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

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article number125
JournalGenome biology
Issue number1
StatePublished - Dec 2023

Bibliographical note

Funding Information:
These studies were supported by funding from NHLBI (P01HL160476), Department of Defense (W81XWH2110606) and Minnesota Regenerative Medicine.

Publisher Copyright:
© 2023, The Author(s).


  • Ascl1
  • Etv2
  • Klf4
  • Nucleosomal DNA
  • Oct4
  • Pioneer factors
  • Sox2

PubMed: MeSH publication types

  • Journal Article
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural


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