Sharim, H. et al. Genome Res. 29, 646–656 (2019).
Methylation of cytosine adjacent to a guanine is a hallmark of many functional elements in the human genome. CpG methylation patterns are most often studied at the population level by means of bisulfite conversion followed by high-throughput sequencing. To investigate methylation at the level of individual DNA molecules, Sharim et al. developed reduced-representation optical methylation mapping (ROM). They use a bacterial methyltransferase that is engineered to incorporate a fluorophore at a TCGA motif only if the C is not methylated. When combined with traditional optical mapping, which labels a region of interest and visualizes the labels on the DNA stretched out in a nanochannel, ROM provides information on the methylation state of 10-kb windows along the human genome. The researchers quantified the methylation state and copy number of DNA tandem repeats, regions that are challenging to resolve by sequencing. They demonstrated that ROM can be used to diagnose a form of muscular dystrophy related to a reduction in the number of tandem repeats on chromosome 4.
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Rusk, N. Optically mapping methylation. Nat Methods 16, 362 (2019). https://doi.org/10.1038/s41592-019-0420-0