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Volumn 110, Issue 6, 2013, Pages 2395-2400

Small open reading frames associated with morphogenesis are hidden in plant genomes

Author keywords

Agilent custom microarray; Peptide hormone; Phenome; Transcriptome; Transgenic plant

Indexed keywords

TRANSCRIPTOME;

EID: 84873479857     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1213958110     Document Type: Article
Times cited : (148)

References (50)
  • 1
    • 33644641676 scopus 로고    scopus 로고
    • Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
    • Kastenmayer JP, et al. (2006) Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res 16(3):365-373.
    • (2006) Genome Res , vol.16 , Issue.3 , pp. 365-373
    • Kastenmayer, J.P.1
  • 2
    • 77954786287 scopus 로고    scopus 로고
    • Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis
    • Kondo T, et al. (2010) Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science 329(5989):336-339.
    • (2010) Science , vol.329 , Issue.5989 , pp. 336-339
    • Kondo, T.1
  • 3
    • 0035197071 scopus 로고    scopus 로고
    • Diversity of Arabidopsis genes encoding precursors for phytosulfokine, a peptide growth factor
    • Yang H, Matsubayashi Y, Nakamura K, Sakagami Y (2001) Diversity of Arabidopsis genes encoding precursors for phytosulfokine, a peptide growth factor. Plant Physiol 127(3):842-851.
    • (2001) Plant Physiol , vol.127 , Issue.3 , pp. 842-851
    • Yang, H.1    Matsubayashi, Y.2    Nakamura, K.3    Sakagami, Y.4
  • 4
    • 0346750619 scopus 로고    scopus 로고
    • Tapetum determinant1 is required for cell specialization in the Arabidopsis anther
    • Yang SL, et al. (2003) Tapetum determinant1 is required for cell specialization in the Arabidopsis anther. Plant Cell 15(12):2792-2804.
    • (2003) Plant Cell , vol.15 , Issue.12 , pp. 2792-2804
    • Yang, S.L.1
  • 5
    • 36749050378 scopus 로고    scopus 로고
    • Tyrosinesulfated glycopeptide involved in cellular proliferation and expansion in Arabidopsis
    • Amano Y, Tsubouchi H, Shinohara H, Ogawa M, Matsubayashi Y (2007) Tyrosinesulfated glycopeptide involved in cellular proliferation and expansion in Arabidopsis. Proc Natl Acad Sci USA 104(46):18333-18338.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.46 , pp. 18333-18338
    • Amano, Y.1    Tsubouchi, H.2    Shinohara, H.3    Ogawa, M.4    Matsubayashi, Y.5
  • 6
    • 40449110666 scopus 로고    scopus 로고
    • The CLE family of plant polypeptide signaling molecules
    • Jun JH, Fiume E, Fletcher JC (2008) The CLE family of plant polypeptide signaling molecules. Cell Mol Life Sci 65(5):743-755.
    • (2008) Cell Mol Life Sci , vol.65 , Issue.5 , pp. 743-755
    • Jun, J.H.1    Fiume, E.2    Fletcher, J.C.3
  • 7
    • 12944270592 scopus 로고    scopus 로고
    • The pollen determinant of self-incompatibility in Brassica campestris
    • Takayama S, et al. (2000) The pollen determinant of self-incompatibility in Brassica campestris. Proc Natl Acad Sci USA 97(4):1920-1925.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.4 , pp. 1920-1925
    • Takayama, S.1
  • 8
    • 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 CA, Liu QL, Williamson VM (2008) Silencing a candidate nematode effector gene corresponding to the tomato resistance gene Mi-1 leads to acquisition of virulence. Mol Plant Microbe Interact 21(5):576-585.
    • (2008) Mol Plant Microbe Interact , vol.21 , Issue.5 , pp. 576-585
    • Gleason, C.A.1    Liu, Q.L.2    Williamson, V.M.3
  • 9
    • 77649220369 scopus 로고    scopus 로고
    • Plant peptides govern terminal differentiation of bacteria in symbiosis
    • Van de Velde W, et al. (2010) Plant peptides govern terminal differentiation of bacteria in symbiosis. Science 327(5969):1122-1126.
    • (2010) Science , vol.327 , Issue.5969 , pp. 1122-1126
    • Van De Velde, W.1
  • 10
    • 0035940404 scopus 로고    scopus 로고
    • RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root growth and development
    • Pearce G, Moura DS, Stratmann J, Ryan CA, Jr. (2001) RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root growth and development. Proc Natl Acad Sci USA 98(22):12843-12847.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.22 , pp. 12843-12847
    • Pearce, G.1    Moura, D.S.2    Stratmann, J.3    Ryan Jr., C.A.4
  • 11
    • 47349120149 scopus 로고    scopus 로고
    • Identification of a biologically active, small, secreted peptide in arabidopsis by in silico gene screening, followed by LC-MSbased structure analysis
    • Ohyama K, Ogawa M, Matsubayashi Y (2008) Identification of a biologically active, small, secreted peptide in Arabidopsis by in silico gene screening, followed by LC-MSbased structure analysis. Plant J 55(1):152-160.
    • (2008) Plant J , vol.55 , Issue.1 , pp. 152-160
    • Ohyama, K.1    Ogawa, M.2    Matsubayashi, Y.3
  • 12
    • 77956097951 scopus 로고    scopus 로고
    • Secreted peptide signals required for maintenance of root stem cell niche in Arabidopsis
    • Matsuzaki Y, Ogawa-Ohnishi M, Mori A, Matsubayashi Y (2010) Secreted peptide signals required for maintenance of root stem cell niche in Arabidopsis. Science 329(5995):1065-1067.
    • (2010) Science , vol.329 , Issue.5995 , pp. 1065-1067
    • Matsuzaki, Y.1    Ogawa-Ohnishi, M.2    Mori, A.3    Matsubayashi, Y.4
  • 13
    • 0142092370 scopus 로고    scopus 로고
    • Inflorescence deficient in abscission controls floral organ abscission in Arabidopsis and identifies a novel family of putative ligands in plants
    • Butenko MA, et al. (2003) Inflorescence deficient in abscission controls floral organ abscission in Arabidopsis and identifies a novel family of putative ligands in plants. Plant Cell 15(10):2296-2307.
    • (2003) Plant Cell , vol.15 , Issue.10 , pp. 2296-2307
    • Butenko, M.A.1
  • 14
    • 62649085569 scopus 로고    scopus 로고
    • Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells
    • Okuda S, et al. (2009) Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells. Nature 458(7236):357-361.
    • (2009) Nature , vol.458 , Issue.7236 , pp. 357-361
    • Okuda, S.1
  • 15
    • 67649348212 scopus 로고    scopus 로고
    • Epidermal cell density is autoregulated via a secretory peptide, EPIDERMAL PATTERNING FACTOR 2 in Arabidopsis leaves
    • Hara K, et al. (2009) Epidermal cell density is autoregulated via a secretory peptide, EPIDERMAL PATTERNING FACTOR 2 in Arabidopsis leaves. Plant Cell Physiol 50(6): 1019-1031.
    • (2009) Plant Cell Physiol , vol.50 , Issue.6 , pp. 1019-1031
    • Hara, K.1
  • 16
    • 74449084030 scopus 로고    scopus 로고
    • Stomagen positively regulates stomatal density in Arabidopsis
    • Sugano SS, et al. (2010) Stomagen positively regulates stomatal density in Arabidopsis. Nature 463(7278):241-244.
    • (2010) Nature , vol.463 , Issue.7278 , pp. 241-244
    • Sugano, S.S.1
  • 17
    • 0028798016 scopus 로고
    • Systemin activates synthesis of wound-inducible tomato leaf polyphenol oxidase via the octadecanoid defense signaling pathway
    • Constabel CP, Bergey DR, Ryan CA (1995) Systemin activates synthesis of wound-inducible tomato leaf polyphenol oxidase via the octadecanoid defense signaling pathway. Proc Natl Acad Sci USA 92(2):407-411.
    • (1995) Proc Natl Acad Sci USA , vol.92 , Issue.2 , pp. 407-411
    • Constabel, C.P.1    Bergey, D.R.2    Ryan, C.A.3
  • 18
    • 33745589774 scopus 로고    scopus 로고
    • An endogenous peptide signal in Arabidopsis activates components of the innate immune response
    • Huffaker A, Pearce G, Ryan CA (2006) An endogenous peptide signal in Arabidopsis activates components of the innate immune response. Proc Natl Acad Sci USA 103(26): 10098-10103.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.26 , pp. 10098-10103
    • Huffaker, A.1    Pearce, G.2    Ryan, C.A.3
  • 19
    • 79953331944 scopus 로고    scopus 로고
    • Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
    • Yang X, et al. (2011) Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res 21(4):634-641.
    • (2011) Genome Res , vol.21 , Issue.4 , pp. 634-641
    • Yang, X.1
  • 20
    • 33847329566 scopus 로고    scopus 로고
    • In search of the small ones: Improved prediction of short exons in vertebrates, plants, fungi and protists
    • Saeys Y, Rouzé P, Van de Peer Y (2007) In search of the small ones: Improved prediction of short exons in vertebrates, plants, fungi and protists. Bioinformatics 23(4):414-420.
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 414-420
    • Saeys, Y.1    Rouzé, P.2    Van De Peer, Y.3
  • 21
    • 26944500600 scopus 로고    scopus 로고
    • Genome organization of more than 300 defensin-like genes in Arabidopsis
    • Silverstein KA, Graham MA, Paape TD, VandenBosch KA (2005) Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol 138(2):600-610.
    • (2005) Plant Physiol , vol.138 , Issue.2 , pp. 600-610
    • Silverstein, K.A.1    Graham, M.A.2    Paape, T.D.3    Vandenbosch, K.A.4
  • 22
    • 34248202149 scopus 로고    scopus 로고
    • A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
    • Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH (2007) A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res 17(5):632-640.
    • (2007) Genome Res , vol.17 , Issue.5 , pp. 632-640
    • Hanada, K.1    Zhang, X.2    Borevitz, J.O.3    Li, W.H.4    Shiu, S.H.5
  • 23
    • 77949511569 scopus 로고    scopus 로고
    • SORF finder: A program package to identify small open reading frames with high coding potential
    • Hanada K, et al. (2010) sORF finder: A program package to identify small open reading frames with high coding potential. Bioinformatics 26(3):399-400.
    • (2010) Bioinformatics , vol.26 , Issue.3 , pp. 399-400
    • Hanada, K.1
  • 24
    • 80052208938 scopus 로고    scopus 로고
    • Small open reading frames: Current prediction techniques and future prospect
    • Cheng H, et al. (2011) Small open reading frames: Current prediction techniques and future prospect. Curr Protein Pept Sci 12(6):503-507.
    • (2011) Curr Protein Pept Sci , vol.12 , Issue.6 , pp. 503-507
    • Cheng, H.1
  • 25
    • 0031856647 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous substitution distances are correlated in mouse and rat genes
    • Makalowski W, Boguski MS (1998) Synonymous and nonsynonymous substitution distances are correlated in mouse and rat genes. J Mol Evol 47(2):119-121.
    • (1998) J Mol Evol , vol.47 , Issue.2 , pp. 119-121
    • Makalowski, W.1    Boguski, M.S.2
  • 26
    • 35348919491 scopus 로고    scopus 로고
    • The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes
    • Hanada K, Shiu SH, Li WH (2007) The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes. Mol Biol Evol 24(10):2235-2241.
    • (2007) Mol Biol Evol , vol.24 , Issue.10 , pp. 2235-2241
    • Hanada, K.1    Shiu, S.H.2    Li, W.H.3
  • 27
    • 58549101102 scopus 로고    scopus 로고
    • Discovery and revision of Arabidopsis genes by proteogenomics
    • Castellana NE, et al. (2008) Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci USA 105(52):21034-21038.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.52 , pp. 21034-21038
    • Castellana, N.E.1
  • 28
    • 34447522197 scopus 로고    scopus 로고
    • The secretory peptide gene EPF1 enforces the stomatal one-cell-spacing rule
    • Hara K, Kajita R, Torii KU, Bergmann DC, Kakimoto T (2007) The secretory peptide gene EPF1 enforces the stomatal one-cell-spacing rule. Genes Dev 21(14):1720-1725.
    • (2007) Genes Dev , vol.21 , Issue.14 , pp. 1720-1725
    • Hara, K.1    Kajita, R.2    Torii, K.U.3    Bergmann, D.C.4    Kakimoto, T.5
  • 29
    • 2542525473 scopus 로고    scopus 로고
    • Overexpression of a novel small peptide ROTUNDIFOLIA4 decreases cell proliferation and alters leaf shape in Arabidopsis thaliana
    • Narita NN, et al. (2004) Overexpression of a novel small peptide ROTUNDIFOLIA4 decreases cell proliferation and alters leaf shape in Arabidopsis thaliana. Plant J 38(4):699-713.
    • (2004) Plant J , vol.38 , Issue.4 , pp. 699-713
    • Narita, N.N.1
  • 30
    • 1542288842 scopus 로고    scopus 로고
    • DVL, a novel class of small polypeptides: Overexpression alters Arabidopsis development
    • Wen J, Lease KA, Walker JC (2004) DVL, a novel class of small polypeptides: Overexpression alters Arabidopsis development. Plant J 37(5):668-677.
    • (2004) Plant J , vol.37 , Issue.5 , pp. 668-677
    • Wen, J.1    Lease, K.A.2    Walker, J.C.3
  • 31
    • 33845523291 scopus 로고    scopus 로고
    • The FOX hunting system: An alternative gain-of-function gene hunting technique
    • Ichikawa T, et al. (2006) The FOX hunting system: An alternative gain-of-function gene hunting technique. Plant J 48(6):974-985.
    • (2006) Plant J , vol.48 , Issue.6 , pp. 974-985
    • Ichikawa, T.1
  • 32
    • 79951562921 scopus 로고    scopus 로고
    • RiceFOX: A database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function
    • Sakurai T, et al. (2011) RiceFOX: A database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. Plant Cell Physiol 52(2):265-273.
    • (2011) Plant Cell Physiol , vol.52 , Issue.2 , pp. 265-273
    • Sakurai, T.1
  • 33
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • Alexa A, Rahnenführer J, Lengauer T (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22(13):1600-1607.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1600-1607
    • Alexa, A.1    Rahnenführer, J.2    Lengauer, T.3
  • 34
    • 36448946146 scopus 로고    scopus 로고
    • Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
    • Grossmann S, Bauer S, Robinson PN, Vingron M (2007) Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics 23(22):3024-3031.
    • (2007) Bioinformatics , vol.23 , Issue.22 , pp. 3024-3031
    • Grossmann, S.1    Bauer, S.2    Robinson, P.N.3    Vingron, M.4
  • 35
    • 79951558745 scopus 로고    scopus 로고
    • ARTADE2DB: Improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses
    • Iida K, et al. (2011) ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. Plant Cell Physiol 52(2):254-264.
    • (2011) Plant Cell Physiol , vol.52 , Issue.2 , pp. 254-264
    • Iida, K.1
  • 36
    • 33645731661 scopus 로고    scopus 로고
    • BRICK1/HSPC300 functions with SCAR and the ARP2/3 complex to regulate epidermal cell shape in Arabidopsis
    • Djakovic S, Dyachok J, Burke M, Frank MJ, Smith LG (2006) BRICK1/HSPC300 functions with SCAR and the ARP2/3 complex to regulate epidermal cell shape in Arabidopsis. Development 133(6):1091-1100.
    • (2006) Development , vol.133 , Issue.6 , pp. 1091-1100
    • Djakovic, S.1    Dyachok, J.2    Burke, M.3    Frank, M.J.4    Smith, L.G.5
  • 38
    • 0031252075 scopus 로고    scopus 로고
    • Promoter trap markers differentiate structural and positional components of polar development in Arabidopsis
    • Topping JF, Lindsey K (1997) Promoter trap markers differentiate structural and positional components of polar development in Arabidopsis. Plant Cell 9(10):1713-1725.
    • (1997) Plant Cell , vol.9 , Issue.10 , pp. 1713-1725
    • Topping, J.F.1    Lindsey, K.2
  • 39
    • 70349225934 scopus 로고    scopus 로고
    • Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice
    • Zou C, et al. (2009) Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol 151(1):3-15.
    • (2009) Plant Physiol , vol.151 , Issue.1 , pp. 3-15
    • Zou, C.1
  • 40
    • 79952131885 scopus 로고    scopus 로고
    • Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation
    • Yang L, Takuno S, Waters ER, Gaut BS (2011) Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation. Mol Biol Evol 28(3):1193-1203.
    • (2011) Mol Biol Evol , vol.28 , Issue.3 , pp. 1193-1203
    • Yang, L.1    Takuno, S.2    Waters, E.R.3    Gaut, B.S.4
  • 41
    • 0042065288 scopus 로고    scopus 로고
    • Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region
    • Vilela C, McCarthy JE (2003) Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region. Mol Microbiol 49(4):859-867.
    • (2003) Mol Microbiol , vol.49 , Issue.4 , pp. 859-867
    • Vilela, C.1    McCarthy, J.E.2
  • 42
    • 74949084336 scopus 로고    scopus 로고
    • Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    • Filichkin SA, et al. (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20(1):45-58.
    • (2010) Genome Res , vol.20 , Issue.1 , pp. 45-58
    • Filichkin, S.A.1
  • 44
    • 77952905505 scopus 로고    scopus 로고
    • Most "dark matter" transcripts are associated with known genes
    • van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol 8(5):e1000371.
    • (2010) PLoS Biol , vol.8 , Issue.5
    • Van Bakel, H.1    Nislow, C.2    Blencowe, B.J.3    Hughes, T.R.4
  • 45
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium
    • Dunham I, et al.; ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
    • Dunham, I.1
  • 46
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 47
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586-1591.
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1
  • 48
    • 84859229975 scopus 로고    scopus 로고
    • Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads
    • Kawaguchi S, et al. (2012) Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads. Bioinformatics 28(7):929-937.
    • (2012) Bioinformatics , vol.28 , Issue.7 , pp. 929-937
    • Kawaguchi, S.1
  • 49
    • 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. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511-515.
    • (2010) Nat Biotechnol , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1
  • 50
    • 0032447801 scopus 로고    scopus 로고
    • Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
    • Clough SJ, Bent AF (1998) Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16(6):735-743.
    • (1998) Plant J , vol.16 , Issue.6 , pp. 735-743
    • Clough, S.J.1    Bent, A.F.2


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