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Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function
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, m...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439971/ https://www.ncbi.nlm.nih.gov/pubmed/22439910 http://dx.doi.org/10.1186/gb-2012-13-3-r20 |
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author | Zhang, Xiaoming Xia, Jing Lii, Yifan E Barrera-Figueroa, Blanca E Zhou, Xuefeng Gao, Shang Lu, Lu Niu, Dongdong Chen, Zheng Leung, Christy Wong, Timothy Zhang, Huiming Guo, Jianhua Li, Yi Liu, Renyi Liang, Wanqi Zhu, Jian-Kang Zhang, Weixiong Jin, Hailing |
author_facet | Zhang, Xiaoming Xia, Jing Lii, Yifan E Barrera-Figueroa, Blanca E Zhou, Xuefeng Gao, Shang Lu, Lu Niu, Dongdong Chen, Zheng Leung, Christy Wong, Timothy Zhang, Huiming Guo, Jianhua Li, Yi Liu, Renyi Liang, Wanqi Zhu, Jian-Kang Zhang, Weixiong Jin, Hailing |
author_sort | Zhang, Xiaoming |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3439971 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34399712012-09-13 Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function Zhang, Xiaoming Xia, Jing Lii, Yifan E Barrera-Figueroa, Blanca E Zhou, Xuefeng Gao, Shang Lu, Lu Niu, Dongdong Chen, Zheng Leung, Christy Wong, Timothy Zhang, Huiming Guo, Jianhua Li, Yi Liu, Renyi Liang, Wanqi Zhu, Jian-Kang Zhang, Weixiong Jin, Hailing Genome Biol Research 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. BioMed Central 2012-03-22 /pmc/articles/PMC3439971/ /pubmed/22439910 http://dx.doi.org/10.1186/gb-2012-13-3-r20 Text en Copyright © 2012 Zhang et al.; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Zhang, Xiaoming Xia, Jing Lii, Yifan E Barrera-Figueroa, Blanca E Zhou, Xuefeng Gao, Shang Lu, Lu Niu, Dongdong Chen, Zheng Leung, Christy Wong, Timothy Zhang, Huiming Guo, Jianhua Li, Yi Liu, Renyi Liang, Wanqi Zhu, Jian-Kang Zhang, Weixiong Jin, Hailing Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function |
title | Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function |
title_full | Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function |
title_fullStr | Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function |
title_full_unstemmed | Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function |
title_short | Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function |
title_sort | genome-wide analysis of plant nat-sirnas reveals insights into their distribution, biogenesis and function |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439971/ https://www.ncbi.nlm.nih.gov/pubmed/22439910 http://dx.doi.org/10.1186/gb-2012-13-3-r20 |
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