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

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…

• DZ
  Deutsches Zentrum für Herz-Kreislaufforschung
• DF
  Deutsche Forschungsgemeinschaft

  Awards: 284237345, 390649896, Cardio-Pulmonary Institute (CPI), EXC 2026, Project ID: 390649896, KFO309, Project ID: 390649896
• BF
  Bundesministerium für Bildung und Forschung
• M
  Max-Planck-Gesellschaft
• CI
  Cardio-Pulmonary Institute

  Awards: 390649896, EXC 2026, Project ID: 390649896, EXC 2026