메뉴 건너뛰기




Volumn 42, Issue 1, 2014, Pages 417-429

Computational prediction and experimental validation of microRNAs in the brown alga Ectocarpus siliculosus

Author keywords

[No Author keywords available]

Indexed keywords

ALGAL PROTEIN; APOPTOTIC PROTEASE ACTIVATING FACTOR 1; CED 4 PROTEIN; COBALAMIN BINDING PROTEIN; KINESIN; MICRORNA; TETRATRICOPEPTIDE REPEAT PROTEIN; UNCLASSIFIED DRUG; ARGONAUTE PROTEIN; MESSENGER RNA; NUCLEOTIDE;

EID: 84891810693     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt856     Document Type: Article
Times cited : (19)

References (67)
  • 1
    • 0035955361 scopus 로고    scopus 로고
    • An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    • Lau, N.C., Lim, L.P., Weinstein, E.G. and Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862
    • (2001) Science , vol.294 , pp. 858-862
    • Lau, N.C.1    Lim, L.P.2    Weinstein, E.G.3    Bartel, D.P.4
  • 2
    • 0035955366 scopus 로고    scopus 로고
    • An extensive class of small RNAs in Caenorhabditis elegans
    • Lee, R.C. and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862-864
    • (2001) Science , vol.294 , pp. 862-864
    • Lee, R.C.1    Ambros, V.2
  • 4
    • 79955379930 scopus 로고    scopus 로고
    • Vive la diffe'rence: Biogenesis and evolution of microRNAs in plants and animals
    • Axtell, M.J., Westholm, J.O. and Lai, E.C. (2011) Vive la diffe'rence: Biogenesis and evolution of microRNAs in plants and animals. Genome Biol., 12, 221
    • (2011) Genome Biol , vol.12 , pp. 221
    • Axtell, M.J.1    Westholm, J.O.2    Lai, E.C.3
  • 11
    • 79959685129 scopus 로고    scopus 로고
    • Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-Throughput sequencing and bioinformatics analysis
    • Huang, A., He, L. and Wang, G. (2011) Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-Throughput sequencing and bioinformatics analysis. BMC Genomics, 12, 337
    • (2011) BMC Genomics , vol.12 , pp. 337
    • Huang, A.1    He, L.2    Wang, G.3
  • 14
    • 34249003938 scopus 로고    scopus 로고
    • Principles and limitations of computational microRNA gene and target finding
    • Lindow, M. and Gorodkin, J. (2007) Principles and limitations of computational microRNA gene and target finding. DNA Cell Biol., 26, 339-351
    • (2007) DNA Cell Biol , vol.26 , pp. 339-351
    • Lindow, M.1    Gorodkin, J.2
  • 15
    • 65849520676 scopus 로고    scopus 로고
    • Current tools for the identification of miRNA genes and their targets
    • Mendes, N.D., Freitas, A.T. and Sagot, M. (2009) Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res., 37, 2419-2433
    • (2009) Nucleic Acids Res , vol.37 , pp. 2419-2433
    • Mendes, N.D.1    Freitas, A.T.2    Sagot, M.3
  • 16
    • 84876136646 scopus 로고    scopus 로고
    • Computational methods for ab initio detection of microRNAs
    • Allmer, J. and Yousef, M. (2012) Computational methods for ab initio detection of microRNAs. Front. Genet., 3, 209
    • (2012) Front. Genet , Issue.3 , pp. 209
    • Allmer, J.1    Yousef, M.2
  • 18
    • 0038825783 scopus 로고    scopus 로고
    • Computational identification of Drosophila microRNA genes
    • Lai, E.C., Tomancak, P., Williams, R.W. and Rubin, G.M. (2003) Computational identification of Drosophila microRNA genes. Genome Biol., 4, R42
    • (2003) Genome Biol , vol.4
    • Lai, E.C.1    Tomancak, P.2    Williams, R.W.3    Rubin, G.M.4
  • 19
    • 33846437079 scopus 로고    scopus 로고
    • Unique folding of precursor microRNAs: Quantitative evidence and implications for de novo identification
    • Ng Kwang Loong, S. and Mishra, S.K. (2007) Unique folding of precursor microRNAs: Quantitative evidence and implications for de novo identification. RNA, 13, 170-187
    • (2007) RNA , vol.13 , pp. 170-187
    • Ng Kwang Loong, S.1    Mishra, S.K.2
  • 20
    • 0037144546 scopus 로고    scopus 로고
    • A microRNA in a multiple-Turnover RNAi enzyme complex
    • Hutvá gner, G. and Zamore, P.D. (2002) A microRNA in a multiple-Turnover RNAi enzyme complex. Science, 297, 2056-2060
    • (2002) Science , vol.297 , pp. 2056-2060
    • Hutvágner, G.1    Zamore, P.D.2
  • 21
    • 56649102410 scopus 로고    scopus 로고
    • Evolution of Arabidopsis MIR genes generates novel microRNA classes
    • Vazquez, F., Blevins, T., Ailhas, J., Boller, T. and Meins, F.J. (2008) Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res., 36, 6429-6438
    • (2008) Nucleic Acids Res , vol.36 , pp. 6429-6438
    • Vazquez, F.1    Blevins, T.2    Ailhas, J.3    Boller, T.4    Meins, F.J.5
  • 24
    • 31844442152 scopus 로고    scopus 로고
    • Computational analysis of microRNA targets in Caenorhabditis elegans
    • Watanabe, Y., Yachie, N., Numata, K., Saito, R., Kanai, A. and Tomita, M. (2006) Computational analysis of microRNA targets in Caenorhabditis elegans. Gene, 365, 2-10
    • (2006) Gene , vol.365 , pp. 2-10
    • Watanabe, Y.1    Yachie, N.2    Numata, K.3    Saito, R.4    Kanai, A.5    Tomita, M.6
  • 25
    • 36749026906 scopus 로고    scopus 로고
    • Switching from repression to activation: MicroRNAs can up-regulate translation
    • Vasudevan, S., Tong, Y. and Steitz, J.A. (2007) Switching from repression to activation: MicroRNAs can up-regulate translation. Science, 318, 1931-1934
    • (2007) Science , vol.318 , pp. 1931-1934
    • Vasudevan, S.1    Tong, Y.2    Steitz, J.A.3
  • 28
    • 38949213142 scopus 로고    scopus 로고
    • Resolving evolutionary relationships among the brown algae using chloroplast and nuclear genes
    • Phillips, N., Burrowes, R., Rousseau, F., de Reviers, B. and Saunders, G.W. (2008) Resolving evolutionary relationships among the brown algae using chloroplast and nuclear genes. J. Phycol., 44, 394-405
    • (2008) J. Phycol , vol.44 , pp. 394-405
    • Phillips, N.1    Burrowes, R.2    Rousseau, F.3    De Reviers, B.4    Saunders, G.W.5
  • 29
    • 84989660650 scopus 로고
    • A linked 5S rRNA gene in Scytosiphon lomentaria (scytosiphonales, phaeophyceae)
    • Kawai, H., Muto, H., Fujii, T. and Kato, A. (1995) A linked 5S rRNA gene in Scytosiphon lomentaria (scytosiphonales, phaeophyceae). J. Phycol., 31, 306-311
    • (1995) J. Phycol , vol.31 , pp. 306-311
    • Kawai, H.1    Muto, H.2    Fujii, T.3    Kato, A.4
  • 30
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 32
    • 53549088310 scopus 로고    scopus 로고
    • Early development pattern of the brown alga Ectocarpus siliculosus (ectocarpales, phaeophyceae) sporophyte
    • Le Bail, A., Billoud, B., Maisonneuve, C., Peters, A., Cock, M. and Charrier, B. (2008) Early development pattern of the brown alga Ectocarpus siliculosus (ectocarpales, phaeophyceae) sporophyte. J. Phycol., 44, 1269-1281
    • (2008) J. Phycol , vol.44 , pp. 1269-1281
    • Le Bail, A.1    Billoud, B.2    Maisonneuve, C.3    Peters, A.4    Cock, M.5    Charrier, B.6
  • 34
    • 84893415745 scopus 로고    scopus 로고
    • R foundation for statistical computing
    • Vienna, Austria R Development Core Team
    • R Development Core Team. (2010) R Foundation for Statistical Computing. R: A Language and Environment for Statistical Computing. Vienna, Austria
    • (2010) R: A Language and Environment for Statistical Computing
  • 36
    • 45449087921 scopus 로고    scopus 로고
    • Q-base relative quantification framework and software for management and automated analysis of real - Time quantitative PCR data
    • Hellemans, J., Mortier, G., De Paepe, A., Speleman, F. and Vandesompele, J. (2007) qBase relative quantification framework and software for management and automated analysis of real- Time quantitative PCR data. Genome Biol., 8, R19
    • (2007) Genome Biol , vol.8
    • Hellemans, J.1    Mortier, G.2    De Paepe, A.3    Speleman, F.4    Vandesompele, J.5
  • 38
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan - An integration platform for the signature-recognition methods in InterPro
    • Zdobnov, E.M. and Apweiler, R. (2001) InterProScan - An integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 39
    • 34447309058 scopus 로고    scopus 로고
    • De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
    • Ng Kwang Loong, S. and Mishra, S.K. (2007) De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics, 23, 1321-1330
    • (2007) Bioinformatics , vol.23 , pp. 1321-1330
    • Ng Kwang Loong, S.1    Mishra, S.K.2
  • 40
    • 77954469325 scopus 로고    scopus 로고
    • Systematic computational analysis of potential rnai regulation
    • In: Nazife, B., Osman, S., Mesude, I.C. and Tolga, C. (eds Middle East Technical University, Ankara, Turkey
    • Ç akir, M. and Allmer, J. (2010) Systematic computational analysis of potential RNAi regulation. In: Nazife, B., Osman, S., Mesude, I.C. and Tolga, C. (eds), Toxoplasma gondii. 5th International Symposium on Health Informatics and Bioinformatics (HIBIT). Middle East Technical University, Ankara, Turkey, Vol. 5, pp. 31-38
    • (2010) Toxoplasma gondii. 5th International Symposium on Health Informatics and Bioinformatics (HIBI , vol.5 , pp. 31-38
    • Ç Akir, M.1    Allmer, J.2
  • 41
    • 30344456035 scopus 로고    scopus 로고
    • Facile means for quantifying microRNA expression by real-Time PCR
    • Shi, R. and Chiang, V.L. (2005) Facile means for quantifying microRNA expression by real-Time PCR. Biotechniques, 39, 519-525
    • (2005) Biotechniques , vol.39 , pp. 519-525
    • Shi, R.1    Chiang, V.L.2
  • 42
    • 0032231378 scopus 로고    scopus 로고
    • The Tpr protein: Linking structure and function in the nuclear interior? Am
    • Paddy, M.R. (1998) The Tpr protein: Linking structure and function in the nuclear interior? Am. J. Hum. Genet., 63, 305-310
    • (1998) J. Hum. Genet , vol.63 , pp. 305-310
    • Paddy, M.R.1
  • 43
    • 66149134483 scopus 로고    scopus 로고
    • Microtubule-nucleus interactions in Dictyostelium discoideum mediated by central motor kinesins
    • Tikhonenko, I., Nag, D.K., Robinson, D.N. and Koonce, M.P. (2009) Microtubule-nucleus interactions in Dictyostelium discoideum mediated by central motor kinesins. Eukaryot. Cell, 8, 723-731
    • (2009) Eukaryot. Cell , vol.8 , pp. 723-731
    • Tikhonenko, I.1    Nag, D.K.2    Robinson, D.N.3    Koonce, M.P.4
  • 44
    • 34748851341 scopus 로고    scopus 로고
    • Cell and molecular biology of Notch
    • Fiú za, U. and Arias, A.M. (2007) Cell and molecular biology of Notch. J. Endocrinol., 194, 459-474
    • (2007) J. Endocrinol , vol.194 , pp. 459-474
    • Fiúza, U.1    Arias, A.M.2
  • 46
    • 77956508095 scopus 로고    scopus 로고
    • MIReNA: Finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data
    • Mathelier, A. and Carbone, A. (2010) MIReNA: Finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics, 26, 2226-2234
    • (2010) Bioinformatics , vol.26 , pp. 2226-2234
    • Mathelier, A.1    Carbone, A.2
  • 47
    • 70350113884 scopus 로고    scopus 로고
    • Abundant conserved microRNA target sites in the 5'-untranslated region and coding sequence
    • Zhou, X., Duan, X., Qian, J. and Li, F. (2009) Abundant conserved microRNA target sites in the 5'-untranslated region and coding sequence. Genetica, 137, 159-164
    • (2009) Genetica , vol.137 , pp. 159-164
    • Zhou, X.1    Duan, X.2    Qian, J.3    Li, F.4
  • 48
    • 58849093262 scopus 로고    scopus 로고
    • Revisiting the principles of microRNA target recognition and mode of action
    • Brodersen, P. and Voinnet, O. (2009) Revisiting the principles of microRNA target recognition and mode of action. Nat. Rev. Mol. Cell Biol., 10, 141-148
    • (2009) Nat. Rev. Mol. Cell Biol , vol.10 , pp. 141-148
    • Brodersen, P.1    Voinnet, O.2
  • 49
    • 70350004858 scopus 로고    scopus 로고
    • An evolutionary perspective of animal microRNAs and their targets
    • Shomron, N., Golan, D. and Hornstein, E. (2009) An evolutionary perspective of animal microRNAs and their targets. J. Biomed. Biotechnol., 2009, 594738
    • (2009) J. Biomed. Biotechnol , vol.2009 , pp. 594738
    • Shomron, N.1    Golan, D.2    Hornstein, E.3
  • 50
    • 58149279263 scopus 로고    scopus 로고
    • Genomic analysis of rice microRNA promoters and clusters
    • Cui, X., Xu, S.M., Mu, D.S. and Yang, Z.M. (2009) Genomic analysis of rice microRNA promoters and clusters. Gene, 431, 61-66
    • (2009) Gene , vol.431 , pp. 61-66
    • Cui, X.1    Xu, S.M.2    Mu, D.S.3    Yang, Z.M.4
  • 51
    • 76349105277 scopus 로고    scopus 로고
    • Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins
    • Merchan, F., Boualem, A., Crespi, M. and Frugier, F. (2009) Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins. Genome Biol., 10, R136
    • (2009) Genome Biol , vol.10
    • Merchan, F.1    Boualem, A.2    Crespi, M.3    Frugier, F.4
  • 52
    • 6344281172 scopus 로고    scopus 로고
    • Identification of mammalian microRNA host genes and transcription units
    • Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L. and Bradley, A. (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res., 14, 1902-1910
    • (2004) Genome Res , vol.14 , pp. 1902-1910
    • Rodriguez, A.1    Griffiths-Jones, S.2    Ashurst, J.L.3    Bradley, A.4
  • 53
    • 50649110065 scopus 로고    scopus 로고
    • A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
    • Zhu, Q., Spriggs, A., Matthew, L., Fan, L., Kennedy, G., Gubler, F. and Helliwell, C. (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res., 18, 1456-1465
    • (2008) Genome Res , vol.18 , pp. 1456-1465
    • Zhu, Q.1    Spriggs, A.2    Matthew, L.3    Fan, L.4    Kennedy, G.5    Gubler, F.6    Helliwell, C.7
  • 56
    • 4644310115 scopus 로고    scopus 로고
    • Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis
    • Pillai, R.S., Artus, C.G. and Filipowicz, W. (2004) Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA, 10, 1518-1525
    • (2004) RNA , vol.10 , pp. 1518-1525
    • Pillai, R.S.1    Artus, C.G.2    Filipowicz, W.3
  • 57
    • 60949102130 scopus 로고    scopus 로고
    • Dicer is regulated by cellular stresses and interferons
    • Wiesen, J.L. and Tomasi, T.B. (2009) Dicer is regulated by cellular stresses and interferons. Mol. Immunol., 46, 1222-1228
    • (2009) Mol. Immunol , vol.46 , pp. 1222-1228
    • Wiesen, J.L.1    Tomasi, T.B.2
  • 58
    • 84856594225 scopus 로고    scopus 로고
    • Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants
    • Khraiwesh, B., Zhu, J. and Zhu, J. (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim. Biophys. Acta, 1819, 137-148
    • (2012) Biochim. Biophys. Acta , vol.1819 , pp. 137-148
    • Khraiwesh, B.1    Zhu, J.2    Zhu, J.3
  • 59
    • 67649921029 scopus 로고    scopus 로고
    • Dicer-like (DCL) proteins in plants
    • Liu, Q., Feng, Y. and Zhu, Z. (2009) Dicer-like (DCL) proteins in plants. Funct. Integr. Genomics, 9, 277-286
    • (2009) Funct. Integr. Genomics , vol.9 , pp. 277-286
    • Liu, Q.1    Feng, Y.2    Zhu, Z.3
  • 60
    • 55249089227 scopus 로고    scopus 로고
    • Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice
    • Kapoor, M., Arora, R., Lama, T., Nijhawan, A., Khurana, J.P., Tyagi, A.K. and Kapoor, S. (2008) Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics, 9, 451
    • (2008) BMC Genomics , vol.9 , pp. 451
    • Kapoor, M.1    Arora, R.2    Lama, T.3    Nijhawan, A.4    Khurana, J.P.5    Tyagi, A.K.6    Kapoor, S.7
  • 61
    • 77949321139 scopus 로고    scopus 로고
    • Targeting of integrin beta1 and kinesin 2alpha by microRNA 183
    • Li, G., Luna, C., Qiu, J., Epstein, D.L. and Gonzalez, P. (2010) Targeting of integrin beta1 and kinesin 2alpha by microRNA 183. J. Biol. Chem., 285, 5461-5471
    • (2010) J. Biol. Chem , Issue.285 , pp. 5461-5471
    • Li, G.1    Luna, C.2    Qiu, J.3    Epstein, D.L.4    Gonzalez, P.5
  • 62
    • 38149042783 scopus 로고    scopus 로고
    • Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells
    • Frankel, L.B., Christoffersen, N.R., Jacobsen, A., Lindow, M., Krogh, A. and Lund, A.H. (2008) Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J. Biol. Chem., 283, 1026-1033
    • (2008) J. Biol. Chem , vol.283 , pp. 1026-1033
    • Frankel, L.B.1    Christoffersen, N.R.2    Jacobsen, A.3    Lindow, M.4    Krogh, A.5    Lund, A.H.6
  • 63
    • 36949014988 scopus 로고    scopus 로고
    • Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants
    • Lindow, M., Jacobsen, A., Nygaard, S., Mang, Y. and Krogh, A. (2007) Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput. Biol., 3, e238
    • (2007) PLoS Comput. Biol , vol.3
    • Lindow, M.1    Jacobsen, A.2    Nygaard, S.3    Mang, Y.4    Krogh, A.5
  • 64
    • 78651468130 scopus 로고    scopus 로고
    • MiR-138 inhibits EZH2 methyltransferase expression and methylation of histone H3 at lysine 27, and affects thermotolerance acquisition
    • Kisliouk, T., Yosefi, S. and Meiri, N. (2010) MiR-138 inhibits EZH2 methyltransferase expression and methylation of histone H3 at lysine 27, and affects thermotolerance acquisition. Eur. J. Neurosci., 33, 224-235
    • (2010) Eur. J. Neurosci , Issue.33 , pp. 224-235
    • Kisliouk, T.1    Yosefi, S.2    Meiri, N.3
  • 65
    • 79951810835 scopus 로고    scopus 로고
    • Targeting Notch signalling by the conserved miR-8/200 microRNA family in development and cancer cells
    • Vallejo, D.M., Caparros, E. and Dominguez, M. (2011) Targeting Notch signalling by the conserved miR-8/200 microRNA family in development and cancer cells. EMBO J., 30, 756-769
    • (2011) EMBO J. , Issue.30 , pp. 756-769
    • Vallejo, D.M.1    Caparros, E.2    Dominguez, M.3
  • 66
    • 79957697370 scopus 로고    scopus 로고
    • ETOILE regulates developmental patterning in the filamentous brown alga Ectocarpus siliculosus
    • Le Bail, A., Billoud, B., Le Panse, S., Chenivesse, S. and Charrier, B. (2011) ETOILE regulates developmental patterning in the filamentous brown alga Ectocarpus siliculosus. Plant Cell, 23, 1666-1678
    • (2011) Plant Cell , vol.23 , pp. 1666-1678
    • Le Bail, A.1    Billoud, B.2    Le Panse, S.3    Chenivesse, S.4    Charrier, B.5
  • 67
    • 67650609762 scopus 로고    scopus 로고
    • Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress
    • Dittami, S.M., Scornet, D., Petit, J., Se'gurens, B., Da Silva, C., Corre, E., Dondrup, M., Glatting, K., König, R., Sterck, L. et al. (2009) Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol., 10, R66
    • (2009) Genome Biol , Issue.10
    • Dittami, S.M.1    Scornet, D.2    Petit, J.3    Se'gurens, B.4    Da Silva, C.5    Corre, E.6    Dondrup, M.7    Glatting, K.8    König, R.9    Sterck, L.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.