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

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 perform a side-by-side comparison of ATAC-seq and MNase-seq in budding yeast and find a large discrepancy between ATAC-seq peaks and MNase-defined NDRs. We show that this discrepancy is not primarily due to the 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 ATAC- NDRs mark more static nucleosome-free regions at promoters. Depletion of SWI/SNF reduces ATAC-seq signals without affecting most NDRs. 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 find that the functional distinctions 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.