UCLA researchers in the Departments of Human Genetics and Biological Chemistry have developed a new approach for measuring DNA methylation levels in mammals based on short and highly conserved nucleotide sequences. This method facilitates the development of chip for measuring DNA methylation that can be used for cross-species comparisons and used for building universal epigenetic aging clocks (age estimators) that apply to all mammals.
DNA methylation, by the attachment of a methyl group to cytosines, is one of the most widely studies epigenetic modifications, due to its implications in regulating gene expression across many biological processes. In humans, DNA methylation levels can be used to accurately predict an individual’s age, as well as age across tissues and cell types. The two most widely used technologies for obtaining DNA methylation levels are bisulfite sequencing and microarray-based methylation chips. Whole genome bisulfite sequencing is an expensive assay, causing reduced representation bisulfite sequencing (RRBS) to become the prevalent sequencing approach. However, the sequencing depth required even for RRBS can still drive up costs even though it is not quantitavely reliable. As a result, array chips (for human samples) containing an increasing number of probes have been the most reliable and widely used technology. The first human methylation chip (Illumina Infinium 27K) was introduced over ten years ago but no analogous chip has been presented for other species. Many researchers study animals that are not widely used, e.g. dogs, cats, cattle, swine, elephants, bats. It is not cost effective to develop a DNA methylation array for species that are rarely analyzed. This delay may reflect the fact that it was not economical to design a methylation chip for non-human species. Even if costs were no impediment, the development of species specific arrays could hinder cross species comparisons as the measurement platforms would be different.
UCLA researchers developed an algorithm, which repurposes the degenerate base technology used to tolerate within-human variation to tolerate cross-species mutations. The technology performs a greedy search to obtain a maximal number of species that can be targeted using a probe for any CpG site in the human genome, based on a multiple sequence alignment. A major advantage of the invention is the focus on highly conserved stretches of DNA, which facilitate cross-species comparisons. For example, the invention allows one to evaluate whether an intervention that affects DNA methylation levels in one species (e.g. mouse) also affects the corresponding DNA methylation levels in another species (e.g. human). The resulting DNA methylation chip is applicable to all mammals and hence drives down the cost per chip through economies of scale. Further, the chip is tailor-made for cross species comparisons. Finally, the researchers have demonstrated that highly conserved sequences lend themselves for building highly accurate epigenetic aging clocks.
The custom methylation chip has been developed and tested against mammalian genomes.
DNA methylation, chip, assay, epigenetics, mammals, algorithm, aging clock, epigenetic clock, preclinical studies