DNA methylation and nucleosome distribution and assembly regulate epigenetic factors of gene expression, and resolving these two essential processes is important for understanding genetic mechanisms. Traditional approaches to accurately track these two processes have relied on stepwise imaging of DNA methylation, nucleosome occupancy, and nucleosome localization in the genome. Lifeasible offers nucleosome occupancy and methylome sequencing (NOMe-seq), which allows customers to observe DNA methylation and nucleosome localization in the same DNA molecule, which will help them perform in-depth epigenetic studies.

We used GpC methyltransferase (MTase) for methylation modification of GpC dinucleotides in the open chromatin region, which allows simultaneous detection of DNA methylation sites in the open chromatin region and genome-wide at high resolution. Importantly, NOMe-seq is not an enrichment method and, therefore requires a relatively large number of sequencing reads to obtain sufficient depth to determine the level of genome-wide accessibility. However, the absence of enrichment bias and the single-molecule nature of the technique makes its detection of chromatin accessibility profiles more quantitatively informative than DNase-seq, ATAC-seq, or MNase-seq, as the relative accessibility levels of each genomic locus can be directly determined.

Analysis flow

During the analysis, we will first methylate the GpC residues of the fixed chromosomes (unpacked with nucleosomes). The crosslink is then inverted, releasing the nucleosome and any bound proteins, such as transcription factors. And this DNA is made to undergo sulfite conversion, which converts unmethylated cytosine to uracil. At this point, DNA sequencing is performed to resolve the DNA methylation profile and the nucleosome occupancy footprint, where the DNA is protected by GpC methylation.

Applications

• Chromatin openness changes under specific conditions can provide a great deal of information on the regulation of gene expression, pointing the way to discovering new sites for the binding of various proteins.
• Explore the very early cytological events during the onset of different stress responses, stress tolerance, or developmental stage transitions.
• This could provide valuable information for early control of crop stresses upstream.

The relationship between nucleosome location and DNA methylation status, which could previously only be inferred from the correlation between DNA methylation and nucleosome localization, can now be determined directly on a genome-wide scale through the technical services provided by Lifeasible. In addition to this, we are actively combining NOMe-seq and post bisulfite adapter tagging (PBAT)-seq technologies in a clever and systematic optimization and enhancement. The analysis of genomic and epigenomic features at five levels, including chromatin status, nucleosome localization, DNA methylation, genomic copy number variation, and chromosome ploidy, was achieved on the same single cell. Please feel free to contact us for a combination of solutions unique to you.

*If your organization requires the signing of a confidentiality agreement, please contact us by email.

For research or industrial use.

Related Services

• Chromatin Remodeling
• DNase-Seq for Plant Epigenetics
• MNase-Seq for Plant Epigenetics
• ATAC-Seq for Plant Epigenetics
• FAIRE-Seq for Plant Epigenetics