RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes

  • Jaime A. Castro-Mondragon
  • Claire Rioualen
  • Bruno Contreras-Moreira
  • Jacques van Helden
Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1482)

Abstract

In this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif discovery algorithms, and compare them with reference motif databases. The protocol is documented with detailed notes explaining the rationale underlying the choice of options. The interpretation of the results is illustrated with an example from the model plant Arabidopsis thaliana.

Key words

Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) Transcription factor (TF) Transcription factor binding motifs (TFBM) Transcription factor binding site (TFBS) Gene ontology (GO) Functional enrichment 
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Notes

Acknowledgements

We thank C. Dubos for feedback on MYBR3 proteins. This work was funded in part by Fundación ARAID and by the Enseignants-Chercheurs invités program of Aix-Marseille Université (to B.C.M.). C.R. was supported by the France Génomique National infrastructure, funded as part of the Investissements d’Avenir, program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09). J.C-M PhD grant is funded by the Ecole Doctorale des Sciences de la Vie et de la Santé (EDSVS), Aix-Marseille Université.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Jaime A. Castro-Mondragon
    • 1
  • Claire Rioualen
    • 1
  • Bruno Contreras-Moreira
    • 2
    • 3
  • Jacques van Helden
    • 1
  1. 1.INSERM, U1090 TAGCAix Marseille UniversityMarseilleFrance
  2. 2.Estación Experimental de Aula Dei-CSICZaragozaSpain
  3. 3.Fundación ARAIDZaragozaSpain

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