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Volumn 52, Issue 5, 2013, Pages 795-807

Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the drosha cleavage site

Author keywords

[No Author keywords available]

Indexed keywords

3D STRUCTURE; CLEAVAGE SITES; DOUBLE-STRANDED RNA; EXPERIMENTAL DETERMINATION; MICRORNA (MIRNA); MICRORNAS; NON-CODING RNAS; RNA JUNCTIONS; STRUCTURAL INFORMATION; STRUCTURE ELEMENTS; STRUCTURE MODELS; THREE DIMENSIONAL (3D) STRUCTURES;

EID: 84873365736     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi301452a     Document Type: Article
Times cited : (21)

References (54)
  • 2
    • 79960611669 scopus 로고    scopus 로고
    • Exploring RNA Structural Codes with SHAPE Chemistry
    • Weeks, K. M. and Mauger, D. M. (2011) Exploring RNA Structural Codes with SHAPE Chemistry Acc. Chem. Res. 44, 1280-1291
    • (2011) Acc. Chem. Res. , vol.44 , pp. 1280-1291
    • Weeks, K.M.1    Mauger, D.M.2
  • 3
    • 40449139010 scopus 로고    scopus 로고
    • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    • DOI 10.1038/nature06684, PII NATURE06684
    • Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data Nature 452, 51-55 (Pubitemid 351355097)
    • (2008) Nature , vol.452 , Issue.7183 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 7
    • 23044502585 scopus 로고    scopus 로고
    • Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences
    • DOI 10.1074/jbc.M504714200
    • Zeng, Y. and Cullen, B. R. (2005) Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences J. Biol. Chem. 280, 27595-27603 (Pubitemid 41076871)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.30 , pp. 27595-27603
    • Zeng, Y.1    Cullen, B.R.2
  • 9
    • 33744520104 scopus 로고    scopus 로고
    • Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex
    • DOI 10.1016/j.cell.2006.03.043, PII S0092867406005162
    • Han, J. J., Lee, Y., Yeom, K. H., Nam, J. W., Heo, I., Rhee, J. K., Sohn, S. Y., Cho, Y. J., Zhang, B. T., and Kim, V. N. (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex Cell 125, 887-901 (Pubitemid 43810154)
    • (2006) Cell , vol.125 , Issue.5 , pp. 887-901
    • Han, J.1    Lee, Y.2    Yeom, K.-H.3    Nam, J.-W.4    Heo, I.5    Rhee, J.-K.6    Sohn, S.Y.7    Cho, Y.8    Zhang, B.-T.9    Kim, V.N.10
  • 10
    • 0037273432 scopus 로고    scopus 로고
    • Sequence requirements for micro RNA processing and function in human cells
    • DOI 10.1261/rna.2780503
    • Zeng, Y. and Cullen, B. R. (2003) Sequence requirements for micro RNA processing and function in human cells RNA 9, 112-123 (Pubitemid 36206307)
    • (2003) RNA , vol.9 , Issue.1 , pp. 112-123
    • Zeng, Y.1    Cullen, B.R.2
  • 11
    • 79952997312 scopus 로고    scopus 로고
    • Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer
    • Warf, M. B., Johnson, W. E., and Bass, B. L. (2011) Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer RNA 17, 563-577
    • (2011) RNA , vol.17 , pp. 563-577
    • Warf, M.B.1    Johnson, W.E.2    Bass, B.L.3
  • 14
    • 4744357297 scopus 로고    scopus 로고
    • Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design
    • DOI 10.1074/jbc.M404931200
    • Krol, J., Sobczak, K., Wilczynska, U., Drath, M., Jasinska, A., Kaczynska, D., and Krzyzosiak, W. J. (2004) Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design J. Biol. Chem. 279, 42230-42239 (Pubitemid 39313672)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.40 , pp. 42230-42239
    • Krol, J.1    Sobczak, K.2    Wilczynska, U.3    Drath, M.4    Jasinska, A.5    Kaczynska, D.6    Krzyzosiak, W.J.7
  • 15
    • 78649870594 scopus 로고    scopus 로고
    • The terminal loop region controls microRNA processing by Drosha and Dicer
    • Zeng, Y. and Zhang, X. X. (2010) The terminal loop region controls microRNA processing by Drosha and Dicer Nucleic Acids Res. 38, 7689-7697
    • (2010) Nucleic Acids Res. , vol.38 , pp. 7689-7697
    • Zeng, Y.1    Zhang, X.X.2
  • 16
    • 84859963228 scopus 로고    scopus 로고
    • Biogenesis of mammalian microRNAs by a non-canonical processing pathway
    • Havens, M. A., Reich, A. A., Duelli, D. M., and Hastings, M. L. (2012) Biogenesis of mammalian microRNAs by a non-canonical processing pathway Nucleic Acids Res. 40, 4626-4640
    • (2012) Nucleic Acids Res. , vol.40 , pp. 4626-4640
    • Havens, M.A.1    Reich, A.A.2    Duelli, D.M.3    Hastings, M.L.4
  • 17
    • 38749095507 scopus 로고    scopus 로고
    • The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of β-site amyloid precursor protein-cleaving enzyme 1
    • DOI 10.1523/JNEUROSCI.5065-07.2008
    • Wang, W. X., Rajeev, B. W., Stromberg, A. J., Ren, N., Tang, G. L., Huang, Q. W., Rigoutsos, I., and Nelson, P. T. (2008) The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of β-site amyloid precursor protein-cleaving enzyme 1 J. Neurosci. 28, 1213-1223 (Pubitemid 351186356)
    • (2008) Journal of Neuroscience , vol.28 , Issue.5 , pp. 1213-1223
    • Wang, W.-X.1    Rajeev, B.W.2    Stromberg, A.J.3    Ren, N.4    Tang, G.5    Huang, Q.6    Rigoutsos, I.7    Nelson, P.T.8
  • 19
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE)
    • DOI 10.1021/ja043822v
    • Merino, E. J., Wilkinson, K. A., Coughlan, J. L., and Weeks, K. M. (2005) RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE) J. Am. Chem. Soc. 127, 4223-4231 (Pubitemid 40463047)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.12 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 20
    • 78650396433 scopus 로고    scopus 로고
    • Dynamic Origins of Differential RNA Binding Function in Two dsRBDs from the miRNA "microprocessor" Complex
    • Wostenberg, C., Quarles, K. A., and Showalter, S. A. (2010) Dynamic Origins of Differential RNA Binding Function in Two dsRBDs from the miRNA "Microprocessor" Complex Biochemistry 49, 10728-10736
    • (2010) Biochemistry , vol.49 , pp. 10728-10736
    • Wostenberg, C.1    Quarles, K.A.2    Showalter, S.A.3
  • 21
    • 13944278373 scopus 로고    scopus 로고
    • SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • DOI 10.1261/rna.7214405
    • Das, R., Laederach, A., Pearlman, S. M., Herschlag, D., and Altman, R. B. (2005) SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments RNA 11, 344-354 (Pubitemid 40270826)
    • (2005) RNA , vol.11 , Issue.3 , pp. 344-354
    • Das, R.1    Laederach, A.2    Pearlman, S.M.3    Herschlag, D.4    Altman, R.B.5
  • 22
    • 80052729501 scopus 로고    scopus 로고
    • Understanding the Errors of SHAPE-Directed RNA Structure Modeling
    • Kladwang, W., Vanlang, C. C., Cordero, P., and Das, R. (2011) Understanding the Errors of SHAPE-Directed RNA Structure Modeling Biochemistry 50, 8049-8056
    • (2011) Biochemistry , vol.50 , pp. 8049-8056
    • Kladwang, W.1    Vanlang, C.C.2    Cordero, P.3    Das, R.4
  • 23
    • 79959458096 scopus 로고    scopus 로고
    • HiTRACE: High-throughput robust analysis for capillary electrophoresis
    • Yoon, S., Kim, J., Hum, J., Kim, H., Park, S., Kladwang, W., and Das, R. (2011) HiTRACE: High-throughput robust analysis for capillary electrophoresis Bioinformatics 27, 1798-1805
    • (2011) Bioinformatics , vol.27 , pp. 1798-1805
    • Yoon, S.1    Kim, J.2    Hum, J.3    Kim, H.4    Park, S.5    Kladwang, W.6    Das, R.7
  • 25
    • 3342977915 scopus 로고    scopus 로고
    • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
    • DOI 10.1261/rna.7650904
    • Mathews, D. H. (2004) Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization RNA 10, 1178-1190 (Pubitemid 38989004)
    • (2004) RNA , vol.10 , Issue.8 , pp. 1178-1190
    • Mathews, D.H.1
  • 27
    • 79951574446 scopus 로고    scopus 로고
    • Structural characterization of naturally occurring RNA single mismatches
    • Davis, A. R., Kirkpatrick, C. C., and Znosko, B. M. (2011) Structural characterization of naturally occurring RNA single mismatches Nucleic Acids Res. 39, 1081-1094
    • (2011) Nucleic Acids Res. , vol.39 , pp. 1081-1094
    • Davis, A.R.1    Kirkpatrick, C.C.2    Znosko, B.M.3
  • 28
    • 0034653899 scopus 로고    scopus 로고
    • RNA bulges as architectural and recognition motifs
    • DOI 10.1016/S0969-2126(00)00110-6
    • Hermann, T. and Patel, D. J. (2000) RNA bulges as architectural and recognition motifs Structure 8, R47-R54 (Pubitemid 30148687)
    • (2000) Structure , vol.8 , Issue.3
    • Hermann, T.1    Patel, D.J.2
  • 29
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • DOI 10.1093/nar/gkg595
    • Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31, 3406-3415 (Pubitemid 37442169)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 30
    • 0033607261 scopus 로고    scopus 로고
    • Thermodynamics of single mismatches in RNA duplexes
    • Kierzek, R., Burkard, M. E., and Turner, D. H. (1999) Thermodynamics of single mismatches in RNA duplexes Biochemistry 38, 14214-14223
    • (1999) Biochemistry , vol.38 , pp. 14214-14223
    • Kierzek, R.1    Burkard, M.E.2    Turner, D.H.3
  • 31
    • 0030929777 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach
    • DOI 10.1021/bi9625915
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach Biochemistry 36, 4449-4460 (Pubitemid 27180291)
    • (1997) Biochemistry , vol.36 , Issue.15 , pp. 4449-4460
    • Wu, M.1    SantaLucia Jr., J.2    Turner, D.H.3
  • 32
    • 0028917227 scopus 로고
    • A periodic table of symmetric tandem mismatches in RNA
    • Wu, M., McDowell, J. A., and Turner, D. H. (1995) A periodic table of symmetric tandem mismatches in RNA Biochemistry 34, 3204-3211
    • (1995) Biochemistry , vol.34 , pp. 3204-3211
    • Wu, M.1    McDowell, J.A.2    Turner, D.H.3
  • 35
    • 84865187135 scopus 로고    scopus 로고
    • Determining RNA three-dimensional structures using low-resolution data
    • Parisien, M. and Major, F. (2012) Determining RNA three-dimensional structures using low-resolution data J. Struct. Biol. 179, 252-260
    • (2012) J. Struct. Biol. , vol.179 , pp. 252-260
    • Parisien, M.1    Major, F.2
  • 37
    • 33744956966 scopus 로고    scopus 로고
    • An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA
    • DOI 10.1021/bi0524464
    • Chen, G., Kennedy, S. D., Qiao, J., Krugh, T. R., and Turner, D. H. (2006) An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA Biochemistry 45, 6889-6903 (Pubitemid 43856674)
    • (2006) Biochemistry , vol.45 , Issue.22 , pp. 6889-6903
    • Chen, G.1    Kennedy, S.D.2    Qiao, J.3    Krugh, T.R.4    Turner, D.H.5
  • 38
    • 36248936612 scopus 로고    scopus 로고
    • Thermodynamic characterization of single mismatches found in naturally occurring RNA
    • DOI 10.1021/bi701311c
    • Davis, A. R. and Znosko, B. M. (2007) Thermodynamic characterization of single mismatches found in naturally occurring RNA Biochemistry 46, 13425-13436 (Pubitemid 350136381)
    • (2007) Biochemistry , vol.46 , Issue.46 , pp. 13425-13436
    • Davis, A.R.1    Znosko, B.M.2
  • 39
    • 0033971758 scopus 로고    scopus 로고
    • Database of non-canonical base pairs found in known RNA structures
    • Nagaswamy, U., Voss, N., Zhang, Z., and Fox, G. E. (2000) Database of non-canonical base pairs found in known RNA structures Nucleic Acids Res. 28, 375-376 (Pubitemid 30047812)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 375-376
    • Nagaswamy, U.1    Voss, N.2    Zhang, Z.3    Fox, G.E.4
  • 40
    • 0000731487 scopus 로고    scopus 로고
    • The energetics of small internal loops in RNA
    • DOI 10.1002/1097-0282(1999)52:4 <157::AID-BIP1001>3.0.CO;2-E
    • Schroeder, S. J., Burkard, M. E., and Turner, D. H. (1999) The energetics of small internal loops in RNA Biopolymers 52, 157-167 (Pubitemid 32472439)
    • (1999) Biopolymers , vol.52 , Issue.4 , pp. 157-167
    • Schroeder, S.J.1    Burkard, M.E.2    Turner, D.H.3
  • 41
    • 79851497250 scopus 로고    scopus 로고
    • Molecular recognition of 6′-N-5-hexynoate kanamycin A and RNA 1 × 1 internal loops containing CA mismatches
    • Tran, T. and Disney, M. D. (2011) Molecular recognition of 6′-N-5-hexynoate kanamycin A and RNA 1 × 1 internal loops containing CA mismatches Biochemistry 50, 962-969
    • (2011) Biochemistry , vol.50 , pp. 962-969
    • Tran, T.1    Disney, M.D.2
  • 42
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
    • DOI 10.1126/science.289.5481.905
    • Ban, N., Nissen, P., Hansen, J., Moore, P. B., and Steitz, T. A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution Science 289, 905-920 (Pubitemid 30659939)
    • (2000) Science , vol.289 , Issue.5481 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 43
    • 0028206986 scopus 로고
    • Structure of a mispaired RNA double helix at 1.6-Å resolution and implications for the prediction of RNA secondary structure
    • Cruse, W. B., Saludjian, P., Biala, E., Strazewski, P., Prange, T., and Kennard, O. (1994) Structure of a mispaired RNA double helix at 1.6-Å resolution and implications for the prediction of RNA secondary structure Proc. Natl. Acad. Sci. U.S.A. 91, 4160-4164
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 4160-4164
    • Cruse, W.B.1    Saludjian, P.2    Biala, E.3    Strazewski, P.4    Prange, T.5    Kennard, O.6
  • 44
    • 0026000848 scopus 로고
    • Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs
    • Holbrook, S. R., Cheong, C., Tinoco, I., Jr., and Kim, S. H. (1991) Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs Nature 353, 579-581 (Pubitemid 21912562)
    • (1991) Nature , vol.353 , Issue.6344 , pp. 579-581
    • Holbrook, S.R.1    Cheong, C.2    Tinoco Jr., L.3    Kim, S.-H.4
  • 45
    • 0025082690 scopus 로고
    • Effects of GA mismatches on the structure and thermodynamics of RNA internal loops
    • DOI 10.1021/bi00489a044
    • SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1990) Effects of GA mismatches on the structure and thermodynamics of RNA internal loops Biochemistry 29, 8813-8819 (Pubitemid 20302780)
    • (1990) Biochemistry , vol.29 , Issue.37 , pp. 8813-8819
    • Santa Lucia Jr., J.1    Kierzek, R.2    Turner, D.H.3
  • 46
    • 41849129277 scopus 로고    scopus 로고
    • Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches
    • DOI 10.1021/bi7020876
    • Christiansen, M. E. and Znosko, B. M. (2008) Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches Biochemistry 47, 4329-4336 (Pubitemid 351499888)
    • (2008) Biochemistry , vol.47 , Issue.14 , pp. 4329-4336
    • Christiansen, M.E.1    Znosko, B.M.2
  • 47
    • 0028085964 scopus 로고
    • The stability and structure of tandem GA mismatches in RNA depend on closing base pairs
    • DOI 10.1021/bi00203a033
    • Walter, A. E., Wu, M., and Turner, D. H. (1994) The stability and structure of tandem GA mismatches in RNA depend on closing base pairs Biochemistry 33, 11349-11354 (Pubitemid 24304301)
    • (1994) Biochemistry , vol.33 , Issue.37 , pp. 11349-11354
    • Walter, A.E.1    Wu, M.2    Turner, D.H.3
  • 49
    • 77954701916 scopus 로고    scopus 로고
    • RNA internal loops with tandem AG pairs: The structure of the 5′GAGU/3′UGAG loop can be dramatically different from others, including 5′AAGU/3′UGAA
    • Hammond, N. B., Tolbert, B. S., Kierzek, R., Turner, D. H., and Kennedy, S. D. (2010) RNA internal loops with tandem AG pairs: The structure of the 5′GAGU/3′UGAG loop can be dramatically different from others, including 5′AAGU/3′UGAA Biochemistry 49, 5817-5827
    • (2010) Biochemistry , vol.49 , pp. 5817-5827
    • Hammond, N.B.1    Tolbert, B.S.2    Kierzek, R.3    Turner, D.H.4    Kennedy, S.D.5
  • 50
    • 30844438338 scopus 로고    scopus 로고
    • Structural basis for double-stranded RNA processing by Dicer
    • DOI 10.1126/science.1121638
    • MacRae, I. J., Zhou, K., Li, F., Repic, A., Brooks, A. N., Cande, W. Z., Adams, P. D., and Doudna, J. A. (2006) Structural basis for double-stranded RNA processing by Dicer Science 311, 195-198 (Pubitemid 43108178)
    • (2006) Science , vol.311 , Issue.5758 , pp. 195-198
    • MacRae, I.J.1    Zhou, K.2    Li, F.3    Repic, A.4    Brooks, A.N.5    Cande, W.Z.6    Adams, P.D.7    Doudna, J.A.8
  • 52
    • 79960185923 scopus 로고    scopus 로고
    • Dicer recognizes the 5′ end of RNA for efficient and accurate processing
    • Park, J. E., Heo, I., Tian, Y., Simanshu, D. K., Chang, H., Jee, D., Patel, D. J., and Kim, V. N. (2011) Dicer recognizes the 5′ end of RNA for efficient and accurate processing Nature 475, 201-205
    • (2011) Nature , vol.475 , pp. 201-205
    • Park, J.E.1    Heo, I.2    Tian, Y.3    Simanshu, D.K.4    Chang, H.5    Jee, D.6    Patel, D.J.7    Kim, V.N.8
  • 54
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty, K., Denise, A., and Ponty, Y. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure Bioinformatics 25, 1974-1975
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3


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