{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE346nnn/GSE346229/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Genomics"],"species":["Saccharomyces cerevisiae"],"gds_type":["Genome binding/occupancy profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE346229"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility [ATAC-seq]","description":"Chromatin accessibility shapes the ability of transcription factors (TFs) and the transcriptional machinery to engage genomic DNA and therefore plays a central role in gene regulation. Two widely used approaches for profiling chromatin accessibility are micrococcal nuclease (MNase)-seq and assay for transposase-accessible chromatin (ATAC)-seq. ATAC-seq peaks are often thought to be equivalent to nucleosome-depleted regions (NDRs) that are defined by MNase-seq; however, these two measurements have not been systematically compared. Here, we performed a side-by-side comparison of ATAC-seq and MNase-seq in budding yeast and found a substantial discrepancy between ATAC-seq peaks and MNase-defined NDRs. This discrepancy is not primarily explained by intrinsic differences between MNase and Tn5 enzymatic activity. Instead, ATAC-seq peaks and NDRs capture distinct chromatin states. Specifically, ATAC-seq peaks are enriched at dynamic nucleosomes associated with transcriptional co-regulators, including SAGA and SWI/SNF, whereas NDRs mark more static nucleosome-free regions at promoters. Depletion of SWI/SNF, but not RSC, reduces ATAC-seq signals. Generation of NDRs and ATAC-seq peaks requires distinct TF properties, and native TFs differ in their ability to produce these two types of open chromatin. Finally, we show that the functional distinction between ATAC-seq peaks and NDRs are widespread across eukaryotic species, including human cells. Together, our results provide new insights into the biological meaning of chromatin accessibility measured by these two assays.","dates":{"publication":"2026/09/08"},"accession":"GSE346229","cross_references":{"GSM":["GSM10029266","GSM10029288","GSM10029265","GSM10029287","GSM10029264","GSM10029286","GSM10029285","GSM10029263","GSM10029269","GSM10029268","GSM10029267","GSM10029280","GSM10029262","GSM10029284","GSM10029261","GSM10029283","GSM10029282","GSM10029260","GSM10029281","GSM10029277","GSM10029255","GSM10029276","GSM10029254","GSM10029275","GSM10029274","GSM10029259","GSM10029258","GSM10029279","GSM10029257","GSM10029256","GSM10029278","GSM10029273","GSM10029272","GSM10029271","GSM10029270"],"GPL":["31112"],"GSE":["346229"],"taxon":["Saccharomyces cerevisiae"]}}