메뉴 건너뛰기




Volumn 44, Issue 2, 2016, Pages e12-

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

Author keywords

[No Author keywords available]

Indexed keywords

BTUB MESSENGER RNA; NUCLEOTIDE; RIBONUCLEASE P; RNA; RNA 5S; UNCLASSIFIED DRUG; UNTRANSLATED RNA; BACTERIAL RNA; BTUB PROTEIN, E COLI; CARRIER PROTEIN; ESCHERICHIA COLI PROTEIN; OUTER MEMBRANE PROTEIN; RIBOSWITCH;

EID: 84966440987     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv879     Document Type: Article
Times cited : (69)

References (61)
  • 1
    • 20644462362 scopus 로고    scopus 로고
    • Micros for microbes: Non-coding regulatory RNAs in bacteria
    • Gottesman,S. (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet., 21, 399-404.
    • (2005) Trends Genet. , vol.21 , pp. 399-404
    • Gottesman, S.1
  • 2
    • 4344682527 scopus 로고    scopus 로고
    • The small RNA regulators of Escherichia coli: Roles and mechanisms
    • Gottesman,S. (2004) The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol., 58, 303-328.
    • (2004) Annu. Rev. Microbiol. , vol.58 , pp. 303-328
    • Gottesman, S.1
  • 3
    • 77954855829 scopus 로고    scopus 로고
    • Non-coding RNAs: Meet thy masters
    • Costa,F.F. (2010) Non-coding RNAs: Meet thy masters. Bioessays, 32, 599-608.
    • (2010) Bioessays , vol.32 , pp. 599-608
    • Costa, F.F.1
  • 4
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn,J.L. and Chang,H.Y. (2012) Genome regulation by long noncoding RNAs. Annu. Rev. Biochem., 81, 145-166.
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 5
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel,D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 9
    • 84859842558 scopus 로고    scopus 로고
    • Rationally designed families of orthogonal RNA regulators of translation
    • Mutalik,V.K., Qi,L., Guimaraes,J.C., Lucks,J.B. and Arkin,A.P. (2012) Rationally designed families of orthogonal RNA regulators of translation. Nat. Chem. Biol., 8, 447-454.
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 447-454
    • Mutalik, V.K.1    Qi, L.2    Guimaraes, J.C.3    Lucks, J.B.4    Arkin, A.P.5
  • 10
    • 79957700542 scopus 로고    scopus 로고
    • Versatile RNA-sensing transcriptional regulators for engineering genetic networks
    • Lucks,J.B., Qi,L., Mutalik,V.K., Wang,D. and Arkin,A.P. (2011) Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc. Natl. Acad. Sci. U.S.A, 108, 8617-8622.
    • (2011) Proc. Natl. Acad. Sci. U.S.A , vol.108 , pp. 8617-8622
    • Lucks, J.B.1    Qi, L.2    Mutalik, V.K.3    Wang, D.4    Arkin, A.P.5
  • 11
    • 84883467214 scopus 로고    scopus 로고
    • A modular strategy for engineering orthogonal chimeric RNA transcription regulators
    • Takahashi,M.K. and Lucks,J.B. (2013) A modular strategy for engineering orthogonal chimeric RNA transcription regulators. Nucleic Acids Res., 41, 7577-7588.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 7577-7588
    • Takahashi, M.K.1    Lucks, J.B.2
  • 12
    • 84863226500 scopus 로고    scopus 로고
    • Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals
    • Qi,L., Lucks,J.B., Liu,C.C., Mutalik,V.K. and Arkin,A.P. (2012) Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res., 40, 5775-5786.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5775-5786
    • Qi, L.1    Lucks, J.B.2    Liu, C.C.3    Mutalik, V.K.4    Arkin, A.P.5
  • 13
    • 84909963314 scopus 로고    scopus 로고
    • Toehold switches: De-novo-designed regulators of gene expression
    • Green,A.A., Silver,P.A., Collins,J.J. and Yin,P. (2014) Toehold switches: de-novo-designed regulators of gene expression. Cell, 159, 925-939.
    • (2014) Cell , vol.159 , pp. 925-939
    • Green, A.A.1    Silver, P.A.2    Collins, J.J.3    Yin, P.4
  • 14
    • 84864258391 scopus 로고    scopus 로고
    • Synthetic biology: An emerging engineering discipline
    • Cheng,A.A. and Lu,T.K. (2012) Synthetic biology: an emerging engineering discipline. Annu. Rev. Biomed. Eng., 14, 155-178.
    • (2012) Annu. Rev. Biomed. Eng. , vol.14 , pp. 155-178
    • Cheng, A.A.1    Lu, T.K.2
  • 15
    • 33845755467 scopus 로고    scopus 로고
    • Illuminating the silence: Understanding the structure and function of small RNAs
    • Rana,T.M. (2007) Illuminating the silence: understanding the structure and function of small RNAs. Nat. Rev. Mol. Cell. Biol., 8, 23-36.
    • (2007) Nat. Rev. Mol. Cell. Biol. , vol.8 , pp. 23-36
    • Rana, T.M.1
  • 16
    • 48249104039 scopus 로고    scopus 로고
    • Riboswitches: Emerging themes in RNA structure and function
    • Montange,R.K. and Batey,R.T. (2008) Riboswitches: emerging themes in RNA structure and function. Annu. Rev. Biophys., 37, 117-133.
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 117-133
    • Montange, R.K.1    Batey, R.T.2
  • 19
    • 84893427735 scopus 로고    scopus 로고
    • In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
    • Ding,Y., Tang,Y., Kwok,C.K., Zhang,Y., Bevilacqua,P.C. and Assmann,S.M. (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature, 505, 696-700.
    • (2014) Nature , vol.505 , pp. 696-700
    • Ding, Y.1    Tang, Y.2    Kwok, C.K.3    Zhang, Y.4    Bevilacqua, P.C.5    Assmann, S.M.6
  • 20
    • 84898949357 scopus 로고    scopus 로고
    • Mod-seq: High-throughput sequencing for chemical probing of RNA structure
    • Talkish,J., May,G., Lin,Y., Woolford,J.L. and McManus,C.J. (2014) Mod-seq: high-throughput sequencing for chemical probing of RNA structure. RNA, 20, 713-720.
    • (2014) RNA , vol.20 , pp. 713-720
    • Talkish, J.1    May, G.2    Lin, Y.3    Woolford, J.L.4    McManus, C.J.5
  • 21
    • 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. and Weissman,J.S. (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature, 505, 701-705.
    • (2014) Nature , vol.505 , pp. 701-705
    • Rouskin, S.1    Zubradt, M.2    Washietl, S.3    Kellis, M.4    Weissman, J.S.5
  • 22
    • 84925225043 scopus 로고    scopus 로고
    • SHAPE-Seq 2.0: Systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing
    • Loughrey,D., Watters,K.E., Settle,A.H. and Lucks,J.B. (2014) SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing. Nucleic Acids Res., 42. e165.
    • (2014) Nucleic Acids Res. , vol.42 , pp. e165
    • Loughrey, D.1    Watters, K.E.2    Settle, A.H.3    Lucks, J.B.4
  • 24
    • 84924584607 scopus 로고    scopus 로고
    • Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
    • Incarnato,D., Neri,F., Anselmi,F. and Oliviero,S. (2014) Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biol., 15, 491.
    • (2014) Genome Biol. , vol.15 , pp. 491
    • Incarnato, D.1    Neri, F.2    Anselmi, F.3    Oliviero, S.4
  • 26
    • 34247162792 scopus 로고    scopus 로고
    • A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
    • Mortimer,S.A. and Weeks,K.M. (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc., 129, 4144-4145.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 4144-4145
    • Mortimer, S.A.1    Weeks, K.M.2
  • 27
    • 77955787630 scopus 로고    scopus 로고
    • Advances in RNA structure analysis by chemical probing
    • Weeks,K.M. (2010) Advances in RNA structure analysis by chemical probing. Curr. Opin. Struct. Biol., 20, 295-304.
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 295-304
    • Weeks, K.M.1
  • 33
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead,B., Trapnell,C., Pop,M. and Salzberg,S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, 1-10.
    • (2009) Genome Biol. , vol.10 , pp. 1-10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 34
    • 84869472916 scopus 로고    scopus 로고
    • An RNA Mapping DataBase for curating RNA structure mapping experiments
    • Cordero,P., Lucks,J.B. and Das,R. (2012) An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics, 28, 3006-3008.
    • (2012) Bioinformatics , vol.28 , pp. 3006-3008
    • Cordero, P.1    Lucks, J.B.2    Das, R.3
  • 35
    • 77949447172 scopus 로고    scopus 로고
    • RNAstructure: Software for RNA secondary structure prediction and analysis
    • Reuter,J.S. and Mathews,D.H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11, 129.
    • (2010) BMC Bioinformatics , vol.11 , pp. 129
    • Reuter, J.S.1    Mathews, D.H.2
  • 36
    • 84863924309 scopus 로고    scopus 로고
    • Bacterial small RNA regulators: Versatile roles and rapidly evolving variations
    • Gottesman,S. and Storz,G. (2011) Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb. Perspect. Biol., 3, 1-16.
    • (2011) Cold Spring Harb. Perspect. Biol. , vol.3 , pp. 1-16
    • Gottesman, S.1    Storz, G.2
  • 37
    • 0020390455 scopus 로고
    • Attenuation in amino acid biosynthetic operons
    • Kolter,R. and Yanofsky,C. (1982) Attenuation in amino acid biosynthetic operons. Annu. Rev. Genet., 16, 113-134.
    • (1982) Annu. Rev. Genet. , vol.16 , pp. 113-134
    • Kolter, R.1    Yanofsky, C.2
  • 40
    • 84889243990 scopus 로고    scopus 로고
    • The cellular environment stabilizes adenine riboswitch RNA structure
    • Tyrrell,J., McGinnis,J.L., Weeks,K.M. and Pielak,G.J. (2013) The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry, 52, 8777-8785.
    • (2013) Biochemistry , vol.52 , pp. 8777-8785
    • Tyrrell, J.1    McGinnis, J.L.2    Weeks, K.M.3    Pielak, G.J.4
  • 41
    • 84901044497 scopus 로고    scopus 로고
    • Ribosome RNA assembly intermediates visualized in living cells
    • McGinnis,J.L. and Weeks,K.M. (2014) Ribosome RNA assembly intermediates visualized in living cells. Biochemistry, 53, 3237-3247.
    • (2014) Biochemistry , vol.53 , pp. 3237-3247
    • McGinnis, J.L.1    Weeks, K.M.2
  • 42
    • 84879681227 scopus 로고    scopus 로고
    • Characterization of 582 natural and synthetic terminators and quantification of their design constraints
    • Chen,Y.-J., Liu,P., Nielsen,A.A.K., Brophy,J.A.N., Clancy,K., Peterson,T. and Voigt,C.A. (2013) Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat. Methods, 10, 659-664.
    • (2013) Nat. Methods , vol.10 , pp. 659-664
    • Chen, Y.-J.1    Liu, P.2    Nielsen, A.A.K.3    Brophy, J.A.N.4    Clancy, K.5    Peterson, T.6    Voigt, C.A.7
  • 43
    • 0033579543 scopus 로고    scopus 로고
    • Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure
    • Franch,T., Petersen,M., Wagner,E.G., Jacobsen,J.P. and Gerdes,K. (1999) Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J. Mol. Biol., 294, 1115-1125.
    • (1999) J. Mol. Biol. , vol.294 , pp. 1115-1125
    • Franch, T.1    Petersen, M.2    Wagner, E.G.3    Jacobsen, J.P.4    Gerdes, K.5
  • 45
    • 0033648805 scopus 로고    scopus 로고
    • Use of dimethyl sulfate to probe RNA structure in vivo
    • Wells,S.E., Hughes,J.M., Igel,A.H. and Ares,M. (2000) Use of dimethyl sulfate to probe RNA structure in vivo. Meth. Enzymol., 318, 479-493.
    • (2000) Meth. Enzymol. , vol.318 , pp. 479-493
    • Wells, S.E.1    Hughes, J.M.2    Igel, A.H.3    Ares, M.4
  • 46
    • 0024844260 scopus 로고
    • Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNA
    • Kittle,J.D., Simons,R.W., Lee,J. and Kleckner,N. (1989) Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNA. J. Mol. Biol., 210, 561-572.
    • (1989) J. Mol. Biol. , vol.210 , pp. 561-572
    • Kittle, J.D.1    Simons, R.W.2    Lee, J.3    Kleckner, N.4
  • 47
    • 84876565196 scopus 로고    scopus 로고
    • Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system
    • Ross,J.A., Ellis,M.J., Hossain,S. and Haniford,D.B. (2013) Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. RNA, 19, 670-684.
    • (2013) RNA , vol.19 , pp. 670-684
    • Ross, J.A.1    Ellis, M.J.2    Hossain, S.3    Haniford, D.B.4
  • 48
    • 0025278320 scopus 로고
    • The IS10 transposase mRNA is destabilized during antisense RNA control
    • Case,C.C., Simons,E.L. and Simons,R.W. (1990) The IS10 transposase mRNA is destabilized during antisense RNA control. EMBO J., 9, 1259-1266.
    • (1990) EMBO J. , vol.9 , pp. 1259-1266
    • Case, C.C.1    Simons, E.L.2    Simons, R.W.3
  • 53
    • 71549154663 scopus 로고    scopus 로고
    • Unexpected diversity of RNase P, an ancient tRNA processing enzyme: Challenges and prospects
    • Lai,L.B., Vioque,A., Kirsebom,L.A. and Gopalan,V. (2010) Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett., 584, 287-296.
    • (2010) FEBS Lett. , vol.584 , pp. 287-296
    • Lai, L.B.1    Vioque, A.2    Kirsebom, L.A.3    Gopalan, V.4
  • 54
    • 0032546728 scopus 로고    scopus 로고
    • Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis
    • Massire,C., Jaeger,L. and Westhof,E. (1998) Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol., 279, 773-793.
    • (1998) J. Mol. Biol. , vol.279 , pp. 773-793
    • Massire, C.1    Jaeger, L.2    Westhof, E.3
  • 55
    • 0034635354 scopus 로고    scopus 로고
    • Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe
    • Biswas,R., Ledman,D.W., Fox,R.O., Altman,S. and Gopalan,V. (2000) Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe. J. Mol. Biol., 296, 19-31.
    • (2000) J. Mol. Biol. , vol.296 , pp. 19-31
    • Biswas, R.1    Ledman, D.W.2    Fox, R.O.3    Altman, S.4    Gopalan, V.5
  • 57
    • 0037462929 scopus 로고    scopus 로고
    • Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme
    • Tsai,H.-Y., Masquida,B., Biswas,R., Westhof,E. and Gopalan,V. (2003) Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J. Mol. Biol., 325, 661-675.
    • (2003) J. Mol. Biol. , vol.325 , pp. 661-675
    • Tsai, H.-Y.1    Masquida, B.2    Biswas, R.3    Westhof, E.4    Gopalan, V.5
  • 58
    • 84881664828 scopus 로고    scopus 로고
    • Structure and function of the T-loop structural motif in noncoding RNAs
    • Chan,C.W., Chetnani,B. and Mondragón,A. (2013) Structure and function of the T-loop structural motif in noncoding RNAs. Wiley Interdiscip. Rev. RNA, 4, 507-522.
    • (2013) Wiley Interdiscip. Rev. RNA , vol.4 , pp. 507-522
    • Chan, C.W.1    Chetnani, B.2    Mondragón, A.3
  • 59
    • 0030598998 scopus 로고    scopus 로고
    • Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P
    • Dong,H., Kirsebom,L.A. and Nilsson,L. (1996) Growth rate regulation of 4.5 S RNA and M1 RNA the catalytic subunit of Escherichia coli RNase P. J. Mol. Biol., 261, 303-308.
    • (1996) J. Mol. Biol. , vol.261 , pp. 303-308
    • Dong, H.1    Kirsebom, L.A.2    Nilsson, L.3
  • 60
    • 1242320304 scopus 로고    scopus 로고
    • Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes
    • Nahvi,A., Barrick,J.E. and Breaker,R.R. (2004) Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res., 32, 143-150.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 143-150
    • Nahvi, A.1    Barrick, J.E.2    Breaker, R.R.3
  • 61
    • 84870539710 scopus 로고    scopus 로고
    • B12 cofactors directly stabilize an mRNA regulatory switch
    • Johnson,J.E., Reyes,F.E., Polaski,J.T. and Batey,R.T. (2012) B12 cofactors directly stabilize an mRNA regulatory switch. Nature, 492, 133-137.
    • (2012) Nature , vol.492 , pp. 133-137
    • Johnson, J.E.1    Reyes, F.E.2    Polaski, J.T.3    Batey, R.T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.