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. 2009 Jan;19(1):70-8.
doi: 10.1101/gr.084806.108. Epub 2008 Oct 29.

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

Xuefeng Zhou  1 , Ramanjulu Sunkar, Hailing Jin, Jian-Kang Zhu, Weixiong Zhang
Affiliations

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

Xuefeng Zhou et al. Genome Res. 2009 Jan.

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.

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Figures

Figure 1.
Figure 1.
Distribution of the first nucleotide of small RNAs generated from cis-NATs and trans-NATs.
Figure 2.
Figure 2.
Distribution of the lengths of small RNAs generated from cis-NATs and trans-NATs.
Figure 3.
Figure 3.
One transcript may form trans-NATs with multiple antisense transcripts. The network formed by these NATs shows a star structure. (A) The positions where the NATs are formed; (B) the annotations of genes that are involved in the NATs.
Figure 4.
Figure 4.
Many-to-many relationship in trans-NAT networks with bipartite structures. Two examples of trans-NAT networks with bipartite structure and the GO annotations of the genes involved in these two networks are shown.
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