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Volumn 112, Issue 10, 2015, Pages 3158-3163

Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit

Author keywords

Competing endogenous RNA; MicroRNA regulation; Quantitative biology; RNA interference efficiency; Synthetic gene circuits

Indexed keywords

COMPETING ENDOGENOUS RNA; LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA; RNA; SMALL INTERFERING RNA; SYNTHETIC DNA; UNCLASSIFIED DRUG;

EID: 84924302007     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1413896112     Document Type: Article
Times cited : (89)

References (31)
  • 1
    • 0037144546 scopus 로고    scopus 로고
    • A microRNA in a multiple-turnover RNAi enzyme complex
    • Hutvágner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297(5589):2056-2060.
    • (2002) Science , vol.297 , Issue.5589 , pp. 2056-2060
    • Hutvágner, G.1    Zamore, P.D.2
  • 2
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel DP (2009) MicroRNAs: Target recognition and regulatory functions. Cell 136(2): 215-233.
    • (2009) Cell , vol.136 , Issue.2 , pp. 215-233
    • Bartel, D.P.1
  • 3
    • 80054689794 scopus 로고    scopus 로고
    • An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma
    • Sumazin P, et al. (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147(2): 370-381.
    • (2011) Cell , vol.147 , Issue.2 , pp. 370-381
    • Sumazin, P.1
  • 4
    • 80054681545 scopus 로고    scopus 로고
    • In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma
    • Karreth FA, et al. (2011) In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147(2):382-395.
    • (2011) Cell , vol.147 , Issue.2 , pp. 382-395
    • Karreth, F.A.1
  • 5
    • 80054715378 scopus 로고    scopus 로고
    • A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
    • Cesana M, et al. (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147(2):358-369.
    • (2011) Cell , vol.147 , Issue.2 , pp. 358-369
    • Cesana, M.1
  • 6
    • 84875372911 scopus 로고    scopus 로고
    • Natural RNA circles function as efficient microRNA sponges
    • Hansen TB, et al. (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495(7441):384-388.
    • (2013) Nature , vol.495 , Issue.7441 , pp. 384-388
    • Hansen, T.B.1
  • 7
    • 84892573723 scopus 로고    scopus 로고
    • The multilayered complexity of ceRNA crosstalk and competition
    • Tay Y, Rinn J, Pandolfi PP (2014) The multilayered complexity of ceRNA crosstalk and competition. Nature 505(7483):344-352.
    • (2014) Nature , vol.505 , Issue.7483 , pp. 344-352
    • Tay, Y.1    Rinn, J.2    Pandolfi, P.P.3
  • 8
    • 84876899530 scopus 로고    scopus 로고
    • Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments
    • Ala U, et al. (2013) Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci USA 110(18):7154-7159.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.18 , pp. 7154-7159
    • Ala, U.1
  • 9
    • 84879486402 scopus 로고    scopus 로고
    • Modelling competing endogenous RNA networks
    • Bosia C, Pagnani A, Zecchina R (2013) Modelling competing endogenous RNA networks. PLoS ONE 8(6):e66609.
    • (2013) PLoS ONE , vol.8 , Issue.6 , pp. e66609
    • Bosia, C.1    Pagnani, A.2    Zecchina, R.3
  • 10
    • 84874833554 scopus 로고    scopus 로고
    • MicroRNAs as a selective channel of communication between competing RNAs: A steady-state theory
    • Figliuzzi M, Marinari E, De Martino A (2013) MicroRNAs as a selective channel of communication between competing RNAs: A steady-state theory. Biophys J 104(5): 1203-1213.
    • (2013) Biophys J , vol.104 , Issue.5 , pp. 1203-1213
    • Figliuzzi, M.1    Marinari, E.2    De Martino, A.3
  • 11
    • 84924285768 scopus 로고    scopus 로고
    • RNAi Synthetic Logic Circuits for Sensing, Information Processing, and Actuation
    • Meyers RA Wiley, Hoboken, NJ
    • Xie Z, Wroblewska L, Weiss R (2014) RNAi synthetic logic circuits for sensing, information processing, and actuation. Encyclopedia of Molecular Cell Biology and Molecular Medicine, ed Meyers RA (Wiley, Hoboken, NJ), pp 1-23.
    • (2014) Encyclopedia of Molecular Cell Biology and Molecular Medicine , pp. 1-23
    • Xie, Z.1    Wroblewska, L.2    Weiss, R.3
  • 12
    • 84885131782 scopus 로고    scopus 로고
    • MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise
    • Siciliano V, et al. (2013) MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise. Nat Commun 4:2364.
    • (2013) Nat Commun , vol.4 , pp. 2364
    • Siciliano, V.1
  • 13
    • 80051486871 scopus 로고    scopus 로고
    • Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template
    • Bleris L, et al. (2011) Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template. Mol Syst Biol 7:519.
    • (2011) Mol Syst Biol , vol.7 , pp. 519
    • Bleris, L.1
  • 14
    • 80052456127 scopus 로고    scopus 로고
    • Multi-input RNAi-based logic circuit for identification of specific cancer cells
    • Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y (2011) Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333(6047):1307-1311.
    • (2011) Science , vol.333 , Issue.6047 , pp. 1307-1311
    • Xie, Z.1    Wroblewska, L.2    Prochazka, L.3    Weiss, R.4    Benenson, Y.5
  • 15
    • 80052266532 scopus 로고    scopus 로고
    • MicroRNAs can generate thresholds in target gene expression
    • Mukherji S, et al. (2011) MicroRNAs can generate thresholds in target gene expression. Nat Genet 43(9):854-859.
    • (2011) Nat Genet , vol.43 , Issue.9 , pp. 854-859
    • Mukherji, S.1
  • 16
    • 34548668642 scopus 로고    scopus 로고
    • Quantitative characteristics of gene regulation by small RNA
    • Levine E, Zhang Z, Kuhlman T, Hwa T (2007) Quantitative characteristics of gene regulation by small RNA. PLoS Biol 5(9):e229.
    • (2007) PLoS Biol , vol.5 , Issue.9 , pp. e229
    • Levine, E.1    Zhang, Z.2    Kuhlman, T.3    Hwa, T.4
  • 17
    • 34250877841 scopus 로고    scopus 로고
    • A mammalian microRNA expression atlas based on small RNA library sequencing
    • Landgraf P, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7):1401-1414.
    • (2007) Cell , vol.129 , Issue.7 , pp. 1401-1414
    • Landgraf, P.1
  • 18
    • 84878695952 scopus 로고    scopus 로고
    • Transcripts for combined synthetic microRNA and gene delivery
    • Kashyap N, Pham B, Xie Z, Bleris L (2013) Transcripts for combined synthetic microRNA and gene delivery. Mol Biosyst 9(7):1919-1925.
    • (2013) Mol Biosyst , vol.9 , Issue.7 , pp. 1919-1925
    • Kashyap, N.1    Pham, B.2    Xie, Z.3    Bleris, L.4
  • 19
    • 55949114921 scopus 로고    scopus 로고
    • MicroRNA-21 down-regulates the expression of tumor suppressor PDCD4 in human glioblastoma cell T98G
    • Chen Y, et al. (2008) MicroRNA-21 down-regulates the expression of tumor suppressor PDCD4 in human glioblastoma cell T98G. Cancer Lett 272(2):197-205.
    • (2008) Cancer Lett , vol.272 , Issue.2 , pp. 197-205
    • Chen, Y.1
  • 20
    • 33747849920 scopus 로고    scopus 로고
    • RNAhybrid: MicroRNA target prediction easy, fast and flexible
    • web server issue
    • Kruger J, RehmsmeierM (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34(web server issue):W451-W454.
    • (2006) Nucleic Acids Res , vol.34 , pp. W451-W454
    • Kruger, J.1    Rehmsmeier, M.2
  • 21
    • 84901838697 scopus 로고    scopus 로고
    • Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance
    • Denzler R, Agarwal V, Stefano J, Bartel DP, Stoffel M (2014) Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell 54(5):766-776.
    • (2014) Mol Cell , vol.54 , Issue.5 , pp. 766-776
    • Denzler, R.1    Agarwal, V.2    Stefano, J.3    Bartel, D.P.4    Stoffel, M.5
  • 22
    • 84870038812 scopus 로고    scopus 로고
    • Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties
    • Wee LM, Flores-Jasso CF, Salomon WE, Zamore PD (2012) Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell 151(5): 1055-1067.
    • (2012) Cell , vol.151 , Issue.5 , pp. 1055-1067
    • Wee, L.M.1    Flores-Jasso, C.F.2    Salomon, W.E.3    Zamore, P.D.4
  • 23
    • 74049124186 scopus 로고    scopus 로고
    • Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application
    • Jackson AL, Linsley PS (2010) Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov 9(1): 57-67.
    • (2010) Nat Rev Drug Discov , vol.9 , Issue.1 , pp. 57-67
    • Jackson, A.L.1    Linsley, P.S.2
  • 25
    • 58749086586 scopus 로고    scopus 로고
    • Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect
    • Ui-Tei K, Naito Y, Nishi K, Juni A, Saigo K (2008) Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect. Nucleic Acids Res 36(22):7100-7109.
    • (2008) Nucleic Acids Res , vol.36 , Issue.22 , pp. 7100-7109
    • Ui-Tei, K.1    Naito, Y.2    Nishi, K.3    Juni, A.4    Saigo, K.5
  • 26
    • 80455154984 scopus 로고    scopus 로고
    • Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
    • Garcia DM, et al. (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18(10):1139-1146.
    • (2011) Nat Struct Mol Biol , vol.18 , Issue.10 , pp. 1139-1146
    • Garcia, D.M.1
  • 27
    • 84924330592 scopus 로고    scopus 로고
    • Competition between target sites of regulators shapes post-transcriptional gene regulation
    • Jens M, Rajewsky N (2015) Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat Rev Genet 16(2):113-126.
    • (2015) Nat Rev Genet , vol.16 , Issue.2 , pp. 113-126
    • Jens, M.1    Rajewsky, N.2
  • 28
    • 84880770383 scopus 로고    scopus 로고
    • Diversifying microRNA sequence and function
    • Ameres SL, Zamore PD (2013) Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol 14(8):475-488.
    • (2013) Nat Rev Mol Cell Biol , vol.14 , Issue.8 , pp. 475-488
    • Ameres, S.L.1    Zamore, P.D.2
  • 29
    • 67349123973 scopus 로고    scopus 로고
    • Redefining microRNA targets
    • Seitz H (2009) Redefining microRNA targets. Curr Biol 19(10):870-873.
    • (2009) Curr Biol , vol.19 , Issue.10 , pp. 870-873
    • Seitz, H.1
  • 30
    • 79952364512 scopus 로고    scopus 로고
    • Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells
    • Baccarini A, et al. (2011) Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Curr Biol 21(5):369-376.
    • (2011) Curr Biol , vol.21 , Issue.5 , pp. 369-376
    • Baccarini, A.1
  • 31
    • 3042602447 scopus 로고    scopus 로고
    • Kinetic analysis of the RNAi enzyme complex
    • Haley B, Zamore PD (2004) Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 11(7):599-606.
    • (2004) Nat Struct Mol Biol , vol.11 , Issue.7 , pp. 599-606
    • Haley, B.1    Zamore, P.D.2


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