Quantitative Assessment of Chromatin Structure: Analysis of Epigenetically Regulated Gene Promoters

Francisco Bizouarn
Bio-Rad Laboratories Inc, United States of America

Epigenetic processes, such as DNA methylation and histone modification, control gene expression by altering chromatin structure. Genes that are actively transcribed are associated with “open” or “accessible” chromatin regions; genes that are transcriptionally silent are often in “closed” or “inaccessible” chromatin. We present a new assay, termed the EpiQ chromatin assay, that quantitatively assesses chromatin structure in cultured cells. The assay is novel, easy to perform, quantitative and produces results on the day of cell harvest. We validated this assay by analyzing 15 genes in four human cancer cell lines (4 housekeeping genes and 11 genes that are epigenetically regulated in human cancer). We observe an excellent correlation between the level of gene expression and the chromatin structure of the corresponding promoter. Importantly, our data indicates that gene promoters exist not just in “open” and “closed” chromatin states, but also exist in intermediate states of chromatin accessibility which act to fine-tune the level of gene expression. The EpiQ chromatin assay compliments and extends existing epigenetic assays and allows researchers to gain novel insights into mechanisms of gene regulation.

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