Work

Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays

Year: 2026

Type: article

Abstract: Transcription factors (TFs) are central to gene regulation and play critical roles in development, cellular homeostasis and disease. The ability to accurately measure TF activity is essential to understanding how TFs respond to signals and regulate target genes. In one commonly used approach, activities of TFs are computationally inferred from genome-wide chromatin accessibility data (ATAC-seq). However, it has remained unclear how well these inferences reflect actual regulatory activity of TFs. An alternative approach employs a collection of synthetic reporters that are designed to each probe the regulatory activity of a single TF. In this study, we systematically compared TF activities as inferred by ATAC-seq with those measured by multiplexed reporters, across diverse perturbations known to alter specific TF activities. We observed considerable overlap between the two methods, but also notable discrepancies. Our findings suggest that reporter assays and chromatin-based inference capture distinct aspects of TF function: reporter assays are more sensitive to signal-responsive TFs, while ATAC-seq better detects chromatin-modifying TFs.

Source: Molecular Systems Biology

DOI: 10.1038/s44320-026-00240-7

Authors: Max Trauernicht, Vinícius H Franceschini-Santos, Hatice Yücel, Teodora Filipovska, Bas van Steensel

Institution: The Netherlands Cancer Institute

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $7,990

Funders: Oncode Institute, European Research Council