title: Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function.
abstract: BACKGROUND
  Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain regarding the features and biogenesis of nat-siRNAs.
  
  
  RESULTS
  Through deep sequencing, we identified more than 17,000 unique siRNAs corresponding to cis-NATs from biotic and abiotic stress-challenged Arabidopsis thaliana and 56,000 from abiotic stress-treated rice. These siRNAs were enriched in the overlapping regions of NATs and exhibited either site-specific or distributed patterns, often with strand bias. Out of 1,439 and 767 cis-NAT pairs identified in Arabidopsis and rice, respectively, 84 and 119 could generate at least 10 siRNAs per million reads from the overlapping regions. Among them, 16 cis-NAT pairs from Arabidopsis and 34 from rice gave rise to nat-siRNAs exclusively in the overlap regions. Genetic analysis showed that the overlapping double-stranded RNAs could be processed by Dicer-like 1 (DCL1) and/or DCL3. The DCL3-dependent nat-siRNAs were also dependent on RNA-dependent RNA polymerase 2 (RDR2) and plant-specific RNA polymerase IV (PolIV), whereas only a fraction of DCL1-dependent nat-siRNAs was RDR- and PolIV-dependent. Furthermore, the levels of some nat-siRNAs were regulated by specific biotic or abiotic stress conditions in Arabidopsis and rice.
  
  
  CONCLUSIONS
  Our results suggest that nat-siRNAs display distinct distribution patterns and are generated by DCL1 and/or DCL3. Our analysis further supported the existence of nat-siRNAs in plants and advanced our understanding of their characteristics.
authors.affiliation: Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Zhang
authors.forename: Jing
authors.initials: J
authors.lastname: Xia
authors.forename: Yifan E
authors.initials: YE
authors.lastname: Lii
authors.forename: Blanca E
authors.initials: BE
authors.lastname: Barrera-Figueroa
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Zhou
authors.forename: Shang
authors.initials: S
authors.lastname: Gao
authors.forename: Lu
authors.initials: L
authors.lastname: Lu
authors.forename: Dongdong
authors.initials: D
authors.lastname: Niu
authors.forename: Zheng
authors.initials: Z
authors.lastname: Chen
authors.forename: Christy
authors.initials: C
authors.lastname: Leung
authors.forename: Timothy
authors.initials: T
authors.lastname: Wong
authors.forename: Huiming
authors.initials: H
authors.lastname: Zhang
authors.forename: Jianhua
authors.initials: J
authors.lastname: Guo
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.forename: Renyi
authors.initials: R
authors.lastname: Liu
authors.forename: Wanqi
authors.initials: W
authors.lastname: Liang
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
authors.forename: Hailing
authors.initials: H
authors.lastname: Jin
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000235:genetics*; D034622:RNA Interference / Q000502:physiology; D012330:RNA, Double-Stranded / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D043244:Ribonuclease III / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D018797:Cell Cycle Proteins; D012330:RNA, Double-Stranded; D018749:RNA, Plant; D034741:RNA, Small Interfering; C499181:RNA polymerase IV, Arabidopsis; C519655:RDR2 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; D012321:DNA-Directed RNA Polymerases; C402383:DCL1 protein, Arabidopsis; C519654:DCL3 protein, Arabidopsis; D043244:Ribonuclease III