Advertisement

Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila

  • Delphine Potier
  • Zeynep Kalender Atak
  • Marina Naval Sanchez
  • Carl Herrmann
  • Stein AertsEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 786)

Abstract

Gene expression regulation is a fundamental biological process leading to complete organism development by controlling processes like cell type specification and differentiation. The accuracy of this process is ­governed by transcription factors (TFs) acting within a complex gene regulatory network. CisTargetX has been developed to enable a user to predict TFs, enhancers, and target genes involved in the regulation of co-expressed genes. It uses a strategy that incorporates the genome-wide prediction of clusters of transcription factor binding sites (TFBSs), starting from a large, unbiased collection of position weight matrices (PWMs) and uses comparative genomics criteria to filter potential TFBS. We describe in this chapter, step-by-step, how to use cisTargetX starting from a set of genes or TF(s) to predict transcriptional targets with their putative binding sites and networks in Drosophila. Next, we illustrate this approach on a particular developmental system, namely, sensory organ development, and identify relevant TFs, DNA regions regulating gene expression, and TF/target gene interactions. CisTargetX is available at http://med.kuleuven.be/lcb/cisTargetX.

Key words

cis-Regulatory module Gene regulatory network Motif discovery Drosophila cisTargetX Transcriptional targets 

Notes

Acknowledgments

We thank P.A. Salmand, A. Aubry, C. Oliva for their advice as cisTargetX users. This work is supported by a PhD fellowship from FWO (to M.N.S.) and KULeuven CREA grant 3 M100189 (to S.A.).

Supplementary material is available online at the following URL: http:// med.kuleuven.be/lcb/resources/.

References

  1. 1.
    Van Loo, P., and Marynen, P. (2009) Computational methods for the detection of cis-regulatory modules, Briefings in Bioinformatics 10, 509–524.PubMedCrossRefGoogle Scholar
  2. 2.
    Stark, A., Lin, M. F., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D., Roy, S., Deoras, A. N., Ruby, J. G., Brennecke, J., Hodges, E., Hinrichs, A. S., Caspi, A., Paten, B., Park, S., Han, M. V., Maeder, M. L., Polansky, B. J., Robson, B. E., Aerts, S., van Helden, J., Hassan, B., Gilbert, D. G., Eastman, D. A., Rice, M., Weir, M., Hahn, M. W., Park, Y., Dewey, C. N., Pachter, L., Kent, W. J., Haussler, D., Lai, E. C., Bartel, D. P., Hannon, G. J., Kaufman, T. C., Eisen, M. B., Clark, A. G., Smith, D., Celniker, S. E., Gelbart, W. M., and Kellis, M. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures, Nature 450, 219–232.PubMedCrossRefGoogle Scholar
  3. 3.
    Li, L., Zhu, Q., He, X., Sinha, S., and Halfon, M. S. (2007) Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses, Genome Biol 8, R101.PubMedCrossRefGoogle Scholar
  4. 4.
    He, X., Ling, X., and Sinha, S. (2009) Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution, PLoS Comput Biol 5, e1000299.PubMedCrossRefGoogle Scholar
  5. 5.
    Sinha, S., Schroeder, M., Unnerstall, U., Gaul, U., and Siggia, E. (2004) Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila, BMC Bioinformatics 5, 129.PubMedCrossRefGoogle Scholar
  6. 6.
    Whitington, T., Perkins, A. C., and Bailey, T. L. (2009) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites, Nucleic Acids Research 37, 14–25.PubMedCrossRefGoogle Scholar
  7. 7.
    Ernst, J., Plasterer, H. L., Simon, I., and Bar-Joseph, Z. (2010) Integrating multiple evidence sources to predict transcription factor binding in the human genome, Genome Res 20, 526–536.PubMedCrossRefGoogle Scholar
  8. 8.
    Aerts, S., van Helden, J., Sand, O., and Hassan, B. A. (2007) Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes, PLoS ONE 2, e1115.PubMedCrossRefGoogle Scholar
  9. 9.
    Schroeder, M. D., Pearce, M., Fak, J., Fan, H., Unnerstall, U., Emberly, E., Rajewsky, N., Siggia, E. D., and Gaul, U. (2004) Transcriptional Control in the Segmentation Gene Network of Drosophila, PLoS Biol 2, e271.PubMedCrossRefGoogle Scholar
  10. 10.
    Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B., Eskin, E., Favorov, A. V., Frith, M. C., Fu, Y., Kent, W. J., Makeev, V. J., Mironov, A. A., Noble, W. S., Pavesi, G., Pesole, G., Regnier, M., Simonis, N., Sinha, S., Thijs, G., van Helden, J., Vandenbogaert, M., Weng, Z., Workman, C., Ye, C., and Zhu, Z. (2005) Assessing computational tools for the discovery of transcription factor binding sites, Nat Biotech 23, 137–144.CrossRefGoogle Scholar
  11. 11.
    Frith, M. C., Fu, Y., Yu, L., Chen, J., Hansen, U., and Weng, Z. (2004) Detection of functional DNA motifs via statistical over-representation, Nucleic Acids Research 32, 1372–1381.PubMedCrossRefGoogle Scholar
  12. 12.
    Ho Sui, S. J., Fulton, D. L., Arenillas, D. J., Kwon, A. T., and Wasserman, W. W. (2007) oPOSSUM: integrated tools for analysis of regulatory motif over-representation, Nucleic Acids Research 35, W245–W252.PubMedCrossRefGoogle Scholar
  13. 13.
    Roider, H. G., Manke, T., O’Keeffe, S., Vingron, M., and Haas, S. A. (2009) PASTAA: identifying transcription factors associated with sets of co-regulated genes, Bioinformatics 25, 435–442.PubMedCrossRefGoogle Scholar
  14. 14.
    Kantorovitz, M. R., Kazemian, M., Kinston, S., Miranda-Saavedra, D., Zhu, Q., Robinson, G. E., Göttgens, B., Halfon, M. S., and Sinha, S. (2009) Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse, Developmental Cell 17, 568–579.Google Scholar
  15. 15.
    Rouault, H., Mazouni, K., Couturier, L., Hakim, V., and Schweisguth, F. (2010) Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny, Proceedings of the National Academy of Sciences 107, 14615–14620.CrossRefGoogle Scholar
  16. 16.
    Warner, J. B., Philippakis, A. A., Jaeger, S. A., He, F. S., Lin, J., and Bulyk, M. L. (2008) Systematic identification of mammalian regulatory motifs’ target genes and functions, Nat Meth 5, 347–353.Google Scholar
  17. 17.
    Van Loo, P., Aerts, S., Thienpont, B., De Moor, B., Moreau, Y., and Marynen, P. (2008) ModuleMiner – improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Genome Biol 9, R66.PubMedCrossRefGoogle Scholar
  18. 18.
    Aerts, S., Quan, X., Claeys, A., Naval Sanchez, M., Tate, P., Yan, J., and Hassan, B. A. (2010) Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification, PLoS Biol 8, e1000435.PubMedCrossRefGoogle Scholar
  19. 19.
    Portales-Casamar, E., Thongjuea, S., Kwon, A. T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W. W., and Sandelin, A. (2009) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles, Nucleic Acids Research 38, D105–D110.PubMedCrossRefGoogle Scholar
  20. 20.
    Matys, V. (2006) TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes, Nucleic Acids Research 34, D108–D110.PubMedCrossRefGoogle Scholar
  21. 21.
    Bergman, C. M., Carlson, J. W., and Celniker, S. E. Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster, Bioinformatics 21, 1747–1749.Google Scholar
  22. 22.
    Elemento, O., and Tavazoie, S. (2005) Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach, Genome Biol 6, R18.PubMedCrossRefGoogle Scholar
  23. 23.
    Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., and Kellis, M. (2005) Systematic discovery of regulatory motifs in human promoters and 3(prime) UTRs by comparison of several mammals, Nature 434, 338–345.PubMedCrossRefGoogle Scholar
  24. 24.
    Down, T. A., Bergman, C. M., Su, J., and Hubbard, T. J. P. (2007) Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster, PLoS Comput Biol 3, e7.PubMedCrossRefGoogle Scholar
  25. 25.
    Newburger, D. E., and Bulyk, M. L. (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions, Nucleic Acids Research 37, D77–D82.PubMedCrossRefGoogle Scholar
  26. 26.
    Mahony, S., and Benos, P. V. (2007) STAMP: a web tool for exploring DNA-binding motif similarities, Nucleic Acids Research 35, W253–W258.PubMedCrossRefGoogle Scholar
  27. 27.
    Frith, M. C., Li, M. C., and Weng, Z. (2003) Cluster-Buster: finding dense clusters of motifs in DNA sequences, Nucleic Acids Research 31, 3666–3668.PubMedCrossRefGoogle Scholar
  28. 28.
    Kim, J., Cunningham, R., James, B., Wyder, S., Gibson, J. D., Niehuis, O., Zdobnov, E. M., Robertson, H. M., Robinson, G. E., Werren, J. H., and Sinha, S. (2010) Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances, PLoS Comput Biol 6, e1000652.PubMedCrossRefGoogle Scholar
  29. 29.
    Reeves, N., and Posakony, J. W. (2005) Genetic Programs Activated by Proneural Proteins in the Developing Drosophila PNS, Developmental Cell 8, 413–425.PubMedCrossRefGoogle Scholar
  30. 30.
    Snel, B., Lehmann, G., Bork, P., and Huynen, M. A. (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene, Nucleic Acids Research 28, 3442–3444.PubMedCrossRefGoogle Scholar
  31. 31.
    Hare, E. E., Peterson, B. K., Iyer, V. N., Meier, R., and Eisen, M. B. (2008) Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation, PLoS Genet 4, e1000106.PubMedCrossRefGoogle Scholar
  32. 32.
    Aerts, S., Lambrechts, D., Maity, S., Van Loo, P., Coessens, B., De Smet, F., Tranchevent, L., De Moor, B., Marynen, P., Hassan, B., Carmeliet, P., and Moreau, Y. (2006) Gene prioritization through genomic data fusion, Nat Biotech 24, 537–544.CrossRefGoogle Scholar
  33. 33.
    Castro, B., Barolo, S., Bailey, A. M., and Posakony, J. W. (2005) Lateral inhibition in proneural clusters: cis-regulatory logic and default repression by Suppressor of Hairless, Development 132, 3333–3344.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Delphine Potier
    • 1
    • 2
  • Zeynep Kalender Atak
    • 3
  • Marina Naval Sanchez
    • 3
  • Carl Herrmann
    • 4
    • 5
  • Stein Aerts
    • 3
    Email author
  1. 1.TAGC Inserm U928 and Université de la MediterranéeMarseilleFrance
  2. 2.IBDML CNRS UMR 6216 and Université de la MediterranéeMarseilleFrance
  3. 3.Laboratory of Computational Biology, Center for Human GeneticsK. U. LeuvenLeuvenBelgium
  4. 4.TAGC Inserm U928MarseilleFrance
  5. 5.Université de la MediterranéeMarseilleFrance

Personalised recommendations