Journal
GENOME BIOLOGY
Volume 20, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-019-1642-2
Keywords
Computational footprinting; Open chromatin; ATAC-seq; Cleavage bias
Funding
- Interdisciplinary Center for Clinical Research (IZKF) Aachen
- RWTH Aachen University Medical School, Aachen, Germany
- Deutsche Forschungsgemeinschaft [DFG-GE 2811/3]
- ITC RWTH Aachen University [rwth0233]
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Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.
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