Wang, A. (2015). Dissecting the Molecular Network of Virus-Plant Interactions: The Complex Roles of Host Factors. Annual Review of Phytopathology, 53(1), 45-66. doi:10.1146/annurev-phyto-080614-120001
Garcia‐Ruiz, H. (2019). Host factors against plant viruses. Molecular Plant Pathology, 20(11), 1588-1601. doi:10.1111/mpp.12851
Garcia-Ruiz, H. (2018). Susceptibility Genes to Plant Viruses. Viruses, 10(9), 484. doi:10.3390/v10090484
[+]
Wang, A. (2015). Dissecting the Molecular Network of Virus-Plant Interactions: The Complex Roles of Host Factors. Annual Review of Phytopathology, 53(1), 45-66. doi:10.1146/annurev-phyto-080614-120001
Garcia‐Ruiz, H. (2019). Host factors against plant viruses. Molecular Plant Pathology, 20(11), 1588-1601. doi:10.1111/mpp.12851
Garcia-Ruiz, H. (2018). Susceptibility Genes to Plant Viruses. Viruses, 10(9), 484. doi:10.3390/v10090484
Han, G. (2019). Origin and evolution of the plant immune system. New Phytologist, 222(1), 70-83. doi:10.1111/nph.15596
García, J. A., & Pallás, V. (2015). Viral factors involved in plant pathogenesis. Current Opinion in Virology, 11, 21-30. doi:10.1016/j.coviro.2015.01.001
Whitham, S. A., Yang, C., & Goodin, M. M. (2006). Global Impact: Elucidating Plant Responses to Viral Infection. Molecular Plant-Microbe Interactions®, 19(11), 1207-1215. doi:10.1094/mpmi-19-1207
Eichten, S. R., Schmitz, R. J., & Springer, N. M. (2014). Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation. Plant Physiology, 165(3), 933-947. doi:10.1104/pp.113.234211
Feng, S., Jacobsen, S. E., & Reik, W. (2010). Epigenetic Reprogramming in Plant and Animal Development. Science, 330(6004), 622-627. doi:10.1126/science.1190614
Matzke, M. A., Kanno, T., & Matzke, A. J. M. (2015). RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants. Annual Review of Plant Biology, 66(1), 243-267. doi:10.1146/annurev-arplant-043014-114633
Zhang, H., Lang, Z., & Zhu, J.-K. (2018). Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology, 19(8), 489-506. doi:10.1038/s41580-018-0016-z
Movahedi, A., Sun, W., Zhang, J., Wu, X., Mousavi, M., Mohammadi, K., … Zhuge, Q. (2015). RNA-directed DNA methylation in plants. Plant Cell Reports, 34(11), 1857-1862. doi:10.1007/s00299-015-1839-0
Matzke, M. A., & Mosher, R. A. (2014). RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Reviews Genetics, 15(6), 394-408. doi:10.1038/nrg3683
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
Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., & Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences, 104(16), 6752-6757. doi:10.1073/pnas.0701861104
Zhu, J.-K. (2009). Active DNA Demethylation Mediated by DNA Glycosylases. Annual Review of Genetics, 43(1), 143-166. doi:10.1146/annurev-genet-102108-134205
Baulcombe, D. C., & Dean, C. (2014). Epigenetic Regulation in Plant Responses to the Environment. Cold Spring Harbor Perspectives in Biology, 6(9), a019471-a019471. doi:10.1101/cshperspect.a019471
Ding, B., & Wang, G.-L. (2015). Chromatin versus pathogens: the function of epigenetics in plant immunity. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00675
Butterbach, P., Verlaan, M. G., Dullemans, A., Lohuis, D., Visser, R. G. F., Bai, Y., & Kormelink, R. (2014). Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection. Proceedings of the National Academy of Sciences, 111(35), 12942-12947. doi:10.1073/pnas.1400894111
Raja, P., Sanville, B. C., Buchmann, R. C., & Bisaro, D. M. (2008). Viral Genome Methylation as an Epigenetic Defense against Geminiviruses. Journal of Virology, 82(18), 8997-9007. doi:10.1128/jvi.00719-08
Yang, L.-P., Fang, Y.-Y., An, C.-P., Dong, L., Zhang, Z.-H., Chen, H., … Guo, H.-S. (2013). C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with beet severe curly top virus. The Plant Journal, 73(6), 910-917. doi:10.1111/tpj.12081
Kanazawa, A., Inaba, J., Shimura, H., Otagaki, S., Tsukahara, S., Matsuzawa, A., … Masuta, C. (2010). Virus-mediated efficient induction of epigenetic modifications of endogenous genes with phenotypic changes in plants. The Plant Journal, 65(1), 156-168. doi:10.1111/j.1365-313x.2010.04401.x
Kon, T., & Yoshikawa, N. (2014). Induction and maintenance of DNA methylation in plant promoter sequences by apple latent spherical virus-induced transcriptional gene silencing. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00595
Otagaki, S., Kawai, M., Masuta, C., & Kanazawa, A. (2011). Size and positional effects of promoter RNA segments on virus-induced RNA-directed DNA methylation and transcriptional gene silencing. Epigenetics, 6(6), 681-691. doi:10.4161/epi.6.6.16214
Diezma‐Navas, L., Pérez‐González, A., Artaza, H., Alonso, L., Caro, E., Llave, C., & Ruiz‐Ferrer, V. (2019). Crosstalk between epigenetic silencing and infection by tobacco rattle virus in
Arabidopsis. Molecular Plant Pathology, 20(10), 1439-1452. doi:10.1111/mpp.12850
Wang, C., Wang, C., Xu, W., Zou, J., Qiu, Y., Kong, J., … Zhu, S. (2018). Epigenetic Changes in the Regulation of Nicotiana tabacum Response to Cucumber Mosaic Virus Infection and Symptom Recovery through Single-Base Resolution Methylomes. Viruses, 10(8), 402. doi:10.3390/v10080402
Wang, C., Wang, C., Zou, J., Yang, Y., Li, Z., & Zhu, S. (2019). Epigenetics in the plant–virus interaction. Plant Cell Reports, 38(9), 1031-1038. doi:10.1007/s00299-019-02414-0
Scheets, K., Jordan, R., White, K. A., & Hernández, C. (2015). Pelarspovirus, a proposed new genus in the family Tombusviridae. Archives of Virology, 160(9), 2385-2393. doi:10.1007/s00705-015-2500-5
Castaño, A., & Hernández, C. (2005). Complete nucleotide sequence and genome organization of Pelargonium line pattern virus and its relationship with the family Tombusviridae. Archives of Virology, 150(5), 949-965. doi:10.1007/s00705-004-0464-y
Castaño, A., Ruiz, L., & Hernández, C. (2009). Insights into the translational regulation of biologically active open reading frames of Pelargonium line pattern virus. Virology, 386(2), 417-426. doi:10.1016/j.virol.2009.01.017
Pérez-Cañamás, M., & Hernández, C. (2015). Key Importance of Small RNA Binding for the Activity of a Glycine-Tryptophan (GW) Motif-containing Viral Suppressor of RNA Silencing. Journal of Biological Chemistry, 290(5), 3106-3120. doi:10.1074/jbc.m114.593707
Alonso, M., & Borja, M. (2005). High incidence of Pelargonium line pattern virus infecting asymptomatic Pelargonium spp. in Spain. European Journal of Plant Pathology, 112(2), 95-100. doi:10.1007/s10658-005-0803-1
Ivars, P., Alonso, M., Borja, M., & Hernández, C. (2004). Development of a Non-radioactive Dot-blot Hybridisation Assay for the Detection of Pelargonium Flower Break Virus and Pelargonium line Pattern Virus. European Journal of Plant Pathology, 110(3), 275-283. doi:10.1023/b:ejpp.0000019798.87567.22
Pérez-Cañamás, M., Blanco-Pérez, M., Forment, J., & Hernández, C. (2017). Nicotiana benthamiana plants asymptomatically infected by Pelargonium line pattern virus show unusually high accumulation of viral small RNAs that is neither associated with DCL induction nor RDR6 activity. Virology, 501, 136-146. doi:10.1016/j.virol.2016.11.018
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
Blanco-Pérez, M., & Hernández, C. (2016). Evidence supporting a premature termination mechanism for subgenomic RNA transcription in Pelargonium line pattern virus: identification of a critical long-range RNA–RNA interaction and functional variants through mutagenesis. Journal of General Virology, 97(6), 1469-1480. doi:10.1099/jgv.0.000459
Pérez-Cañamás, M., & Hernández, C. (2018). New Insights into the Nucleolar Localization of a Plant RNA Virus-Encoded Protein That Acts in Both RNA Packaging and RNA Silencing Suppression: Involvement of Importins Alpha and Relevance for Viral Infection. Molecular Plant-Microbe Interactions®, 31(11), 1134-1144. doi:10.1094/mpmi-02-18-0050-r
Li, L.-C., & Dahiya, R. (2002). MethPrimer: designing primers for methylation PCRs. Bioinformatics, 18(11), 1427-1431. doi:10.1093/bioinformatics/18.11.1427
Hetzl, J., Foerster, A. M., Raidl, G., & Scheid, O. M. (2007). CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. The Plant Journal, 51(3), 526-536. doi:10.1111/j.1365-313x.2007.03152.x
Liu, D., Shi, L., Han, C., Yu, J., Li, D., & Zhang, Y. (2012). Validation of Reference Genes for Gene Expression Studies in Virus-Infected Nicotiana benthamiana Using Quantitative Real-Time PCR. PLoS ONE, 7(9), e46451. doi:10.1371/journal.pone.0046451
McStay, B., & Grummt, I. (2008). The Epigenetics of rRNA Genes: From Molecular to Chromosome Biology. Annual Review of Cell and Developmental Biology, 24(1), 131-157. doi:10.1146/annurev.cellbio.24.110707.175259
Pikaard, C. S. (2000). The epigenetics of nucleolar dominance. Trends in Genetics, 16(11), 495-500. doi:10.1016/s0168-9525(00)02113-2
Buchmann, R. C., Asad, S., Wolf, J. N., Mohannath, G., & Bisaro, D. M. (2009). Geminivirus AL2 and L2 Proteins Suppress Transcriptional Gene Silencing and Cause Genome-Wide Reductions in Cytosine Methylation. Journal of Virology, 83(10), 5005-5013. doi:10.1128/jvi.01771-08
Rodríguez‐Negrete, E., Lozano‐Durán, R., Piedra‐Aguilera, A., Cruzado, L., Bejarano, E. R., & Castillo, A. G. (2013). Geminivirus
R
ep protein interferes with the plant
DNA
methylation machinery and suppresses transcriptional gene silencing. New Phytologist, 199(2), 464-475. doi:10.1111/nph.12286
Yang, L., Xu, Y., Liu, Y., Meng, D., Jin, T., & Zhou, X. (2016). HC-Pro viral suppressor from tobacco vein banding mosaic virus interferes with DNA methylation and activates the salicylic acid pathway. Virology, 497, 244-250. doi:10.1016/j.virol.2016.07.024
Alonso, C., Ramos‐Cruz, D., & Becker, C. (2018). The role of plant epigenetics in biotic interactions. New Phytologist, 221(2), 731-737. doi:10.1111/nph.15408
Sáez-Vásquez, J., & Delseny, M. (2019). Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors. The Plant Cell, 31(9), 1945-1967. doi:10.1105/tpc.18.00874
Jan, E., Mohr, I., & Walsh, D. (2016). A Cap-to-Tail Guide to mRNA Translation Strategies in Virus-Infected Cells. Annual Review of Virology, 3(1), 283-307. doi:10.1146/annurev-virology-100114-055014
Cao, M., Du, P., Wang, X., Yu, Y.-Q., Qiu, Y.-H., Li, W., … Ding, S.-W. (2014). Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs inArabidopsis. Proceedings of the National Academy of Sciences, 111(40), 14613-14618. doi:10.1073/pnas.1407131111
Martinez, G., Castellano, M., Tortosa, M., Pallas, V., & Gomez, G. (2013). A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants. Nucleic Acids Research, 42(3), 1553-1562. doi:10.1093/nar/gkt968
Csorba, T., Kontra, L., & Burgyán, J. (2015). viral silencing suppressors: Tools forged to fine-tune host-pathogen coexistence. Virology, 479-480, 85-103. doi:10.1016/j.virol.2015.02.028
Deleris, A., Halter, T., & Navarro, L. (2016). DNA Methylation and Demethylation in Plant Immunity. Annual Review of Phytopathology, 54(1), 579-603. doi:10.1146/annurev-phyto-080615-100308
Le, T.-N., Schumann, U., Smith, N. A., Tiwari, S., Au, P. C. K., Zhu, Q.-H., … Wang, M.-B. (2014). DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biology, 15(9). doi:10.1186/s13059-014-0458-3
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
Palukaitis, P., & García-Arenal, F. (2003). Cucumoviruses. Advances in Virus Research, 241-323. doi:10.1016/s0065-3527(03)62005-1
Ratcliff, F., Martin-Hernandez, A. M., & Baulcombe, D. C. (2008). Technical Advance: Tobacco rattle virus as a vector for analysis of gene function by silencing. The Plant Journal, 25(2), 237-245. doi:10.1046/j.0960-7412.2000.00942.x
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