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Article: Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars
Title | Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars |
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Authors | |
Keywords | Chloroplasts MiRNAs Mitochondria MORF PPR TasiRNAs and natsiRNAs |
Issue Date | 2014 |
Publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/ |
Citation | BMC Genomics, 2014, v. 15, article no. 116 How to Cite? |
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. |
Persistent Identifier | http://hdl.handle.net/10722/198225 |
ISSN | 2023 Impact Factor: 3.5 2023 SCImago Journal Rankings: 1.047 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Liang, C | en_US |
dc.contributor.author | Liu, X | en_US |
dc.contributor.author | Sun, Y | en_US |
dc.contributor.author | Yiu, SM | en_US |
dc.contributor.author | Lim, BL | en_US |
dc.date.accessioned | 2014-06-25T02:56:25Z | - |
dc.date.available | 2014-06-25T02:56:25Z | - |
dc.date.issued | 2014 | en_US |
dc.identifier.citation | BMC Genomics, 2014, v. 15, article no. 116 | en_US |
dc.identifier.issn | 1471-2164 | - |
dc.identifier.uri | http://hdl.handle.net/10722/198225 | - |
dc.description.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. | en_US |
dc.language | eng | en_US |
dc.publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/ | - |
dc.relation.ispartof | BMC Genomics | en_US |
dc.rights | BMC Genomics. Copyright © BioMed Central Ltd. | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Chloroplasts | - |
dc.subject | MiRNAs | - |
dc.subject | Mitochondria | - |
dc.subject | MORF | - |
dc.subject | PPR | - |
dc.subject | TasiRNAs and natsiRNAs | - |
dc.title | Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars | en_US |
dc.type | Article | en_US |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | en_US |
dc.identifier.email | Lim, BL: bllim@hkucc.hku.hk | en_US |
dc.identifier.authority | Yiu, SM=rp00207 | en_US |
dc.identifier.authority | Lim, BL=rp00744 | en_US |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1186/1471-2164-15-116 | en_US |
dc.identifier.pmid | 24507710 | - |
dc.identifier.pmcid | PMC3925372 | - |
dc.identifier.scopus | eid_2-s2.0-84893690779 | - |
dc.identifier.hkuros | 229141 | en_US |
dc.identifier.volume | 15 | en_US |
dc.identifier.isi | WOS:000332598600001 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1471-2164 | - |