title: Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa.
abstract: Natural antisense transcripts (NATs) have been shown to play important roles in post-transcriptional regulation through the RNA interference pathway. We have combined pyrophosphate-based high-throughput sequencing and computational analysis to identify and analyze, in genome scale, cis-NAT and trans-NAT small RNAs that are derived under normal conditions and in response to drought and salt stresses in the staple plant Oryza sativa. Computationally, we identified 344 cis-NATs and 7,142 trans-NATs that are formed by protein-coding genes. From the deep sequencing data, we found 108 cis-NATs and 7,141 trans-NATs that gave rise to small RNAs from their overlapping regions. Consistent with early findings, the majority of these 108 cis-NATs seem to be associated with specific conditions or developmental stages. Our analyses also revealed several interesting results. The overlapping regions of the cis-NATs and trans-NATs appear to be more enriched with small RNA loci than non-overlapping regions. The small RNAs generated from cis-NATs and trans-NATs have a length bias of 21 nt, even though their lengths spread over a large range. Furthermore, >40% of the small RNAs from cis-NATs and trans-NATs carry an A as their 5'-terminal nucleotides. A substantial portion of the transcripts are involved in both cis-NATs and trans-NATs, and many trans-NATs can form many-to-many relationships, indicating that NATs may form complex regulatory networks in O. sativa. This study is the first genome-wide investigation of NAT-derived small RNAs in O. sativa. It reveals the importance of NATs in biogenesis of small RNAs and broadens our understanding of the roles of NAT-derived small RNAs in gene regulation, particularly in response to environmental stimuli.
authors.affiliation: Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, USA.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Zhou
authors.forename: Ramanjulu
authors.initials: R
authors.lastname: Sunkar
authors.forename: Hailing
authors.initials: H
authors.lastname: Jin
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
mesh_terms: D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D034622:RNA Interference; D018749:RNA, Plant / Q000032:analysis / Q000235:genetics*; D034741:RNA, Small Interfering / Q000032:analysis / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D018749:RNA, Plant; D034741:RNA, Small Interfering