Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia

BMC Genomics

Research Article

Hideo Matsumura¹  Akito Taneda²  Ryohei Terauchi³  Kentaro Yoshida³  Megumi Kasai⁴  Akira Kanazawa⁴ 

[1] Gene Research Center, Shinshu University, 386-8567, Ueda, Japan;Graduate School of Science and Technology, Hirosaki University, 036-8561, Hirosaki, Aomori, Japan;Iwate Biotechnology Research Center, 024-0003, Kitakami, Japan;Research Faculty of Agriculture, Hokkaido University, 060-8589, Sapporo, Japan;

关键词: Chalcone synthase;    Cosuppression;    Deep-sequencing analysis;    Flower color pattern;    Naturally occurring RNA silencing;    Short interfering RNA;   

DOI  :  10.1186/1471-2164-14-63

 received in 2012-11-01, accepted in 2013-01-22,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundIntroduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties. Although the mechanism by which white sectors are generated in nontransgenic petunia is known to be due to RNA silencing of the CHS-A gene as in cosuppression, whether the same trigger(s) and/or pattern of RNA degradation are involved in these phenomena has not been known. Here, we addressed this question using deep-sequencing and bioinformatic analyses of small RNAs.ResultsWe analyzed short interfering RNAs (siRNAs) produced in nonpigmented sectors of petal tissues in transgenic petunia plants that have CHS-A cosuppression and a nontransgenic petunia variety Red Star, that has naturally occurring CHS-A RNA silencing. In both silencing systems, 21-nt and 22-nt siRNAs were the most and the second-most abundant size classes, respectively. CHS-A siRNA production was confined to exon 2, indicating that RNA degradation through the RNA silencing pathway occurred in this exon. Common siRNAs were detected in cosuppression and naturally occurring RNA silencing, and their ranks based on the number of siRNAs in these plants were correlated with each other. Noticeably, highly abundant siRNAs were common in these systems. Phased siRNAs were detected in multiple phases at multiple sites, and some of the ends of the regions that produced phased siRNAs were conserved.ConclusionsThe features of siRNA production found to be common to cosuppression and naturally occurring silencing of the CHS-A gene indicate mechanistic similarities between these silencing systems especially in the biosynthetic processes of siRNAs including cleavage of CHS-A transcripts and subsequent production of secondary siRNAs in exon 2. The data also suggest that these events occurred at multiple sites, which can be a feature of these silencing phenomena.

【 授权许可】

Unknown   
© Kasai et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.