NOMe-Seq

Nucleosome Occupancy Methylome-Sequencing

NOMe-Seq is a single-molecule, high-resolution nucleosome positioning assay (Han et al., 2011). 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 (Wallner et al., 2016)

Advantages:

• High resolution

Disadvantages:

• Relies on the presence of GpC residues (Ishii et al., 2015)

Reagents:
Illumina Library prep and Array Kit Selector

Reviews:
Shull A. Y., Noonepalle S. K., Lee E. J., Choi J. H. and Shi H. Sequencing the cancer methylome. Methods Mol Biol. 2015;1238:627-651

References:

Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. Genome Res. 2012 Dec;22(12):2497-506.

Lay FD, Kelly TK, Jones PA.Lay FD, Kelly TK, Jones PA. 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

Edit: NOMe-Seq

You must be logged in to edit this entry.

History: NOMe-Seq

Revision by tkkelly on 2018-04-06 23:11:01 - Show/Hide

Nucleosome Occupancy Methylome-Sequencing NOMe-Seq is a single-molecule, high-resolution nucleosome positioning assay (Han et al., 2011). 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 (Wallner et al., 2016) Advantages:

• High resolution

Disadvantages:

• Relies on the presence of GpC residues (Ishii et al., 2015)

Reagents: Illumina Library prep and Array Kit Selector Reviews: Shull A. Y., Noonepalle S. K., Lee E. J., Choi J. H. and Shi H. Sequencing the cancer methylome. Methods Mol Biol. 2015;1238:627-651 References: Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. Genome Res. 2012 Dec;22(12):2497-506. Lay FD, Kelly TK, Jones PA.Lay FD, Kelly TK, Jones PA. 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

Revision by sbrumpton on 2017-06-21 09:37:46 - Show/Hide