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Related Experiment Videos

PRECISE: software for prediction of cis-acting regulatory elements.

L M Trindade1, R van Berloo, M Fiers

  • 1Graduate School of Experimental Plant Sciences, Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands. luisa.trindade@wur.nl

The Journal of Heredity
|September 2, 2005
PubMed
Summary

A new tool, PRECISE, accurately predicts cis-acting elements involved in gene regulation. It identifies regulatory motifs in plant genomes, aiding research in plant biology and starch biosynthesis.

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Area of Science:

  • Genetics and Molecular Biology
  • Bioinformatics
  • Plant Science

Background:

  • Gene expression regulation relies on transcription factors binding to cis-acting elements in promoter regions.
  • Predicting these cis-acting elements is crucial for understanding gene regulation.
  • Existing methods may lack user-friendliness or efficient filtering capabilities.

Purpose of the Study:

  • To introduce PRECISE (Prediction of REgulatory CIS-acting Elements), a novel computer program for predicting cis-acting elements.
  • To evaluate PRECISE's efficacy using empirical motif frequency tables and case studies in Arabidopsis.

Main Methods:

  • Development of the PRECISE software with a user-friendly interface.
  • Integration of tools for creating empirical motif frequency tables from genomic sequences.

Related Experiment Videos

  • Application of PRECISE to analyze upstream regions of Arabidopsis genes involved in starch metabolism and gibberellin-induced transcription.

    • Main Results:

    • PRECISE identified 15 out of 20 highly specific motifs homologous to known cis-acting elements regulating light, auxin, and abscisic acid in starch biosynthesis genes.
    • In a second case study, PRECISE successfully identified 6 out of 17 known gibberellin-responsive motifs in Arabidopsis.

    Conclusions:

    • The PRECISE software package demonstrates significant power and accuracy in predicting regulatory elements.
    • PRECISE facilitates the discovery of cis-acting elements involved in crucial plant biological processes like starch metabolism and hormone signaling.