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.
*The authors of this chapter contributed equally to the work.
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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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Castro-Mondragon, J.A., Rioualen, C., Contreras-Moreira, B., van Helden, J. (2016). RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes. In: Hehl, R. (eds) Plant Synthetic Promoters. Methods in Molecular Biology, vol 1482. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6396-6_19
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DOI: https://doi.org/10.1007/978-1-4939-6396-6_19
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