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…
Chromatin accessibility is crucial for gene regulation, and two primary methods to assess it are micrococcal nuclease (MNase)-seq and assay for transposase-accessible chromatin (ATAC)-seq. While ATAC-seq peaks are often equated with nucleosome-depleted regions (NDRs) defined by MNase-seq, a recent study has analyzed both techniques in budding yeast and discovered significant differences between the two.
These findings suggest that ATAC-seq peaks and NDRs identify distinct chromatin states. The ATAC-seq peaks are associated with dynamic nucleosomes that interact with transcriptional co-regulators such as SAGA and SWI/SNF, while ATAC-NDRs mark more stable nucleosome-free regions near promoter regions. The study also reveals that the depletion of SWI/SNF impacts ATAC-seq signals but does not significantly alter NDRs.
Moreover, the formation of NDRs and ATAC-seq peaks relies on different transcription factor (TF) characteristics, and native TFs exhibit varying abilities to generate these two types of open chromatin. Notably, the functional distinctions between ATAC-seq peaks and NDRs are consistently observed across various eukaryotic species, including human cells.
These results offer novel insights into the biological implications of chromatin accessibility as measured by ATAC-seq and MNase-seq.
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