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Review

Competitive endogenous RNA network: potential implication for systemic lupus erythematosus

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Pages 639-648 | Received 15 Jan 2017, Accepted 12 Apr 2017, Published online: 23 Apr 2017

References

  • Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature. 2012;489(7414):101–108.
  • Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505(7483):344–352.
  • Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281–297.
  • Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet. 2010;11(9):597–610.
  • Rueegger S, Grosshans H. MicroRNA turnover: when, how, and why. Trends Biochem Sci. 2012;37(10):436–446.
  • Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215–233.
  • Thomson DW, Bracken CP, Goodall GJ. Experimental strategies for microRNA target identification. Nucleic Acids Res. 2011;39(16):6845–6853.
  • Seitz H. Redefining MicroRNA Targets. Curr Biol. 2009;19(10):870–873.
  • Salmena L, Poliseno L, Tay Y, et al. A ceRNA hypothesis: the rosetta stone of a hidden RNA language? Cell. 2011;146(3):353–358.
  • Bosia C, Pagnani A, Zecchina R. Modelling competing endogenous RNA networks. Plos One. 2013;8(6):e66609.
  • Ala U, Karreth FA, Bosia C, et al. Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci U S A. 2013;110(18):7154–7159.
  • Yuan Y, Liu B, Xie P, et al. Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit. Proc Natl Acad Sci U S A. 2015;112(10):3158–3163.
  • Figliuzzi M, Marinari E, de Martino A. MicroRNAs as a selective channel of communication between competing RNAs: a steady-state theory. Biophys J. 2013;104(5):1203–1213.
  • Chiu Y-C, Hsiao T-H, Chen Y, et al. Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers. BMC Genomics. 2015;16(Suppl 4):S1.
  • D’Cruz DP, Khamashta MA, Hughes GRV. Systemic lupus erythematosus. Lancet. 2007;369(9561):587–596.
  • Tsokos GC. MECHANISMS OF DISEASE systemic lupus erythematosus. New England J Med. 2011;365(22):2110–2121.
  • Smith PP, Gordon C. Systemic lupus erythematosus: clinical presentations. Autoimmun Rev. 2010;10(1):43–45.
  • Deapen D, Escalante A, Weinrib L, et al. A revised estimate of twin concordance in systemic lupus erythematosus. Arthritis Rheum. 1992;35(3):311–318.
  • Sun C, Molineros JE, Looger LL, et al. High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry. Nat Genet. 2016;48(3):323–330.
  • Bentham J, Morris DL, Graham DSC, et al. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nat Genet. 2015;47(12):1457–1464.
  • Altorok N1, Sawalha AH. Epigenetics in the pathogenesis of systemic lupus erythematosus. Curr Opin Rheumatol. 2013;25(5):569–576.
  • Zhao M, Liu S, Luo S, et al. DNA methylation and mRNA and microRNA expression of SLE CD4+T cells correlate with disease phenotype. J Autoimmun. 2014;54:127–136.
  • Shi L, Zhang Z, Yu AM, et al. The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs. Plos One. 2014;9(5):e93846.
  • Rodriguez-Pla A, Patel P, Maecker HT, et al. IFN priming is necessary but not sufficient to turn on a migratory dendritic cell program in lupus monocytes. J Immunol. 2014;192(12):5586–5598.
  • Becker AM, Dao KH, Han BK, et al. SLE peripheral blood B Cell, T Cell and myeloid cell transcriptomes display unique profiles and each subset contributes to the interferon signature. Plos One. 2013;8(6):e67003.
  • Bradley SJ, Suarez-Fueyo A, Moss DR, et al. T Cell transcriptomes describe patient subtypes in systemic lupus erythematosus. Plos One. 2015;10(11):e0141171.
  • Denzler R, Agarwal V, Stefano J, et al. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell. 2014;54(5):766–776.
  • Jens M, Rajewsky N. Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat Rev Genet. 2015;16(2):113–126.
  • Bosson AD, Zamudio JR, Sharp PA. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell. 2014;56(3):347–359.
  • Franco-Zorrilla JM, Valli A, Todesco M, et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet. 2007;39(8):1033–1037.
  • Cazalla D, Yario T, Steitz J. Down-regulation of a host MicroRNA by a herpesvirus saimiri noncoding RNA. Science. 2010;328(5985):1563–1566.
  • Sumazin P, Yang X, Chiu H-S, et al. An extensive MicroRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell. 2011;147(2):370–381.
  • Mighell AJ, Smith NR, Robinson PA, et al. Vertebrate pseudogenes. FEBS Lett. 2000;468(2–3):109–114.
  • Zhang ZD, Frankish A, Hunt T, et al. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol. 2010;11(3):R26.
  • Poliseno L. Pseudogenes: newly discovered players in human cancer. Sci Signal. 2012;5(242):re5.
  • Harrison PM, Zheng DY, Zhang ZL, et al. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res. 2005;33(8):2374–2383.
  • Pei B, Sisu C, Frankish A, et al. The GENCODE pseudogene resource. Genome Biol. 2012;13(9):R51.
  • Hawkins PG, Morris KV. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription. 2010;1(3):165–175.
  • Poliseno L, Salmena L, Zhang J, et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010;465(7301):1033–U90.
  • Wang L, Guo Z-Y, Zhang R, et al. Pseudogene OCT4-pg4 functions as a natural micro RNA sponge to regulate OCT4 expression by competing for miR-145 in hepatocellular carcinoma. Carcinogenesis. 2013;34(8):1773–1781.
  • Marques AC, Tan J, Lee S, et al. Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs. Genome Biol. 2012;13(11):R102.
  • Karreth FA, Reschke M, Ruocco A, et al. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell. 2015;161(2):319–332.
  • Esposito F, de Martino M, Petti MG, et al. HMGA1 pseudogenes as candidate proto-oncogenic competitive endogenous RNAs. Oncotarget. 2014;5(18):8341–8354.
  • Zheng L, Li X, Gu Y, et al. The 3ʹUTR of the pseudogene CYP4Z2P promotes tumor angiogenesis in breast cancer by acting as a ceRNA for CYP4Z1. Breast Cancer Res Treat. 2015;150(1):105–118.
  • Yang W, Du WW, Li X, et al. Foxo3 activity promoted by non-coding effects of circular RNA and Foxo3 pseudogene in the inhibition of tumor growth and angiogenesis. Oncogene. 2016;35(30):3919–3931.
  • Chen X, Zhu H, Wu X, et al. Downregulated pseudogene CTNNAP1 promote tumor growth in human cancer by downregulating its cognate gene CTNNA1 expression. Oncotarget. 2016;7(34):55518–55528.
  • Cech TR, Steitz JA. The noncoding RNA revolution-trashing old rules to forge new ones. Cell. 2014;157(1):77–94.
  • Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25(18):1915–1927.
  • Iyer MK, Niknafs YS, Malik R, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015;47(3):199–208.
  • Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012;482(7385):339–346.
  • Satpathy AT, Chang HY. Long noncoding RNA in hematopoiesis and immunity. Immunity. 2015;42(5):792–804.
  • Carrieri C, Cimatti L, Biagioli M, et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature. 2012;491(7424):454–457.
  • Cesana M, Cacchiarelli D, Legnini I, et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011;147(2):358–369.
  • Wang J, Liu X, Wu H, et al. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res. 2010;38(16):5366–5383.
  • Li S-P, Xu H-X, Yu Y, et al. LncRNA HULC enhances epithelial-mesenchymal transition to promote tumorigenesis and metastasis of hepatocellular carcinoma via the miR-200a-3p/ZEB1 signaling pathway. Oncotarget. 2016;7(27):42431–42446.
  • Wang Y, Xu Z, Jiang J, et al. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell. 2013;25(1):69–80.
  • Liu XH, Sun M, Nie FQ, et al. Lnc RNA HOTAIR functions as a competing endogenous RNA to regulate HER2 expression by sponging miR-331-3p in gastric cancer. Mol Cancer. 2014;13:92.
  • Xia T, Chen SC, Jiang Z, et al. Long noncoding RNA FER1L4 suppresses cancer cell growth by acting as a competing endogenous RNA and regulating PTEN expression. Sci Rep. 2015;5:13445.
  • Fan M, Li X, Jiang W, et al. A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells. Exp Ther Med. 2013;5(4):1143–1146.
  • Yu F, Lu Z, Cai J, et al. MALAT1 functions as a competing endogenous RNA to mediate Rac1 expression by sequestering miR-101b in liver fibrosis. Cell Cycle. 2015;14(24):3885–3896.
  • Wang S-H, Zhang W-J, Wu X-C, et al. Long non-coding RNA Malat1 promotes gallbladder cancer development by acting as a molecular sponge to regulate miR-206. Oncotarget. 2016;7:37857–37867.
  • Lu MH, Tang B, Zeng S, et al. Long noncoding RNA BC032469, a novel competing endogenous RNA, upregulates hTERT expression by sponging miR-1207-5p and promotes proliferation in gastric cancer. Oncogene. 2016;35(27):3524–3534.
  • Liu L, Yang J, Zhu X, et al. Long noncoding RNA H19 competitively binds miR-17-5p to regulate YES1 expression in thyroid cancer. Febs J. 2016;283(12):2326–2339.
  • Su Z, Zhi X, Zhang Q, et al. LncRNA H19 functions as a competing endogenous RNA to regulate AQP3 expression by sponging miR-874 in the intestinal barrier. FEBS Lett. 2016;590(9):1354–1364.
  • Du Z, Sun T, Hacisuleyman E, et al. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nat Commun. 2016;7:10982.
  • Huang G, Wu X, Li S, et al. The long noncoding RNA CASC2 functions as a competing endogenous RNA by sponging miR-18a in colorectal cancer. Sci Rep. 2016;6:26524.
  • Wang S-H, Ma F, Tang Z-H, et al. Long non-coding RNA H19 regulates FOXM1 expression by competitively binding endogenous miR-342-3p in gallbladder cancer. J Exp Clin Cancer Res. 2016;35(1):160.
  • Liu Q, Guo X, Que S, et al. LncRNA RSU1P2 contributes to tumorigenesis by acting as a ceRNA against let-7a in cervical cancer cells. Oncotarget. 2016. DOI:10.18632/oncotarget.10844.
  • Maldotti M, Incarnato D, Neri F, et al. The long intergenic non-coding RNA CCR492 functions as a let-7 competitive endogenous RNA to regulate c-Myc expression. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms. 2016;1859(10):1322–1332.
  • Cao C, Zhang T, Zhang D, et al. The long non-coding RNA, SNHG6-003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma. Oncogene. 2016;36(8):1112–1122.
  • Salzman J, Gawad C, Wang PL, et al. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. Plos One. 2012;7(2):e30733.
  • Chen -L-L, Yang L. Regulation of circRNA biogenesis. RNA Biol. 2015;12(4):381–388.
  • Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–338.
  • Salzman J, Chen RE, Olsen MN, et al. Cell-type specific features of circular RNA expression. Plos Genet. 2013;9(9):e1003777.
  • Memczak S, Papavasileiou P, Peters O, et al. Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood. Plos One. 2015;10(10):e0141214.
  • Rybak-Wolf A, Stottmeister C, Glazar P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58(5):870–885.
  • Zhang Y, Zhang XO, Chen T, et al. Circular intronic long noncoding RNAs. Mol Cell. 2013;51(6):792–806.
  • Li Z, Huang C, Bao C, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015;22(3):256–264.
  • Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. circRNA biogenesis competes with Pre-mRNA splicing. Mol Cell. 2014;56(1):55–66.
  • Li LJ, Huang Q, Pan HF, et al. Circular RNAs and systemic lupus erythematosus. Exp Cell Res. 2016;346(2):248–254.
  • Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–388.
  • Zheng Q, Bao C, Guo W, et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nat Commun. 2016;7:11215.
  • Zhong Z, Lv M, Chen J. Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma. Sci Rep. 2016;6:30919.
  • Li F, Zhang LY, Li W, et al. Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/beta-catenin pathway. Oncotarget. 2015;6(8):6001–6013.
  • Xie HJ, Ren XL, Xin SN, et al. Emerging roles of circRNA_001569 targeting miR-145 in the proliferation and invasion of colorectal cancer. Oncotarget. 2016;7(18):26680–26691.
  • Tay Y, Kats L, Salmena L, et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell. 2011;147(2):344–357.
  • Jeyapalan Z, Deng Z, Shatseva T, et al. Expression of CD44 3ʹ-untranslated region regulates endogenous microRNA functions in tumorigenesis and angiogenesis. Nucleic Acids Res. 2011;39(8):3026–3041.
  • Fang L, Du WW, Yang X, et al. Versican 3 ‘-untranslated region (3 ‘-UTR) functions as a ceRNA in inducing the development of hepatocellular carcinoma by regulating miRNA activity. Faseb J. 2013;27(3):907–919.
  • Yang J, Li T, Gao C, et al. FOXO1 3 ‘ UTR functions as a ceRNA in repressing the metastases of breast cancer cells via regulating miRNA activity. FEBS Lett. 2014;588(17):3218–3224.
  • Liu T, Zu C-H, Wang -S-S, et al. PIK3C2A mRNA functions as a miR-124 sponge to facilitate CD151 expression and enhance malignancy of hepatocellular carcinoma cells. Oncotarget. 2016;7(28):43376–43389.
  • Shen K, Mao R, Ma L, et al. Post-transcriptional regulation of the tumor suppressor miR-139-5p and a network of miR-139-5p-mediated mRNA interactions in colorectal cancer. Febs J. 2014;281(16):3609–3624.
  • Li X, Zheng L, Zhang F, et al. STARD13-correlated ceRNA network inhibits EMT and metastasis of breast cancer. Oncotarget. 2016;7(17):23197–23211.
  • Mercer TR, Wilhelm D, Dinger ME, et al. Expression of distinct RNAs from 3 ‘ untranslated regions. Nucleic Acids Res. 2011;39(6):2393–2403.
  • Karreth FA, Tay Y, Pema D, et al. In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell. 2011;147(2):382–395.
  • Vandewalle C, Comijn J, de Craene B, et al. SIP1/ZEB2 induces EMT by repressing genes of different epithelial cell-cell junctions. Nucleic Acids Res. 2005;33(20):6566–6578.
  • Ling S, Birnbaum Y, Nanhwan MK, et al. MicroRNA-dependent cross-talk between VEGF and HIF1 alpha in the diabetic retina. Cell Signal. 2013;25(12):2840–2847.
  • Li D, Yang Z-K, Bu J-Y, et al. OCT4B modulates OCT4A expression as ceRNA in tumor cells. Oncol Rep. 2015;33(5):2622–2630.
  • Ding Y, Wang ZC, Zheng Y, et al. C-Myc functions as a competing endogenous RNA in acute promyelocytic leukemia. Oncotarget. 2016; 30;735:56422–56430.
  • Ren Y, Ji N, Kang X, et al. Aberrant ceRNA-mediated regulation of KNG1 contributes to glioblastoma-induced angiogenesis. Oncotarget. 2016. DOI:10.18632/oncotarget.12659.
  • Das S, Ghosal S, Sen R, et al. InCeDB: database of human long noncoding RNA acting as competing endogenous RNA. Plos One. 2014;9(6):e98965.
  • Xiao F, Zuo Z, Cai G, et al. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 2009;37:D105–D10.
  • Jeggari A, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 2012;28(15):2062–2063.
  • Helwak A, Kudla G, Dudnakova T, et al. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell. 2013;153(3):654–665.
  • Sarver AL, Subramanian S. Competing endogenous RNA database. Bioinformation. 2012;8(15):731–733.
  • Liu K, Yan Z, Li Y, et al. Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis. Bioinformatics. 2013;29(17):2221–2222.
  • Xu J, Li Y, Lu J, et al. The mRNA related ceRNA-ceRNA landscape and significance across 20 major cancer types. Nucleic Acids Res. 2015;43(17):8169–8182.
  • Li J-H, S L, Zhou H, et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42:D92–D7.
  • Flores M, Chen Y, Huang Y. TraceRNA A web application for competing endogenous RNA exploration. Circulation-Cardiovascular Genet. 2014;7(4):548–557.
  • Sardina DS, Alaimo S, Ferro A, et al. A novel computational method for inferring competing endogenous interactions. Brief Bioinform. 2016;pii:bbw084.
  • Paci P, Colombo T, Farina L. Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. BMC Syst Biol. 2014;8:83.
  • Zhang Y, Xu Y, Feng L, et al. Comprehensive characterization of lncRNA-mRNA related ceRNA network across 12 major cancers. Oncotarget. 2016;7(39):64148–64167.
  • Wang P, Zhi H, Zhang Y, et al. miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs. Database (Oxford). 2015;pii:bav098.
  • Le TD, Zhang J, Liu L, et al. Computational methods for identifying miRNA sponge interactions. Brief Bioinform. 2016;pii:bbw042.
  • Yang C, Wu D, Gao L, et al. Competing endogenous RNA networks in human cancer: hypothesis, validation, and perspectives. Oncotarget. 2016;7(12):13479–13490.
  • Zhou M, Wang X, Shi H, et al. Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer. Oncotarget. 2016;7(11):12598–12611.
  • Xia T, Liao Q, Jiang X, et al. Long noncoding RNA associated-competing endogenous RNAs in gastric cancer. Sci Rep. 2014;4:6088.
  • Zhou X, Liu J, Wang W. Construction and investigation of breast-cancer-specific ceRNA network based on the mRNA and miRNA expression data. IET Syst Biol. 2014;8(3):96–103.
  • Cao Y, Wang P, Ning S, et al. Identification of prognostic biomarkers in glioblastoma using a long non-coding RNA-mediated, competitive endogenous RNA network. Oncotarget. 2016;7(27):41737–41747.
  • Zhou M, Diao Z, Yue X, et al. Construction and analysis of dysregulated lncRNA-associated ceRNA network identified novel lncRNA biomarkers for early diagnosis of human pancreatic cancer. Oncotarget. 2016;7(35):56383–56394.
  • Liu D, Yu X, Wang S, et al. The gain and loss of long noncoding RNA associated-competing endogenous RNAs in prostate cancer. Oncotarget. 2016;35:57228–57238.
  • Lukiw WJ. Circular RNA (circRNA) in Alzheimer’s disease (AD). Front Genet. 2013;4:307.
  • Sanchez-Taltavull D, MacLeod M, Perkins TJ. On cross-conditional and fluctuation correlations in competitive RNA networks. Bioinformatics. 2016;32(17):i790–i797.
  • Nitzan M, Steiman-Shimony A, Altuvia Y, et al. Interactions between distant ceRNAs in regulatory networks. Biophys J. 2014;106(10):2254–2266.

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