Extinct Genomes in PLOS One

ResearchBlogging.orgtasmanian tigerA paper published today in PLoS One reports on research that shows the feasibility of taking a gene or genomic region from an extinct species and inserting it into the genome of an extant species and resurrect the extinct species DNA function in the transgenic mice. The extinct species was the Tasmanian tiger or Thylacine (that links to the wikipedia page, anyone want to become the curator for the EOL page which is pretty minimal at this point?) and the ‘surrogate’ species was Mus musculus.

And, as the abstract says,

While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

It is an fascinating piece of research.

Just for fun, I’m embedding the paper here (docstoc is a new toy of mine) for your viewing pleasure in case you just want to skim, but download the paper from PLoS One*, it’s an interesting read.


Resurrection of DNA Function In Vivo from an Extinct – Get more documents

The researchers used a conserved and well-characterised transcriptional enhancer element of the
proa1(II) collagen (Col2a1) gene. After amplifying and isolating this region,

Four copies of the thylacine sequence were multimerised and ligated to the human b-globin basal promoter fused to lacZ and followed by a polyadenylation signal.

The reporter gene was then expressed in mouse fetus and

confirms that the thylacine Col2a1 gene had a conserved developmental role in cartilage formation, and that its promoter directed expression in chondrocytes in this extinct marsupial mammal.

The researchers were able then to determine which part of the sequence was essential for expression. Though a repeat is conserved in other mammals and not conserved in Thylacine, the enhancer still functions in the developing mouse.

It’s a fascinating piece of work and demonstrates quite well that we can use both in vitro and in vivo studies to study the function of genes and non-coding regions in both extinct and extant species, giving us some useful insights into genome evolution. Additionally, it points to some interesting implications in studying the genetic variation in extinct species and how that variation might have informed different phenotypic differences. In a world with an increasing extinction rate, this will prove important. Not as an important as actually making inroads to _stopping_ the extinctions through habitat restoration, global warming abatement, etc, but important nonetheless.

Perhaps hoarding genomes isn’t such a bad idea.

Pask, A.J., Behringer, R.R., Renfree , M.B. (2008). Resurrection of DNA Function In Vivo from an Extinct Genome. PLoS One, 3(5), e2240-e2240. DOI: 10.1371/journal.pone.0002240

*Creative Commons License

Other Blogs discussing this: Greg Laden discusses this paper and points to an important point

This assumes that the word “function” is used very carefully, of course. The exact effects of a gene may depend on context to the extent that one bit of DNA may function in one organism in a different way than other organism to the extent that we would normally assign the two outcomes to two different functions. It is that kind of context based functionality that makes genes a) really interesting and b) able to do so much work despite the fact that there are actually not that many different kinds of genes.

A commenter on that post is confused as to why the PLoS authors are claiming “this is the first instance of the “resurrection” of an extinct gene.” He points to a Science paper from 2006 using Mammoth DNA to determine the function of hair color genes. This research though was in vitro (mouse cells), not in vivo (mouse organism) which is what the paper is claiming was a first:

While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo.