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

By Mette Bentsen, Philipp Goymann, Hendrik Schultheis, Anastasiia Petrova, Kathrin Klee, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Johnny Kim, Mario Looso

Posted 09 Dec 2019
bioRxiv DOI: 10.1101/869560

While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational method implementing both footprinting, visualization and downstream analysis has hindered the widespread application of this method. Here we present TOBIAS, a comprehensive footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TF simultaneously. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation (ZGA) in both humans and mice, and explore how the TF Dux activates cascades of TF, binds to repeat elements and induces expression of novel genetic elements. TOBIAS is freely available at: https://github.com/loosolab/TOBIAS.

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