Published online 23 September 2004
Nucleic Acids Research, Vol. 32 No. 17 © Oxford University Press 2004; all rights reserved
In silico identification of transcriptional regulators associated with c-Myc
The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics, Sackler School of Medicine, 1 School of Computer Science, Tel Aviv University, Israel, 2 Division of Hematology, Department of Medicine and 3 The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21212 USA
* To whom correspondence should be addressed at Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Room 1002, Tel Aviv University, Ramat Aviv 69978, Israel. Tel: +972 3 6409760; Fax: +972 3 6407471; Email: yossih{at}post.tau.ac.il
Received July 22, 2004; Revised and Accepted August 21, 2004
The development of powerful experimental strategies for functional genomics and accompanying computational tools has brought major advances in the delineation of transcriptional networks in organisms ranging from yeast to human. Regulation of transcription of eukaryotic genes is to a large extent combinatorial. Here, we used an in silico approach to identify transcription factors (TFs) that form recurring regulatory modules with c-Myc, a protein encoded by an oncogene that is frequently disregulated in human malignancies. A recent study identified, on a genomic scale, human genes whose promoters are bound by c-Myc and its heterodimer partner Max in Burkitt's lymphoma cells. Using computational methods, we identified nine TFs whose binding-site signatures are highly overrepresented in this promoter set of c-Myc targets, pointing to possible functional links between these TFs and c-Myc. Binding sites of most of these TFs are also enriched on the set of mouse homolog promoters, suggesting functional conservation. Among the enriched TFs, there are several regulators known to control cell cycle progression. Another TF in this set, EGR-1, is rapidly activated by numerous stress challenges and plays a central role in angiogenesis. Experimental investigation confirmed that c-Myc and EGR-1 bind together on several target promoters. The approach applied here is general and demonstrates how computational analysis of functional genomics experiments can identify novel modules in complex networks of transcriptional regulation.
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