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Volumn 32, Issue 6, 2014, Pages 562-568

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOPHYSICS; CELL MEMBRANES; DISSOCIATION; GENE ENCODING; MOLECULAR BIOLOGY; PROTEINS;

EID: 84901804745     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2880     Document Type: Article
Times cited : (160)

References (50)
  • 1
    • 34250735674 scopus 로고    scopus 로고
    • RNA regulons: Coordination of post-transcriptional events
    • Keene, J.D. RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet. 8, 533-543 (2007).
    • (2007) Nat. Rev. Genet , vol.8 , pp. 533-543
    • Keene, J.D.1
  • 2
    • 0021111044 scopus 로고
    • Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site
    • Carey, J., Cameron, V., De Haseth, P.L. & Uhlenbeck, O.C. Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site. Biochemistry 22, 2601-2610 (1983).
    • (1983) Biochemistry , vol.22 , pp. 2601-2610
    • Carey, J.1    Cameron, V.2    De Haseth, P.L.3    Uhlenbeck, O.C.4
  • 3
    • 77958594113 scopus 로고    scopus 로고
    • Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae
    • Tsvetanova, N.G., Klass, D.M., Salzman, J. & Brown, P.O. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS ONE 5, e12671 (2010).
    • (2010) PLoS ONE , vol.5
    • Tsvetanova, N.G.1    Klass, D.M.2    Salzman, J.3    Brown, P.O.4
  • 4
    • 78649736872 scopus 로고    scopus 로고
    • A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes
    • Scherrer, T., Mittal, N., Janga, S.C. & Gerber, A.P. A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PLoS ONE 5, e15499 (2010).
    • (2010) PLoS ONE , vol.5
    • Scherrer, T.1    Mittal, N.2    Janga, S.C.3    Gerber, A.P.4
  • 5
    • 67649774581 scopus 로고    scopus 로고
    • Unbiased RNA-protein interaction screen by quantitative proteomics
    • Butter, F., Scheibe, M., Morl, M. & Mann, M. Unbiased RNA-protein interaction screen by quantitative proteomics. Proc. Natl. Acad. Sci. USA 106, 10626-10631 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 10626-10631
    • Butter, F.1    Scheibe, M.2    Morl, M.3    Mann, M.4
  • 6
    • 84861969926 scopus 로고    scopus 로고
    • Insights into RNA biology from an atlas of mammalian mRNA-binding proteins
    • Castello, A. et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149, 1393-1406 (2012).
    • (2012) Cell , vol.149 , pp. 1393-1406
    • Castello, A.1
  • 7
    • 79953748673 scopus 로고    scopus 로고
    • A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
    • Wang, K.C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-124 (2011).
    • (2011) Nature , vol.472 , pp. 120-124
    • Wang, K.C.1
  • 8
    • 77954572735 scopus 로고    scopus 로고
    • Long noncoding RNA as modular scaffold of histone modification complexes
    • Tsai, M.C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689-693 (2010).
    • (2010) Science , vol.329 , pp. 689-693
    • Tsai, M.C.1
  • 9
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • Guttman, M. & Rinn, J.L. Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346 (2012).
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 10
    • 78649429678 scopus 로고    scopus 로고
    • Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins
    • Culler, S.J., Hoff, K.G. & Smolke, C.D. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330, 1251-1255 (2010).
    • (2010) Science , vol.330 , pp. 1251-1255
    • Culler, S.J.1    Hoff, K.G.2    Smolke, C.D.3
  • 12
    • 0031462334 scopus 로고    scopus 로고
    • Measuring the thermodynamics of RNA secondary structure formation
    • SantaLucia, J. & Turner, D.H. Measuring the thermodynamics of RNA secondary structure formation. Biopolymers 44, 309-319 (1997).
    • (1997) Biopolymers , vol.44 , pp. 309-319
    • Santalucia, J.1    Turner, D.H.2
  • 13
    • 77956306662 scopus 로고    scopus 로고
    • Genome-wide measurement of RNA secondary structure in yeast
    • Kertesz, M. et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103-107 (2010).
    • (2010) Nature , vol.467 , pp. 103-107
    • Kertesz, M.1
  • 14
    • 84893427735 scopus 로고    scopus 로고
    • In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
    • Ding, Y. et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505, 696-700 (2014).
    • (2014) Nature , vol.505 , pp. 696-700
    • Ding, Y.1
  • 15
    • 84893351549 scopus 로고    scopus 로고
    • Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
    • Rouskin, S., Zubradt, M., Washietl, S., Kellis, M. & Weissman, J. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505, 701-705 (2014).
    • (2014) Nature , vol.505 , pp. 701-705
    • Rouskin, S.1    Zubradt, M.2    Washietl, S.3    Kellis, M.4    Weissman, J.5
  • 16
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
    • Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905-920 (2000).
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 18
    • 84870845464 scopus 로고    scopus 로고
    • Systematic reconstruction of RNA functional motifs with high-throughput microfluidics
    • Martin, L. et al. Systematic reconstruction of RNA functional motifs with high-throughput microfluidics. Nat. Methods 9, 1192-1194 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 1192-1194
    • Martin, L.1
  • 19
    • 67650484984 scopus 로고    scopus 로고
    • Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
    • Ray, D. et al. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat. Biotechnol. 27, 667-670 (2009).
    • (2009) Nat. Biotechnol , vol.27 , pp. 667-670
    • Ray, D.1
  • 20
    • 84880427394 scopus 로고    scopus 로고
    • A compendium of RNA-binding motifs for decoding gene regulation
    • Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172-177 (2013).
    • (2013) Nature , vol.499 , pp. 172-177
    • Ray, D.1
  • 21
    • 84867644046 scopus 로고    scopus 로고
    • A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
    • Araya, C.L. et al. A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function. Proc. Natl. Acad. Sci. USA 109, 16858-16863 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 16858-16863
    • Araya, C.L.1
  • 22
    • 77957963240 scopus 로고    scopus 로고
    • Rapid construction of empirical RNA fitness landscapes
    • Pitt, J.N. & Ferre-D'Amare, A.R. Rapid construction of empirical RNA fitness landscapes. Science 330, 376-379 (2010).
    • (2010) Science , vol.330 , pp. 376-379
    • Pitt, J.N.1    Ferre-D'Amare, A.R.2
  • 23
    • 84885842840 scopus 로고    scopus 로고
    • Hidden specificity in an apparently nonspecific RNA-binding protein
    • Guenther, U.-P. et al. Hidden specificity in an apparently nonspecific RNA-binding protein. Nature 502, 385-388 (2013).
    • (2013) Nature , vol.502 , pp. 385-388
    • Guenther, U.-P.1
  • 24
    • 78650023082 scopus 로고    scopus 로고
    • High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing
    • Matzas, M. et al. High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat. Biotechnol. 28, 1291-1294 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 1291-1294
    • Matzas, M.1
  • 25
    • 80755142727 scopus 로고    scopus 로고
    • Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing
    • Myllykangas, S., Buenrostro, J.D., Natsoulis, G., Bell, J.M. & Ji, H.P. Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing. Nat. Biotechnol. 29, 1024-1027 (2011).
    • (2011) Nat. Biotechnol , vol.29 , pp. 1024-1027
    • Myllykangas, S.1    Buenrostro, J.D.2    Natsoulis, G.3    Bell, J.M.4    Ji, H.P.5
  • 26
    • 77951107295 scopus 로고    scopus 로고
    • Real-time tRNA transit on single translating ribosomes at codon resolution
    • Uemura, S. et al. Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 464, 1012-1017 (2010).
    • (2010) Nature , vol.464 , pp. 1012-1017
    • Uemura, S.1
  • 27
    • 79960277492 scopus 로고    scopus 로고
    • Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument
    • Nutiu, R. et al. Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat. Biotechnol. 29, 659-664 (2011).
    • (2011) Nat. Biotechnol , vol.29 , pp. 659-664
    • Nutiu, R.1
  • 28
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 29
    • 0021113926 scopus 로고
    • Interaction of R17 coat protein with synthetic variants of its ribonucleic acid binding site
    • Carey, J., Lowary, P.T. & Uhlenbeck, O.C. Interaction of R17 coat protein with synthetic variants of its ribonucleic acid binding site. Biochemistry 22, 4723-4730 (1983).
    • (1983) Biochemistry , vol.22 , pp. 4723-4730
    • Carey, J.1    Lowary, P.T.2    Uhlenbeck, O.C.3
  • 30
    • 0028060580 scopus 로고
    • Mutations that increase the affinity of a translational repressor for RNA
    • Lim, F. & David, S.P. Mutations that increase the affinity of a translational repressor for RNA. Nucleic Acids Res. 22, 3748-3752 (1994).
    • (1994) Nucleic Acids Res , vol.22 , pp. 3748-3752
    • Lim, F.1    David, S.P.2
  • 31
    • 0027960331 scopus 로고
    • Crystal structure of an RNA bacteriophage coat protein-operator complex
    • Valegård, K., Murray, J.B., Stockley, P.G., Stonehouse, N.J. & Liljas, L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature 371, 623-626 (1994).
    • (1994) Nature , vol.371 , pp. 623-626
    • Valegård, K.1    Murray, J.B.2    Stockley, P.G.3    Stonehouse, N.J.4    Liljas, L.5
  • 33
    • 0035175230 scopus 로고    scopus 로고
    • Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex
    • Grahn, E. et al. Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex. RNA 7, 1616-1627 (2001).
    • (2001) RNA , vol.7 , pp. 1616-1627
    • Grahn, E.1
  • 34
    • 0025145063 scopus 로고
    • Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method
    • Bardwell, V.J. & Wickens, M. Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method. Nucleic Acids Res. 18, 6587-6594 (1990).
    • (1990) Nucleic Acids Res , vol.18 , pp. 6587-6594
    • Bardwell, V.J.1    Wickens, M.2
  • 35
    • 0032185810 scopus 로고    scopus 로고
    • Localization of ASH1 mRNA particles in living yeast
    • Bertrand, E. et al. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2, 437-445 (1998).
    • (1998) Mol. Cell , vol.2 , pp. 437-445
    • Bertrand, E.1
  • 36
    • 84856484968 scopus 로고    scopus 로고
    • Counting absolute numbers of molecules using unique molecular identifiers
    • Kivioja, T. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72-74 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 72-74
    • Kivioja, T.1
  • 37
    • 38849204944 scopus 로고    scopus 로고
    • Direct observation of hierarchical folding in single riboswitch aptamers
    • Greenleaf, W.J., Frieda, K.L., Foster, D.A., Woodside, M.T. & Block, S.M. Direct observation of hierarchical folding in single riboswitch aptamers. Science 319, 630-633 (2008).
    • (2008) Science , vol.319 , pp. 630-633
    • Greenleaf, W.J.1    Frieda, K.L.2    Foster, D.A.3    Woodside, M.T.4    Block, S.M.5
  • 38
    • 31344459813 scopus 로고    scopus 로고
    • Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots
    • Hobson, D. & Uhlenbeck, O.C. Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots. J. Mol. Biol. 356, 613-624 (2006).
    • (2006) J. Mol. Biol , vol.356 , pp. 613-624
    • Hobson, D.1    Uhlenbeck, O.C.2
  • 39
    • 0034232357 scopus 로고    scopus 로고
    • The G·U wobble base pair
    • Varani, G. & McClain, W.H. The G·U wobble base pair. EMBO Rep. 1, 18-23 (2000).
    • (2000) EMBO Rep , vol.1 , pp. 18-23
    • Varani, G.1    McClain, W.H.2
  • 40
    • 0031213649 scopus 로고    scopus 로고
    • The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions
    • Valegård, K. et al. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J. Mol. Biol. 270, 724-738 (1997).
    • (1997) J. Mol. Biol , vol.270 , pp. 724-738
    • Valegård, K.1
  • 43
    • 33645666942 scopus 로고    scopus 로고
    • Darwinian evolution can follow only very few mutational paths to fitter proteins
    • Weinreich, D.M. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111-114 (2006).
    • (2006) Science , vol.312 , pp. 111-114
    • Weinreich, D.M.1
  • 44
    • 70349464621 scopus 로고    scopus 로고
    • An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
    • Bridgham, J.T., Ortlund, E.A. & Thornton, J.W. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461, 515-519 (2009).
    • (2009) Nature , vol.461 , pp. 515-519
    • Bridgham, J.T.1    Ortlund, E.A.2    Thornton, J.W.3
  • 45
    • 84878935899 scopus 로고    scopus 로고
    • Epistasis among adaptive mutations in deer mouse hemoglobin
    • Natarajan, C. et al. Epistasis among adaptive mutations in deer mouse hemoglobin. Science 340, 1324-1327 (2013).
    • (2013) Science , vol.340 , pp. 1324-1327
    • Natarajan, C.1
  • 46
    • 0025721938 scopus 로고
    • Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA
    • Rousset, F., Pélandakis, M. & Solignac, M. Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA. Proc. Natl. Acad. Sci. USA 88, 10032-10036 (1991).
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10032-10036
    • Rousset, F.1    Pélandakis, M.2    Solignac, M.3
  • 47
    • 54249159094 scopus 로고    scopus 로고
    • Single-molecule fluorescence resonance energy transfer assays reveal heterogeneous folding ensembles in a simple RNA stem-loop
    • Gell, C. et al. Single-molecule fluorescence resonance energy transfer assays reveal heterogeneous folding ensembles in a simple RNA stem-loop. J. Mol. Biol. 384, 264-278 (2008).
    • (2008) J. Mol. Biol , vol.384 , pp. 264-278
    • Gell, C.1
  • 48
    • 56549105330 scopus 로고    scopus 로고
    • HITS-CLIP yields genome-wide insights into brain alternative RNA processing
    • Licatalosi, D.D. et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464-469 (2008).
    • (2008) Nature , vol.456 , pp. 464-469
    • Licatalosi, D.D.1
  • 49
    • 78650253763 scopus 로고    scopus 로고
    • Genome-wide identification of polycomb-associated RNAs by RIP-seq
    • Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939-953 (2010).
    • (2010) Mol. Cell , vol.40 , pp. 939-953
    • Zhao, J.1
  • 50
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin DNA-binding proteins and nucleosome position
    • Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y. & Greenleaf, W.J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5


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