Genetics, Molecular and Cellular Biology Program
USC Epigenome Center
Mapping nucleosome organization in cancer cells using NOMe-seq
One of the hallmarks of cancer is aberrant epigenetic changes which include alterations in DNA methylation, nucleosome positioning and histone modifications. DNA methylation changes have been studied extensively. However, their relationship to other epigenetic changes and the genome-wide organization of chromatin structure in cancer remain unclear. Here, we describe the use of our Nucleosome Occupancy and Methylation whole-genome sequencing (NOMe-seq) assay to address these questions using normal and cancer cell lines. We demonstrate that epigenetic changes that occur in cancer cells show coordination between DNA methylation and nucleosome organization. I will describe the analysis methods we use to analyze NOMe-seq data, including statistical approaches we have developed to identify individual nucleosomes and nucleosome depleted regions.