RNA Used in Sequencing Ancient DNA

A Peruvian Mummy 

            Oftentimes, when ancient samples of DNA are taken, they have inhabited warm soil and are contaminated by bacteria (unlike the pure samples of hair, tooth, or bone that had been preserved in frozen ice or soil). Less than 1% of human DNA (which is often short and degraded) is found in these samples.  The techniques that exist, such as zooming in on the DNA or filtering the sample using modern DNA that are similar to the sample sequence, are costly and only expose some of the genome. At the American Society of Human Genetics, a technique using RNA to purify the ancient DNA was reported. At Stanford University, a team has found a “cheap” way to create RNA sequences that are close to the sample DNA sequence. The RNA probes can analyze a whole genome at a low cost, only $50 per sample (saving about $300,000).

            RNA probes attach to beads and the nonhuman DNA is washed away when the probes and DNA sample are mixed. Then, the probe is removed by an RNA-chewing enzyme. Finally, the pure DNA goes through the genome sequencing machine. Two to thirteen times more genetic sequence was recovered (as compared to just sequencing) when using this method on 500 to 3500 year old samples from teeth, hair, and bone.

            Thus far, the technique has already proven that a Peruvian mummy was not of European descent, as previously believed. Currently, it is being used to study ancient dog DNA to understand dog domestication. The technique may also prove helpful for microbial genomics researchers (to rid samples of human DNA) and forensics (when dealing with human DNA with unwanted bacteria).

            Similarly, researchers in Germany were able to sequence an archaic Siberian girl’s genome. The new technique using the amplification of small DNA strands. An enzyme copies the sequence of one strand of DNA. The genome was sequenced thirty-one times. The genome of the girl more than 50,000 years old was as clear as a sequence of a living person’s genome.

            I found that the revelations of “RNA Helps Resurrect Ancient DNA” were fascinating.  When I learned that we are able to have our entire genome sequenced, I was riveted. To learn that scientists can sequence the genome of DNA from thousands of years ago is even more captivating! I was surprised to read that the technique of using RNA to purify DNA is so effective, that it is able to sequence from samples that have less than 1% of DNA. Further, I was amazed by the fact that it costs a mere $50. The fact that we are able to know such a great deal about our ancestors captivates me and stimulates my interest to see what these techniques can teach us. 

Primary Article: http://www.sciencemag.org/content/342/6158/543.full

Secondary Article: http://www.sciencemag.org/content/337/6098/1028.full?sid=5bb97fdf-27a3-41b8-bf1e-89a3fd5ab007