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Published in:
2013 | OriginalPaper | Chapter
Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors
Authors : Alina Munteanu, Raluca Gordân
Published in: Research in Computational Molecular Biology
Publisher: Springer Berlin Heidelberg
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Transcription factors (TFs) regulate gene expression by binding to specific DNA sites in cis regulatory regions of genes. Most eukaryotic TFs are members of protein families that share a common DNA binding domain and often recognize highly similar DNA sequences. Currently, it is not well understood why closely related TFs are able to bind different genomic regions
in vivo
, despite having the potential to interact with the same DNA sites. Here, we use the Myc/Max/Mad family as a model system to investigate whether interactions with additional proteins (co-factors) can explain why paralogous TFs with highly similar DNA binding preferences interact with different genomic sites
in vivo
. We use a classification approach to distinguish between targets of c-Myc versus Mad2, using features that reflect the DNA binding specificities of putative co-factors. When applied to c-Myc/Mad2 DNA binding data, our algorithm can distinguish between genomic regions bound uniquely by c-Myc versus Mad2 with 87% accuracy.