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Open Access Highly Accessed Research article

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors

Xueping Yu1, Jimmy Lin1, Donald J Zack1234 and Jiang Qian1*

Author Affiliations

1 Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA

2 Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA

3 Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA

4 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA

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BMC Bioinformatics 2007, 8:437  doi:10.1186/1471-2105-8-437

Published: 9 November 2007

Abstract

Background

Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by increasing evidence that some DNA regulatory regions are not evolutionary conserved, we have developed an approach for cis-regulatory region identification that does not rely upon evolutionary sequence conservation.

Results

The conservation-independent approach is based on an empirical potential energy between interacting transcription factors (TFs). In this analysis, the potential energy is defined as a function of the number of TF interactions in a genomic region and the strength of the interactions. By identifying sets of interacting TFs, the analysis locates regions enriched with the binding sites of these interacting TFs. We applied this approach to 30 human tissues and identified 6232 putative cis-regulatory modules (CRMs) regulating 2130 tissue-specific genes. Interestingly, some genes appear to be regulated by different CRMs in different tissues. Known regulatory regions are highly enriched in our predicted CRMs. In addition, DNase I hypersensitive sites, which tend to be associated with active regulatory regions, significantly overlap with the predicted CRMs, but not with more conserved regions. We also find that conserved and non-conserved CRMs regulate distinct gene groups. Conserved CRMs control more essential genes and genes involved in fundamental cellular activities such as transcription. In contrast, non-conserved CRMs, in general, regulate more non-essential genes, such as genes related to neural activity.

Conclusion

These results demonstrate that identifying relevant sets of binding motifs can help in the mapping of DNA regulatory regions, and suggest that non-conserved CRMs play an important role in gene regulation.