Work

Protocol for discovering genetic variants associated with ATAC-seq footprint-inferred transcription factor binding

Year: 2025

Type: article

Abstract: Transcription factor (TF) binding is detectable in assay for transposase-accessible chromatin using sequencing (ATAC-seq) experiments, where bound TFs block transposase insertions, leaving a depletion of insertions known as a “footprint.” Here, we present a computational protocol for detecting genetic variants associated with footprint-inferred TF binding. We describe steps to run the PRINT footprinting software to quantify TF binding likelihood at variants across multiple genotyped ATAC-seq samples and then run regressions to measure genetic associations. This protocol can implicate causal variants in disease-associated loci. For complete details on the use and execution of this protocol, please refer to Dudek et al. 1

Source: STAR Protocols

DOI: 10.1016/j.xpro.2025.104148

Authors: Max F. Dudek, Brandon M. Wenz, Benjamin F. Voight, Laura Almasy, Struan F.A. Grant

Institutions: Children's Hospital of Philadelphia, University of Pennsylvania

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,550