ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility [ATAC-seq]

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE346229 | GEO | 2026/09/08

REPOSITORIES: GEO