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Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors

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Research in Computational Molecular Biology (RECOMB 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7821))

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Abstract

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.

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Author information

Authors and Affiliations

  1. Faculty of Computer Science, Alexandru I. Cuza University, Iasi, Romania

    Alina Munteanu

  2. Institute for Genome Sciences and Policy, Departments of Biostatistics & Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, Durham, NC, 27708, USA

    Raluca Gordân

Authors
  1. Alina Munteanu
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  2. Raluca Gordân
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Editor information

Editors and Affiliations

  1. School of Mathematics, Peking University, Beijing, P.R. China

    Minghua Deng

  2. Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, 100084, Beijing, P.R. China

    Rui Jiang

  3. Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA

    Fengzhu Sun

  4. Department of Automation, Tsinghua University, P.O. Box, 100084, Beijing, China

    Xuegong Zhang

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Munteanu, A., Gordân, R. (2013). Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science(), vol 7821. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37195-0_12

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  • DOI: https://doi.org/10.1007/978-3-642-37195-0_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-37194-3

  • Online ISBN: 978-3-642-37195-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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