Transcriptional regulation of E-cadherin by small activating RNA: A new double-stranded RNA

Wu,Zhiming; Li,Yan; Li,Zhiyong; Liu,Zhuowei; Qin,Zike; Li,Xiangdong; Ye,Yunlin; Bu,Lei; Lin,Bin; Wang,Zhanyu; Jia,Guojin; Chen,Gang

doi:10.3892/ijo.2016.3643

Transcriptional regulation of E-cadherin by small activating RNA: A new double-stranded RNA

Authors:
- Zhiming Wu
- Yan Li
- Zhiyong Li
- Zhuowei Liu
- Zike Qin
- Xiangdong Li
- Yunlin Ye
- Lei Bu
- Bin Lin
- Zhanyu Wang
- Guojin Jia
- Gang Chen
View Affiliations

Affiliations: Department of Urology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, P.R. China, Department of Urology, Jinshan Hospital, Fudan University, Shanghai, P.R. China, Langone Medical Center School of Medicine, NYU, New York, NY, USA
Published online on: August 3, 2016 https://doi.org/10.3892/ijo.2016.3643
Pages: 1620-1628

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Recent studies have reported that chemically synthesized small activating RNA (saRNA) targeting the promoter regions of a gene can activate its expression in different cell lines. This technique can be a powerful therapeutic method for diseases caused by complete inactivation or reduced expression of specific genes. E-cadherin is a typical tumor suppressor gene. Loss of E-cadherin mediates the transition from benign lesions to invasive, metastatic cancer. In this study, several 21-nt small double-stranded RNAs (dsRNAs) targeting the promoter regions of human E-cadherin were designed and synthesized and the features of their function were investigated to study the regulatory role of dsRNA on E-cadherin expression. A new saRNA (dsEcad‑661) that can enhance E-cadherin expression by targeting non-coding regulatory regions in gene promoters was identified. Using dsRNA with modified base quantity and cholesterol-conjugated dsRNA, we found the antisense strand may be the guide strand of saRNA in the upregulation of E-cadherin. These findings provide several important pieces of evidence that may improve understanding of the function of saRNA and may promote its development for clinical application.

View Figures

View References

1	Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC: Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 391:806–811. 1998. View Article : Google Scholar : PubMed/NCBI
2	Janowski BA, Younger ST, Hardy DB, Ram R, Huffman KE and Corey DR: Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat Chem Biol. 3:166–173. 2007. View Article : Google Scholar : PubMed/NCBI
3	Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K and Tuschl T: Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 411:494–498. 2001. View Article : Google Scholar : PubMed/NCBI
4	Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H and Dahiya R: Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci USA. 103:17337–17342. 2006. View Article : Google Scholar : PubMed/NCBI
5	Ting AH, Schuebel KE, Herman JG and Baylin SB: Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet. 37:906–910. 2005. View Article : Google Scholar : PubMed/NCBI
6	Place RF, Noonan EJ, Földes-Papp Z and Li LC: Defining features and exploring chemical modifications to manipulate RNAa activity. Curr Pharm Biotechnol. 11:518–526. 2010. View Article : Google Scholar : PubMed/NCBI
7	Pushparaj PN, Aarthi JJ, Kumar SD and Manikandan J: RNAi and RNAa - the yin and yang of RNAome. Bioinformation. 2:235–237. 2008. View Article : Google Scholar : PubMed/NCBI
8	Wang T, Li M, Yuan H, Zhan Y, Xu H, Wang S, Yang W, Liu J, Ye Z and Li LC: saRNA guided iNOS up-regulation improves erectile function of diabetic rats. J Urol. 190:790–798. 2013. View Article : Google Scholar : PubMed/NCBI
9	Zheng L, Wang L, Gan J and Zhang H: RNA activation: Promise as a new weapon against cancer. Cancer Lett. 355:18–24. 2014. View Article : Google Scholar : PubMed/NCBI
10	van Roy F and Berx G: The cell-cell adhesion molecule E-cadherin. Cell Mol Life Sci. 65:3756–3788. 2008. View Article : Google Scholar : PubMed/NCBI
11	Repetto O, De Paoli P, De Re V, Canzonieri V and Cannizzaro R: Levels of soluble E-cadherin in breast, gastric, and colorectal cancers. Biomed Res Int. 2014:4080472014. View Article : Google Scholar : PubMed/NCBI
12	Canel M, Serrels A, Frame MC and Brunton VG: E-cadherin-integrin crosstalk in cancer invasion and metastasis. J Cell Sci. 126:393–401. 2013. View Article : Google Scholar : PubMed/NCBI
13	Schmalhofer O, Brabletz S and Brabletz T: E-cadherin, beta-catenin, and ZEB1 in malignant progression of cancer. Cancer Metastasis Rev. 28:151–166. 2009. View Article : Google Scholar : PubMed/NCBI
14	Place RF, Li LC, Pookot D, Noonan EJ and Dahiya R: MicroRNA 373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA. 105:1608–1613. 2008. View Article : Google Scholar
15	Sun X, Rogoff HA and Li CJ: Asymmetric RNA duplexes mediate RNA interference in mammalian cells. Nat Biotechnol. 26:1379–1382. 2008. View Article : Google Scholar : PubMed/NCBI
16	Sano M, Sierant M, Miyagishi M, Nakanishi M, Takagi Y and Sutou S: Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection. Nucleic Acids Res. 36:5812–5821. 2008. View Article : Google Scholar : PubMed/NCBI
17	Morris KV, Santoso S, Turner AM, Pastori C and Hawkins PG: Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet. 4:e10002582008. View Article : Google Scholar : PubMed/NCBI
18	Schwartz JC, Younger ST, Nguyen NB, Hardy DB, Monia BP, Corey DR and Janowski BA: Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol. 15:842–848. 2008. View Article : Google Scholar : PubMed/NCBI
19	Hu J, Chen Z, Xia D, Wu J, Xu H and Ye ZQ: Promoter-associated small double-stranded RNA interacts with heterogeneous nuclear ribonucleoprotein A2/B1 to induce transcriptional activation. Biochem J. 447:407–416. 2012. View Article : Google Scholar : PubMed/NCBI
20	Portnoy V, Huang V, Place RF and Li LC: Small RNA and transcriptional upregulation. Wiley Interdiscip Rev RNA. 2:748–760. 2011. View Article : Google Scholar : PubMed/NCBI
21	Morris KV, Chan SW, Jacobsen SE and Looney DJ: Small interfering RNA-induced transcriptional gene silencing in human cells. Science. 305:1289–1292. 2004. View Article : Google Scholar : PubMed/NCBI
22	Guo D, Barry L, Lin SS, Huang V and Li LC: RNAa in action: From the exception to the norm. RNA Biol. 11:1221–1225. 2014. View Article : Google Scholar
23	Nakagawa H, Hikiba Y, Hirata Y, Font-Burgada J, Sakamoto K, Hayakawa Y, Taniguchi K, Umemura A, Kinoshita H, Sakitani K, et al: Loss of liver E-cadherin induces sclerosing cholangitis and promotes carcinogenesis. Proc Natl Acad Sci USA. 111:1090–1095. 2014. View Article : Google Scholar : PubMed/NCBI
24	Corso G, Carvalho J, Marrelli D, Vindigni C, Carvalho B, Seruca R, Roviello F and Oliveira C: Somatic mutations and deletions of the E-cadherin gene predict poor survival of patients with gastric cancer. J Clin Oncol. 31:868–875. 2013. View Article : Google Scholar : PubMed/NCBI
25	Zhang H, Stephens LC and Kumar R: Metastasis tumor antigen family proteins during breast cancer progression and metastasis in a reliable mouse model for human breast cancer. Clin Cancer Res. 12:1479–1486. 2006. View Article : Google Scholar : PubMed/NCBI
26	Yue X, Schwartz JC, Chu Y, Younger ST, Gagnon KT, Elbashir S, Janowski BA and Corey DR: Transcriptional regulation by small RNAs at sequences downstream from 3′ gene termini. Nat Chem Biol. 6:621–629. 2010. View Article : Google Scholar : PubMed/NCBI
27	Jiao AL and Slack FJ: RNA-mediated gene activation. Epigenetics. 9:27–36. 2014. View Article : Google Scholar :
28	Li LC: Chromatin remodeling by the small RNA machinery in mammalian cells. Epigenetics. 9:45–52. 2014. View Article : Google Scholar :
29	Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H and Li LC: saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res. 26:320–335. 2016. View Article : Google Scholar : PubMed/NCBI
30	Meng X, Jiang Q, Chang N, Wang X, Liu C, Xiong J, Cao H and Liang Z: Small activating RNA binds to the genomic target site in a seed-region-dependent manner. Nucleic Acids Res. 44:2274–2282. 2016. View Article : Google Scholar : PubMed/NCBI
31	Janowski BA, Huffman KE, Schwartz JC, Ram R, Nordsell R, Shames DS, Minna JD and Corey DR: Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat Struct Mol Biol. 13:787–792. 2006. View Article : Google Scholar : PubMed/NCBI
32	Kim DH, Saetrom P, Snøve O Jr and Rossi JJ: MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci USA. 105:16230–16235. 2008. View Article : Google Scholar : PubMed/NCBI
33	Morris KV: RNA-directed transcriptional gene silencing and activation in human cells. Oligonucleotides. 19:299–306. 2009. View Article : Google Scholar : PubMed/NCBI
34	Gagnon KT, Li L, Chu Y, Janowski BA and Corey DR: RNAi factors are present and active in human cell nuclei. Cell Rep. 6:211–221. 2014. View Article : Google Scholar : PubMed/NCBI
35	Chang CI, Yoo JW, Hong SW, Lee SE, Kang HS, Sun X, Rogoff HA, Ban C, Kim S, Li CJ, et al: Asymmetric shorter-duplex siRNA structures trigger efficient gene silencing with reduced nonspecific effects. Mol Ther. 17:725–732. 2009. View Article : Google Scholar : PubMed/NCBI