MicroRNA promoter element discovery in Arabidopsis

  1. Molly Megraw1,5,
  2. Vesselin Baev4,5,
  3. Ventsislav Rusinov4,
  4. Shane T. Jensen2,
  5. Kriton Kalantidis4, and
  6. Artemis G. Hatzigeorgiou1,3
  1. 1Center for Bioinformatics and Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
  2. 2Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
  3. 3Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
  4. 4Institute of Molecular Biology and Biotechnology, GR 711 Heraklion, Crete, Greece

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

Footnotes

  • ↵5 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: artemis{at}pcbi.upenn.edu; fax: (215) 573-3111; or Kriton Kalantidis, Institute of Molecular Biology and Biotechnology, Heraklion, Crete, Greece; e-mail: kriton{at}imbb.forth.gr.

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

    • Received April 27, 2006.
    • Accepted June 12, 2006.
« Previous | Next Article »Table of Contents

This Article

  1. Published in Advance August 3, 2006, doi: 10.1261/rna.130506 RNA 2006. 12: 1612-1619 Copyright © 2006 RNA Society

Current Issue

  1. December 2008, 14 (12)
  1. Current Issue
  1. Alert me to new issues of RNA