ArticleEpigenetics & chromatin2020
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation.
Article in Epigenetics & chromatin, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 105 citations in OpenAlex.
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- DNA-damage dependent interaction of Orc6 to SMARCA1 in S-phase modulates chromatin remodeling.Nucleic acids research · 2026Article
- Organ-Specific and Conserved Regulatory Logic Orchestrates Gene Expression in the Embryonic Mesothelium.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Folate-dependent one-carbon metabolism controls meiotic and post-meiotic epigenome remodeling in the male germline.bioRxiv : the preprint server for biology · 2026Article
- Article
- Tumor-specific lncRNA IGF1R-AS1 trans-regulates chromatin interactions associated with oncogenic MYC signaling.Nature communications · 2026Article
- Deep Invaginations of Nuclear Envelope Coordinate Spatial Organization of Chromatin in Epithelium.bioRxiv : the preprint server for biology · 2026Article
- SoxB1-mediated chromatin remodeling promotes sensory neuron differentiation in planarians.Genetics · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- SoxB1-Mediated Chromatin Remodeling Promotes Sensory Neuron Differentiation in Planarians.bioRxiv : the preprint server for biology · 2025Article
- Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach.Plant & cell physiology · 2025Article
- The SWI/SNF-related protein SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer.Molecular cell · 2025Article
- Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments.Nucleic acids research · 2025Article
- Selecting ChIP-seq normalization methods from the perspective of their technical conditions.Briefings in bioinformatics · 2025Article
- Large-scale discovery of chromatin dysregulation induced by oncofusions and other protein-coding variants.Nature biotechnology · 2025Article
- METTL3-dependent m6A RNA methylation regulates transposable elements and represses human naïve pluripotency through transposable element-derived enhancers.Nucleic acids research · 2025Article
- Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.BMC genomics · 2025Article
- DUBR non-coding RNA regulates gene expression by affecting AP-1 enhancer accessibility.Functional & integrative genomics · 2025Article
- Chromatin remodeling protein BPTF mediates chromatin accessibility at gene promoters in planarian stem cells.BMC genomics · 2025Article
- Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3.Communications biology · 2025Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundChromatin dysregulation is associated with developmental disorders and cancer. Numerous methods for measuring genome-wide chromatin accessibility have been developed in the genomic era to interrogate the function of chromatin regulators. A recent technique which has gained widespread use due to speed and low input requirements with native chromatin is the Assay for Transposase-Accessible Chromatin, or ATAC-seq. Biologists have since used this method to compare chromatin accessibility between two cellular conditions. However, approaches for calculating differential accessibility can yield conflicting results, and little emphasis is placed on choice of normalization method during differential ATAC-seq analysis, especially when global chromatin alterations might be expected.
resultsUsing an in vivo ATAC-seq data set generated in our recent report, we observed differences in chromatin accessibility patterns depending on the data normalization method used to calculate differential accessibility. This observation was further verified on published ATAC-seq data from yeast. We propose a generalized workflow for differential accessibility analysis using ATAC-seq data. We further show this workflow identifies sites of differential chromatin accessibility that correlate with gene expression and is sensitive to differential analysis using negative controls.
conclusionsWe argue that researchers should systematically compare multiple normalization methods before continuing with differential accessibility analysis. ATAC-seq users should be aware of the interpretations of potential bias within experimental data and the assumptions of the normalization method implemented.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.