ArticleNucleic acids research2019
Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis.Genome biology · 2025Article
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel.BMC genomics · 2024Article
- Characterization of the DNA accessibility of chloroplast genomes in grasses.Communications biology · 2024Article
- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
- One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.Cell chemical biology · 2024Article
- Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids.Nature cell biology · 2023Article
- Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.Nucleic acids research · 2023Article
- Multimodal analysis methods in predictive biomedicine.Computational and structural biotechnology journal · 2023Review
- TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors.GigaScience · 2022Article
- Increased chromatin accessibility facilitates intron retention in specific cell differentiation states.Nucleic acids research · 2022Article
- Multi-omics analysis for potential inflammation-related genes involved in tumour immune evasion via extended application of epigenetic data.Open biology · 2022Article
- Broad domains of histone marks in the highly compactGenome research · 2022Article
- Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.Cell genomics · 2022Article
- Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler.Nature neuroscience · 2022Article
- Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification.NAR genomics and bioinformatics · 2021Article
- The native cistrome and sequence motif families of the maize ear.PLoS genetics · 2021Article
- Article
- Tumor suppressor p53: from engaging DNA to target gene regulation.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin accessibility maps are important for the functional interpretation of the genome. Here, we systematically analysed assay specific differences between DNase I-seq, ATAC-seq and NOMe-seq in a side by side experimental and bioinformatic setup. We observe that most prominent nucleosome depleted regions (NDRs, e.g. in promoters) are roboustly called by all three or at least two assays. However, we also find a high proportion of assay specific NDRs that are often 'called' by only one of the assays. We show evidence that these assay specific NDRs are indeed genuine open chromatin sites and contribute important information for accurate gene expression prediction. While technically ATAC-seq and DNase I-seq provide a superb high NDR calling rate for relatively low sequencing costs in comparison to NOMe-seq, NOMe-seq singles out for its genome-wide coverage allowing to not only detect NDRs but also endogenous DNA methylation and as we show here genome wide segmentation into heterochromatic B domains and local phasing of nucleosomes outside of NDRs. In summary, our comparisons strongly suggest to consider assay specific differences for the experimental design and for generalized and comparative functional interpretations.
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