Cleavage (geology)

Footprinting

Transcription factor

Biology

Promoter

Gene

Gene expression

Genome

Paleontology

Transposase

DNA footprinting

Computational biology

Nucleosome

DNA-binding protein

DNA binding site

Fracture (geology)

Transposable element

Genetics

Chromatin

Genome biology

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.

Identification of transcription factor binding sites using ATAC-seq