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

26 Pags.- 8 Figs.- 2 Tabls. The definitive version is available at: http://link.springer.com/bookseries/7651 and http://link.springer.com/book/10.1007/978-1-4939-6396-6
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.
This work was funded in part by Fundación ARAID and by the EnseignantsChercheurs 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), AixMarseille Université.