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Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

Xiaoming Zhang1, Jing Xia2, Yifan E Lii1, Blanca E Barrera-Figueroa34, Xuefeng Zhou2, Shang Gao1, Lu Lu15, Dongdong Niu16, Zheng Chen2, Christy Leung1, Timothy Wong1, Huiming Zhang7, Jianhua Guo16, Yi Li5, Renyi Liu3, Wanqi Liang8, Jian-Kang Zhu7, Weixiong Zhang29* and Hailing Jin1*

Author affiliations

1 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA

2 Department of Computer Science and Engineering, Washington University in St Louis, St Louis, MO 63130, USA

3 Department of Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA

4 Instituto de Biotecnologia, Universidad del Papaloapan, Tuxtepec Oaxaca 68301, Mexico

5 Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China

6 Department of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China

7 Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA

8 School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China

9 Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA

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Citation and License

Genome Biology 2012, 13:R20  doi:10.1186/gb-2012-13-3-r20

Published: 22 March 2012

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.