• Login
    View Item 
    •   Home
    • UMass Chan Faculty and Staff Research and Publications
    • UMass Chan Faculty and Researcher Publications
    • View Item
    •   Home
    • UMass Chan Faculty and Staff Research and Publications
    • UMass Chan Faculty and Researcher Publications
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of eScholarship@UMassChanCommunitiesPublication DateAuthorsUMass Chan AffiliationsTitlesDocument TypesKeywordsThis CollectionPublication DateAuthorsUMass Chan AffiliationsTitlesDocument TypesKeywordsProfilesView

    My Account

    LoginRegister

    Help

    AboutSubmission GuidelinesData Deposit PolicySearchingUsage StatisticsAccessibilityTerms of UseWebsite Migration FAQ

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    NAR_2011_DeMasi_4553.full.pdf
    Size:
    871.2Kb
    Format:
    PDF
    Download
    Authors
    De Masi, Federico
    Grove, Christian A.
    Vedenko, Anastasia
    Alibés, Andreu
    Gisselbrecht, Stephen S.
    Serrano, Luis
    Bulyk, Martha L.
    Walhout, Albertha J. M.
    UMass Chan Affiliations
    Program in Molecular Medicine
    Program in Gene Function and Expression
    Document Type
    Journal Article
    Publication Date
    2011-06-01
    Keywords
    Gene Regulatory Networks
    Transcription Factors
    Basic Helix-Loop-Helix Transcription Factors
    DNA-Binding Proteins
    Genetics and Genomics
    
    Metadata
    Show full item record
    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.
    Source
    Nucleic Acids Res. 2011 Jun 1;39(11):4553-4563. Epub 2011 Feb 18. Link to article on publisher's site
    DOI
    10.1093/nar/gkr070
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/43945
    PubMed ID
    21335608
    Related Resources
    Link to Article in PubMed
    Rights
    © The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
    ae974a485f413a2113503eed53cd6c53
    10.1093/nar/gkr070
    Scopus Count
    Collections
    UMass Chan Faculty and Researcher Publications

    entitlement

    DSpace software (copyright © 2002 - 2023)  DuraSpace
    Lamar Soutter Library, UMass Chan Medical School | 55 Lake Avenue North | Worcester, MA 01655 USA
    Quick Guide | escholarship@umassmed.edu
    Works found in eScholarship@UMassChan are protected by copyright unless otherwise indicated.
    Open Repository is a service operated by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.