Genome Biology (May 2023)

SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors

  • Wuming Gong,
  • Nikita Dsouza,
  • Daniel J. Garry

DOI
https://doi.org/10.1186/s13059-023-02954-5
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 28

Abstract

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Abstract Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor-induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data.

Keywords