Methylome Analysis

DNA methylation is the most studied form of epigenetic modification of the genome. Thought primarily to be related to the regulation of gene expression via the inhibition of transcription factor binding, analysis of methylated cytosines within a genome, and across a species’ genomes, can shed light on which genes and regulatory elements are required, or not, at a given point in time. Therefore, the methylome – a genome’s collection of methyl marks – is a changeable snapshot of an organism’s (or a population’s) genomic response to its environment.  
Historically, whole genome bisulfite sequencing (WGBS) has been the gold standard technique for methyl sequencing, but it relies on harsh chemical treatments at high temperatures that were extremely damaging to DNA. In the wake of bisulfite conversion, the DNA sample was often so damaged that the resulting libraries were significantly shortened and more difficult to sequence. It was these challenges with bisulfite sequencing that led to the development of the NEBNext® Enzymatic Methyl-seq (EM-seq™) Kit and now the NEBNext Enzymatic 5hmC-seq Kit.

This animated workflow will introduce the NEBNext Enzymatic Methyl-seq Kit’s gentler alternative to bisulfite-based cytosine conversion.


Figure 1: NEBNext Enzymatic Methyl-seq and Sodium Bisulfite Conversion Methods

The EM-seq kit is a combination of new reagents for enzymatic cytosine protection and conversion and the trusted Ultra® II DNA library prep reagents. The addition of Q5U®, a modified version of Q5® High-Fidelity DNA Polymerase, enables amplification through the uracil-containing converted DNA. The result is superior detection of CpGs with fewer sequencing reads. 
For a closer look at the extensive performance data behind EM-seq, download our technical note

The EM-seq product line has now been expanded to enable the specific detection of 5hmC at the single base level, with the NEBNext Enzymatic 5hmC-seq Kit.
The EpiMark® suite of products were the first generation of New England Biolabs’ epigenetics offering. You can find the current list of available EpiMark products here. 


Figure 2: E5hmC-seq conversion method


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FAQs for Methylome Analysis
Application Notes for Methylome Analysis
Microbiome DNA Enrichment Workflow


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