We are analyzing https://link.springer.com/protocol/10.1007/978-1-4939-1242-1_16.

Title:
SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes | SpringerLink
Description:
The closely related members of the Hox family of homeodomain transcription factors have similar DNA-binding preferences as monomers, yet carry out distinct functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that...
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Keywords {🔍}

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Topics {✒️}

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Schema {🗺️}

ScholarlyArticle:
      headline:SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes
      pageEnd:278
      pageStart:255
      image:https://media.springernature.com/w153/springer-static/cover/book/978-1-4939-1242-1.jpg
      genre:
         Springer Protocols
      isPartOf:
         name:Hox Genes
         isbn:
            978-1-4939-1242-1
            978-1-4939-1241-4
         type:Book
      publisher:
         name:Springer New York
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Todd R. Riley
            affiliation:
                  name:Columbia University
                  address:
                     name:Department of Biological Sciences, Columbia University, New York, USA
                     type:PostalAddress
                  type:Organization
                  name:University of Massachusetts - Boston
                  address:
                     name:Department of Biology, University of Massachusetts - Boston, Boston, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Matthew Slattery
            affiliation:
                  name:Columbia University Medical Center
                  address:
                     name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
                     type:PostalAddress
                  type:Organization
                  name:University of Minnesota Medical School
                  address:
                     name:Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Namiko Abe
            affiliation:
                  name:Columbia University Medical Center
                  address:
                     name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Chaitanya Rastogi
            affiliation:
                  name:Columbia University
                  address:
                     name:Department of Biological Sciences, Columbia University, New York, USA
                     type:PostalAddress
                  type:Organization
                  name:Columbia University
                  address:
                     name:Department of Applied Physics and Applied Mathematics, Columbia University, New York, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Dahong Liu
            affiliation:
                  name:Columbia University
                  address:
                     name:Department of Biological Sciences, Columbia University, New York, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Richard S. Mann
            affiliation:
                  name:Columbia University Medical Center
                  address:
                     name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
            name:Harmen J. Bussemaker
            affiliation:
                  name:Columbia University
                  address:
                     name:Department of Biological Sciences, Columbia University, New York, USA
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
      keywords:Hox proteins, Transcription factor specificity, Extradenticle, Pbx, SELEX, Next-generation sequencing, Computational analysis
      description:The closely related members of the Hox family of homeodomain transcription factors have similar DNA-binding preferences as monomers, yet carry out distinct functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA-binding specificities. To test this hypothesis we developed a new experimental and computational platform, termed SELEX-seq, to characterize DNA-binding specificities of Hox-based multiprotein complexes. We found that complex formation with the same cofactor reveals latent specificities that are not observed for monomeric Hox factors. The findings from this in vitro platform are consistent with in vivo data, and the “latent specificity” concept serves as a precedent for how the specificities of similar transcription factors might be distinguished in vivo. Importantly, the SELEX-seq platform is flexible and can be used to determine the relative affinities to any DNA sequence for any transcription factor or multiprotein complex.
      datePublished:2014
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Book:
      name:Hox Genes
      isbn:
         978-1-4939-1242-1
         978-1-4939-1241-4
Organization:
      name:Springer New York
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:Columbia University
      address:
         name:Department of Biological Sciences, Columbia University, New York, USA
         type:PostalAddress
      name:University of Massachusetts - Boston
      address:
         name:Department of Biology, University of Massachusetts - Boston, Boston, USA
         type:PostalAddress
      name:Columbia University Medical Center
      address:
         name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
         type:PostalAddress
      name:University of Minnesota Medical School
      address:
         name:Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, USA
         type:PostalAddress
      name:Columbia University Medical Center
      address:
         name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
         type:PostalAddress
      name:Columbia University
      address:
         name:Department of Biological Sciences, Columbia University, New York, USA
         type:PostalAddress
      name:Columbia University
      address:
         name:Department of Applied Physics and Applied Mathematics, Columbia University, New York, USA
         type:PostalAddress
      name:Columbia University
      address:
         name:Department of Biological Sciences, Columbia University, New York, USA
         type:PostalAddress
      name:Columbia University Medical Center
      address:
         name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
         type:PostalAddress
      name:Columbia University
      address:
         name:Department of Biological Sciences, Columbia University, New York, USA
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Todd R. Riley
      affiliation:
            name:Columbia University
            address:
               name:Department of Biological Sciences, Columbia University, New York, USA
               type:PostalAddress
            type:Organization
            name:University of Massachusetts - Boston
            address:
               name:Department of Biology, University of Massachusetts - Boston, Boston, USA
               type:PostalAddress
            type:Organization
      name:Matthew Slattery
      affiliation:
            name:Columbia University Medical Center
            address:
               name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
               type:PostalAddress
            type:Organization
            name:University of Minnesota Medical School
            address:
               name:Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, USA
               type:PostalAddress
            type:Organization
      name:Namiko Abe
      affiliation:
            name:Columbia University Medical Center
            address:
               name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
               type:PostalAddress
            type:Organization
      name:Chaitanya Rastogi
      affiliation:
            name:Columbia University
            address:
               name:Department of Biological Sciences, Columbia University, New York, USA
               type:PostalAddress
            type:Organization
            name:Columbia University
            address:
               name:Department of Applied Physics and Applied Mathematics, Columbia University, New York, USA
               type:PostalAddress
            type:Organization
      name:Dahong Liu
      affiliation:
            name:Columbia University
            address:
               name:Department of Biological Sciences, Columbia University, New York, USA
               type:PostalAddress
            type:Organization
      name:Richard S. Mann
      affiliation:
            name:Columbia University Medical Center
            address:
               name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Harmen J. Bussemaker
      affiliation:
            name:Columbia University
            address:
               name:Department of Biological Sciences, Columbia University, New York, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Biological Sciences, Columbia University, New York, USA
      name:Department of Biology, University of Massachusetts - Boston, Boston, USA
      name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
      name:Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, USA
      name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
      name:Department of Biological Sciences, Columbia University, New York, USA
      name:Department of Applied Physics and Applied Mathematics, Columbia University, New York, USA
      name:Department of Biological Sciences, Columbia University, New York, USA
      name:Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, USA
      name:Department of Biological Sciences, Columbia University, New York, USA
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