NOMeseq

NOMeseq, often written NOMe-seq and expanding to nucleosome occupancy and methylome sequencing, is a genome-wide assay that concurrently maps chromatin accessibility and DNA methylation. It provides integrated information about regulatory landscapes by reading methylation patterns that reflect both nucleosome positioning and CpG methylation status on the same DNA molecule.

Method overview: The method uses an ex vivo methyltransferase to label accessible DNA. Nuclei are treated with a GpC methyltransferase, which methylates GpC dinucleotides in regions not protected by nucleosomes or bound factors. DNA is then extracted, subjected to bisulfite conversion, and sequenced. In the resulting data, endogenous CpG methylation reports the native methylome, while the newly introduced GpC methylation marks indicate chromatin accessibility. Analysis yields per-molecule information on both methylation state and nucleosome occupancy, enabling fine-grained maps of regulatory elements and chromatin structure.

Applications: NOMeseq has been used to characterize nucleosome landscapes and methylation in diverse cell types, developmental stages, and disease contexts. It supports discovery of regulatory elements, assessment of allele-specific methylation, and studies of how chromatin accessibility relates to DNA methylation across the genome. The single-molecule readout allows phasing of methylation and accessibility signals along long DNA fragments.

Limitations and considerations: The technique requires intact nuclei and careful experimental handling; input material can be limiting for some primary samples, and data analysis is complex due to the dual methylation signals. Technical biases in methyltransferase activity and bisulfite sequencing can influence results, and interpretation depends on robust computational pipelines.

History: NOMe-seq was introduced in the early 2010s as a method to couple chromatin accessibility with DNA methylation in a single assay, enabling integrated epigenomic insights.