MicroRNA Promoter Analysis

  • Molly Megraw
  • Artemis G. Hatzigeorgiou
Part of the Methods in Molecular Biology book series (MIMB, volume 592)


In this chapter, we present a brief overview of current knowledge about the promoters of plant microRNAs (miRNAs), and provide a step-by-step guide for predicting plant miRNA promoter elements using known transcription factor binding motifs. The approach to promoter element prediction is based on a carefully constructed collection of Positional Weight Matrices (PWMs) for known transcription factors (TFs) in Arabidopsis. A key concept of the method is to use scoring thresholds for potential binding sites that are appropriate to each individual transcription factor. While the procedure can be applied to search for Transcription Factor Binding Sites (TFBSs) in any pol-II promoter region, it is particularly practical for the case of plant miRNA promoters where upstream sequence regions and binding sites are not readily available in existing databases. The majority of the material described in this chapter is available for download at

Key words:

MicroRNA Transcription factors Promoter Sequence scanning Position-specific weight matrices 



The authors thank Shane Jensen, Vesselin Baev, Ventsislav Rusinov, and Kriton Kalantidis for their contributions to the study from which this work was derived. This work was supported by an NSF Career Award (DBI-0238295).


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Molly Megraw
    • 1
    • 2
  • Artemis G. Hatzigeorgiou
    • 3
    • 4
  1. 1.Department of Genetics, Center for Bioinformatics, School of MedicineUniversity of PennsylvaniaPhiladelphiaUSA
  2. 2.Institute for Genome Sciences & Policy, Duke UniversityDurhamUSA
  3. 3.Department of Genetics, Center for Bioinformatics, School of Medicine, Department of Computer and Information Science, School of EngineeringUniversity of PennsylvaniaPhiladelphiaUSA
  4. 4.Institute of Molecular Oncology, Biomedical Sciences Research Center “Alexander Fleming”Vari-AthensGreece

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