An Overview of Epigenetic Assays

Abstract

A significant portion of ongoing epigenetic research involves the investigation of DNA methylation and chromatin modification patterns seen throughout many biological processes. Over the last few years, epigenetic research has undergone a gradual shift and recent studies have been directed toward a genome-wide assessment. DNA methylation and chromatin modifications are essential components of the regulation of gene activity. DNA methylation effectively down-regulates gene activity by addition of a methyl group to the five-carbon of a cytosine base. Less specifically, modification of the chromatin structure can be carried out by multiple mechanisms leading to either the upregulation or down-regulation of the associated gene. Of the many assays used to assess the effects of epigenetic modifications, chromatin immunoprecipitation (ChIP), which serves to monitor changes in chromatin structure, and bisulfite modification, which tracks changes in DNA methylation, are the two most commonly used techniques.

A microarray‐based approach for the identification of epigenetic biomarkers for the noninvasive diagnosis of fetal disease

“…A second approach relies upon the fact that bisulfite treatment of genomic DNA results in a DNA sequence change that can be detected and quantified using standard molecular methods (Sulewska et al, 2007;Zilberman and Henikoff, 2007;DeAngelis et al, 2008;Hayatsu, 2008a,b). The major drawback of this approach is that bisulfite conversion results in dramatic degradation and loss of sample DNA.…”

Phosphorus and osmium as elemental tags for the determination of global DNA methylation—A novel application of high performance liquid chromatography inductively coupled plasma mass spectrometry in epigenetic studies

“…In molecular biology, site-specific sequence techniques are in use to detect subtle differences in the methylation status of individual genes [7][8][9][10]. On the other hand, global methylation of DNA has often been evaluated as an indicator of large-scale epigenetic effects [11][12][13][14][15][16][17].…”

Targeting epigenetic mechanisms for chronic visceral pain: A valid approach for the development of novel therapeutics

“…These assays provide a relatively high throughput (24 or more samples depending on the number of technical replicates) for minimal cost (most assays are $300‐$500). The same technical weaknesses occur as with other commercial kits with generating enough sample to test duplicate/triplicate replicates in the assay; however, by testing for activity of broad classes of histone‐modifying enzymes, these assays can be useful when evaluating novel therapeutics or for assessing potential epigenetic regulation in specific diseases, such as cancer . Caution must also be used with interpretation of the results of the enzymatic assays as global changes in activity of the enzyme may or may not affect the expression of your gene of interest.…”