ArticleGenome biology2019
Identification of transcription factor binding sites using ATAC-seq.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 304 papers.
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Who cites it
304 citing papers in PubMed.
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- Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina.PLoS genetics · 2026Article
- Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.Nature neuroscience · 2026Article
- Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.Genomics, proteomics & bioinformatics · 2026Article
244 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.
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