Advertisement
Research Article

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

  • Robert K. Bradley equal contributor,

    equal contributor Contributed equally to this work with: Robert K. Bradley, Xiao-Yong Li

    Affiliations: Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America

    X
  • Xiao-Yong Li equal contributor,

    equal contributor Contributed equally to this work with: Robert K. Bradley, Xiao-Yong Li

    Affiliations: Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America

    X
  • Cole Trapnell,

    Affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America

    X
  • Stuart Davidson,

    Affiliation: Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America

    X
  • Lior Pachter,

    Affiliations: Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America

    X
  • Hou Cheng Chu,

    Affiliation: Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America

    X
  • Leath A. Tonkin,

    Affiliations: California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States of America, Vincent J. Coates Genome Sequencing Laboratory, University of California Berkeley, Berkeley, California, United States of America

    X
  • Mark D. Biggin,

    Affiliation: Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America

    X
  • Michael B. Eisen mail

    mbeisen@lbl.gov

    Affiliations: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America, California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States of America

    X
  • Published: March 23, 2010
  • DOI: 10.1371/journal.pbio.1000343

About the Authors

Robert K. Bradley, Lior Pachter
Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
Robert K. Bradley, Lior Pachter, Michael B. Eisen
Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
Xiao-Yong Li, Michael B. Eisen
Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
Xiao-Yong Li, Stuart Davidson, Hou Cheng Chu, Mark D. Biggin, Michael B. Eisen
Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America
Cole Trapnell
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
Leath A. Tonkin, Michael B. Eisen
California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States of America
Leath A. Tonkin
Vincent J. Coates Genome Sequencing Laboratory, University of California Berkeley, Berkeley, California, United States of America

Corresponding Author

Email: mbeisen@lbl.gov

Competing Interests

MBE is a co-founder and member of the Board of Directors of PLoS.

Author Contributions

The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: RKB XYL MDB MBE. Performed the experiments: XYL HCC LAT. Analyzed the data: RKB CT SD LP MBE. Contributed reagents/materials/analysis tools: RKB CT LAT. Wrote the paper: RKB MBE.