title: Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction.
abstract: BACKGROUND
  Viroids are circular, highly structured, non-protein-coding RNAs that, usurping cellular enzymes and escaping host defense mechanisms, are able to replicate and move through infected plants. Similarly to viruses, viroid infections are associated with the accumulation of viroid-derived 21-24 nt small RNAs (vd-sRNAs) with the typical features of the small interfering RNAs characteristic of RNA silencing, a sequence-specific mechanism involved in defense against invading nucleic acids and in regulation of gene expression in most eukaryotic organisms.
  
  
  RESULTS
  To gain further insights on the genesis and possible role of vd-sRNAs in plant-viroid interaction, sRNAs isolated from Vitis vinifera infected by Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1) were sequenced by the high-throughput platform Solexa-Illumina, and the vd-sRNAs were analyzed. The large majority of HSVd- and GYSVd1-sRNAs derived from a few specific regions (hotspots) of the genomic (+) and (-) viroid RNAs, with a prevalence of those from the (-) strands of both viroids. When grouped according to their sizes, vd-sRNAs always assumed a distribution with prominent 21-, 22- and 24-nt peaks, which, interestingly, mapped at the same hotspots.
  
  
  CONCLUSIONS
  These findings show that different Dicer-like enzymes (DCLs) target viroid RNAs, preferentially accessing to the same viroid domains. Interestingly, our results also suggest that viroid RNAs may interact with host enzymes involved in the RNA-directed DNA methylation pathway, indicating more complex scenarios than previously thought for both vd-sRNAs genesis and possible interference with host gene expression.
authors.affiliation: Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino and Bari, Italy.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Navarro
authors.forename: Vitantonio
authors.initials: V
authors.lastname: Pantaleo
authors.forename: Andreas
authors.initials: A
authors.lastname: Gisel
authors.forename: Simon
authors.initials: S
authors.lastname: Moxon
authors.forename: Tamas
authors.initials: T
authors.lastname: Dalmay
authors.forename: György
authors.initials: G
authors.lastname: Bisztray
authors.forename: Francesco
authors.initials: F
authors.lastname: Di Serio
authors.forename: József
authors.initials: J
authors.lastname: Burgyán
mesh_terms: D015152:Blotting, Northern; D017931:DNA Primers / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D008957:Models, Genetic; D009841:Oligonucleotides / Q000737:chemistry; D010935:Plant Diseases / Q000235:genetics / Q000821:virology; D010944:Plants / Q000235:genetics*; D034622:RNA Interference; D018749:RNA, Plant / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D014772:Viroids / Q000235:genetics*; D027843:Vitis / Q000235:genetics
chemical_list: D017931:DNA Primers; D035683:MicroRNAs; D009841:Oligonucleotides; D018749:RNA, Plant