Ding, B. (2009). The Biology of Viroid-Host Interactions. Annual Review of Phytopathology, 47(1), 105-131. doi:10.1146/annurev-phyto-080508-081927
Ding, B. (2010). Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs. Wiley Interdisciplinary Reviews: RNA, 1(3), 362-375. doi:10.1002/wrna.22
Navarro, B., Gisel, A., Rodio, M.-E., Delgado, S., Flores, R., & Di Serio, F. (2012). Viroids: How to infect a host and cause disease without encoding proteins. Biochimie, 94(7), 1474-1480. doi:10.1016/j.biochi.2012.02.020
[+]
Ding, B. (2009). The Biology of Viroid-Host Interactions. Annual Review of Phytopathology, 47(1), 105-131. doi:10.1146/annurev-phyto-080508-081927
Ding, B. (2010). Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs. Wiley Interdisciplinary Reviews: RNA, 1(3), 362-375. doi:10.1002/wrna.22
Navarro, B., Gisel, A., Rodio, M.-E., Delgado, S., Flores, R., & Di Serio, F. (2012). Viroids: How to infect a host and cause disease without encoding proteins. Biochimie, 94(7), 1474-1480. doi:10.1016/j.biochi.2012.02.020
Zhao, Y., Hammond, R. W., & Owens, R. A. (2001). Use of a vector based on Potato virus X in a whole plant assay to demonstrate nuclear targeting of Potato spindle tuber viroid. Journal of General Virology, 82(6), 1491-1497. doi:10.1099/0022-1317-82-6-1491
Gómez, G., & Pallas, V. (2012). Studies on Subcellular Compartmentalization of Plant Pathogenic Noncoding RNAs Give New Insights into the Intracellular RNA-Traffic Mechanisms. Plant Physiology, 159(2), 558-564. doi:10.1104/pp.112.195214
Navarro, J.-A., Vera, A., & Flores, R. (2000). A Chloroplastic RNA Polymerase Resistant to Tagetitoxin Is Involved in Replication of Avocado Sunblotch Viroid. Virology, 268(1), 218-225. doi:10.1006/viro.1999.0161
Nohales, M.-A., Flores, R., & Daros, J.-A. (2012). Viroid RNA redirects host DNA ligase 1 to act as an RNA ligase. Proceedings of the National Academy of Sciences, 109(34), 13805-13810. doi:10.1073/pnas.1206187109
Nohales, M.-A., Molina-Serrano, D., Flores, R., & Daros, J.-A. (2012). Involvement of the Chloroplastic Isoform of tRNA Ligase in the Replication of Viroids Belonging to the Family Avsunviroidae. Journal of Virology, 86(15), 8269-8276. doi:10.1128/jvi.00629-12
Zhong, X., & Ding, B. (2008). Distinct RNA motifs mediate systemic RNA trafficking. Plant Signaling & Behavior, 3(1), 58-59. doi:10.4161/psb.3.1.4890
Gomez, G., & Pallas, V. (2004). A Long-Distance Translocatable Phloem Protein from Cucumber Forms a Ribonucleoprotein Complex In Vivo with Hop Stunt Viroid RNA. Journal of Virology, 78(18), 10104-10110. doi:10.1128/jvi.78.18.10104-10110.2004
Gómez, G., & Pallás, V. (2001). Identification of an In Vitro Ribonucleoprotein Complex Between a Viroid RNA and a Phloem Protein from Cucumber Plants. Molecular Plant-Microbe Interactions, 14(7), 910-913. doi:10.1094/mpmi.2001.14.7.910
Owens, R. A., Blackburn, M., & Ding, B. (2001). Possible Involvement of the Phloem Lectin in Long-Distance Viroid Movement. Molecular Plant-Microbe Interactions, 14(7), 905-909. doi:10.1094/mpmi.2001.14.7.905
Gómez, G., & Pallás, V. (2013). Viroids: a light in the darkness of thelncRNA-directed regulatory networks in plants. New Phytologist, 198(1), 10-15. doi:10.1111/nph.12196
Diener, T. O. (1981). Are viroids escaped introns? Proceedings of the National Academy of Sciences, 78(8), 5014-5015. doi:10.1073/pnas.78.8.5014
Haas, B., Klanner, A., Ramm, K., & Sänger, H. L. (1988). The 7S RNA from tomato leaf tissue resembles a signal recognition particle RNA and exhibits a remarkable sequence complementarity to viroids. The EMBO Journal, 7(13), 4063-4074. doi:10.1002/j.1460-2075.1988.tb03300.x
Visvader, J. E., & Symons, R. H. (1985). Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity. Nucleic Acids Research, 13(8), 2907-2920. doi:10.1093/nar/13.8.2907
Schnölzer, M., Haas, B., Ramm, K., Hofmann, H., & Sänger, H. L. (1985). Correlation between structure and pathogenicity of potato spindle tuber viroid (PSTV). The EMBO Journal, 4(9), 2181-2190. doi:10.1002/j.1460-2075.1985.tb03913.x
Papaefthimiou, I. (2001). Replicating potato spindle tuber viroid RNA is accompanied by short RNA fragments that are characteristic of post-transcriptional gene silencing. Nucleic Acids Research, 29(11), 2395-2400. doi:10.1093/nar/29.11.2395
Wang, M.-B., Bian, X.-Y., Wu, L.-M., Liu, L.-X., Smith, N. A., Isenegger, D., … Waterhouse, P. M. (2004). On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proceedings of the National Academy of Sciences, 101(9), 3275-3280. doi:10.1073/pnas.0400104101
Gómez, G., Martínez, G., & Pallás, V. (2009). Interplay between viroid-induced pathogenesis and RNA silencing pathways. Trends in Plant Science, 14(5), 264-269. doi:10.1016/j.tplants.2009.03.002
Gómez, G., Martínez, G., & Pallás, V. (2008). Viroid-Induced Symptoms in Nicotiana benthamiana Plants Are Dependent on RDR6 Activity. Plant Physiology, 148(1), 414-423. doi:10.1104/pp.108.120808
Navarro, B., Gisel, A., Rodio, M. E., Delgado, S., Flores, R., & Di Serio, F. (2012). Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. The Plant Journal, 70(6), 991-1003. doi:10.1111/j.1365-313x.2012.04940.x
Dowen, R. H., Pelizzola, M., Schmitz, R. J., Lister, R., Dowen, J. M., Nery, J. R., … Ecker, J. R. (2012). Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences, 109(32), E2183-E2191. doi:10.1073/pnas.1209329109
Law, J. A., & Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics, 11(3), 204-220. doi:10.1038/nrg2719
Matzke, M., Kanno, T., Daxinger, L., Huettel, B., & Matzke, A. J. (2009). RNA-mediated chromatin-based silencing in plants. Current Opinion in Cell Biology, 21(3), 367-376. doi:10.1016/j.ceb.2009.01.025
Zhang, X., Henderson, I. R., Lu, C., Green, P. J., & Jacobsen, S. E. (2007). Role of RNA polymerase IV in plant small RNA metabolism. Proceedings of the National Academy of Sciences, 104(11), 4536-4541. doi:10.1073/pnas.0611456104
Haag, J. R., & Pikaard, C. S. (2011). Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nature Reviews Molecular Cell Biology, 12(8), 483-492. doi:10.1038/nrm3152
Gong, Z., Morales-Ruiz, T., Ariza, R. R., Roldán-Arjona, T., David, L., & Zhu, J.-K. (2002). ROS1, a Repressor of Transcriptional Gene Silencing in Arabidopsis, Encodes a DNA Glycosylase/Lyase. Cell, 111(6), 803-814. doi:10.1016/s0092-8674(02)01133-9
Nuthikattu, S., McCue, A. D., Panda, K., Fultz, D., DeFraia, C., Thomas, E. N., & Slotkin, R. K. (2013). The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs. Plant Physiology, 162(1), 116-131. doi:10.1104/pp.113.216481
Wassenegger, M., Heimes, S., Riedel, L., & Sänger, H. L. (1994). RNA-directed de novo methylation of genomic sequences in plants. Cell, 76(3), 567-576. doi:10.1016/0092-8674(94)90119-8
Itaya, A., Matsuda, Y., Gonzales, R. A., Nelson, R. S., & Ding, B. (2002). Potato spindle tuber viroidStrains of Different Pathogenicity Induces and Suppresses Expression of Common and Unique Genes in Infected Tomato. Molecular Plant-Microbe Interactions, 15(10), 990-999. doi:10.1094/mpmi.2002.15.10.990
Owens, R. A., Tech, K. B., Shao, J. Y., Sano, T., & Baker, C. J. (2012). Global Analysis of Tomato Gene Expression DuringPotato spindle tuber viroidInfection Reveals a Complex Array of Changes Affecting Hormone Signaling. Molecular Plant-Microbe Interactions, 25(4), 582-598. doi:10.1094/mpmi-09-11-0258
Tessitori, M., Maria, G., Capasso, C., Catara, G., Rizza, S., De Luca, V., … Carginale, V. (2007). Differential display analysis of gene expression in Etrog citron leaves infected by Citrus viroid III. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1769(4), 228-235. doi:10.1016/j.bbaexp.2007.03.004
Herranz, M. C., Niehl, A., Rosales, M., Fiore, N., Zamorano, A., Granell, A., & Pallas, V. (2013). A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid. Virology Journal, 10(1). doi:10.1186/1743-422x-10-164
Lisón, P., Tárraga, S., López-Gresa, P., Saurí, A., Torres, C., Campos, L., … Rodrigo, I. (2013). A noncoding plant pathogen provokes both transcriptional and posttranscriptional alterations in tomato. PROTEOMICS, 13(5), 833-844. doi:10.1002/pmic.201200286
GÓMEZ, G., & PALLÁS, V. (2006). Hop stunt viroid is processed and translocated in transgenic Nicotiana benthamiana plants. Molecular Plant Pathology, 7(6), 511-517. doi:10.1111/j.1364-3703.2006.00356.x
MARTINEZ, G., DONAIRE, L., LLAVE, C., PALLAS, V., & GOMEZ, G. (2010). High-throughput sequencing ofHop stunt viroid-derived small RNAs from cucumber leaves and phloem. Molecular Plant Pathology, 11(3), 347-359. doi:10.1111/j.1364-3703.2009.00608.x
Pallas, V., Navarro, A., & Flores, R. (1987). Isolation of a Viroid-like RNA from Hop Different from Hop Stunt Viroid. Journal of General Virology, 68(12), 3201-3205. doi:10.1099/0022-1317-68-12-3201
Gómez, G., & Pallás, V. (2007). Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants. The Plant Journal, 51(6), 1041-1049. doi:10.1111/j.1365-313x.2007.03203.x
Dellaporta, S. L., Wood, J., & Hicks, J. B. (1983). A plant DNA minipreparation: Version II. Plant Molecular Biology Reporter, 1(4), 19-21. doi:10.1007/bf02712670
Martínez, G., Forment, J., Llave, C., Pallás, V., & Gómez, G. (2011). High-Throughput Sequencing, Characterization and Detection of New and Conserved Cucumber miRNAs. PLoS ONE, 6(5), e19523. doi:10.1371/journal.pone.0019523
Long, E. O., & Dawid, I. B. (1980). Repeated Genes in Eukaryotes. Annual Review of Biochemistry, 49(1), 727-764. doi:10.1146/annurev.bi.49.070180.003455
Henras, A. K., Soudet, J., Gérus, M., Lebaron, S., Caizergues-Ferrer, M., Mougin, A., & Henry, Y. (2008). The post-transcriptional steps of eukaryotic ribosome biogenesis. Cellular and Molecular Life Sciences, 65(15), 2334-2359. doi:10.1007/s00018-008-8027-0
Pontvianne, F., Blevins, T., Chandrasekhara, C., Feng, W., Stroud, H., Jacobsen, S. E., … Pikaard, C. S. (2012). Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes & Development, 26(9), 945-957. doi:10.1101/gad.182865.111
Preuss, S., & Pikaard, C. S. (2007). rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1769(5-6), 383-392. doi:10.1016/j.bbaexp.2007.02.005
Earley, K. W., Pontvianne, F., Wierzbicki, A. T., Blevins, T., Tucker, S., Costa-Nunes, P., … Pikaard, C. S. (2010). Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation. Genes & Development, 24(11), 1119-1132. doi:10.1101/gad.1914110
Tucker, S., Vitins, A., & Pikaard, C. S. (2010). Nucleolar dominance and ribosomal RNA gene silencing. Current Opinion in Cell Biology, 22(3), 351-356. doi:10.1016/j.ceb.2010.03.009
Layat, E., Cotterell, S., Vaillant, I., Yukawa, Y., Tutois, S., & Tourmente, S. (2012). Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA control 5S rRNA accumulation during Arabidopsis thaliana development. The Plant Journal, 71(1), 35-44. doi:10.1111/j.1365-313x.2012.04948.x
Rodio, M.-E., Delgado, S., De Stradis, A., Gómez, M.-D., Flores, R., & Di Serio, F. (2007). A Viroid RNA with a Specific Structural Motif Inhibits Chloroplast Development. The Plant Cell, 19(11), 3610-3626. doi:10.1105/tpc.106.049775
Yu, A., Lepere, G., Jay, F., Wang, J., Bapaume, L., Wang, Y., … Navarro, L. (2013). Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proceedings of the National Academy of Sciences, 110(6), 2389-2394. doi:10.1073/pnas.1211757110
Sha, A. H., Lin, X. H., Huang, J. B., & Zhang, D. P. (2005). Analysis of DNA methylation related to rice adult plant resistance to bacterial blight based on methylation-sensitive AFLP (MSAP) analysis. Molecular Genetics and Genomics, 273(6), 484-490. doi:10.1007/s00438-005-1148-3
Boyko, A., Kathiria, P., Zemp, F. J., Yao, Y., Pogribny, I., & Kovalchuk, I. (2007). Transgenerational changes in the genome stability and methylation in pathogen-infected plants. Nucleic Acids Research, 35(5), 1714-1725. doi:10.1093/nar/gkm029
Rodríguez-Negrete, E., Lozano-Durán, R., Piedra-Aguilera, A., Cruzado, L., Bejarano, E. R., & Castillo, A. G. (2013). Geminivirus Rep protein interferes with the plant DNA methylation machinery and suppresses transcriptional gene silencing. New Phytologist, 199(2), 464-475. doi:10.1111/nph.12286
Vaillant, I., Tutois, S., Cuvillier, C., Schubert, I., & Tourmente, S. (2007). Regulation of Arabidopsis thaliana 5S rRNA Genes. Plant and Cell Physiology, 48(5), 745-752. doi:10.1093/pcp/pcm043
MÜHLBACH, H.-P., & SÄNGER, H. L. (1979). Viroid replication is inhibited by α-amanitin. Nature, 278(5700), 185-188. doi:10.1038/278185a0
Li, L.-C., & Dahiya, R. (2002). MethPrimer: designing primers for methylation PCRs. Bioinformatics, 18(11), 1427-1431. doi:10.1093/bioinformatics/18.11.1427
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