Array identifies suppressed genes associated with disease

Researchers from North Carolina State University have developed a panel that assesses the methylation levels of genes located in imprint control regions (ICRs) within the human genome. The array represents a cost-effective and efficient method to explore potential links between environmental exposures and epigenetic dysregulation during the early developmental origins of disease and behavioral disorders.

ICRs regulate the expression of imprinted genes—genes where only one parental copy of the gene is active, while the other copy is silenced early in development. Imprinted genes are of particular interest to epidemiologists, geneticists, and toxicologists studying the links between environmental influences and disease because the methylation marks that control their expression are sensitive to environmental influences.

These DNA methylation modifications can be persistent throughout the affected individual’s life and can even be passed on to their children. This is of particular interest in epigenetics, which is the study of heritable changes in gene expression in the absence of DNA sequence changes.

“Methylation—whether a gene is ‘off’ or ‘on’—is the easiest thing to look at when you’re investigating epigenetic effects,” says Cathrine Hoyo, NC State professor of biological sciences and co-corresponding author of the paper. . “It serves as a jumping off point for understanding the relationship between environment and gene expression.”

While methylation arrays exist to probe gene expression, those most commonly used do not include probes specific for ICRs. Instead, scientists interested in the regulation of imprinted genes must sequence a subject’s entire genome, which is expensive, time-consuming, and impractical in large population studies.

The new array contains 22,000 fluorescent probes that are specific for 1,000 of the 1,488 known ICRs in the human genome. Probes are short DNA sequences that target specific methylation sites within these ICRs, with alternative probes binding methylated and unmethylated versions. Alternative probes for each target site have different fluorescent signals, so the relative amount of each bound probe can be measured and the level of methylation for each site determined by the ratio of specific probes.

As a proof of concept, the research team used DNA from a cohort of Alzheimer’s patients to compare ICR methylation data from the cohort data with methylation results obtained from whole genome sequencing and found a significant correlation between two methods. At most for clinical application, results were complete after a week, compared to the months potentially needed to interpret whole genomes.

“In large studies we have to screen participants,” says Hoyo. “If there are 1,000 people in a study, it’s simply not possible to do that many whole genome sequences in a timely and cost-effective manner. It’s especially pointless when you consider that we’re only interested in 22,000 sites out of millions. genome.

“This group does the screening for us – it only looks at the sites of interest and allows us to focus time and energy on the full sequence only when necessary. It essentially sifts the wheat from the chaff so we can focus only on the ICRs that can be involved in disease”.

The work appears in Epigenetics Communications and was supported by the National Institutes of Health under grant numbers R01ES093351, R01HD098857, R01MD011746, and R21HD093351, and by funding from the NC State Center for Human Health and the Environment. Technology licensed from TruDiagnostic, Inc. Ryan Smith of TruDiagnostic is the co-corresponding author. Other co-authors include first author Natalia Carreras-Gallo, Varun B. Dwaraka, and Tavis L. Mendez of TruDiagnostic; Dereje D. Jima, David A. Skaar, Antonio Planchart and Randy L. Jirtle from NC State University; and Wanding Zhou from the University of Pennsylvania.

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