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MicroRNA Promoter Analysis

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Plant MicroRNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 592))

Abstract

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 http://microrna.gr.

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Acknowledgments

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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Authors and Affiliations

  1. Department of Genetics, Center for Bioinformatics, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Molly Megraw

  2. Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA

    Molly Megraw

  3. Department of Genetics, Center for Bioinformatics, School of Medicine, Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, USA

    Artemis G. Hatzigeorgiou

  4. Institute of Molecular Oncology, Biomedical Sciences Research Center “Alexander Fleming”, Vari-Athens, Greece

    Artemis G. Hatzigeorgiou

Authors
  1. Molly Megraw
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  2. Artemis G. Hatzigeorgiou
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Editor information

Editors and Affiliations

  1. Delaware Biotechnology Institute, University of Delaware, Innovation Way 15, Newark, 19711, U.S.A.

    Blake C. Meyers

  2. Delaware Biotechnology Institute, University of Delaware, Innovation Way 15, Newark, 19711, U.S.A.

    Pamela J. Green

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

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Megraw, M., Hatzigeorgiou, A.G. (2010). MicroRNA Promoter Analysis. In: Meyers, B., Green, P. (eds) Plant MicroRNAs. Methods in Molecular Biology, vol 592. Humana Press. https://doi.org/10.1007/978-1-60327-005-2_11

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  • DOI: https://doi.org/10.1007/978-1-60327-005-2_11

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-004-5

  • Online ISBN: 978-1-60327-005-2

  • eBook Packages: Springer Protocols

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