One of the challenges of working with ancient DNA samples is that damage accumulates over time, breaking the double helix structure into ever-smaller fragments. In the samples we worked with, these fragments were scattered and mixed with contaminants, making genome reconstruction a major technical challenge.
But a shocking paper published Thursday shows that this isn’t always true: Damage can make fragments of DNA progressively smaller over time. But if locked into the right kind of material, the fragments can stay in place, essentially preserving key features of ancient chromosomes even as the underlying DNA breaks down. Researchers have now used this to uncover more of the chromosome structure of mammoths, which offers some hints about how these mammals regulated some key genes.
DNA meets Hi-C
The backbone of DNA’s double helix is made up of alternating sugars and phosphates, chemically bonded together (the bases of DNA are chemically bonded to these sugars). Damage, such as from radiation, breaks these chemical bonds, leading to increased fragmentation over time. By the time a sample reaches a Neanderthal-like age, there are very few fragments longer than 100 base pairs. Because chromosomes are millions of base pairs long, it was thought that many of the fragments would simply diffuse away, inevitably destroying the chromosome structure.
But that’s only true if the mammoths’ environments allow them to spread, and some scientists suspect that the permafrost that preserves the tissues of extinct Arctic animals might hinder their spread. So they decided to test this using mammoth tissue from a sample called Yakinhu, which is about 50,000 years old.
The problem is that the molecular techniques they use to study chromosomes are carried out in liquid solutions, which means the pieces would separate from each other anyway. An approach called Hi-Cspecifically stores information about which pieces of DNA were near each other. It does this by exposing the chromosomes to chemicals that bind together pieces of DNA that are physically close together, so that even though they are fragments, they are still stuck together by the time they reach a liquid solution.
Then, using several enzymes, they convert these linked molecules into a single piece of DNA and sequence it. This data contains sequence information for two different parts of the genome, and shows that these parts were once close to each other in the cell.
Interpretation of Hi-C
A single bit of data like this isn’t particularly interesting on its own — any two bits of the genome might be randomly next to each other — but with millions of bits like this, we can begin to build a map that shows the structure of the genome.
There are two basic rules that govern the patterns of interactions we expect to see: first, interactions within a chromosome are more common than interactions between two chromosomes, and within a chromosome, parts of a molecule that are physically close together are more likely to interact than parts that are far apart.
So, for example, if you’re looking at a particular segment of chromosome 12, most of the places where Hi-C interacts are also on chromosome 12. And the closer you get to the sequence of interest, the higher the frequency of interactions.
Hi-C can be used to reconstruct chromosomes even starting with just fragments. But exceptions to expected patterns can also tell us about biology. For example, active genes tend to lie on loops of DNA, with the ends of the loop tethered by proteins. This is also true for inactive genes. Interactions within these loops tend to occur more frequently than interactions between the loops, subtly altering how often two fragments end up linked during Hi-C.
