(Invited) Properties of Chromatin Extracted By Salt Fractionation from a Cancerous and Non-Cancerous Esophageal Cell Line

Abstract

While cancer is mostly viewed as a genetic disease and characterized by genetic markers and expression of mutant proteins, there is considerable evidence that there is more to cancer than somatic mutations. For example, the first signature looked for by a pathologist is a grossly aberrant cell nucleus. Chromatin compaction and structure play a major role in the overall nuclear structure. We compared chromatin compaction, structure and gene expression for two esophageal cell lines, EPC2 (non-cancerous) and CP-D (cancerous) by using a combination of salt fractionation, DNA quantification by spectroscopy, atomic force microscopy, and sequencing.Salt fractionation is believed to be an efficient method for quantitative extraction of intact chromatin fragments from cell nuclei. We found that this method is not quantitative unless the supernatant fraction is included. For EPC2 and CP-D cells, about half of the genomic content is solved in the supernatant fraction. Further, we found significant differences for DNA amounts, and chromatin morphology for the cancerous and non-cancerous cell lines, as well as variations in the nucleosome partitioning. We anticipate that our results will help to get insights into the mechanisms of cell phenotype changes from normal to cancerous.