메뉴 건너뛰기




Volumn 7, Issue 2, 2011, Pages

Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations

Author keywords

[No Author keywords available]

Indexed keywords

FORECASTING; GENE EXPRESSION; PHYSIOLOGY; RNA;

EID: 79952478894     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1001090     Document Type: Article
Times cited : (70)

References (40)
  • 1
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: target recognition and regulatory functions
    • Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 2
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee RC, Feinbaum RL, Ambros V, (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 3
    • 0034708122 scopus 로고    scopus 로고
    • The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
    • Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
    • (2000) Nature , vol.403 , pp. 901-906
    • Reinhart, B.J.1    Slack, F.J.2    Basson, M.3    Pasquinelli, A.E.4    Bettinger, J.C.5
  • 4
    • 33645124258 scopus 로고    scopus 로고
    • Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs
    • Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, et al. (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312: 75-79.
    • (2006) Science , vol.312 , pp. 75-79
    • Giraldez, A.J.1    Mishima, Y.2    Rihel, J.3    Grocock, R.J.4    Van Dongen, S.5
  • 5
    • 20444460289 scopus 로고    scopus 로고
    • MicroRNA expression profiles classify human cancers
    • Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435: 834-838.
    • (2005) Nature , vol.435 , pp. 834-838
    • Lu, J.1    Getz, G.2    Miska, E.A.3    Alvarez-Saavedra, E.4    Lamb, J.5
  • 10
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
    • (2007) Nat Genet , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 11
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman RC, Farh KK, Burge CB, Bartel DP, (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
    • (2009) Genome Res , vol.19 , pp. 92-105
    • Friedman, R.C.1    Farh, K.K.2    Burge, C.B.3    Bartel, D.P.4
  • 12
    • 57749206034 scopus 로고    scopus 로고
    • Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    • Wang Y, Juranek S, Li H, Sheng G, Tuschl T, et al. (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456: 921-926.
    • (2008) Nature , vol.456 , pp. 921-926
    • Wang, Y.1    Juranek, S.2    Li, H.3    Sheng, G.4    Tuschl, T.5
  • 13
    • 15244354492 scopus 로고    scopus 로고
    • Incorporating structure to predict microRNA targets
    • Robins H, Li Y, Padgett RW, (2005) Incorporating structure to predict microRNA targets. Proc Natl Acad Sci U S A 102: 4006-4009.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 4006-4009
    • Robins, H.1    Li, Y.2    Padgett, R.W.3
  • 15
    • 34447102459 scopus 로고    scopus 로고
    • Molecular basis for target RNA recognition and cleavage by human RISC
    • Ameres SL, Martinez J, Schroeder R, (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130: 101-112.
    • (2007) Cell , vol.130 , pp. 101-112
    • Ameres, S.L.1    Martinez, J.2    Schroeder, R.3
  • 17
    • 66749109861 scopus 로고    scopus 로고
    • Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH
    • Ragan C, Cloonan N, Grimmond SM, Zuker M, Ragan MA, (2009) Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH. PLoS One 4: e5745.
    • (2009) PLoS One , vol.4
    • Ragan, C.1    Cloonan, N.2    Grimmond, S.M.3    Zuker, M.4    Ragan, M.A.5
  • 18
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: software for nucleic acid folding and hybridization
    • Markham NR, Zuker M, (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol 453: 3-31.
    • (2008) Methods Mol Biol , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 19
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH, (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 20
    • 45249120816 scopus 로고    scopus 로고
    • Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells
    • Subkhankulova T, Gilchrist MJ, Livesey FJ, (2008) Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells. BMC Genomics 9: 268.
    • (2008) BMC Genomics , vol.9 , pp. 268
    • Subkhankulova, T.1    Gilchrist, M.J.2    Livesey, F.J.3
  • 21
    • 34347376692 scopus 로고    scopus 로고
    • Characterization of microRNA expression profiles in normal human tissues
    • Liang Y, Ridzon D, Wong L, Chen C, (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8: 166.
    • (2007) BMC Genomics , vol.8 , pp. 166
    • Liang, Y.1    Ridzon, D.2    Wong, L.3    Chen, C.4
  • 23
    • 27344456287 scopus 로고    scopus 로고
    • microRNA target predictions across seven Drosophila species and comparison to mammalian targets
    • Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N, (2005) microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1: e13.
    • (2005) PLoS Comput Biol , vol.1
    • Grun, D.1    Wang, Y.L.2    Langenberger, D.3    Gunsalus, K.C.4    Rajewsky, N.5
  • 25
    • 54249136806 scopus 로고    scopus 로고
    • MicroRNA-21 targets a network of key tumor-suppressive pathways in glioblastoma cells
    • Papagiannakopoulos T, Shapiro A, Kosik KS, (2008) MicroRNA-21 targets a network of key tumor-suppressive pathways in glioblastoma cells. Cancer Res 68: 8164-8172.
    • (2008) Cancer Res , vol.68 , pp. 8164-8172
    • Papagiannakopoulos, T.1    Shapiro, A.2    Kosik, K.S.3
  • 26
    • 33144490646 scopus 로고    scopus 로고
    • A microRNA expression signature of human solid tumors defines cancer gene targets
    • Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, et al. (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103: 2257-2261.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 2257-2261
    • Volinia, S.1    Calin, G.A.2    Liu, C.G.3    Ambs, S.4    Cimmino, A.5
  • 27
    • 70349741005 scopus 로고    scopus 로고
    • A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis
    • Sætrom P, Biesinger J, Li SM, Smith D, Thomas LF, et al. (2009) A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis. Cancer Res 69: 7459-7465.
    • (2009) Cancer Res , vol.69 , pp. 7459-7465
    • Sætrom, P.1    Biesinger, J.2    Li, S.M.3    Smith, D.4    Thomas, L.F.5
  • 30
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
    • (2010) Cell , vol.141 , pp. 129-141
    • Hafner, M.1    Landthaler, M.2    Burger, L.3    Khorshid, M.4    Hausser, J.5
  • 31
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    • Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
    • (2007) Mol Cell , vol.27 , pp. 91-105
    • Grimson, A.1    Farh, K.K.2    Johnston, W.K.3    Garrett-Engele, P.4    Lim, L.P.5
  • 32
    • 34249856066 scopus 로고    scopus 로고
    • Distance constraints between microRNA target sites dictate efficacy and cooperativity
    • Sætrom P, Heale BS, Snøve O Jr, Aagaard L, Alluin J, et al. (2007) Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res 35: 2333-2342.
    • (2007) Nucleic Acids Res , vol.35 , pp. 2333-2342
    • Sætrom, P.1    Heale, B.S.2    Snøve Jr., O.3    Aagaard, L.4    Alluin, J.5
  • 33
    • 67149115119 scopus 로고    scopus 로고
    • Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
    • Khan AA, Betel D, Miller ML, Sander C, Leslie CS, et al. (2009) Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 27: 549-555.
    • (2009) Nat Biotechnol , vol.27 , pp. 549-555
    • Khan, A.A.1    Betel, D.2    Miller, M.L.3    Sander, C.4    Leslie, C.S.5
  • 35
    • 27944473306 scopus 로고    scopus 로고
    • Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency
    • Patzel V, Rutz S, Dietrich I, Koberle C, Scheffold A, et al. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat Biotechnol 23: 1440-1444.
    • (2005) Nat Biotechnol , vol.23 , pp. 1440-1444
    • Patzel, V.1    Rutz, S.2    Dietrich, I.3    Koberle, C.4    Scheffold, A.5
  • 36
    • 36849060584 scopus 로고    scopus 로고
    • Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state
    • Brown BD, Gentner B, Cantore A, Colleoni S, Amendola M, et al. (2007) Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state. Nat Biotechnol 25: 1457-1467.
    • (2007) Nat Biotechnol , vol.25 , pp. 1457-1467
    • Brown, B.D.1    Gentner, B.2    Cantore, A.3    Colleoni, S.4    Amendola, M.5
  • 38
    • 3042735602 scopus 로고    scopus 로고
    • Prediction of hybridization and melting for double-stranded nucleic acids
    • Dimitrov RA, Zuker M, (2004) Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J 87: 215-226.
    • (2004) Biophys J , vol.87 , pp. 215-226
    • Dimitrov, R.A.1    Zuker, M.2
  • 39
    • 13344279384 scopus 로고    scopus 로고
    • Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
    • Doshi KJ, Cannone JJ, Cobaugh CW, Gutell RR, (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5: 105.
    • (2004) BMC Bioinformatics , vol.5 , pp. 105
    • Doshi, K.J.1    Cannone, J.J.2    Cobaugh, C.W.3    Gutell, R.R.4
  • 40
    • 39149106448 scopus 로고    scopus 로고
    • Efficient siRNA selection using hybridization thermodynamics
    • Lu ZJ, Mathews DH, (2008) Efficient siRNA selection using hybridization thermodynamics. Nucl Acids Res 36: 640-647.
    • (2008) Nucl Acids Res , vol.36 , pp. 640-647
    • Lu, Z.J.1    Mathews, D.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.