RNA. 2006 Sep;12(9):1612-9. Epub 2006 Aug 3.

MicroRNA promoter element discovery in Arabidopsis.

Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG.

Source

Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

Abstract

In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these elements in miRNA promoters, protein-coding gene promoters, and random genomic sequences. We report five transcription factor (TF) binding motifs that show evidence of overrepresentation in miRNA promoter regions relative to the promoter regions of protein-coding genes. This investigation is based on the analysis of 800-nucleotide regions upstream of 63 experimentally verified Transcription Start Sites (TSS) for miRNA primary transcripts in Arabidopsis. While the TATA-box binding motif was also previously reported by Xie and colleagues, the transcription factors AtMYC2, ARF, SORLREP3, and LFY are identified for the first time as overrepresented binding motifs in miRNA promoters.

PMID:: 16888323; [PubMed - indexed for MEDLINE]
PMCID: PMC1557699

Free PMC Article

Images from this publication.See all images (7) Free text

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Supplemental Content

Related citations

Genomic analysis of rice microRNA promoters and clusters. [Gene. 2009]
Genomic analysis of rice microRNA promoters and clusters.
Cui X, Xu SM, Mu DS, Yang ZM. Gene. 2009 Feb 15; 431(1-2):61-6. Epub 2008 Nov 24.
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. [BMC Genomics. 2010]
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.
Bernard V, Brunaud V, Lecharny A. BMC Genomics. 2010 Mar 12; 11:166. Epub 2010 Mar 12.
MicroRNA promoter analysis. [Methods Mol Biol. 2010]
MicroRNA promoter analysis.
Megraw M, Hatzigeorgiou AG. Methods Mol Biol. 2010; 592:149-61.
Review The DPE, a core promoter element for transcription by RNA polymerase II. [Exp Mol Med. 2002]
Review The DPE, a core promoter element for transcription by RNA polymerase II.
Kadonaga JT. Exp Mol Med. 2002 Sep 30; 34(4):259-64.
Review rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites. [Hum Mutat. 2002]
Review rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites.
Ponomarenko JV, Orlova GV, Merkulova TI, Gorshkova EV, Fokin ON, Vasiliev GV, Frolov AS, Ponomarenko MP. Hum Mutat. 2002 Oct; 20(4):239-48.

See reviews... See all...

Cited by 16 PubMed Central articles

Regulation of microRNA expression and function by nuclear receptor signaling. [Cell Biosci. 2011]
Regulation of microRNA expression and function by nuclear receptor signaling.
Yang Z, Wang L. Cell Biosci. 2011 Sep 21; 1(1):31. Epub 2011 Sep 21.
The plant Mediator and its role in noncoding RNA production. [Front Biol. 2011]
The plant Mediator and its role in noncoding RNA production.
Kim YJ, Chen X. Front Biol. 2011 Apr 1; 6(2):125-132.
Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis. [BMC Genomics. 2011]
Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis.
Peng FY, Weselake RJ. BMC Genomics. 2011 Jun 2; 12:286. Epub 2011 Jun 2.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

MicroRNA promoter element discovery in Arabidopsis.
MicroRNA promoter element discovery in Arabidopsis.
RNA. 2006 Sep ;12(9):1612-9. Epub 2006 Aug 3 .

PubMed
microRNAs exhibit high frequency genomic alterations in human cancer.
microRNAs exhibit high frequency genomic alterations in human cancer.
Proc Natl Acad Sci U S A. 2006 Jun 13 ;103(24):9136-41. Epub 2006 Jun 5 .

PubMed
Tonic shock induces detachment of Giardia lamblia.
Tonic shock induces detachment of Giardia lamblia.
PLoS Negl Trop Dis. 2008 Feb 13 ;2(2):e169.

PubMed
Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryon...
Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells.
Genes Dev. 2007 Oct 15 ;21(20):2545-57.

PubMed
GeneE: gene and protein query expansion with disambiguation.
GeneE: gene and protein query expansion with disambiguation.
Bioinformatics. 2010 Jan 1 ;26(1):147-8. Epub 2009 Oct 16 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: