CUTANA™ meCUT&RUN Kit for DNA Methylation Sequencing

Unlock Deeper Methylome Insights at Lower Cost

Product Description

CUTANA™ meCUT&RUN enriches methylated DNA for streamlined 5-methylcytosine sequencing, delivering high-quality, genome-wide insights at a fraction of the sequencing required for WGBS. 

• Captures 80% of methylated CpGs
• 20-fold reduced sequencing costs
• Robust down to 10,000 cells
• Avoids bisulfite conversion, minimizing bias

CUTANA™ meCUT&RUN: Genome-wide DNA methylation insights for a fraction of the cost!

How it works

The CUTANA™ meCUT&RUN Kit for DNA Methylation Sequencing enables streamlined, high-resolution mapping of DNA methylation at >20-fold reduced sequencing depths compared to whole genome strategies like bisulfite sequencing. In meCUT&RUN, a GST-tagged MeCP2 methyl binding domain binds methylated DNA, directing the selective cleavage and release of DNA methylation-enriched chromatin fragments into solution by an immunotethered nuclease (pAG-MNase). Enriched DNA is separated from bead-bound cells, purified, and prepared for sequencing by one of two methods:

• Option 1 uses a traditional library prep method, such as the CUTANA™ CUT&RUN Library Prep Kit (14-1001-EPC/14-1002-EPC), to provide ~150 bp resolution profiles of DNA methylation enrichment. Only 15-20 million total sequencing reads are required for this strategy, and data are analyzed using standard CUT&RUN bioinformatic pipelines.
• Option 2 uses a cytosine conversion strategy such as Enzymatic Methyl-seq (NEB® EM-seq™, preferred) or bisulfite sequencing to provide base-pair resolution of 5-methylcytosine (5mC). This workflow requires 30-50 million total sequencing reads and is analyzed using standard DNA methylation bioinformatic tools; see User Manual for detailed information.

The meCUT&RUN Kit is designed for 8-strip tubes and multi-channel pipetting, enabling a seamless workflow that maximizes throughput and reproducibility. The kit is compatible with a variety of inputs including cells or nuclei derived from native, cryopreserved, or cross-linked samples. While it is recommended to start with 500,000 cells, comparable data can be generated using as few as 10,000 cells. The low sequencing depth requirements, as well as compatibility with diverse sample inputs and low cell numbers, make this kit an ideal solution for DNA methylation sequencing. 

Figure 1: meCUT&RUN methods

Validation Data

Figure 2: meCUT&RUN DNA fragment size distribution analysis
meCUT&RUN was performed as described in Figure 1. Library DNA was analyzed by Agilent TapeStation®. This analysis confirmed that mononucleosomes were predominantly enriched in meCUT&RUN (~300 bp peaks represent 150 bp nucleosomes + sequencing adapters).

Figure 3: Gene browser tracks
meCUT&RUN was performed as described in Figure 1. A 30 kb window at the AJM1 gene is shown for anti-GST antibody and meCUT&RUN. Tracks are also shown with representative data for meCUT&RUN followed by EM-seq (meCUT&RUN-EM) and whole genome EM-seq (WGEM), using the New England Biolabs NEBNext® Enzymatic Methyl-seq v2 Kit (NEB E8015). The meCUT&RUN kit produced the expected genomic distribution, showing enrichment of methylated DNA that approximates the methylated CpG pattern observed in WGEM. Images were generated using the Integrative Genomics Viewer (IGV, Broad Institute).