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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Regulatory motifs identified from a maize developmental coexpression network.

Gregory S Downs1, Christophe Liseron-Monfils, Lewis N Lukens

  • 1a Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada.

Genome
|June 3, 2014
PubMed
Summary

Researchers identified 244 regulatory motifs controlling gene expression in maize development. This study reveals novel motifs and variants of known ones, enhancing our understanding of plant transcriptional control.

Keywords:
5′ upstream regulatory sequencesPromzeaZea mayscoexpression networkdéveloppement de la planteidentification de motifsmotif identificationplant developmentréseau de coexpressionséquences régulatrices en 5′

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Transcriptomics

Background:

  • Transcriptional control is crucial for plant development.
  • Gene expression patterns are regulated by upstream sequences.
  • Maize developmental transcriptome exhibits distinct gene expression modules.

Purpose of the Study:

  • Identify regulatory motifs within maize gene expression modules.
  • Characterize novel and known regulatory motifs.
  • Understand the role of motifs in controlling the developmental transcriptome.

Main Methods:

  • Analysis of 34,876 Zea mays gene models.
  • Identification of 244 enriched regulatory motifs.
  • Comparison of identified motifs with experimentally verified motifs.

Main Results:

  • 244 regulatory motifs significantly enriched in 24 gene expression modules.
  • Identification of previously uncharacterized motifs.
  • Functional overlap between identified motifs and predicted module functions.

Conclusions:

  • Transcript-level coexpression modules are powerful tools for motif discovery.
  • This work identified novel motifs and variants of known motifs in maize.
  • The findings advance the understanding of transcriptional control in plant development.