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Open Access Highly Accessed Research article

Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars

Chao Liang1, Xuan Liu2, Yuzhe Sun1, Siu-Ming Yiu2 and Boon Leong Lim13*

  • * Corresponding author: Boon L Lim bllim@hku.hk

  • † Equal contributors

Author Affiliations

1 School of Biological Sciences, the University of Hong Kong, Pokfulam, Hong Kong, China

2 Department of Computer Science, the University of Hong Kong, Pokfulam, Hong Kong, China

3 State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China

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BMC Genomics 2014, 15:116  doi:10.1186/1471-2164-15-116

Published: 10 February 2014

Abstract

Background

In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) and trans-acting siRNAs (tasiRNAs) biogenesis were significantly changed in the fast-growing lines. In this study, the sRNA profiles of the leaf and the root of 20-day-old plants were sequenced and the impacts of high energy status on sRNA expression were analyzed.

Results

9-13 million reads from each library were mapped to genome. miRNAs, tasiRNAs and natural antisense transcripts-generated small interfering RNAs (natsiRNAs) were identified and compared between libraries. In the leaf of OE lines, 15 known miRNAs increased in abundance and 9 miRNAs decreased in abundance, whereas in the root of OE lines, 2 known miRNAs increased in abundance and 9 miRNAs decreased in abundance. miRNAs with increased abundance in the leaf and root samples of both OE lines (miR158b and miR172a/b) were predicted to target mRNAs coding for Dof zinc finger protein and Apetala 2 (AP2) proteins, respectively. Furthermore, a significant change in the miR173-tasiRNAs-PPR/TPR network was observed in the leaves of both OE lines.

Conclusion

In this study, the impact of high energy content on the sRNA profiles of Arabidopsis is reported. While the abundance of many stress-induced miRNAs is unaltered, the abundance of some miRNAs related to plant growth and development (miR172 and miR319) is elevated in the fast-growing lines. An induction of miR173-tasiRNAs-PPR/TPR network was also observed in the OE lines. In contrast, only few cis- and trans-natsiRNAs are altered in the fast-growing lines.

Keywords:
Chloroplasts; Mitochondria; miRNAs; MORF; PPR; tasiRNAs and natsiRNAs