Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa

  1. Xuefeng Zhou1,
  2. Ramanjulu Sunkar2,
  3. Hailing Jin3,
  4. Jian-Kang Zhu4 and
  5. Weixiong Zhang1,5,6
  1. 1 Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, USA;
  2. 2 Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA;
  3. 3 Department of Plant Pathology and Department of Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA;
  4. 4 Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA;
  5. 5 Department of Genetics, Washington University in St. Louis, Saint Louis, Missouri 63130-4899, USA

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 7142 trans-NATs that are formed by protein-coding genes. From the deep sequencing data, we found 108 cis-NATs and 7141 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.

Footnotes

  • 6 Corresponding author.

    E-mail zhang{at}cse.wustl.edu; fax (314) 935-7302.

  • [Supplemental material is available online at www.genome.org. The small-RNA sequence data from this study have been submitted to NCBI Gene Expression Omnibus (http:www.ncbi.nlm.nih.gov/geo/) under accession no. GSE12317.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.084806.108.

    • Received August 15, 2008.
    • Accepted October 16, 2008.
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