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.

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MicroRNA promoter element discovery in <em>Arabidopsis</em>

Artemis Hatzigeorgiou

^{Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA}

^{Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA}

^{Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA}

^{Institute of Molecular Biology and Biotechnology, GR 711 Heraklion, Crete, Greece}

^{These authors contributed equally to this work.}

Reprint requests to: Artemis G. Hatzigeorgiou, Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; e-mail: ude.nnepu.ibcp@simetra; fax: (215) 573-3111; or Kriton Kalantidis, Institute of Molecular Biology and Biotechnology, Heraklion, Crete, Greece; e-mail: rg.htrof.bbmi@notirk.

Received 2006 Apr 27; Accepted 2006 Jun 12.

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.

Keywords: microRNA, transcription factors, promoter, sequence scanning, position-specific weight matrices

Abstract

ACKNOWLEDGMENTS

We thank Praveen Sethupathy for his insightful suggestion to examine experimentally supported Arabidopsis miRNA targets contained in Tarbase for potential regulatory feedback loops. We are also grateful to Zissimos Mourelatos and Fernando Pereira for their helpful comments. A.G.H. and M.M. are supported by an NSF Career Award (DBI-0238295). S.T.J. is supported by a University of Pennsylvania Research Foundation Grant. K.K., V.B., and V.R. are supported by the FAMED-contract EST 7295 and FOSRAK-STREP 2004-005120 European grants.

ACKNOWLEDGMENTS

Footnotes

Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.130506.

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