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Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

Nature Protocols volume 3, pages 1578–1588 (2008)Cite this article

Abstract

This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour.

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Figure 1: Representations of the binding specificity for the Krüppel transcription factor of Drososphila melanogaster.
Figure 2: Graphical flowchart showing the links between regulatory sequence analysis tool (RSAT) programs used in the protocol.
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Figure 7: A matrix-scan result for the detection of individual sites.
Figure 8: Feature-maps for the even-skipped example.

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Acknowledgements

This work was supported by the Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture, FRIA (J.-V.T. PhD grant), the Vrije Universiteit Brussel (Geconcerteerde Onderzoeksactie 29) (M.T.-C. PhD grant), and by the BioSapiens Network of Excellence funded under the sixth Framework program of the European Communities (LSHG-CT-2003-503265). The postdoctoral grant of M.D. was funded by the Belgian Program on Interuniversity Attraction Poles, initiated by the Belgian Federal Science Policy Office, project P6/25 (BioMaGNet).

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  1. Jean-Valery Turatsinze and Morgane Thomas-Chollier: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, Bruxelles, B-1050, Belgium

    Jean-Valery Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance & Jacques van Helden

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  1. Jean-Valery Turatsinze
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Correspondence to Jacques van Helden.

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Turatsinze, JV., Thomas-Chollier, M., Defrance, M. et al. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc 3, 1578–1588 (2008). https://doi.org/10.1038/nprot.2008.97

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