메뉴 건너뛰기




Volumn 515, Issue 7525, 2014, Pages 143-146

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

Author keywords

[No Author keywords available]

Indexed keywords

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

EID: 84922180958     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13802     Document Type: Article
Times cited : (756)

References (44)
  • 1
    • 0000568977 scopus 로고
    • Ribonucleic acids from yeast which contain a fifth nucleotide
    • Davis, F. F. & Allen, F. W. Ribonucleic acids from yeast which contain a fifth nucleotide. J. Biol. Chem. 227, 907-915 (1957).
    • (1957) J. Biol. Chem. , vol.227 , pp. 907-915
    • Davis, F.F.1    Allen, F.W.2
  • 2
    • 0028239805 scopus 로고
    • Gln complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure
    • Gln complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry 33, 7560-7567 (1994).
    • (1994) Biochemistry , vol.33 , pp. 7560-7567
    • Arnez, J.G.1    Steitz, T.A.2
  • 3
    • 0033935223 scopus 로고    scopus 로고
    • Pseudouridine in RNA: What, where, how, and why
    • Charette, M. & Gray, M. W. Pseudouridine in RNA: what, where, how, and why. IUBMB Life 49, 341-351 (2000).
    • (2000) IUBMB Life , vol.49 , pp. 341-351
    • Charette, M.1    Gray, M.W.2
  • 4
    • 0025922011 scopus 로고
    • Phe from hisT mutants: A structural role for pseudouridine
    • Phe from hisT mutants: a structural role for pseudouridine. Biochemistry 30, 4223-4231 (1991).
    • (1991) Biochemistry , vol.30 , pp. 4223-4231
    • Davis, D.R.1    Poulter, C.D.2
  • 6
    • 0025805268 scopus 로고
    • Properties of a U1/mRNA 5′ splice site duplex containing pseudouridine as measured by thermodynamic and NMR methods
    • Hall, K. B. & Mclaughlin, L. W. Properties of a U1/mRNA 5′ splice site duplex containing pseudouridine as measured by thermodynamic and NMR methods. Biochemistry 30, 1795-1801 (1991).
    • (1991) Biochemistry , vol.30 , pp. 1795-1801
    • Hall, K.B.1    Mclaughlin, L.W.2
  • 7
    • 84886027613 scopus 로고    scopus 로고
    • Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides
    • Hudson, G. A., Bloomingdale, R. & Znosko, B. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides. RNA 19, 1474-1482 (2013).
    • (2013) RNA , vol.19 , pp. 1474-1482
    • Hudson, G.A.1    Bloomingdale, R.2    Znosko, B.3
  • 8
    • 0033199501 scopus 로고    scopus 로고
    • Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39
    • Yarian, C. S. et al. Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39. Nucleic Acids Res. 27, 3543-3549 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 3543-3549
    • Yarian, C.S.1
  • 9
    • 84881477474 scopus 로고    scopus 로고
    • Unusual base pairing during the decoding of a stop codon by the ribosome
    • Fernández, I. S. et al. Unusual base pairing during the decoding of a stop codon by the ribosome. Nature 500, 107-110 (2013).
    • (2013) Nature , vol.500 , pp. 107-110
    • Fernández, I.S.1
  • 10
    • 79959284255 scopus 로고    scopus 로고
    • Converting nonsense codons into sense codons by targeted pseudouridylation
    • Karijolich, J. & Yu, Y.-T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature 474, 395-398 (2011).
    • (2011) Nature , vol.474 , pp. 395-398
    • Karijolich, J.1    Yu, Y.-T.2
  • 11
    • 2442691791 scopus 로고    scopus 로고
    • Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA)
    • Bykhovskaya, Y., Casas, K., Mengesha, E., Inbal, A. & Fischel-Ghodsian, N. Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA). Am. J. Hum. Genet. 74, 1303-1308 (2004).
    • (2004) Am. J. Hum. Genet. , vol.74 , pp. 1303-1308
    • Bykhovskaya, Y.1    Casas, K.2    Mengesha, E.3    Inbal, A.4    Fischel-Ghodsian, N.5
  • 12
    • 0031799895 scopus 로고    scopus 로고
    • X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions
    • Heiss, N. S. et al. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nature Genet. 19, 32-38 (1998).
    • (1998) Nature Genet. , vol.19 , pp. 32-38
    • Heiss, N.S.1
  • 13
    • 84861697187 scopus 로고    scopus 로고
    • Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis
    • Mei, Y.-P. et al. Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis. Oncogene 31, 2794-2804 (2012).
    • (2012) Oncogene , vol.31 , pp. 2794-2804
    • Mei, Y.-P.1
  • 14
    • 78651335915 scopus 로고    scopus 로고
    • The RNA Modification Database, RNAMDB: 2011 update
    • Cantara, W. A. et al. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res. 39, D195-D201 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. D195-D201
    • Cantara, W.A.1
  • 15
    • 84880360716 scopus 로고    scopus 로고
    • Characterization and comparison of human nuclear and cytosolic editomes
    • Chen, L. Characterization and comparison of human nuclear and cytosolic editomes. Proc. Natl Acad. Sci. USA 110, E2741-E2747 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. E2741-E2747
    • Chen, L.1
  • 16
  • 17
    • 66349122954 scopus 로고    scopus 로고
    • Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    • Li, J. B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210-1213 (2009).
    • (2009) Science , vol.324 , pp. 1210-1213
    • Li, J.B.1
  • 18
    • 84862649489 scopus 로고    scopus 로고
    • Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons
    • Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635-1646 (2012).
    • (2012) Cell , vol.149 , pp. 1635-1646
    • Meyer, K.D.1
  • 19
    • 84860751168 scopus 로고    scopus 로고
    • Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA
    • Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40, 5023-5033 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5023-5033
    • Squires, J.E.1
  • 20
    • 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
    • Bakin, A. & Ofengand, J. 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, 9754-9762 (1993).
    • (1993) Biochemistry , vol.32 , pp. 9754-9762
    • Bakin, A.1    Ofengand, J.2
  • 21
    • 78650905534 scopus 로고    scopus 로고
    • U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP
    • Wu, G., Xiao, M., Yang, C. & Yu, Y.-T. U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP. EMBO J. 30, 79-89 (2011).
    • (2011) EMBO J. , vol.30 , pp. 79-89
    • Wu, G.1    Xiao, M.2    Yang, C.3    Yu, Y.-T.4
  • 23
    • 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
    • Arluison, V., Buckle, M. & Grosjean, H. Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA. J. Mol. Biol. 289, 491-502 (1999).
    • (1999) J. Mol. Biol. , vol.289 , pp. 491-502
    • Arluison, V.1    Buckle, M.2    Grosjean, H.3
  • 24
    • 0031565927 scopus 로고    scopus 로고
    • Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs
    • Becker, H. F., Motorin, Y., Sissler, M., Florentz, C. & Grosjean, H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs. J. Mol. Biol. 274, 505-518 (1997).
    • (1997) J. Mol. Biol. , vol.274 , pp. 505-518
    • Becker, H.F.1    Motorin, Y.2    Sissler, M.3    Florentz, C.4    Grosjean, H.5
  • 25
    • 0142147324 scopus 로고    scopus 로고
    • The Saccharomyces cerevisiae U2 snRNA:Pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs
    • Behm-Ansmant, I. et al. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs. RNA 9, 1371-1382 (2003).
    • (2003) RNA , vol.9 , pp. 1371-1382
    • Behm-Ansmant, I.1
  • 26
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255-258 (2009).
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 27
    • 84879345901 scopus 로고    scopus 로고
    • Rate-limiting steps in yeast protein translation
    • Shah, P., Ding, Y., Niemczyk, M., Kudla, G. & Plotkin, J. B. Rate-limiting steps in yeast protein translation. Cell 153, 1589-1601 (2013).
    • (2013) Cell , vol.153 , pp. 1589-1601
    • Shah, P.1    Ding, Y.2    Niemczyk, M.3    Kudla, G.4    Plotkin, J.B.5
  • 28
    • 0027494569 scopus 로고
    • Ribosomal pausing during translation of an RNA pseudoknot
    • Somogyi, P., Jenner, A. J., Brierley, I. & Inglis, S. C. Ribosomal pausing during translation of an RNA pseudoknot. Mol. Cell. Biol. 13, 6931-6940 (1993).
    • (1993) Mol. Cell. Biol. , vol.13 , pp. 6931-6940
    • Somogyi, P.1    Jenner, A.J.2    Brierley, I.3    Inglis, S.C.4
  • 29
    • 34247329067 scopus 로고    scopus 로고
    • Cis-acting determinants of asymmetric, cytoplasmic RNA transport
    • Jambhekar, A. & Derisi, J. L. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA 13, 625-642 (2007).
    • (2007) RNA , vol.13 , pp. 625-642
    • Jambhekar, A.1    Derisi, J.L.2
  • 30
    • 84863012654 scopus 로고    scopus 로고
    • Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy
    • Tan, X. et al. Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy. Proc. Natl Acad. Sci. USA 109, 869-874 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 869-874
    • Tan, X.1
  • 31
    • 0031820288 scopus 로고    scopus 로고
    • Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae
    • Longtine, M. S. et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953-961 (1998).
    • (1998) Yeast , vol.14 , pp. 953-961
    • Longtine, M.S.1
  • 32
    • 0033529707 scopus 로고    scopus 로고
    • Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
    • Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
    • (1999) Science , vol.285 , pp. 901-906
    • Winzeler, E.A.1
  • 35
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10-12 (2011).
    • (2011) EMBnet.Journal , vol.17 , pp. 10-12
    • Martin, M.1
  • 36
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1
  • 37
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 38
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 39
    • 60549108380 scopus 로고    scopus 로고
    • Bidirectional promoters generate pervasive transcription in yeast
    • Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033-1037 (2009).
    • (2009) Nature , vol.457 , pp. 1033-1037
    • Xu, Z.1
  • 40
    • 33847270751 scopus 로고    scopus 로고
    • New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA
    • Piekna-Przybylska, D., Decatur, W. A. & Fournier, M. J. New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13, 305-312(2007).
    • (2007) RNA , vol.13 , pp. 305-312
    • Piekna-Przybylska, D.1    Decatur, W.A.2    Fournier, M.J.3
  • 42
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty, K., Denise, A. & Ponty, Y. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics 25, 1974-1975 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 43
    • 58149191272 scopus 로고    scopus 로고
    • tRNAdb 2009: Compilation of tRNA sequences and tRNA genes
    • Jühling, F. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, D159-D162 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. D159-D162
    • Jühling, F.1
  • 44
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: A 2D graphics environment
    • Hunter, J. D. Matplotlib: A 2D graphics environment. Comput. Sci. Eng. 9, 90-95 (2007).
    • (2007) Comput. Sci. Eng. , vol.9 , pp. 90-95
    • Hunter, J.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.