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

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.

SUBMITTER: Gong W

PROVIDER: S-EPMC10204251 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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

Gong Wuming W Dsouza Nikita N Garry Daniel J DJ

Genome biology 20230522 1

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 inducti ...[more]

PMID: 37218013

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