Document Detail


Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis.
MedLine Citation:
PMID:  23295247     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Endogenous microRNAs (miRNAs) modulate gene expression at the post-transcription level. In plants, a vast majority of MIR genes are thought to be transcribed by RNA Polymerase II (Pol II). However, promoter organization is currently unknown for most plant MIR genes. This deficiency prevents a comprehensive understanding of miRNA-mediated gene networks. In this study, we performed Pol II chromatin immunoprecipitation (ChIP) analysis in Arabidopsis using a genome tiling microarray. Distinct Pol II binding was found at most MIR loci, which allowed prediction of the transcription start sites (TSSs) for 167 MIR genes in Arabidopsis that was validated by average free energy profiling. By employing 99 position weight matrices (PWM), we systematically scanned the regulatory regions upstream of the TSSs. We discovered eleven and ten cis-elements that are statistically over- and under-represented in MIR promoters, respectively. Thus, analysis of Pol II binding provides a new perspective for studying miRNAs in plants.
Authors:
Xin Zhao; Huiyong Zhang; Lei Li
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-1-4
Journal Detail:
Title:  Genomics     Volume:  -     ISSN:  1089-8646     ISO Abbreviation:  Genomics     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-1-8     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8800135     Medline TA:  Genomics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012. Published by Elsevier Inc.
Affiliation:
Department of Biology, University of Virginia, Charlottesville VA 22904, USA.
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