Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays

Liu, Z. J., Kumari, S., Zhang, L. F., Zheng, Y. L., Ware, D. (2012) Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays. PLoS ONE, 7 (6). e39786. ISSN 1932-6203

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URL: http://www.ncbi.nlm.nih.gov/pubmed/22768123
DOI: e3978610.1371/journal.pone.0039786

Abstract

Waterlogging of plants leads to low oxygen levels (hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and protein synthesis. Our research seeks to characterize the microRNA-mediated gene regulatory networks associated with short-term waterlogging. MicroRNAs (miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic stress responses. To characterize the involvement of miRNAs and their targets in response to short-term hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature miRNA signatures (22 known and 2 novel mature miRNAs, representing 66 miRNA loci) and their 92 predicted targets in three inbred Zea mays lines (waterlogging tolerant Hz32, mid-tolerant B73, and sensitive Mo17). Based on our studies, miR159, miR164, miR167, miR393, miR408 and miR528, which are mainly involved in root development and stress responses, were found to be key regulators in the post-transcriptional regulatory mechanisms under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress and development related cis-regulatory elements on the promoters of these miRNAs; and a probable miRNA-mediated gene regulatory network in response to short-term waterlogging stress was constructed. The differential expression patterns of miRNAs and their targets in these three inbred lines suggest that the miRNAs are active participants in the signal transduction at the early stage of hypoxia conditions via a gene regulatory network; and crosstalk occurs between different biochemical pathways.

Item Type: Paper
Uncontrolled Keywords: stress-regulated micrornas box transcription factors dna-binding specificity barley aleurone cells pea plastocyanin gene zinc-finger protein loop rt-pcr arabidopsis-thaliana abscisic-acid plant micrornas
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA

organism description > plant
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date Deposited: 30 Jan 2013 17:50
Last Modified: 30 Jan 2013 17:50
PMCID: PMC3387268
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26998

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