In genomics, ‘epigenomics’ (or ‘epigenetics’) refers to a phenomenon whereby the function and activity of a genome is altered or modified but without changes to the underlying DNA sequence. It is what allows cells to differentiate their function – i.e. a liver cell and a brain cell have the same DNA, but do very different things. One of the ways in which epigenomic modifications occur is through a process called cytosine methylation, which is a chemical ‘addition’ to a cytosine base). These modifications act as blockers, which prevent the cellular machinery from performing the process which converts DNA-to-RNA-to-protein. In life, these epigenomic modifications are controlled by a complex network of interactions between DNA and RNA. They are also modified in response to environmental stress, and can be passed down between generations. Therefore they are sometimes seen as a ‘driver’ for evolutionary change.
We wanted to see if these modifications were detectable in ancient and archaeological samples, and if we could detect meaningful genomic activity related to them. We chose dogs as a model, because their evolution is becoming more and more understood, and because over one quarter of EU households own a dog, and so the project is both relatable and important to society in terms of breeding programmes etc. Further, their status as the first domesticate allows to us explore whether domestication and epigenomics go hand in hand, since domestication is an evolutionary process in itself. To do this, we sequenced DNA and RNA from dogs and wolves from a range of geographical locations, from the Pleisotocene (14,000 years old) up to around 100 years old. We aimed to compare tissues, individuals, times and locations.
We also wanted to see if RNA could be sequenced from ancient mammalian remains, for both proof-of-principle and to confirm the epigenomic data. Despite the advances in sequencing DNA from ancient contexts, the general instability of RNA has discouraged researchers from attempting to sequence it, especially in enzyme-rich mammalian tissues which are thought to break down RNA quickly. There has been some success in sequencing RNA from plants seeds which are adapted for this sort of preservation, and so we decided to try with some ancient dog tissues.
