MNaseseq

MNaseseq is a genome-wide sequencing method designed to map chromatin structure by profiling nucleosome occupancy. The technique builds on the principle that micrococcal nuclease preferentially digests linker DNA between nucleosomes, allowing researchers to infer nucleosome positions and chromatin organization across the genome. By generating high-resolution maps of where nucleosomes are positioned, MNaseseq provides insights into regulatory regions, transcription factor access, and the broader organization of chromatin in different cell types and conditions.

In practice, chromatin is isolated and subjected to micrococcal nuclease digestion under controlled conditions to yield predominantly mononucleosome-sized DNA fragments. These fragments are then prepared for high-throughput sequencing, and the resulting reads are aligned to a reference genome. The density and distribution of mapped reads reflect nucleosome occupancy, while regions with reduced signal indicate nucleosome-depleted or open chromatin. The method typically achieves near-nucleosome resolution, enabling detailed analysis of how nucleosome positioning correlates with gene expression and regulatory element activity.

History and scope: MNaseseq evolved from earlier MNase-seq approaches developed in the 2000s as a means to study chromatin organization. It has been applied across a range of organisms and cell types to compare nucleosome landscapes under different developmental stages, environmental conditions, or disease states. Limitations include potential biases from MNase digestion preferences and the need for carefully controlled experimental conditions. Results are commonly interpreted alongside complementary assays of chromatin accessibility, such as ATAC-seq or NOMe-seq, to provide a more comprehensive view of genome regulation.