메뉴 건너뛰기




Volumn 31, Issue 16, 2015, Pages 2668-2675

StructureFold: Genome-wide RNA secondary structure mapping and reconstruction in vivo

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA; REGULATORY RNA SEQUENCE; RNA; RNA 18S; TRANSCRIPTOME;

EID: 84939548714     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv213     Document Type: Article
Times cited : (36)

References (44)
  • 1
    • 84911494311 scopus 로고    scopus 로고
    • Rational experiment design for sequencingbased RNA structure mapping
    • Aviran, S. and Pachter, L. (2014) Rational experiment design for sequencingbased RNA structure mapping. RNA, 20, 1864-1877.
    • (2014) RNA , vol.20 , pp. 1864-1877
    • Aviran, S.1    Pachter, L.2
  • 2
    • 79960581588 scopus 로고    scopus 로고
    • Modeling and automation of sequencing-based characterization of RNA structure
    • Aviran, S. et al. (2011) Modeling and automation of sequencing-based characterization of RNA structure. Proc. Natl. Acad. Sci. USA, 108, 11069-11074.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 11069-11074
    • Aviran, S.1
  • 3
    • 84859746198 scopus 로고    scopus 로고
    • Cooperative tertiary interaction network guides RNA folding
    • Behrouzi, R. et al. (2012) Cooperative tertiary interaction network guides RNA folding. Cell, 149, 348-357.
    • (2012) Cell , vol.149 , pp. 348-357
    • Behrouzi, R.1
  • 4
    • 2942571539 scopus 로고    scopus 로고
    • The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    • Cannone, J. J. et al. (2002) The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.J.1
  • 5
    • 84866060803 scopus 로고    scopus 로고
    • Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference
    • Cordero, P. et al. (2012) Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry, 51, 7037-7039.
    • (2012) Biochemistry , vol.51 , pp. 7037-7039
    • Cordero, P.1
  • 6
    • 58549109608 scopus 로고    scopus 로고
    • Accurate SHAPE-directed RNA structure determination
    • Deigan, K. E. et al. (2009) Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA, 106, 97-102.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 97-102
    • Deigan, K.E.1
  • 7
    • 84893427735 scopus 로고    scopus 로고
    • In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
    • Ding, Y. et al. (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
  • 8
    • 0023665268 scopus 로고
    • Probing the structure of RNAs in solution
    • Ehresmann, C. et al. (1987) Probing the structure of RNAs in solution. Nucleic Acids Res. , 15, 9109-9128.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 9109-9128
    • Ehresmann, C.1
  • 9
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J. et al. (2010) Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. , 11, R86.
    • (2010) Genome Biol. , vol.11 , pp. R86
    • Goecks, J.1
  • 10
    • 84875865461 scopus 로고    scopus 로고
    • Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
    • Hajdin, C. E. et al. (2013) Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc. Natl. Acad. Sci. USA, 110, 5498-5503.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 5498-5503
    • Hajdin, C.E.1
  • 11
    • 84924584607 scopus 로고    scopus 로고
    • Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
    • Incarnato, D. et al. (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
  • 12
    • 77956306662 scopus 로고    scopus 로고
    • Genome-wide measurement of RNA secondary structure in yeast
    • Kertesz, M. et al. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature, 467, 103-107.
    • (2010) Nature , vol.467 , pp. 103-107
    • Kertesz, M.1
  • 13
    • 0024841809 scopus 로고
    • Enzymatic approaches to probing of RNA secondary and tertiary structure
    • Knapp, G. (1989) Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol. , 180, 192-212.
    • (1989) Methods Enzymol. , vol.180 , pp. 192-212
    • Knapp, G.1
  • 14
    • 84890771087 scopus 로고    scopus 로고
    • Determination of in vivo RNA structure in lowabundance transcripts
    • Kwok, C. K. et al. (2013) Determination of in vivo RNA structure in lowabundance transcripts. Nat. Commun. , 4, 2971.
    • (2013) Nat. Commun. , vol.4 , pp. 2971
    • Kwok, C.K.1
  • 15
    • 84925301356 scopus 로고    scopus 로고
    • The RNA structurome: Transcriptome-wide structure probing with next-generation sequencing
    • Kwok, C. K. et al. (2015) The RNA structurome: Transcriptome-wide structure probing with next-generation sequencing. Trends Biochem. Sci. , 40, 221-232.
    • (2015) Trends Biochem. Sci. , vol.40 , pp. 221-232
    • Kwok, C.K.1
  • 16
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. , 10, R25.
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1
  • 17
    • 84861121932 scopus 로고    scopus 로고
    • Global analysis of RNA secondary structure in two metazoans
    • Li, F. et al. (2012a) Global analysis of RNA secondary structure in two metazoans. Cell Rep. , 1, 69-82.
    • (2012) Cell Rep. , vol.1 , pp. 69-82
    • Li, F.1
  • 18
    • 84864469631 scopus 로고    scopus 로고
    • SAVoR: A server for sequencing annotation and visualization of RNA structures
    • Li, F. et al. (2012b) SAVoR: A server for sequencing annotation and visualization of RNA structures. Nucleic Acids Res. , 40, W59-W64.
    • (2012) Nucleic Acids Res. , vol.40 , pp. W59-W64
    • Li, F.1
  • 19
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 20
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 21
    • 82055164092 scopus 로고    scopus 로고
    • Vienna RNA package 2.0
    • Lorenz, R. et al. (2011) ViennaRNA Package 2. 0. Algorithms Mol. Biol. , 6, 26.
    • (2011) Algorithms Mol. Biol. , vol.6 , pp. 26
    • Lorenz, R.1
  • 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. et al. (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
  • 23
    • 77957139491 scopus 로고    scopus 로고
    • SHAPE-directed RNA secondary structure prediction
    • Low, J. T. and Weeks, K. M. (2010) SHAPE-directed RNA secondary structure prediction. Methods, 52, 150-158.
    • (2010) Methods , vol.52 , pp. 150-158
    • Low, J.T.1    Weeks, K.M.2
  • 24
    • 79960571755 scopus 로고    scopus 로고
    • Multiplexed RNA structure characterization with selective 20-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) Proc
    • Lucks, J. B. et al. (2011) Multiplexed RNA structure characterization with selective 20-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) Proc. Natl. Acad. Sci. USA, 108, 11063-11068.
    • (2011) Natl. Acad. Sci. USA , vol.108 , pp. 11063-11068
    • Lucks, J.B.1
  • 25
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17, 10-12.
    • (2011) EMBnet. Journal , vol.17 , pp. 10-12
    • Martin, M.1
  • 26
    • 84902830900 scopus 로고    scopus 로고
    • Insights into RNA structure and function from genome-wide studies
    • Mortimer, S. A. et al. (2014) Insights into RNA structure and function from genome-wide studies. Nat. Rev. Genet. , 15, 469-479.
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 469-479
    • Mortimer, S.A.1
  • 27
    • 84873325566 scopus 로고    scopus 로고
    • SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
    • Ouyang, Z. et al. (2013) SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res. , 23, 377-387.
    • (2013) Genome Res. , vol.23 , pp. 377-387
    • Ouyang, Z.1
  • 28
    • 40449139010 scopus 로고    scopus 로고
    • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    • Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
    • (2008) Nature , vol.452 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 29
    • 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
  • 30
    • 84893351549 scopus 로고    scopus 로고
    • Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
    • Rouskin, S. et al. (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
  • 31
    • 67449104206 scopus 로고    scopus 로고
    • Advances in RNA structure prediction from sequence: New tools for generating hypotheses about viral RNA structure-function relationships
    • Schroeder, S. J. (2009) Advances in RNA structure prediction from sequence: New tools for generating hypotheses about viral RNA structure-function relationships. J. Virol. , 83, 6326-6334.
    • (2009) J. Virol. , vol.83 , pp. 6326-6334
    • Schroeder, S.J.1
  • 32
    • 60149103676 scopus 로고    scopus 로고
    • The centrality of RNA
    • Sharp, P. A. (2009) The centrality of RNA. Cell, 136, 577-580.
    • (2009) Cell , vol.136 , pp. 577-580
    • Sharp, P.A.1
  • 33
    • 85027926010 scopus 로고    scopus 로고
    • RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) Nat
    • Siegfried, N. A. et al. (2014) RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) Nat. Methods, 11, 959-965.
    • (2014) Methods , vol.11 , pp. 959-965
    • Siegfried, N.A.1
  • 34
    • 84871298684 scopus 로고    scopus 로고
    • RNA SHAPE analysis in living cells
    • Spitale, R. C. et al. (2013) RNA SHAPE analysis in living cells. Nat. Chem. Biol. , 9, 18-20.
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 18-20
    • Spitale, R.C.1
  • 35
    • 84894281794 scopus 로고    scopus 로고
    • Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions
    • Strulson, C. A. et al. (2014) Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. RNA, 20, 331-347.
    • (2014) RNA , vol.20 , pp. 331-347
    • Strulson, C.A.1
  • 36
    • 84898949357 scopus 로고    scopus 로고
    • Mod-seq: High-throughput sequencing for chemical probing of RNA structure
    • Talkish, J. et al. (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
  • 37
    • 75549088409 scopus 로고    scopus 로고
    • NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
    • Turner, D. H. and Mathews, D. H. (2010) NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res. , 38, D280-D282.
    • (2010) Nucleic Acids Res. , vol.38 , pp. D280-D282
    • Turner, D.H.1    Mathews, D.H.2
  • 38
    • 78649690492 scopus 로고    scopus 로고
    • FragSeq: Transcriptome-wide RNA structure probing using high-throughput sequencing
    • Underwood, J. G. et al. (2010) FragSeq: Transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods, 7, 995-1001.
    • (2010) Nat. Methods , vol.7 , pp. 995-1001
    • Underwood, J.G.1
  • 39
    • 84893358533 scopus 로고    scopus 로고
    • Landscape and variation of RNA secondary structure across the human transcriptome
    • Wan, Y. et al. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature, 505, 706-709.
    • (2014) Nature , vol.505 , pp. 706-709
    • Wan, Y.1
  • 40
    • 0033648805 scopus 로고    scopus 로고
    • Use of dimethyl sulfate to probe RNA structure in vivo
    • Wells, S. E. et al. (2000) Use of dimethyl sulfate to probe RNA structure in vivo. Methods Enzymol. , 318, 479-493.
    • (2000) Methods Enzymol. , vol.318 , pp. 479-493
    • Wells, S.E.1
  • 41
    • 33947720028 scopus 로고    scopus 로고
    • Selective 20-hydroxyl acylation analyzed by primer extension (SHAPE) : Quantitative RNA structure analysis at single nucleotide resolution
    • Wilkinson, K. A. et al. (2006) Selective 20-hydroxyl acylation analyzed by primer extension (SHAPE) : quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. , 1, 1610-1616.
    • (2006) Nat. Protoc. , vol.1 , pp. 1610-1616
    • Wilkinson, K.A.1
  • 42
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearestneighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia, T. et al. (1998) Thermodynamic parameters for an expanded nearestneighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1
  • 43
    • 0029312758 scopus 로고
    • Analysis of the structure of Tetrahymena nuclear RNAs in vivo: Telomerase RNA, the self-splicing rRNA intron, and U2 snRNA
    • Zaug, A. J. and Cech, T. R. (1995) Analysis of the structure of Tetrahymena nuclear RNAs in vivo: Telomerase RNA, the self-splicing rRNA intron, and U2 snRNA. RNA, 1, 363-374.
    • (1995) RNA , vol.1 , pp. 363-374
    • Zaug, A.J.1    Cech, T.R.2
  • 44
    • 78049445573 scopus 로고    scopus 로고
    • Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
    • Zheng, Q. et al. (2010) Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet. , 6, e1001141.
    • (2010) PLoS Genet. , vol.6 , pp. e1001141
    • Zheng, Q.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.