MNase-seq Service

MNase-seq (Micrococcal Nuclease Sequencing) is a powerful, high-resolution approach for mapping nucleosome positioning and chromatin accessibility. By leveraging controlled MNase digestion of chromatin, this method reveals how DNA is packaged, where nucleosomes are precisely located, and how accessible each genomic region is to regulatory proteins. Unlike ATAC-seq, which focuses on sharply defined open chromatin peaks, MNase-seq provides genome-wide structural insights spanning accessible, permissive, and repressive chromatin states.

CD BioSciences integrates the most advanced developments in the field—including MNase titration (MACC), MNase-SSP, and histone-IP MNase (h-MACC)—to deliver highly quantitative and unbiased profiling of nucleosome organization.

Introduction to MNase-seq

MNase is an endo/exonuclease that preferentially digests linker DNA while protecting nucleosome-bound DNA fragments (~150 bp). Sequencing these fragments allows direct visualization of:

Modern MNase-seq methodologies also address known limitations of early protocols:

1. Sequence bias (MNase favors AT-rich DNA)
2. Digestion sensitivity (small variations drastically alter results)
3. Underrepresentation of sub-nucleosomal fragments

Newer strategies such as MACC accessibility modeling, q-MNase, and MNase-SSP significantly improve interpretability and biological accuracy.

Fig.1 MNase concentration affects the results of nucleosome occupancy profiling. (Mieczkowski, J., et al., 2016)

Features of MNase-seq

High-Resolution Nucleosome Mapping

MNase-seq precisely defines nucleosome dyad positions and nucleosome spacing, revealing chromatin organization with far higher resolution than ATAC-seq or DNase-seq.

Quantitative Accessibility Through MNase Titration

By integrating multiple MNase digestion levels (light → deep digestion), our service estimates MNase Accessibility (MACC) or q-MNase metrics, resolving:

1. Accessible vs. inaccessible chromatin
2. Fragile vs. stable nucleosomes
3. Regulatory nucleosome remodeling signatures

Superior Detection of Local Chromatin Features

1. TF-bound footprints in nucleosome-adjacent regions
2. Polycomb, HP1, and chromatin compactness signatures
3. Subtle nucleosome phasing across enhancers, promoters, TSS/TES windows

Our Services

To support high-resolution chromatin accessibility and nucleosome positioning studies, CD BioSciences offers a complete MNase-seq service—from experimental planning to data delivery. Our workflow is optimized for both standard mono-nucleosome mapping and quantitative MNase titration approaches (e.g., q-MNase or MACC), enabling flexible applications across cell types, treatment conditions, and chromatin states.

Sample QC & Chromatin Preparation

1. Cell or nucleus isolation
2. Crosslinking optional (native vs. fixed MNase-seq)
3. Chromatin integrity QC

Nase Digestion (Single-Point or Multi-Point Titration)

1. Controlled MNase dosage to generate mono- and oligo-nucleosomes
2. Optional 4-point MNase titration to compute MACC/q-MNase accessibility metrics
3. Size selection to remove high-molecular fragments

Bioinformatic Analysis

1. Alignment & fragment size stratification
2. Nucleosome dyad calling
3. Occupancy and phasing analysis
4. Low-MNase vs. high-MNase comparison
5. MACC / q-MNase-based accessibility scoring

Library Construction & High-Depth Sequencing

1. Short-fragment libraries prepared using optimized adapters
2. Paired-end sequencing for accurate dyad inference
3. Recommended depth: 50–100M PE reads per sample

Supported Sample Types

1. Purified Genomic DNA
2. Cultured Cells (e.g., mammalian)
3. Fresh-Frozen Tissue

1. FFPE Tissue Sections
2. Low-Input and Micro-Dissected Samples
3. Other Types (Please Inquire)

Our Advantages

1. High-Resolution Mapping: Precisely defines nucleosome positions and chromatin structure.
2. Quantitative Accessibility: Supports MACC or q-MNase to quantify chromatin openness.
3. Dual Digestion Strategy: Integrates low- and high-MNase digests for full chromatin profiling.
4. Expert Data Analysis: Includes dyad mapping, phasing, and occupancy scoring.
5. Flexible Sample Types: Optimized for diverse sources from cells to tissues.
6. Integration Ready: Compatible with ATAC-seq, RNA-seq, and ChIP-seq for multi-omic analysis.

Interested in implementing MNase-seq as part of your chromatin accessibility and profiling program? Please contact us for a free consultation, custom workflow design and full project quotation.

Reference

1. Mieczkowski, J., et al. (2016). MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nature communications, 7, 11485.