Abstract
In spite of numerous advances in recent years, the complete list of direct target genes for nuclear receptors remains elusive. The integrated application of new computational and experimental methods reviewed in this chapter provides insight into the complex network of regulatory pathways mediated by nuclear receptors which is expected to improve the understanding of the physiology and the pathology of metabolism, development, homeostasis, and other fundamental processes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Locker, J. (2001) Transcription factors. Humana Molecular Genetics. Academic Press 167–214.
Overington, J.P., Al-Lazikani, B., Hopkins, A.L. (2006) How many drug targets are there? Nat Rev Drug Discov 5, 993–996.
Olefsky, J.M. (2001) Nuclear receptor minireview series. J Biol Chem 276, 36863–36864.
He, J., Cheng, Q., Xie, W. (2009) Minireview: nuclear receptor-controlled steroid hormone synthesis and metabolism. Mol Endocrinol 23, 1–11.
Okuno, M., Arimoto, E., Nishihara, T., Imagawa, M. (2001) Dual DNA-binding specificity of peroxisome-proliferator-activated receptor gamma controlled by heterodimer formation. Biochem J 353, 193–198.
Sandelin, A., Alkema, W., Engstrom, P. et al. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32, D91–D94.
Cartharius, K., Frech, K., Grote, K. et al. (2005) MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21, 2933–2942.
Lemay, D., and Hwang, D. (2006) Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics. J Lipid Res 47, 1583–1587.
Podvinec, M., Kaufmann, M.R., Handschin, C., and Meyer, U.A. (2002) NUBIScan, an in silico approach for prediction of nuclear receptor response elements. Mol Endocrinol 16, 1269–1279.
Moehren, U., Denayer, S., Podvinec, M. et al. (2008) Identification of androgen-selective androgen-response elements in the human aquaporin-5 and Rad9 genes. Biochem J 411, 679–686.
Sandelin, A., and Wassermen, W.W. (2005) Prediction of nuclear hormone receptor response elements. Mol Endocrinol 19, 595–606.
Varga, G., and Su, C. (2007) Classification and predictive modeling of liver X receptor response elements BioDrugs 21, 117–124.
Schmid, C.D., Perier, R., Praz, V., and Bucher, P. (2006) EPD in its twentieth year: towards complete promoter coverage of selected model organisms Nucleic Acids Res 34, D82–D85.
Stayrook, K.R., Rogers, P.M., Savkur, R.S. et al. (2008) Regulation of human 3 alpha-hydroxysteroid dehydrogenase (AKR1C4) expression by the liver X receptor alpha. Mol Pharmacol 73, 607–612.
Wang, Y., Rogers, P.M., Su, C. et al. (2008) Regulation of cholesterologenesis by the oxysterol receptor, LXRalpha. J Biol Chem 283, 26332–26339.
Wang, Y., Rogers, P.M., Stayrook, K.R. et al. (2008) The selective Alzheimer’s disease indicator-1 gene (Seladin-1/DHCR24) is a liver X receptor target gene. Mol Pharmacol 74, 1716–1721.
Fogel, G.B., Porto, V.W., Varga, G. et al. (2008) Evolutionary computation for discovery of composite transcription factor binding sites. Nucleic Acids Res 36, e142.
Pape, U.J., Klein, H., Vingron, M. (2009) Statistical detection of cooperative transcription factors with similarity adjustment Bioinformatics 15, 2103–2109.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Varga, G. (2010). Target Gene Identification via Nuclear Receptor Binding Site Prediction. In: Ladunga, I. (eds) Computational Biology of Transcription Factor Binding. Methods in Molecular Biology, vol 674. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-854-6_15
Download citation
DOI: https://doi.org/10.1007/978-1-60761-854-6_15
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-853-9
Online ISBN: 978-1-60761-854-6
eBook Packages: Springer Protocols