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Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

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  • Colin R. Lickwar

    (Carolina Center for the Genome Sciences, Curriculum in Genetics and Molecular Biology, and Lineberger Comprehensive Cancer Center, CB 3280, 408 Fordham Hall, University of North Carolina at Chapel Hill)

  • Florian Mueller

    (LRBGE-National Cancer Institute, The National Institutes of Health, 41 Library Drive, Bethesda, Maryland 20892, USA
    Institut Pasteur, Groupe Imagerie et Modélisation, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, 25-28 rue du Docteur Roux, 75015 Paris, France
    Present addresses: Institut de Biologie de l’Ecole Normale Supérieure, Functional Imaging of Transcription, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, 45 rue d’Ulm, 75005 Paris, France (F.M.); Office of Physical Sciences-Oncology, CSSI, NCI, NIH, 31 Center Drive, Room 10A03, Bethesda, Maryland 20892, USA (S.E.H.).)

  • Sean E. Hanlon

    (Carolina Center for the Genome Sciences, Curriculum in Genetics and Molecular Biology, and Lineberger Comprehensive Cancer Center, CB 3280, 408 Fordham Hall, University of North Carolina at Chapel Hill
    Present addresses: Institut de Biologie de l’Ecole Normale Supérieure, Functional Imaging of Transcription, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, 45 rue d’Ulm, 75005 Paris, France (F.M.); Office of Physical Sciences-Oncology, CSSI, NCI, NIH, 31 Center Drive, Room 10A03, Bethesda, Maryland 20892, USA (S.E.H.).)

  • James G. McNally

    (LRBGE-National Cancer Institute, The National Institutes of Health, 41 Library Drive, Bethesda, Maryland 20892, USA)

  • Jason D. Lieb

    (Carolina Center for the Genome Sciences, Curriculum in Genetics and Molecular Biology, and Lineberger Comprehensive Cancer Center, CB 3280, 408 Fordham Hall, University of North Carolina at Chapel Hill)

Abstract

Competition ChIP with a sequence-specific S. cerevisiae transcription factor, Rap1, reveals that long Rap1 residence is coupled to transcriptional activation, whereas fast binding turnover is linked to low transcriptional output, suggesting that DNA-binding events that appear identical by conventional ChIP may have different underlying modes of interaction, leading to opposing functional outcomes.

Suggested Citation

  • Colin R. Lickwar & Florian Mueller & Sean E. Hanlon & James G. McNally & Jason D. Lieb, 2012. "Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function," Nature, Nature, vol. 484(7393), pages 251-255, April.
    • Handle: RePEc:nat:nature:v:484:y:2012:i:7393:d:10.1038_nature10985
    DOI: 10.1038/nature10985
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    Cited by:

    1. Ziad Ibrahim & Tao Wang & Olivier Destaing & Nicola Salvi & Naghmeh Hoghoughi & Clovis Chabert & Alexandra Rusu & Jinjun Gao & Leonardo Feletto & Nicolas Reynoird & Thomas Schalch & Yingming Zhao & Ma, 2022. "Structural insights into p300 regulation and acetylation-dependent genome organisation," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
    2. Marta Losa & Iros Barozzi & Marco Osterwalder & Viviana Hermosilla-Aguayo & Angela Morabito & Brandon H. Chacón & Peyman Zarrineh & Ausra Girdziusaite & Jean Denis Benazet & Jianjian Zhu & Susan Macke, 2023. "A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    3. Zing Tsung-Yeh Tsai & Shin-Han Shiu & Huai-Kuang Tsai, 2015. "Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-22, August.
    4. Amir Shahein & Maria López-Malo & Ivan Istomin & Evan J. Olson & Shiyu Cheng & Sebastian J. Maerkl, 2022. "Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Pakavarin Louphrasitthiphol & Alessia Loffreda & Vivian Pogenberg & Sarah Picaud & Alexander Schepsky & Hans Friedrichsen & Zhiqiang Zeng & Anahita Lashgari & Benjamin Thomas & E. Elizabeth Patton & M, 2023. "Acetylation reprograms MITF target selectivity and residence time," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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