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Volumn 560, Issue , 2015, Pages 219-245

Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA

Author keywords

Next generation sequencing; Pseudouridine; RNA modification

Indexed keywords

MESSENGER RNA; PSEUDOURIDINE; PSEUDOURIDINE SYNTHASE; RNA; SYNTHETASE; UNCLASSIFIED DRUG; MUTASE; PSEUDOURIDINE SYNTHASES;

EID: 84938955375     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2015.03.011     Document Type: Chapter
Times cited : (46)

References (46)
  • 1
    • 61949133492 scopus 로고    scopus 로고
    • A pseudouridine synthase homologue is critical to cellular differentiation in Toxoplasma gondii
    • M.Z. Anderson, J. Brewer, U. Singh, and J.C. Boothroyd A pseudouridine synthase homologue is critical to cellular differentiation in Toxoplasma gondii Eukaryotic Cell 8 2009 398 409
    • (2009) Eukaryotic Cell , vol.8 , pp. 398-409
    • Anderson, M.Z.1    Brewer, J.2    Singh, U.3    Boothroyd, J.C.4
  • 2
    • 0033546399 scopus 로고    scopus 로고
    • Pseudouridine synthetase pus1 of Saccharomyces cerevisiae: Kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA
    • V. Arluison, M. Buckle, and H. Grosjean Pseudouridine synthetase pus1 of Saccharomyces cerevisiae: Kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA Journal of Molecular Biology 289 1999 491 502
    • (1999) Journal of Molecular Biology , vol.289 , pp. 491-502
    • Arluison, V.1    Buckle, M.2    Grosjean, H.3
  • 3
    • 0027438034 scopus 로고
    • Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: Analysis by the application of a new sequencing technique
    • A. Bakin, and J. Ofengand Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: Analysis by the application of a new sequencing technique Biochemistry 32 1993 9754 9762
    • (1993) Biochemistry , vol.32 , pp. 9754-9762
    • Bakin, A.1    Ofengand, J.2
  • 4
    • 2442691791 scopus 로고    scopus 로고
    • Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA)
    • Y. Bykhovskaya, K. Casas, E. Mengesha, A. Inbal, and N. Fischel-Ghodsian Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA) American Journal of Human Genetics 74 2004 1303 1308
    • (2004) American Journal of Human Genetics , vol.74 , pp. 1303-1308
    • Bykhovskaya, Y.1    Casas, K.2    Mengesha, E.3    Inbal, A.4    Fischel-Ghodsian, N.5
  • 6
    • 84922180958 scopus 로고    scopus 로고
    • Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
    • T.M. Carlile, M.F. Rojas-Duran, B. Zinshteyn, H. Shin, K.M. Bartoli, and W.V. Gilbert Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells Nature 515 2014 143 146
    • (2014) Nature , vol.515 , pp. 143-146
    • Carlile, T.M.1    Rojas-Duran, M.F.2    Zinshteyn, B.3    Shin, H.4    Bartoli, K.M.5    Gilbert, W.V.6
  • 7
    • 0033935223 scopus 로고    scopus 로고
    • Pseudouridine in RNA: What, where, how, and why
    • M. Charette, and M.W. Gray Pseudouridine in RNA: What, where, how, and why IUBMB Life 49 2000 341 351
    • (2000) IUBMB Life , vol.49 , pp. 341-351
    • Charette, M.1    Gray, M.W.2
  • 8
    • 0018198062 scopus 로고
    • Modified nucleotides in T1 RNase oligonucleotides of 18S ribosomal RNA of the Novikoff hepatoma
    • Y.C. Choi, and H. Busch Modified nucleotides in T1 RNase oligonucleotides of 18S ribosomal RNA of the Novikoff hepatoma Biochemistry 17 1978 2551 2560
    • (1978) Biochemistry , vol.17 , pp. 2551-2560
    • Choi, Y.C.1    Busch, H.2
  • 9
    • 0000661146 scopus 로고
    • Pseudouridine, a carbon-carbon linked ribonucleoside in ribonucleic acids: Isolation, structure, and chemical characteristics
    • W.E. Cohn Pseudouridine, a carbon-carbon linked ribonucleoside in ribonucleic acids: Isolation, structure, and chemical characteristics The Journal of Biological Chemistry 235 1960 1488 1498
    • (1960) The Journal of Biological Chemistry , vol.235 , pp. 1488-1498
    • Cohn, W.E.1
  • 11
    • 84893684258 scopus 로고    scopus 로고
    • 28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures
    • F.C. Courtes, C. Gu, N.S.C. Wong, P.C. Dedon, M.G.S. Yap, and D.-Y. Lee 28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures Journal of Biotechnology 174 2014 16 21
    • (2014) Journal of Biotechnology , vol.174 , pp. 16-21
    • Courtes, F.C.1    Gu, C.2    Wong, N.S.C.3    Dedon, P.C.4    Yap, M.G.S.5    Lee, D.-Y.6
  • 12
    • 0000568977 scopus 로고
    • Ribonucleic acids from yeast which contain a fifth nucleotide
    • F.F. Davis, and F.W. Allen Ribonucleic acids from yeast which contain a fifth nucleotide The Journal of Biological Chemistry 227 1957 907 915
    • (1957) The Journal of Biological Chemistry , vol.227 , pp. 907-915
    • Davis, F.F.1    Allen, F.W.2
  • 14
    • 40849139057 scopus 로고    scopus 로고
    • Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection
    • A. Durairaj, and P.A. Limbach Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection Analytica Chimica Acta 612 2008 173 181
    • (2008) Analytica Chimica Acta , vol.612 , pp. 173-181
    • Durairaj, A.1    Limbach, P.A.2
  • 16
    • 84881477474 scopus 로고    scopus 로고
    • Unusual base pairing during the decoding of a stop codon by the ribosome
    • I.S. Fernández, C.L. Ng, A.C. Kelley, G. Wu, Y.-T. Yu, and V. Ramakrishnan Unusual base pairing during the decoding of a stop codon by the ribosome Nature 500 2013 107 110
    • (2013) Nature , vol.500 , pp. 107-110
    • Fernández, I.S.1    Ng, C.L.2    Kelley, A.C.3    Wu, G.4    Yu, Y.-T.5    Ramakrishnan, V.6
  • 17
    • 0030711050 scopus 로고    scopus 로고
    • Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs
    • P. Ganot, M.L. Bortolin, and T. Kiss Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs Cell 89 1997 565 573
    • (1997) Cell , vol.89 , pp. 565-573
    • Ganot, P.1    Bortolin, M.L.2    Kiss, T.3
  • 18
    • 84875514519 scopus 로고    scopus 로고
    • RNA pseudouridylation: New insights into an old modification
    • J. Ge, and Y.-T. Yu RNA pseudouridylation: New insights into an old modification Trends in Biochemical Sciences 38 2013 210 218
    • (2013) Trends in Biochemical Sciences , vol.38 , pp. 210-218
    • Ge, J.1    Yu, Y.-T.2
  • 19
    • 0018787015 scopus 로고
    • Rapid print-readout technique for sequencing of RNA's containing modified nucleotides
    • R.C. Gupta, and K. Randerath Rapid print-readout technique for sequencing of RNA's containing modified nucleotides Nucleic Acids Research 6 1979 3443 3458
    • (1979) Nucleic Acids Research , vol.6 , pp. 3443-3458
    • Gupta, R.C.1    Randerath, K.2
  • 20
    • 0031799895 scopus 로고    scopus 로고
    • X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions
    • N.S. Heiss, S.W. Knight, T.J. Vulliamy, S.M. Klauck, S. Wiemann, P.J. Mason, and et al. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions Nature Genetics 19 1998 32 38
    • (1998) Nature Genetics , vol.19 , pp. 32-38
    • Heiss, N.S.1    Knight, S.W.2    Vulliamy, T.J.3    Klauck, S.M.4    Wiemann, S.5    Mason, P.J.6
  • 22
    • 84886027613 scopus 로고    scopus 로고
    • Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides
    • G.A. Hudson, R.J. Bloomingdale, and B.M. Znosko Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides RNA 19 2013 1474 1482
    • (2013) RNA , vol.19 , pp. 1474-1482
    • Hudson, G.A.1    Bloomingdale, R.J.2    Znosko, B.M.3
  • 23
    • 34247329067 scopus 로고    scopus 로고
    • Cis-acting determinants of asymmetric, cytoplasmic RNA transport
    • A. Jambhekar, and J.L. DeRisi Cis-acting determinants of asymmetric, cytoplasmic RNA transport RNA 13 2007 625 642
    • (2007) RNA , vol.13 , pp. 625-642
    • Jambhekar, A.1    Derisi, J.L.2
  • 24
    • 79959284255 scopus 로고    scopus 로고
    • Converting nonsense codons into sense codons by targeted pseudouridylation
    • J. Karijolich, and Y.-T. Yu Converting nonsense codons into sense codons by targeted pseudouridylation Nature 474 2011 395 398
    • (2011) Nature , vol.474 , pp. 395-398
    • Karijolich, J.1    Yu, Y.-T.2
  • 25
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S.L. Salzberg TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biology 14 2013 R36
    • (2013) Genome Biology , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 26
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • G. Kudla, A.W. Murray, D. Tollervey, and J.B. Plotkin Coding-sequence determinants of gene expression in Escherichia coli Science 324 2009 255 258
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 27
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology 10 2009 R25
    • (2009) Genome Biology , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 28
    • 66349122954 scopus 로고    scopus 로고
    • Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    • J.B. Li, E.Y. Levanon, J.-K. Yoon, J. Aach, B. Xie, E. Leproust, and et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing Science 324 2009 1210 1213
    • (2009) Science , vol.324 , pp. 1210-1213
    • Li, J.B.1    Levanon, E.Y.2    Yoon, J.-K.3    Aach, J.4    Xie, B.5    Leproust, E.6
  • 29
    • 84908626586 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of pseudouridines: Pseudouridine synthases modify specific mRNAs in S. Cerevisiae
    • A.F. Lovejoy, D.P. Riordan, and P.O. Brown Transcriptome-wide mapping of pseudouridines: Pseudouridine synthases modify specific mRNAs in S. Cerevisiae PLoS One 9 2014 e110799
    • (2014) PLoS One , vol.9 , pp. e110799
    • Lovejoy, A.F.1    Riordan, D.P.2    Brown, P.O.3
  • 30
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • M. Martin Cutadapt removes adapter sequences from high-throughput sequencing reads EMBnet Journal 17 2011 10 12
    • (2011) EMBnet Journal , vol.17 , pp. 10-12
    • Martin, M.1
  • 31
    • 84861697187 scopus 로고    scopus 로고
    • Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis
    • Y.-P. Mei, J.-P. Liao, J. Shen, L. Yu, B.-L. Liu, L. Liu, and et al. Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis Oncogene 31 2011 2794 2804
    • (2011) Oncogene , vol.31 , pp. 2794-2804
    • Mei, Y.-P.1    Liao, J.-P.2    Shen, J.3    Yu, L.4    Liu, B.-L.5    Liu, L.6
  • 32
    • 84862649489 scopus 로고    scopus 로고
    • Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons
    • K.D. Meyer, Y. Saletore, P. Zumbo, O. Elemento, C.E. Mason, and S.R. Jaffrey Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons Cell 149 2012 1635 1646
    • (2012) Cell , vol.149 , pp. 1635-1646
    • Meyer, K.D.1    Saletore, Y.2    Zumbo, P.3    Elemento, O.4    Mason, C.E.5    Jaffrey, S.R.6
  • 34
    • 84893736852 scopus 로고    scopus 로고
    • Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry
    • A.M. Popova, and J.R. Williamson Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry Journal of the American Chemical Society 136 2014 2058 2069
    • (2014) Journal of the American Chemical Society , vol.136 , pp. 2058-2069
    • Popova, A.M.1    Williamson, J.R.2
  • 36
    • 84907527348 scopus 로고    scopus 로고
    • Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA
    • S. Schwartz, D.A. Bernstein, M.R. Mumbach, M. Jovanovic, R.H. Herbst, B.X. León-Ricardo, and et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA Cell 159 2014 148 162
    • (2014) Cell , vol.159 , pp. 148-162
    • Schwartz, S.1    Bernstein, D.A.2    Mumbach, M.R.3    Jovanovic, M.4    Herbst, R.H.5    León-Ricardo, B.X.6
  • 37
    • 84879345901 scopus 로고    scopus 로고
    • Rate-limiting steps in yeast protein translation
    • P. Shah, Y. Ding, M. Niemczyk, G. Kudla, and J.B. Plotkin Rate-limiting steps in yeast protein translation Cell 153 2013 1589 1601
    • (2013) Cell , vol.153 , pp. 1589-1601
    • Shah, P.1    Ding, Y.2    Niemczyk, M.3    Kudla, G.4    Plotkin, J.B.5
  • 40
    • 84897571308 scopus 로고    scopus 로고
    • Poly(A)-tail profiling reveals an embryonic switch in translational control
    • A.O. Subtelny, S.W. Eichhorn, G.R. Chen, H. Sive, and D.P. Bartel Poly(A)-tail profiling reveals an embryonic switch in translational control Nature 508 2014 66 71
    • (2014) Nature , vol.508 , pp. 66-71
    • Subtelny, A.O.1    Eichhorn, S.W.2    Chen, G.R.3    Sive, H.4    Bartel, D.P.5
  • 42
    • 0019332378 scopus 로고
    • An improved direct RNA sequence method; Its application to Vida faba 5.8S ribosomal RNA
    • Y. Tanaka, T.A. Dyer, and G.G. Brownlee An improved direct RNA sequence method; its application to Vida faba 5.8S ribosomal RNA Nucleic Acids Research 8 1980 1259 1272
    • (1980) Nucleic Acids Research , vol.8 , pp. 1259-1272
    • Tanaka, Y.1    Dyer, T.A.2    Brownlee, G.G.3
  • 43
    • 0032541654 scopus 로고    scopus 로고
    • RNA-catalysed nucleotide synthesis
    • P.J. Unrau, and D.P. Bartel RNA-catalysed nucleotide synthesis Nature 395 1998 260 263
    • (1998) Nature , vol.395 , pp. 260-263
    • Unrau, P.J.1    Bartel, D.P.2
  • 44
    • 65549084855 scopus 로고    scopus 로고
    • RNA sequence and two-dimensional structure features required for efficient substrate modification by the Saccharomyces cerevisiae RNA:Ψ-synthase Pus7p
    • A. Urban, I. Behm-Ansmant, C. Branlant, and Y. Motorin RNA sequence and two-dimensional structure features required for efficient substrate modification by the Saccharomyces cerevisiae RNA:Ψ-synthase Pus7p Journal of Biological Chemistry 284 2009 5845 5858
    • (2009) Journal of Biological Chemistry , vol.284 , pp. 5845-5858
    • Urban, A.1    Behm-Ansmant, I.2    Branlant, C.3    Motorin, Y.4
  • 45
    • 78650905534 scopus 로고    scopus 로고
    • U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP
    • G. Wu, M. Xiao, C. Yang, and Y.-T. Yu U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP The EMBO Journal 30 2011 79 89
    • (2011) The EMBO Journal , vol.30 , pp. 79-89
    • Wu, G.1    Xiao, M.2    Yang, C.3    Yu, Y.-T.4
  • 46
    • 2442643944 scopus 로고    scopus 로고
    • Detection and quantitation of RNA base modifications
    • X.L. Zhao, and Y.T. Yu Detection and quantitation of RNA base modifications RNA 10 2004 996 1002
    • (2004) RNA , vol.10 , pp. 996-1002
    • Zhao, X.L.1    Yu, Y.T.2


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