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

TitleGlobal small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars
Authors
Issue Date2014
PublisherBioMed 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?
AbstractBACKGROUND: 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 Identifierhttp://hdl.handle.net/10722/198225
ISSN
2015 Impact Factor: 3.867
2015 SCImago Journal Rankings: 2.343
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLiang, Cen_US
dc.contributor.authorLiu, Xen_US
dc.contributor.authorSun, Yen_US
dc.contributor.authorYiu, SMen_US
dc.contributor.authorLim, BLen_US
dc.date.accessioned2014-06-25T02:56:25Z-
dc.date.available2014-06-25T02:56:25Z-
dc.date.issued2014en_US
dc.identifier.citationBMC Genomics, 2014, v. 15, article no. 116en_US
dc.identifier.issn1471-2164-
dc.identifier.urihttp://hdl.handle.net/10722/198225-
dc.description.abstractBACKGROUND: 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.languageengen_US
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/-
dc.relation.ispartofBMC Genomicsen_US
dc.rightsBMC Genomics. Copyright © BioMed Central Ltd.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleGlobal small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugarsen_US
dc.typeArticleen_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.emailLim, BL: bllim@hkucc.hku.hken_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.authorityLim, BL=rp00744en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1471-2164-15-116en_US
dc.identifier.pmid24507710-
dc.identifier.pmcidPMC3925372-
dc.identifier.hkuros229141en_US
dc.identifier.volume15en_US
dc.identifier.isiWOS:000332598600001-
dc.publisher.placeUnited Kingdom-

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