NOMe-Seq
NOMe-Seq
NOMe-Seq is a single-molecule, high-resolution nucleosome positioning assay. This method is based on the ability of the GpC methyltransferase M.CviPI to methylate GpC sites that are not bound by nucleosomes, to create a digital footprint of nucleosome positioning. M.CviPI can map nucleosome positions at CpG-poor promoters, irrespective of their endogenous methylation status. In this method, native chromatin is treated with M.CviPI, following which the DNA is treated with sodium bisulfite and subjected to WGBS. From these data, CpG methylation patterns as well as nucleosome-free regions (GpC methylation) can be identified.1
Pros:
- High resolution
Cons:
- Relies on the presence of GpC residues2
- NOMe-Seq: Kelly T. K., Liu Y., Lay F. D., Liang G., Berman B. P. and Jones P. A. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 2012;22:2497-2506
- 1. Wallner S., Schroder C., Leitao E., et al. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016;9:33
- 2. Ishii H., Kadonaga J. T. and Ren B. MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A. 2015;112:E3457-3465
- Lay F. D., Kelly T. K. and Jones P. A. Nucleosome Occupancy and Methylome Sequencing (NOMe-seq). Methods Mol Biol. 2018;1708:267-284
- Wallner S., Schroder C., Leitao E., Berulava T., Haak C., et al. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016;9:33
- Lay F. D., Liu Y., Kelly T. K., et al. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res. 2015;25:467-477
- Statham A. L., Taberlay P. C., Kelly T. K., Jones P. A. and Clark S. J. Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines. Genom Data. 2015;3:94-96