Identification of Transcription Factor Binding Sites Using ATAC-seq

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2019 Feb 28

PMID 30808370

Citations 234

Authors

Zhijian Li

Marcel H Schulz

Thomas Look

Matthias Begemann

Martin Zenke

Ivan G Costa

Affiliations

Soon will be listed here.

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.

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