title: Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.
abstract: BACKGROUND
  Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs.
  
  
  RESULTS
  We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa). Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks.
  
  
  CONCLUSIONS
  Our study profiles an abundance of cis-NATs and nat-siRNAs in rice. These data are valuable for gaining insight into the complex function of the rice transcriptome.
authors.affiliation: National Center for Gene Research & Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China. ttlu@ncgr.ac.cn
authors.forename: Tingting
authors.initials: T
authors.lastname: Lu
authors.forename: Chuanrang
authors.initials: C
authors.lastname: Zhu
authors.forename: Guojun
authors.initials: G
authors.lastname: Lu
authors.forename: Yunli
authors.initials: Y
authors.lastname: Guo
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Zhang
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Wenjun
authors.initials: W
authors.lastname: Li
authors.forename: Ying
authors.initials: Y
authors.lastname: Lu
authors.forename: Weihua
authors.initials: W
authors.lastname: Tang
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern; D017931:DNA Primers / Q000235:genetics; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D061346:Laser Capture Microdissection; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059467:Transcriptome / Q000235:genetics*
chemical_list: D017931:DNA Primers; D034741:RNA, Small Interfering