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A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility

Nature Biotechnology volume 36, pages 521529 (2018) | Download Citation

Abstract

No existing method to characterize transcription factor (TF) binding to DNA allows genome-wide measurement of all TF-binding activity in cells. Here we present a massively parallel protein activity assay, active TF identification (ATI), that measures the DNA-binding activity of all TFs in cell or tissue extracts. ATI is based on electrophoretic separation of protein-bound DNA sequences from a highly complex DNA library and subsequent mass-spectrometric identification of the DNA-bound proteins. We applied ATI to four mouse tissues and mouse embryonic stem cells and found that, in a given tissue or cell type, a small set of TFs, which bound to only 10 distinct motifs, displayed strong DNA-binding activity. Some of these TFs were found in all cell types, whereas others were specific TFs known to determine cell fate in the analyzed tissue or cell type. We also show that a small number of TFs determined the accessible chromatin landscape of a cell, suggesting that gene regulatory logic may be simpler than previously appreciated.

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Acknowledgements

We thank J. Yan, E. Kaasinen, B. Schmierer and Y. Yin for critical review of the manuscript, and S. Augsten, L. Hu and P. Pandey for technical assistance. This work was supported by the Center for Innovative Medicine at the Karolinska Institutet (2015–2017; J.T.), the Knut and Alice Wallenberg Foundation (KAW 2013.0088; J.T.), the Göran Gustafsson Foundation (2011–2013; J.T.) and the Swedish Research Council (Vetenskapsrådet; Rådsprofessorprogrammet D0815201; J.T.).

Author information

Affiliations

  1. Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

    • Bei Wei
    • , Arttu Jolma
    • , Fan Zhong
    • , Fangjie Zhu
    • , Inderpreet Sur
    • , Minna Taipale
    •  & Jussi Taipale
  2. Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland.

    • Biswajyoti Sahu
    • , Teemu Kivioja
    •  & Jussi Taipale
  3. Department of Oncology–Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.

    • Lukas M Orre
    •  & Janne Lehtiö
  4. Department of Biochemistry, University of Cambridge, Cambridge, UK.

    • Jussi Taipale

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Contributions

I.S. collected mouse tissue samples; B.W. extracted proteins, performed ATI experiments and analyzed the data; F. Zhong and F. Zhu performed the DHS analysis; B.S. performed the iHep reprogramming experiment; L.M.O. and J.L. performed the MS experiments and data analysis; A.J., T.K. and M.T. helped to supervise the project or related experiments; and B.W. and J.T. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jussi Taipale.

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    Comparison of the motif analysis result and MS identification result in ATI from nuclear extract of mouse ES cells.

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https://doi.org/10.1038/nbt.4138

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