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Research Abstracts - 2007
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Motif Discovery in Human Enhancer Regions Using 10 Mammals

Pouya Kheradpour, Alexander Stark & Manolis Kellis

While the motif composition of promoter regions is well studied [1,2,3], that of enhancer regions is largely unknown due to their large distance from genes, varying roles in development, and unknown sequence characteristics [4]. Recent technological advances enable the genome-wide assessment of chromatin state using ChIP [5]. Through a collaboration with the Ren Lab, we obtained a list of 40,000 human genomic loci with chromatin marks indicative of enhancer activity, which we used to study the motif content of enhancer regions.

We used ten mammals for genome-wide de-novo motif discovery in enhancer regions, resulting in approximately 40 unique motifs with significant conservation. While these motifs were discovered by their preferential conservation, many also show specific enrichment in the human enhancers, regardless of conservation. Some of these motifs are similar to known transcription factor motifs and motifs found conserved near promoters, yet many appear to be novel. Thus, we expect that the factors that bind to enhancers may be partially distinct from those that bind to the promoter regions.

We also studied the pairwise relationships between enhancer motifs based on their patterns of preferential joint conservation. We find that many of our motifs exhibit a tendency to cluster with multiple instances of the same motif. We also find that certain pairs of motifs tend to co-occur near one-another, suggesting the associated factors may work cooperatively. Additionally, groups of motifs appeared enriched in distinct sets of enhancers, suggesting that different classes of enhancers may exist, each defined with an associated set of motifs.

We have also found that the discovered motifs frequently cluster across the human genome, and that most large clusters are indicative of enhancer regions, suggesting putative novel enhancers. Although this methodology is not sufficient for identifying all known enhancers, experimental validation of candidate regions may reveal a significant number of novel elements.

The motif discovery approaches we developed are general, and may be applicable to the understanding and prediction of diverse types of regulatory regions, including promoters, silencers, and boundary elements. They may also shed light into the motif composition of ultra-conserved elements [6], and help understand the molecular basis for their function and their role in gene regulation.


[1] 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' UTRs by comparison of several mammals. Nature 434, 338-345.

[2] Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V., et al. (2003). TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31, 374-378.

[3] Tompa, M. (2001). Identifying functional elements by comparative DNA sequence analysis. Genome Res 11, 1143-1144.

[4] West, A.G., and Fraser, P. (2005). Remote control of gene transcription. Human molecular genetics 14 Spec No 1, R101-111.

[5] Mukherjee, S., Berger, M.F., Jona, G., Wang, X.S., Muzzey, D., Snyder, M., Young, R.A., and Bulyk, M.L. (2004). Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet 36, 1331-1339.

[6] Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS and Haussler D. (2004) Ultraconserved elements in the human genome. Science 304, 1321-1325.


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