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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

Author

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  • Mette Bentsen

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • Philipp Goymann

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • Hendrik Schultheis

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • Kathrin Klee

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • Anastasiia Petrova

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • René Wiegandt

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • Annika Fust

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • Jens Preussner

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research
    German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main)

  • Carsten Kuenne

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research)

  • Thomas Braun

    (German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main
    Max Planck Institute for Heart and Lung Research)

  • Johnny Kim

    (German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main
    Max Planck Institute for Heart and Lung Research)

  • Mario Looso

    (Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research
    German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main)

Abstract

While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.

Suggested Citation

  • Mette Bentsen & Philipp Goymann & Hendrik Schultheis & Kathrin Klee & Anastasiia Petrova & René Wiegandt & Annika Fust & Jens Preussner & Carsten Kuenne & Thomas Braun & Johnny Kim & Mario Looso, 2020. "ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18035-1
    DOI: 10.1038/s41467-020-18035-1
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