs (shRNAs). Such promoter targeted dsRNAs have been termed antigene RNA (agRNAs) or small activating RNA (saRNA).
Mechanism of RNAa
The molecular mechanism of RNAa is not fully understood. Similar to RNAi, it has been shown that mammalian RNAa requires members of the Ago clade of Argonaute proteins, particularly Ago2, but possesses kinetics distinct from RNAi. In contrast to RNAi, promoter-targeted agRNAs induce prolonged activation of gene expression associated with epigenetic changes. It is currently suggested that agRNAs are first loaded and processed by an Ago protein to form an Ago-RNA complex which is then guided by the RNA to its promoter target. The target can be a non-coding transcript overlapping the promoter or the chromosomal DNA. Ago then recruits histone modifying enzymes such as histone methyltransferase to the promoter to activate transcription by causing permissive epigenetic changes.
In 2008, Place et al. identified targets for miRNA miR-373 on the promoters of several human genes and found that introduction of miR-373 mimics into human cells induced the expression of its predicted target genes. This study provided the first example that RNAa could be mediated by naturally occurring non-coding RNA (ncRNA). In 2011, Huang et al. further demonstrated in mouse cells that endogenous RNAa mediated by miRNAs functions in a physiological context and is possibly exploited by cancer cells to gain a growth advantage.
In C. elegans, Argonaute CSR-1 interacts with 22G small RNAs derived from RNA-dependent RNA polymerase and antisense to germline-expressed transcripts to protect these mRNAs from Piwi-piRNA mediated silencing via promoting epigenetic activation. In C. elegans hypodermal seam cells, the transcription of lin-4 miRNA is positively regulated by lin-4 itself which binds to a conserved lin-4 complementary element in its promoter, constituting a positive autoregulatory loop. 
Applications of RNAa
- Li, Long-Cheng; Okino, Steven T.; Zhao, Hong; Pookot, Deepa; Place, Robert F.; Urakami, Shinji; Enokida, Hideki; Dahiya, Rajvir (2006). "Small dsRNAs induce transcriptional activation in human cells". Proceedings of the National Academy of Sciences 103 (46): 17337–42. doi:10.1073/pnas.0607015103. PMC 1859931. PMID 17085592.[non-primary source needed]
- Janowski, Bethany A; Younger, Scott T; Hardy, Daniel B; Ram, Rosalyn; Huffman, Kenneth E; Corey, David R (2007). "Activating gene expression in mammalian cells with promoter-targeted duplex RNAs". Nature Chemical Biology 3 (3): 166–73. doi:10.1038/nchembio860. PMID 17259978.
- Turunen, Mikko P.; Lehtola, Tiia; Heinonen, Suvi E.; Assefa, Genet S.; Korpisalo, Petra; Girnary, Roseanne; Glass, Christopher K.; Väisänen, Sami; Ylä-Herttuala, Seppo (2009). "Efficient Regulation of VEGF Expression by Promoter-Targeted Lentiviral shRNAs Based on Epigenetic Mechanism: A Novel Example of Epigenetherapy". Circulation Research 105 (6): 604–9. doi:10.1161/CIRCRESAHA.109.200774. PMID 19696410.
- Huang, Vera; Qin, Yi; Wang, Ji; Wang, Xiaoling; Place, Robert F.; Lin, Guiting; Lue, Tom F.; Li, Long-Cheng (2010). "RNAa is Conserved in Mammalian Cells". In Jin, Dong-Yan. PLoS ONE 5 (1): e8848. doi:10.1371/journal.pone.0008848. PMC 2809750. PMID 20107511.
- Matsui, Masayuki; Sakurai, Fuminori; Elbashir, Sayda; Foster, Donald J.; Manoharan, Muthiah; Corey, David R. (2010). "Activation of LDL Receptor Expression by Small RNAs Complementary to a Noncoding Transcript that Overlaps the LDLR Promoter". Chemistry & Biology 17 (12): 1344–55. doi:10.1016/j.chembiol.2010.10.009. PMC 3071588. PMID 21168770.
- Voutila, J; Sætrom, P; Mintz, P; Sun, G; Alluin, J; Rossi, JJ; Habib, NA; Kasahara, N (Aug 7, 2012). "Gene Expression Profile Changes After Short-activating RNA-mediated Induction of Endogenous Pluripotency Factors in Human Mesenchymal Stem Cells.". Molecular therapy. Nucleic acids 1: e35. PMID 23344177.
- Shibuya, Kenichi; Fukushima, Setsuko; Takatsuji, Hiroshi (2009). "RNA-directed DNA methylation induces transcriptional activation in plants". Proceedings of the National Academy of Sciences 106 (5): 1660–5. doi:10.1073/pnas.0809294106. PMC 2629447. PMID 19164525.
- Seth, M; Shirayama, M; Gu, W; Ishidate, T; Conte D, Jr; Mello, CC (Dec 18, 2013). "The C. elegans CSR-1 Argonaute Pathway Counteracts Epigenetic Silencing to Promote Germline Gene Expression.". Developmental cell. PMID 24360782.
- Turner, MJ; Jiao, AL; Slack, FJ (Jan 7, 2014). "Autoregulation of lin-4 microRNA transcription by RNA activation (RNAa) in C. elegans.". Cell cycle (Georgetown, Tex.) 13 (5). PMID 24398561.
- Chu, Yongjun; Yue, Xuan; Younger, Scott T.; Janowski, Bethany A.; Corey, David R. (2010). "Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter". Nucleic Acids Research 38 (21): 7736–48. doi:10.1093/nar/gkq648. PMC 2995069. PMID 20675357.
- Li, Long-Cheng (2008). "Small RNA-mediated gene activation". In Morris, Kevin V. RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Caister Academic Press. pp. 189–99. ISBN 978-1-904455-25-7.
- Portnoy, Victoria; Huang, Vera; Place, Robert F.; Li, Long-Cheng (2011). "Small RNA and transcriptional upregulation". Wiley Interdisciplinary Reviews: RNA 2 (5): 748–60. doi:10.1002/wrna.90. PMC 3154074. PMID 21823233.
- Place, Robert F.; Li, Long-Cheng; Pookot, Deepa; Noonan, Emily J.; Dahiya, Rajvir (2008). "MicroRNA-373 induces expression of genes with complementary promoter sequences". Proceedings of the National Academy of Sciences 105 (5): 1608–13. doi:10.1073/pnas.0707594105. PMC 2234192. PMID 18227514.[non-primary source needed]
- Huang, Vera; Place, Robert F.; Portnoy, Victoria; Wang, Ji; Qi, Zhongxia; Jia, Zhejun; Yu, Angela; Shuman, Marc et al. (2011). "Upregulation of Cyclin B1 by miRNA and its implications in cancer". Nucleic Acids Research 40 (4): 1695–707. doi:10.1093/nar/gkr934. PMC 3287204. PMID 22053081.[non-primary source needed]
- Conine, CC; Moresco, JJ; Gu, W; Shirayama, M; Conte D, Jr; Yates JR, 3rd; Mello, CC (Dec 19, 2013). "Argonautes Promote Male Fertility and Provide a Paternal Memory of Germline Gene Expression in C. elegans.". Cell 155 (7): 1532–44. PMID 24360276.
- Wedeles, CJ; Wu, MZ; Claycomb, JM (Dec 18, 2013). "Protection of Germline Gene Expression by the C. elegans Argonaute CSR-1.". Developmental cell. PMID 24360783.
- Wang, Ji; Place, Robert F.; Huang, Vera; Wang, Xiaoling; Noonan, Emily J.; Magyar, Clara E.; Huang, Jiaoti; Li, Long-Cheng (2010). "Prognostic Value and Function of KLF4 in Prostate Cancer: RNAa and Vector-Mediated Overexpression Identify KLF4 as an Inhibitor of Tumor Cell Growth and Migration". Cancer Research 70 (24): 10182–91. doi:10.1158/0008-5472.CAN-10-2414. PMC 3076047. PMID 21159640.
- Chen, Ruibao; Wang, Tao; Rao, Ke; Yang, Jun; Zhang, Shilin; Wang, Shaogang; Liu, Jihong; Ye, Zhangqun (2011). "Up-regulation of VEGF by Small Activator RNA in Human Corpus Cavernosum Smooth Muscle Cells". The Journal of Sexual Medicine 8 (10): 2773–80. doi:10.1111/j.1743-6109.2011.02412.x. PMID 21819543.
- Kang, MR; Yang, G; Place, RF; Charisse, K; Epstein-Barash, H; Manoharan, M; Li, LC (Oct 1, 2012). "Intravesical delivery of small activating RNA formulated into lipid nanoparticles inhibits orthotopic bladder tumor growth.". Cancer research 72 (19): 5069–79. PMID 22869584.
- Place, RF; Wang, J; Noonan, EJ; Meyers, R; Manoharan, M; Charisse, K; Duncan, R; Huang, V; Wang, X; Li, LC (Mar 27, 2012). "Formulation of Small Activating RNA Into Lipidoid Nanoparticles Inhibits Xenograft Prostate Tumor Growth by Inducing p21 Expression.". Molecular therapy. Nucleic acids 1: e15. PMID 23343884.
- Check, Erika (2007). "RNA interference: Hitting the on switch". Nature 448 (7156): 855–8. doi:10.1038/448855a. PMID 17713502.
- Morris, Kevin L. (2008). RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Norfolk, England: Caister Academic Press. ISBN 1-904455-25-5.
- Jorg Tost (2008). Epigenetics. Norfolk, England: Caister Academic Press. ISBN 1-904455-23-9.