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Volumn 9, Issue 1, 2013, Pages 59-64

Peptidomic discovery of short open reading frame-encoded peptides in human cells

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; POLYPEPTIDE; PROTEOME; UNTRANSLATED RNA;

EID: 84871325792     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1120     Document Type: Article
Times cited : (480)

References (50)
  • 1
    • 33646483032 scopus 로고    scopus 로고
    • The abundance of short proteins in the mammalian proteome
    • Frith, M.C. et al. The abundance of short proteins in the mammalian proteome. PLoS Genet. 2, e52 (2006).
    • (2006) PLoS Genet. , vol.2
    • Frith, M.C.1
  • 2
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • Ingolia, N.T., Lareau, L.F. & Weissman, J.S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802 (2011).
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 3
    • 79955575834 scopus 로고    scopus 로고
    • An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA
    • Zhang, F. & Hinnebusch, A.G. An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA. Nucleic Acids Res. 39, 3128-3140 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. 3128-3140
    • Zhang, F.1    Hinnebusch, A.G.2
  • 4
    • 66149118241 scopus 로고    scopus 로고
    • Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
    • Calvo, S.E., Pagliarini, D.J. & Mootha, V.K. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc. Natl. Acad. Sci. USA 106, 7507-7512 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 7507-7512
    • Calvo, S.E.1    Pagliarini, D.J.2    Mootha, V.K.3
  • 5
    • 0025728532 scopus 로고
    • A quantitative model for translational control of the GCN4 gene of Saccharomyces cerevisiae
    • Abastado, J.P., Miller, P.F. & Hinnebusch, A.G. A quantitative model for translational control of the GCN4 gene of Saccharomyces cerevisiae. New Biol. 3, 511-524 (1991).
    • (1991) New Biol. , vol.3 , pp. 511-524
    • Abastado, J.P.1    Miller, P.F.2    Hinnebusch, A.G.3
  • 6
    • 0023054773 scopus 로고
    • Bifunctional messenger RNAs in eukaryotes
    • Kozak, M. Bifunctional messenger RNAs in eukaryotes. Cell 47, 481-483 (1986).
    • (1986) Cell , vol.47 , pp. 481-483
    • Kozak, M.1
  • 7
    • 0028145741 scopus 로고
    • The peptide product of a 5′ leader cistron in the β2 adrenergic receptor mRNA inhibits receptor synthesis
    • Parola, A.L. & Kobilka, B.K. The peptide product of a 5′ leader cistron in the β2 adrenergic receptor mRNA inhibits receptor synthesis. J. Biol. Chem. 269, 4497-4505 (1994).
    • (1994) J. Biol. Chem. , vol.269 , pp. 4497-4505
    • Parola, A.L.1    Kobilka, B.K.2
  • 8
    • 0023659507 scopus 로고
    • The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression
    • Werner, M., Feller, A. & Messenguy, F. The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression. Cell 49, 805-813 (1987).
    • (1987) Cell , vol.49 , pp. 805-813
    • Werner, M.1    Feller, A.2    Messenguy, F.3
  • 9
    • 38049115217 scopus 로고    scopus 로고
    • A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide
    • Wadler, C.S. & Vanderpool, C.K. A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. Proc. Natl. Acad. Sci. USA 104, 20454-20459 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 20454-20459
    • Wadler, C.S.1    Vanderpool, C.K.2
  • 10
    • 0019410218 scopus 로고
    • Identification of the SV40 agnogene product: A DNA binding protein
    • Jay, G., Nomura, S., Anderson, C.W. & Khoury, G. Identification of the SV40 agnogene product: a DNA binding protein. Nature 8, 346-349 (1981).
    • (1981) Nature , vol.8 , pp. 346-349
    • Jay, G.1    Nomura, S.2    Anderson, C.W.3    Khoury, G.4
  • 11
    • 0036670296 scopus 로고    scopus 로고
    • The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning
    • Casson, S.A. et al. The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning. Plant Cell 14, 1705-1721 (2002).
    • (2002) Plant Cell , vol.14 , pp. 1705-1721
    • Casson, S.A.1
  • 13
    • 33644641676 scopus 로고    scopus 로고
    • Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
    • Kastenmayer, J.P. et al. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res. 16, 365-373 (2006).
    • (2006) Genome Res. , vol.16 , pp. 365-373
    • Kastenmayer, J.P.1
  • 14
    • 43549119321 scopus 로고    scopus 로고
    • Silencing a candidate nematode effector gene corresponding to the tomato resistance gene Mi-1 leads to acquisition of virulence
    • Gleason, C.A., Liu, Q.L. & Williamson, V.M. Silencing a candidate nematode effector gene corresponding to the tomato resistance gene Mi-1 leads to acquisition of virulence. Mol. Plant Microbe Interact. 21, 576-585 (2008).
    • (2008) Mol. Plant Microbe Interact. , vol.21 , pp. 576-585
    • Gleason, C.A.1    Liu, Q.L.2    Williamson, V.M.3
  • 15
    • 34249021370 scopus 로고    scopus 로고
    • Peptides encoded by short ORFs control development and define a new eukaryotic gene family
    • Galindo, M.I., Pueyo, J.I., Fouix, S., Bishop, S.A. & Couso, J.P. Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol. 5, e106 (2007).
    • (2007) PLoS Biol. , vol.5
    • Galindo, M.I.1    Pueyo, J.I.2    Fouix, S.3    Bishop, S.A.4    Couso, J.P.5
  • 16
    • 34447573973 scopus 로고    scopus 로고
    • Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA
    • Kondo, T. et al. Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nat. Cell Biol. 9, 660-665 (2007).
    • (2007) Nat. Cell Biol. , vol.9 , pp. 660-665
    • Kondo, T.1
  • 17
    • 4243333514 scopus 로고    scopus 로고
    • A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer′s disease genes and Aβ
    • Hashimoto, Y. et al. A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer′s disease genes and Aβ. Proc. Natl. Acad. Sci. USA 98, 6336-6341 (2001).
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 6336-6341
    • Hashimoto, Y.1
  • 18
    • 56749151013 scopus 로고    scopus 로고
    • Small membrane proteins found by comparative genomics and ribosome binding site models
    • Hemm, M.R., Paul, B.J., Schneider, T.D., Storz, G. & Rudd, K.E. Small membrane proteins found by comparative genomics and ribosome binding site models. Mol. Microbiol. 70, 1487-1501 (2008).
    • (2008) Mol. Microbiol. , vol.70 , pp. 1487-1501
    • Hemm, M.R.1    Paul, B.J.2    Schneider, T.D.3    Storz, G.4    Rudd, K.E.5
  • 19
    • 34347392057 scopus 로고    scopus 로고
    • Diversity of translation start sites may define increased complexity of the human short ORFeome
    • Oyama, M. et al. Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol. Cell. Proteomics 6, 1000-1006 (2007).
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1000-1006
    • Oyama, M.1
  • 20
    • 77949821699 scopus 로고    scopus 로고
    • Expanding the dipeptidyl peptidase 4-regulated peptidome via an optimized peptidomics platform
    • Tinoco, A.D., Tagore, D.M. & Saghatelian, A. Expanding the dipeptidyl peptidase 4-regulated peptidome via an optimized peptidomics platform. J. Am. Chem. Soc. 132, 3819-3830 (2010).
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 3819-3830
    • Tinoco, A.D.1    Tagore, D.M.2    Saghatelian, A.3
  • 22
    • 57749105226 scopus 로고    scopus 로고
    • Peptidase substrates via global peptide profiling
    • Tagore, D.M. et al. Peptidase substrates via global peptide profiling. Nat. Chem. Biol. 5, 23-25 (2009).
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 23-25
    • Tagore, D.M.1
  • 23
    • 77949786295 scopus 로고    scopus 로고
    • Value of using multiple proteases for large-scale mass spectrometry-based proteomics
    • Swaney, D.L., Wenger, C.D. & Coon, J.J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 9, 1323-1329 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 1323-1329
    • Swaney, D.L.1    Wenger, C.D.2    Coon, J.J.3
  • 24
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J.K., McCormack, A.L. & Yates Iii, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994).
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates Iii, J.R.3
  • 25
    • 0029644596 scopus 로고
    • Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
    • Yates, J.R. III, Eng, J.K., McCormack, A.L. & Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426-1436 (1995).
    • (1995) Anal. Chem. , vol.67 , pp. 1426-1436
    • Yates III, J.R.1    Eng, J.K.2    McCormack, A.L.3    Schieltz, D.4
  • 27
    • 80052978224 scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
    • (1915) Genes Dev. , vol.25 , pp. 2011
    • Cabili, M.N.1
  • 28
    • 66349086264 scopus 로고    scopus 로고
    • Identifying novel constrained elements by exploiting biased substitution patterns
    • Garber, M. et al. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics 25, i54-i62 (2009).
    • (2009) Bioinformatics , vol.25
    • Garber, M.1
  • 29
    • 0022552131 scopus 로고
    • Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes
    • Kozak, M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44, 283-292 (1986).
    • (1986) Cell , vol.44 , pp. 283-292
    • Kozak, M.1
  • 30
    • 49549113643 scopus 로고    scopus 로고
    • Global mapping of the topography and magnitude of proteolytic events in apoptosis
    • Dix, M.M., Simon, G.M. & Cravatt, B.F. Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 134, 679-691 (2008).
    • (2008) Cell , vol.134 , pp. 679-691
    • Dix, M.M.1    Simon, G.M.2    Cravatt, B.F.3
  • 31
    • 83055176451 scopus 로고    scopus 로고
    • Mapping intact protein isoforms in discovery mode using top-down proteomics
    • Tran, J.C. et al. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480, 254-258 (2011).
    • (2011) Nature , vol.480 , pp. 254-258
    • Tran, J.C.1
  • 32
    • 80054865417 scopus 로고    scopus 로고
    • A mass spectrometry-guided genome mining approach for natural product peptidogenomics
    • Kersten, R.D. et al. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat. Chem. Biol. 7, 794-802 (2011).
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 794-802
    • Kersten, R.D.1
  • 33
    • 38349068918 scopus 로고    scopus 로고
    • Quantitative multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution
    • Keshishian, H., Addona, T., Burgess, M., Kuhn, E. & Carr, S.A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229 (2007).
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 2212-2229
    • Keshishian, H.1    Addona, T.2    Burgess, M.3    Kuhn, E.4    Carr, S.A.5
  • 34
    • 55249096894 scopus 로고    scopus 로고
    • Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    • de Godoy, L.M. et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254 (2008).
    • (2008) Nature , vol.455 , pp. 1251-1254
    • De Godoy, L.M.1
  • 35
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhäusser, B.1
  • 36
    • 80855128111 scopus 로고    scopus 로고
    • The quantitative proteome of a human cell line
    • Beck, M. et al. The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549 (2011).
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 549
    • Beck, M.1
  • 37
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K.D., Tatusova, T. & Maglott, D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-D65 (2007).
    • (2007) Nucleic Acids Res. , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 38
    • 80052742721 scopus 로고    scopus 로고
    • Molecular mechanism of scanning and start codon selection in eukaryotes
    • Hinnebusch, A.G. Molecular mechanism of scanning and start codon selection in eukaryotes. Microbiol. Mol. Biol. Rev. 75, 434-467 (2011).
    • (2011) Microbiol. Mol. Biol. Rev. , vol.75 , pp. 434-467
    • Hinnebusch, A.G.1
  • 40
    • 0345270035 scopus 로고    scopus 로고
    • Messenger RNA editing in mammals: New members of the APOBEC family seeking roles in the family business
    • Wedekind, J.E., Dance, G.S., Sowden, M.P. & Smith, H.C. Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. Trends Genet. 19, 207-216 (2003).
    • (2003) Trends Genet. , vol.19 , pp. 207-216
    • Wedekind, J.E.1    Dance, G.S.2    Sowden, M.P.3    Smith, H.C.4
  • 41
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1
  • 42
    • 60349120914 scopus 로고    scopus 로고
    • Long non-coding RNAs: Insights into functions
    • Mercer, T.R., Dinger, M.E. & Mattick, J.S. Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 10, 155-159 (2009).
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 155-159
    • Mercer, T.R.1    Dinger, M.E.2    Mattick, J.S.3
  • 43
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 503-510
    • Guttman, M.1
  • 44
    • 67650921949 scopus 로고    scopus 로고
    • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    • Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106, 11667-11672 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 11667-11672
    • Khalil, A.M.1
  • 45
    • 79961212595 scopus 로고    scopus 로고
    • Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT
    • Fonslow, B.R. et al. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J. Proteome Res. 10, 3690-3700 (2011).
    • (2011) J. Proteome Res. , vol.10 , pp. 3690-3700
    • Fonslow, B.R.1
  • 46
    • 41149110237 scopus 로고    scopus 로고
    • Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides
    • Alpert, A.J. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal. Chem. 80, 62-76 (2008).
    • (2008) Anal. Chem. , vol.80 , pp. 62-76
    • Alpert, A.J.1
  • 47
    • 77954368187 scopus 로고    scopus 로고
    • Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: Comprehensive profiling of rat kidney proteome
    • Hao, P. et al. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. J. Proteome Res. 9, 3520-3526 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 3520-3526
    • Hao, P.1
  • 48
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 49
    • 77956340995 scopus 로고    scopus 로고
    • Comprehensive comparative analysis of strand-specific RNA sequencing methods
    • Levin, J.Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 709-715
    • Levin, J.Z.1
  • 50
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3


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