Artículo

Amor, B.B.; Wirth, S.; Merchan, F.; Laporte, P.; D'Aubenton-Carafa, Y.; Hirsch, J.; Maizel, A.; Mallory, A.; Lucas, A.; Deragon, J.M.; Vaucheret, H.; Thermes, C.; Crespi, M. "Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses" (2009) Genome Research. 19(1):57-69
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Abstract:

Long non-protein coding RNAs (npcRNA) represent an emerging class of riboregulators, which either act directly in this long form or are processed to shorter miRNA and siRNA. Genome-wide bioinformatic analysis of full-length cDNA databases identified 76 Arabidopsis npcRNAs. Fourteen npcRNAs were antisense to protein-coding mRNAs, suggesting cis-regulatory roles. Numerous 24-nt siRNA matched to five different npcRNAs, suggesting that these npcRNAs are precursors of this type of siRNA. Expression analyses of the 76 npcRNAs identified a novel npcRNA that accumulates in a dcll mutant but does not appear to produce trans-acting siRNA or miRNA. Additionally, another npcRNA was the precursor of miR869 and shown to be up-regulated in dcl4 but not in dcll mutants, indicative of a young miRNA gene. Abiotic stress altered the accumulation of 22 npcRNAs among the 76, a fraction significantly higher than that observed for the RNA binding protein-coding fraction of the transcriptome. Overexpression analyses in Arabidopsis identified two npcRNAs as regulators of root growth during salt stress and leaf morphology, respectively. Hence, together with small RNAs, long npcRNAs encompass a sensitive component of the transcriptome that have diverse roles during growth and differentiation.

Registro:

Documento: Artículo
Título:Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
Autor:Amor, B.B.; Wirth, S.; Merchan, F.; Laporte, P.; D'Aubenton-Carafa, Y.; Hirsch, J.; Maizel, A.; Mallory, A.; Lucas, A.; Deragon, J.M.; Vaucheret, H.; Thermes, C.; Crespi, M.
Filiación:Institut des Sciences du Végétal (ISV), CNRS, 91198 Gif-sur-Yvette, France
Centre de Génétique Moléculaire (CGM), CNRS, 91198 Gif-sur-Yvette, France
Biomedal S.L, 41092 Sevilla, Spain
Université de Perpignan Via Domitia, CNRS UMR5096 LGDP, 66860 Perpignan Cedex, France
INRA Laboratoire de Biologie Cellulaire, 78026 Versailles Cedex, France
Laboratorio de Agrobiotecnologia, Piso 2, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Buenos Aires, Argentina
INRA, Campus International de Baillarguet, UMR BGPI, TA A-54/K 34398, Montpellier, France
Alten Ouest, ZAC Saint-Sulpice, 12i Rue du Patis Tatelin, 35000 Rennes, France
Palabras clave:plant RNA; RNA binding protein; transcriptome; Arabidopsis protein; cell cycle protein; DCL1 protein, Arabidopsis; DCL4 protein, Arabidopsis; microRNA; plant RNA; ribonuclease; ribonuclease III; RNA precursor; small interfering RNA; untranslated RNA; abiotic stress; Arabidopsis; article; bioinformatics; cell differentiation; gene overexpression; nonhuman; plant genetics; plant growth; plant stress; priority journal; RNA analysis; DNA microarray; gene expression profiling; genetics; growth, development and aging; molecular genetics; mutation; nucleotide sequence; physiological stress; physiology; plant gene; transgenic plant; Arabidopsis; Arabidopsis; Arabidopsis Proteins; Base Sequence; Cell Cycle Proteins; Gene Expression Profiling; Genes, Plant; MicroRNAs; Molecular Sequence Data; Mutation; Oligonucleotide Array Sequence Analysis; Plants, Genetically Modified; Ribonuclease III; Ribonucleases; RNA Precursors; RNA, Plant; RNA, Small Interfering; RNA, Untranslated; Stress, Physiological
Año:2009
Volumen:19
Número:1
Página de inicio:57
Página de fin:69
DOI: http://dx.doi.org/10.1101/gr.080275.108
Título revista:Genome Research
Título revista abreviado:Genome Res.
ISSN:10889051
CODEN:GEREF
CAS:ribonuclease III, 78413-14-6, 9073-62-5; ribonuclease, 59794-03-5, 9001-99-4; Arabidopsis Proteins; Cell Cycle Proteins; DCL1 protein, Arabidopsis, EC 3.1.26.3; DCL4 protein, Arabidopsis, EC 3.1.-; MicroRNAs; Ribonuclease III, EC 3.1.26.3; Ribonucleases, EC 3.1.-; RNA Precursors; RNA, Plant; RNA, Small Interfering; RNA, Untranslated
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10889051_v19_n1_p57_Amor

Referencias:

  • Adenot, X., Elmayan, T., Lauressergues, D., Boutet, S., Bouche, N., Gasciolli, V., Vaucheret, H., DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7 (2006) Curr. Biol, 16, pp. 927-932
  • Argaman, L., Hershberg, R., Vogel, J., Bejerano, G., Wagner, E.G., Margalit, H., Altuvia, S., Novel small RNA-encoding genes in the intergenic regions of Escherichia coli (2001) Curr. Biol, 11, pp. 941-950
  • Bechtold, N., Pelletier, G., In planta Agrobacterium- mediated transformation of adult Arabidopsis thaliana plants by vacuum infiltration (1998) Methods Mol. Biol, 82, pp. 259-266
  • Bonnet, E., Wuyts, J., Rouze, P., Van de Peer, Y., Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes (2004) Proc. Natl. Acad. Sci, 101, pp. 11511-11516
  • Borsani, O., Zhu, J., Verslues, P.E., Sunkar, R., Zhu, J.K., Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis (2005) Cell, 123, pp. 1279-1291
  • Bouche, N., Lauressergues, D., Gasciolli, V., Vaucheret, H., An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs (2006) EMBO J, 25, pp. 3347-3356
  • Brosius, J., Gene duplication and other evolutionary strategies: From the RNA world to the future (2003) J. Struct. Funct. Genomics, 3, pp. 1-17
  • Campalans, A., Kondorosi, A., Crespi, M., Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula (2004) Plant Cell, 16, pp. 1047-1059
  • Castelli, V., Aury, J.M., Jaillon, O., Wincker, P., Clepet, C., Menard, M., Cruaud, C., Schachter, V., Whole genome sequence comparisons and "full-length" cDNA sequences: A combined approach to evaluate and improve Arabidopsis genome annotation (2004) Genome Res, 14, pp. 406-413
  • Chapman, E.J., Carrington, J.C., Specialization and evolution of endogenous small RNA pathways (2007) Nat. Rev. Genet, 8, pp. 884-896
  • Chekanova, J.A., Gregory, B.D., Reverdatto, S.V., Chen, H., Kumar, R., Hooker, T., Yazaki, J., Peng, Q., (2007); Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131: 1340-1353; Chen, Y., Dougherty, E.R., Bittner, M.L., Ratio-based decisions and the quantitative analysis of cDNA microarray images (1997) J. Biomed. Opt, 2, pp. 364-374
  • Costa, F.F., Non-coding RNAs: Lost in translation? (2007) Gene, 386, pp. 1-10
  • Deak, K.I., Malamy, J., Osmotic regulation of root system architecture (2005) Plant J, 43, pp. 17-28
  • Erdmann, V.A., Barciszewska, M.Z., Szymanski, M., Hochberg, A., de Groot, N., Barciszewski, J., The non-coding RNAs as riboregulators (2001) Nucleic Acids Res, 29, pp. 189-193
  • Filipowicz, W., Bhattacharyya, S.N., Sonenberg, N., Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight? (2008) Nat. Rev. Genet, 9, pp. 102-114
  • Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., Miller, W., A computer program for aligning a cDNA sequence with a genomic DNA sequence (1998) Genome Res, 8, pp. 967-974
  • Franco-Zorrilla, J.M., Martin, A.C., Solano, R., Rubio, V., Leyva, A., Paz-Ares, J., Mutations at CRE1 impair cytokinin-induced repression of phosphate starvation responses in Arabidopsis (2002) Plant J, 32, pp. 353-360
  • Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Paz-Ares, J., Target mimicry provides a new mechanism for regulation of microRNA activity (2007) Nat. Genet, 39, pp. 1033-1037
  • Gasciolli, V., Mallory, A.C., Bartel, D.P., Vaucheret, H., Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs (2005) Curr. Biol, 15, pp. 1494-1500
  • He, H., Cai, L., Skogerbo, G., Deng, W., Liu, T., Zhu, X., Wang, Y., Tao, Y., Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray (2006) Nucleic Acids Res, 34, pp. 2976-2983
  • Henz, S.R., Cumbie, J.S., Kasschau, K.D., Lohmann, J.U., Carrington, J.C., Weigel, D., Schmid, M., Distinct expression patterns of natural antisense transcripts in Arabidopsis (2007) Plant Physiol, 144, pp. 1247-1255
  • Hirsch, J., Lefort, V., Vankersschaver, M., Boualem, A., Lucas, A., Thermes, C., d'Aubenton-Carafa, Y., Crespi, M., Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts (2006) Plant Physiol, 140, pp. 1192-1204
  • Huttenhofer, A., Brosius, J., Bachellerie, J.P., RNomics: Identification and function of small, non-messenger RNAs (2002) Curr. Opin. Chem. Biol, 6, pp. 835-843
  • Jones-Rhoades, M.W., Bartel, D.P., Bartel, B., MicroRNAS and their regulatory roles in plants (2006) Annu. Rev. Plant Biol, 57, pp. 19-53
  • Karimi, M., Inze, D., Depicker, A., GATEWAY vectors for Agrobacterium-mediated plant transformation (2002) Trends Plant Sci, 7, pp. 193-195
  • Kastenmayer, J.P., Ni, L., Chu, A., Kitchen, L.E., Au, W.C., Yang, H., Carter, C.D., Boeke, J.D., Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae (2006) Genome Res, 16, pp. 365-373
  • Katiyar-Agarwal, S., Morgan, R., Dahlbeck, D., Borsani, O., Villegas Jr., A., Zhu, J.K., Staskawicz, B.J., Jin, H., A pathogen-inducible endogenous siRNA in plant immunity (2006) Proc. Natl. Acad. Sci, 103, pp. 18002-18007
  • Katiyar-Agarwal, S., Gao, S., Vivian-Smith, A., Jin, H., A novel class of bacteria-induced small RNAs in Arabidopsis (2007) Genes & Dev, 21, pp. 3123-3134
  • Kondo, T., Hashimoto, Y., Kato, K., Inagaki, S., Hayashi, S., Kageyama, Y., Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA (2007) Nat. Cell Biol, 9, pp. 660-665
  • Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Johnson, J.M., Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs (2005) Nature, 433, pp. 769-773
  • Lobbes, D., Rallapalli, G., Schmidt, D.D., Martin, C., Clarke, J., SERRATE: A new player on the plant microRNA scene (2006) EMBO Rep, 7, pp. 1052-1058
  • Lu, S., Sun, Y.H., Shi, R., Clark, C., Li, L., Chiang, V.L., Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis (2005) Plant Cell, 17, pp. 2186-2203
  • Manavella, P.A., Arce, A.L., Dezar, C.A., Bitton, F., Renou, J.P., Crespi, M., Chan, R.L., Cross-talk between ethylene and drought signalling pathways is mediated by the sunflower Hahb-4 transcription factor (2006) Plant J, 48, pp. 125-137
  • March-Diaz, R., Garcia-Dominguez, M., Florencio, F.J., Reyes, J.C., SEF, a new protein required for flowering repression in Arabidopsis, interacts with PIE1 and ARP6 (2007) Plant Physiol, 143, pp. 893-901
  • Mendes Soares, L.M., Valcarcel, J., The expanding transcriptome: The genome as the Book of Sand (2006) EMBO J, 25, pp. 923-931
  • Newton, M.A., Kendziorski, C.M., Richmond, C.S., Blattner, F.R., Tsui, K.W., On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data (2001) J. Comput. Biol, 8, pp. 37-52
  • Nikovics, K., Blein, T., Peaucelle, A., Ishida, T., Morin, H., Aida, M., Laufs, P., The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis (2006) Plant Cell, 18, pp. 2929-2945
  • Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L.G., Hume, D.A., Tomita, M., Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection (2003) Genome Res, 13, pp. 1301-1306
  • Okazaki, Y.M., Furuno, T., Kasukawa, J., Adachi, H., Bono, S., Kondo, I., Nikaido, N., Suzuki, T., Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs (2002) Nature, 420, pp. 563-573
  • Osato, N., Yamada, H., Satoh, K., Ooka, H., Yamamoto, M., Suzuki, K., Kawai, J., Murakami, K., Antisense transcripts with rice full-length cDNAs (2003) Genome Biol, 5, pp. R5
  • Ota, T.Y., Suzuki, T., Nishikawa, T., Otsuki, T., Sugiyama, R., Irie, A., Wakamatsu, K., Nagai, K., Complete sequencing and characterization of 21,243 full-length human cDNAs (2004) Nat. Genet, 36, pp. 40-45
  • Prasanth, K.V., Spector, D.L., Eukaryotic regulatory RNAs: An answer to the "genome complexity" conundrum (2007) Genes & Dev, 21, pp. 11-42
  • Rajagopalan, R., Vaucheret, H., Trejo, J., Bartel, D.P., A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana (2006) Genes & Dev, 20, pp. 3407-3425
  • Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., Bartel, D.P., MicroRNAs in plants (2002) Genes & Dev, 16, pp. 1616-1626
  • Riano-Pachon, D.M., Dreyer, I., Mueller-Roeber, B., Orphan transcripts in Arabidopsis thaliana: Identification of several hundred previously unrecognized genes (2005) Plant J, 43, pp. 205-212
  • Rinn, J.L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N.M., Hartman, S., Harrison, P.M., Gerstein, M., The transcriptional activity of human chromosome 22 (2003) Genes & Dev, 17, pp. 529-540
  • Sapir, M. and Churchill, G.A. 2000. Estimating the posterior probability of differential gene expression from microarray data. The Jackson Laboratory. http://research.jax.org/faculty/churchill/pubs/marina.pdf.Sasidharan, R. and Gerstein, M. 2008. Genomics: Protein fossils live on as RNA. Nature 453: 729-731; Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Lohmann, J.U., A gene expression map of Arabidopsis thaliana development (2005) Nat. Genet, 37, pp. 501-506
  • Stolc, V., Gauhar, Z., Mason, C., Halasz, G., van Batenburg, M.F., Rifkin, S.A., Hua, S., Barbano, P.E., A gene expression map for the euchromatic genome of Drosophila melanogaster (2004) Science, 306, pp. 655-660
  • Storz, G., Opdyke, J.A., Zhang, A., Controlling mRNA stability and translation with small, noncoding RNAs (2004) Curr. Opin. Microbiol, 7, pp. 140-144
  • Sunkar, R., Girke, T., Jain, P.K., Zhu, J.K., Cloning and characterization of microRNAs from rice (2005) Plant Cell, 17, pp. 1397-1411
  • Sunkar, R., Chinnusamy, V., Zhu, J., Zhu, J.K., Small RNAs as big players in plant abiotic stress responses and nutrient deprivation (2007) Trends Plant Sci, 12, pp. 301-309
  • Swarup, K., Benkova, E., Swarup, R., Casimiro, I., Peret, B., Yang, Y., Parry, G., Vanneste, S., The auxin influx carrier LAX3 promotes lateral root emergence (2008) Nat. Cell Biol, 10, pp. 946-954
  • Tenson, T., DeBlasio, A., Mankin, A., A functional peptide encoded in the Escherichia coli 23S rRNA (1996) Proc. Natl. Acad. Sci, 93, pp. 5641-5646
  • Touchon, M., Arneodo, A., d'Aubenton-Carafa, Y., Thermes, C., Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes (2004) Nucleic Acids Res, 32, pp. 4969-4978
  • Vaucheret, H., Post-transcriptional small RNA pathways in plants: Mechanisms and regulations (2006) Genes & Dev, 20, pp. 759-771
  • Vaucheret, H., Mallory, A.C., Bartel, D.P., AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1 (2006) Mol. Cell, 22, pp. 129-136
  • Wang, J.W., Wang, L.J., Mao, Y.B., Cai, W.J., Xue, H.W., Chen, X.Y., Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis (2005) Plant Cell, 17, pp. 2204-2216
  • Wang, X.J., Gaasterland, T., Chua, N.H., Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana (2005) Genome Biol, 6, pp. R30
  • Wang, H., Chua, N.H., Wang, X.J., Prediction of trans-antisense transcripts in Arabidopsis thaliana (2006) Genome Biol, 7, pp. R92
  • Wang, X., Arai, S., Song, X., Reichart, D., Du, K., Pascual, G., Tempst, P., Kurokawa, R., Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription (2008) Nature, 454, pp. 126-130
  • Washietl, S., Hofacker, I.L., Lukasser, M., Huttenhofer, A., Stadler, P.F., Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome (2005) Nat. Biotechnol, 23, pp. 1383-1390
  • Wernersson, R., Nielsen, H.B., OligoWiz 2.0-Integrating sequence feature annotation into the design of microarray probes (2005) Nucleic Acids Res, 33, pp. W611-W615
  • Xiong, L., Wang, R.G., Mao, G., Koczan, J.M., Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic acid (2006) Plant Physiol, 142, pp. 1065-1074
  • Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Nguyen, M., Empirical analysis of transcriptional activity in the Arabidopsis genome (2003) Science, 302, pp. 842-846
  • Yamashita, A., Watanabe, Y., Nukina, N., Yamamoto, M., RNA-assisted nuclear transport of the meiotic regulator Mei2p in fission yeast (1998) Cell, 95, pp. 115-123

Citas:

---------- APA ----------
Amor, B.B., Wirth, S., Merchan, F., Laporte, P., D'Aubenton-Carafa, Y., Hirsch, J., Maizel, A.,..., Crespi, M. (2009) . Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Research, 19(1), 57-69.
http://dx.doi.org/10.1101/gr.080275.108
---------- CHICAGO ----------
Amor, B.B., Wirth, S., Merchan, F., Laporte, P., D'Aubenton-Carafa, Y., Hirsch, J., et al. "Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses" . Genome Research 19, no. 1 (2009) : 57-69.
http://dx.doi.org/10.1101/gr.080275.108
---------- MLA ----------
Amor, B.B., Wirth, S., Merchan, F., Laporte, P., D'Aubenton-Carafa, Y., Hirsch, J., et al. "Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses" . Genome Research, vol. 19, no. 1, 2009, pp. 57-69.
http://dx.doi.org/10.1101/gr.080275.108
---------- VANCOUVER ----------
Amor, B.B., Wirth, S., Merchan, F., Laporte, P., D'Aubenton-Carafa, Y., Hirsch, J., et al. Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 2009;19(1):57-69.
http://dx.doi.org/10.1101/gr.080275.108