NOME-seq (Nucleosome Occupancy and Methylome Sequencing) made a big splash when it was introduced just over a year ago because of its novel ability to profile nucleosome positions and DNA methylation at the same time, on a single DNA strand. Now researchers from the University of Southern California Epigenome Center have powered-up the technique by teaming NOME-seq with next-generation sequencing to get genome-wide coverage and really crank out the research hits like an epigenomic version of Jay Z.
The project was a collaboration of authors Theresa Kelly and Yaping Liu from the labs of Peter Jones and Benjamin Berman at USC that examined nucleosome occupancy and endogenous DNA methylation genome-wide with the amped up NOMe-Seq approach. The group was able to footprint chromatin architecture at a variety of promoter and non-promoter regions.
“We have previously used a locus specific version of NOMe-seq, so here we expanded the methodology to include next generation sequencing which allows us to ask more global questions. In developing NOMe-seq, our goal was to provide a methodology that was able to measure nucleosome occupancy, genome-wide, as accurately as nuclease based nucleosome mapping, using a fraction of the input materials and while also maintaining DNA methylation information. Combining both of these pieces of information allows one to footprint active (unmethylated/nucleosome depleted), repressed (unmethylated/nucleosome occupied) and silent promoters (methylated/nucleosome occupied) using a single technique.” Says Kelly.
Filtering through the gigabytes of data with a novel bioinformatics pipeline the team uncovered lots of useful new insights.
“Using NOMe-seq led to a number of novel findings, including:
- The identification of a striking anti-correlation between nucleosome occupancy and DNA methylation surrounding CTCF sites, that is not present at promoters.
- Genome-wide evidence that CpG island and non-CpG island promoters have similar chromatin structures.
- Nucleosome depleted regions of expressed promoters can accommodate several nucleosomes and are more prominent in highly expressed genes as well as group of promoters whose chromatin configurations are consistent with mono-allelic expression
These have not been described previously.” Dr. Kelly explained.
The So Cal scientists predict that NOME-seq will have a big impact on future epigenomic research. “Mutations in chromatin remodelers have increasingly been identified in cancer and we think that NOMe-seq will be incredibly useful in studying the effects of these mutations in chromatin organization. In addition, we believe that deep-sequencing using NOMe-seq will someday allow investigation of epi-alleles present in particular sub-populations of cells in heterogenous tissues such as tumors, and thus may have advantages over other epigenomic sequencing techniques. Furthermore, NOMe-seq will be useful in investigating things like the loss of imprinting that happens in cancer and whether the presence of an individual SNP correlates with a specific chromatin structure.” Kelly commented.
Take in all of the latest NOMe-seq action at Genome Research, September 2012.
Click here to learn more about NOMe-Seq Kits that are now available from Active Motif.