Using a Structural and Logics Systems Approach to Infer bHLH-DNA Binding Specificity Determinants

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Using a Structural and Logics Systems Approach to Infer bHLH-DNA Binding Specificity Determinants

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Title: Using a Structural and Logics Systems Approach to Infer bHLH-DNA Binding Specificity Determinants
Author: De Masi, Federico; Grove, Christian A.; Vedenko, Anastasia; Gisselbrecht, Stephen S.; Serrano, Luis; Walhout, Albertha J. M.; Alibés, Andreu; Bulyk, Martha Leonia

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Citation: De Masi, Federico, Christian A. Grove, Anastasia Vedenko, Andreu Alibés, Stephen S. Gisselbrecht, Luis Serrano, Martha L. Bulyk, and Albertha J. M. Walhout. 2011. Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Research 39(11): 4553-4563.
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Abstract: Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein–DNA recognition by paralogous TFs is of central importance for understanding how small differences in DNA specificities can dictate target gene selection. Previously, we determined the \(in\) \(vitro\) DNA binding specificities of 19 \(Caenorhabditis\) \(elegans\) basic helix-loop-helix (bHLH) dimers using protein binding microarrays. These TFs bind E-box (CANNTG) and E-box-like sequences. Here, we combine these data with logics, bHLH–DNA co-crystal structures and computational modeling to infer which bHLH monomer can interact with which CAN E-box half-site and we identify a critical residue in the protein that dictates this specificity. Validation experiments using mutant bHLH proteins provide support for our inferences. Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans.
Published Version: doi://10.1093/nar/gkr070
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113581/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:5136967

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