This is a story about a transposon aptly named Sleeping Beauty, it could have been named Rip van Winkle, but I do think Sleeping Beauty is more apt. Now I am not going to go into the details of what a transposon is, that information can be found many places. Suffice it to say that transposons are small bits of DNA that hop around another organism's genome. There are bacterial transposons, yeast, drosophila, worm, fish, primate transposons. Basically there are transposons found in all cellular lifeforms. What is great about transposons for a geneticist is that if you can control when they hop, you can generate a series of essentially random mutations in a heartbeat. If the transposon hops into a gene whose product is required to make the amino acid arginine, your mutant will not be able to grow in the absence of arginine in the medium. This is great if you are interested in understanding how a cell makes arginine and this approach has been used since the 1960s to study and understand many basic cellular processes in bacteria and in eukaryotes. In the post-genomics universe, transposons are also a powerful tool because you know the DNA sequence of the given transposon you are using (if not get another job). So, once you have a mutant you are interested in, identifying the gene disrupted by the transposon is fairly trivial.
Now transposon were used to study primarily "simple" organisms, such as bacteria and yeast for half a century. However, transposons were not used for genetic studies in mammalian organisms because active/functional transposons did not exist. This despite the fact that a major part of our (and other mammals) genome is composed of nothing but transposons and transposon remnants. Although many transposons are intact within the genome, they are non-functional because they contain mutations that have accumulated over time. (Tangential creationist bash - one tenet of the creationist/ID movement is that mutations are uniformly bad. From the perspective of the transposon these mutations are bad, from our perspective having transposons hopping around in our cells is a bad idea so the mutations are good).
In 1997 Ivics and colleagues published a paper in Cell that changed all this. They looked at a non-functional transposon called Tc1/Mariner, which is found in fish humans and other organisms. The idea was to recreate a functional transposon from these Mariners that all contain mutations. However, a transposon can move through a population vertically (think mother to child) or horizontally (think person to person, like the flu although this is not to suggest that transposons are infectious.) So if a transposon picks up mutation in one cell then all the descendants of that cell will have a transposon with that mutation due to vertical transmission. The idea here is that just because all the Mariner transposon in a salmon have a given nucleotide at some position in the sequence does not mean that the nucleotide is not a mutation. So how do you figure out the original "functional" transposon sequence? Ivics obtained the Mariner sequence from 8 different fish species and aligned them using standard sequence analysis computer programs. From this they established a consensus sequence, that is the DNA sequence of Mariner found most often in the different species and identified the important domains (Fig A) of the transposase (the enzyme that carries out the transposition reaction).
When compared to the salmon Mariner a number of mutations were identified (Fig B). Ivics and colleagues then first fixed all the premature stop codon mutations to the correct amino acid (changing SB1 to SB3. The protein expressed from this sequence still did not do too much.
Next, they changed a number of amino acids to make SB4, the protein made from this sequence was not functional as a transposase, but it did localize to the nucleus! This is an important step forward as the transposase needs to be in the nucleus to carry out its function. The researchers then went through a number of steps SB5-SB8 and finally obtained a protein capable of binding DNA, and 2 steps later they generated a functional transposase. This transposase also works when introduced into mammalian cells. Genetic researchers working on vertebrate organisms rejoice! This is why Sleeping Beauty is an apt name, the transposon was relatively simply to reactivate and has been essentially sleeping in our genomes for hundreds of millennia but is now such a powerful tool for understanding ourselves it is indeed beautiful.
Step forward to 2008, by introducing the transposon into mammalian cell lines or into mice, we have a system where we can generate essentially random mutations when and where we want simply by turning on Mariner (the transposase) when and where we want (this is done using specific promoters). The transposase is expressed causing the transposon to hop into new sites in the genome, some of which will have an effect you are interested in. For example, this approach has been used to identify genes involved in the progression of specific type of cancers (do a pubmed search for sleeping beauty for a ton of references). In short, adapting transposon mutagenesis to higher eukaryotic organisms is revolutionizing our understanding of ourselves.
So lets go back to the beginning, if you doubt evolution and believe in creation/ID you must not allow any medical benefits arising from this research to be used on you. How do you justify the approach taken by Ivics and colleagues without evolution? From evolutionary theory, it makes perfect sense to take Ivics' approach. In order to think you can regenerate an active Mariner from these disparate sequences from different species, you have to assume that there was an original active Mariner in the ancient history of the ancestor of these species. After speciation occurred the Mariners could accumulate mutations that inactivated them. However, these mutations occurred independently in the different lineages. Because this happened, it is possible to predict what the ancestral active sequence was by determining the consensus sequence. Now its possible that the ancestor sequence was already non-functional, but that is not the case here. Regardless, how do you begin this research project from a creationist perspective.....you don't, it makes no sense whatsoever. What about an ID perspective? Well I guess if you believe the designer is a sloppy lazy stupid drunk, then maybe you could go down the right path, but I have yet to hear an IDiot say they thought god was either sloppy, lazy, stupid, or drunk much less all four simultaneously.
2016 Nobel Prize predictions
3 hours ago in The Curious Wavefunction