Genome-wide binding analysis of 195 DNA binding proteins reveals “reservoir” promoters and human specific SVA-repeat family regulation

Michael J. Smallegan; Soraya Shehata; Savannah F. Spradlin; Alison Swearingen; Graycen Wheeler; Arpan Das; Giulia Corbet; Benjamin Nebenfuehr; Daniel Ahrens; Devin Tauber; Shelby Lennon; Kevin Choi; Thao Huynh; Tom Wieser; Kristen Schneider; Michael Bradshaw; Joel Basken; Maria Lai; Timothy Read; Matt Hynes-Grace; Dan Timmons; Jon Demasi; John L. Rinn

doi:10.1371/journal.pone.0237055

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Research Article

Genome-wide binding analysis of 195 DNA binding proteins reveals “reservoir” promoters and human specific SVA-repeat family regulation

Michael J. Smallegan ,

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

* E-mail: michael.smallegan@colorado.edu (MS); john.rinn@colorado.edu (JR)

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Molecular and Cellular Biology, University of Colorado Boulder, Boulder, Colorado, United States of America

https://orcid.org/0000-0002-5919-6736

⨯
Soraya Shehata ,

Contributed equally to this work with: Soraya Shehata, Savannah F. Spradlin, Alison Swearingen, Graycen Wheeler

Roles Formal analysis, Software, Visualization, Writing – original draft

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Savannah F. Spradlin ,

Contributed equally to this work with: Soraya Shehata, Savannah F. Spradlin, Alison Swearingen, Graycen Wheeler

Roles Formal analysis, Software, Visualization, Writing – original draft

Affiliations Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Alison Swearingen ,

Contributed equally to this work with: Soraya Shehata, Savannah F. Spradlin, Alison Swearingen, Graycen Wheeler

Roles Formal analysis, Software, Visualization, Writing – original draft

Affiliations Department of Molecular and Cellular Biology, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America

https://orcid.org/0000-0001-7072-5603

⨯
Graycen Wheeler ,

Contributed equally to this work with: Soraya Shehata, Savannah F. Spradlin, Alison Swearingen, Graycen Wheeler

Roles Formal analysis, Resources, Visualization, Writing – original draft

Affiliations Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Arpan Das,

Roles Formal analysis, Software, Visualization

Affiliations Department of Molecular and Cellular Biology, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Giulia Corbet,

Roles Formal analysis, Software, Visualization

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Benjamin Nebenfuehr,

Roles Formal analysis, Software, Visualization

Affiliations Department of Molecular and Cellular Biology, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America

https://orcid.org/0000-0002-1561-6815

⨯
Daniel Ahrens,

Roles Formal analysis, Software, Visualization

Affiliations Department of Molecular and Cellular Biology, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Devin Tauber,

Roles Formal analysis, Software, Visualization

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Shelby Lennon,

Roles Formal analysis, Software, Visualization

Affiliations Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America

https://orcid.org/0000-0002-4049-8865

⨯
Kevin Choi,

Roles Formal analysis, Software, Visualization

Affiliations Department of Molecular and Cellular Biology, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Thao Huynh,

Roles Formal analysis, Software, Visualization

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Tom Wieser,

Roles Formal analysis, Software, Visualization

Affiliations Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Kristen Schneider,

Roles Formal analysis, Software, Visualization

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Michael Bradshaw,

Roles Formal analysis, Software, Visualization

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Biochemistry 5631 Spring 2020, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Joel Basken,

Roles Investigation, Resources

Affiliation Arpeggio Biosciences, Boulder, Colorado, United States of America

https://orcid.org/0000-0003-3205-177X

⨯
Maria Lai,

Roles Investigation, Resources

Affiliation Arpeggio Biosciences, Boulder, Colorado, United States of America
⨯
Timothy Read,

Roles Investigation, Resources

Affiliation Arpeggio Biosciences, Boulder, Colorado, United States of America
⨯
Matt Hynes-Grace,

Roles Resources

Affiliation BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Dan Timmons,

Roles Resources

Affiliation BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
Jon Demasi,

Roles Resources

Affiliation BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
[ ... ],
John L. Rinn

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

* E-mail: michael.smallegan@colorado.edu (MS); john.rinn@colorado.edu (JR)

Affiliations BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Molecular and Cellular Biology, University of Colorado Boulder, Boulder, Colorado, United States of America, Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
⨯
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Genome-wide binding analysis of 195 DNA binding proteins reveals “reservoir” promoters and human specific SVA-repeat family regulation

Michael J. Smallegan,
Soraya Shehata,
Savannah F. Spradlin,
Alison Swearingen,
Graycen Wheeler,
Arpan Das,
Giulia Corbet,
Benjamin Nebenfuehr,
Daniel Ahrens,
Devin Tauber

Published: June 24, 2021
https://doi.org/10.1371/journal.pone.0237055
See the preprint

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DNA-binding proteins
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Binding analysis
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DNA replication
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