Abstract:
: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.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Li Z,Schulz MH,Look T,Begemann M,Zenke M,Costa IGdoi
10.1186/s13059-019-1642-2subject
Has Abstractpub_date
2019-02-26 00:00:00pages
45issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-019-1642-2journal_volume
20pub_type
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