DNA methylation is an epigenetic modification crucial to normal development, with its dysregulation leading to various diseases including cancer. As interest in epigenomics grows, an innovative library prep kit provides researchers with a low-cost yet efficient method for mapping DNA methylation across the genome.
There are massive costs associated with whole-genome bisulfite sequencing for methylation analysis, which requires deep sequencing to obtain comprehensive results. Many enrichment-based approaches diminish these costs, but they may not capture all of the relevant genomic areas prior to sequencing. EpiCypher’s CUTANA™ meCUT&RUN, short for Cleavage Under Targets and Release Using Nuclease, is an innovative DNA methylation profiling assay that allows for high-resolution mapping thanks to the efficient capture of methylated areas.
“It’s built on the CUT&RUN assay,1 which was first described by Peter Skene and Steven Henikoff in 2017,” said Bryan Venters, the senior director of genomic technologies at EpiCypher. “What's novel about meCUT&RUN is that it takes advantage of a naturally occurring 5-methylcytosine reader protein called MeCP2.”
By coupling MeCP2’s natural affinity for methylated DNA with nuclease cleavage, CUTANA™ meCUT&RUN efficiently targets and cuts DNA methylation sites.
EpiCypher
Scientists at EpiCypher engineered MeCP2 to seamlessly work with the existing CUTANA™ CUT&RUN assay, which typically uses antibodies to capture protein-DNA interactions. meCUT&RUN scans the entire genome via MeCP2, and once the protein binds methylated DNA, an associated nuclease cleaves and releases the targeted chromatin fragments into solution. Researchers can then purify the enriched DNA and prepare it for sequencing to identify methylated areas throughout the genome.
meCUT&RUN can capture 80 percent of DNA methylation with an input as low as 10,000 cells from native, cryopreserved, or cross-linked samples. Sequencing experiments using meCUT&RUN kits for enrichment and library preparation require 20-fold fewer sequencing reads compared to whole-genome bisulfite sequencing.
“CUTANA™ meCUT&RUN was introduced to the market earlier this year, and the response has been fantastic,” said Venters. “Scientists interested in DNA methylation love this assay because it can capture nearly all the DNA methylation locations in a simple, cost-effective assay.”
- Skene PJ, Henikoff S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife. 2017;6:e21856.
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