Genes out of Junk (DNA)

Genes Sometimes Form Spontaneously in DNA
Scientists used to think that that so many things had to happen for a gene to form from a random piece of DNA that it would never actually happen. They were wrong. In a new study, scientists have identified 60 brand new, never before seen genes in human DNA. And this isn't the first time this sort of thing has been seen either. Others have seen these kinds of genes in people, baker's yeast and most spectacularly in fruit flies. These studies are adding a new chapter to how scientists think about new genes forming.

Some of our genes are totally unique
to humans.
Until they found this class of newly formed genes, scientists thought that most new genes were built off of old ones. This is a much simpler proposition than cooking a gene up from scratch and there are plenty of examples of old genes mutating to new ones. But now it looks like at least a few new genes can appear from a piece of DNA that hasn't been used as a gene before. Scientists don't yet know how important a role this form of making new genes is in evolution. They simply haven't known about these genes long enough to even know how common they are. Rest assured that now that they know what to look for, scientists will go all out studying this new way of making genes. In a very short time, they will have a better handle on whether these genes have been pivotal to evolution. Or whether they are really just nice add-ons.
Making New Genes
Until recently, scientists pretty much thought that new genes arose from old ones. A big reason for this is that there are lots of ways for a cell to get a hold of a gene that can be used as the starting point for a new gene. And there are plenty of examples of new genes forming this way. One way a cell can get a new gene is if it accidentally makes an extra copy of a gene when it is dividing. Scientists call this gene duplication. The extra gene can now undergo mutation without affecting the health of the cell. Over time, many mutations lead to a new gene. Another way to get an extra gene is when a virus inserts itself into a cell's DNA and leaves one of its genes behind. Again, this gene can now undergo random mutation to become a useful new gene.

An extra copy of a gene
is a great canvas for
the formation of a new gene.
And there are plenty of other ways for a cell to get hold of a gene that can be molded into a different gene. This is a fairly common process and there are many genes that fit this description. But apparently this isn't how it always happens. Sometimes a gene will appear in a place where there wasn't a gene before. This isn't some designed piece of DNA that has just appeared out of the blue. The DNA that was always there built up a set of DNA changes over time that converted it into a gene. Scientists can tell this has happened by comparing various beasts' DNA. In this case, they compared human DNA to a number of other primates' DNA. They found 60 genes in humans that weren't in the other primates. These genes were simple as would be predicted for newly emerged genes. And the scientists could look at the other primate DNA and see how the human gene arose from just a few minor tweaks. The trickiest part, though, is to show that these 60 pieces of DNA are actually genes. Just because a piece of DNA looks like a gene, that doesn't mean a cell uses it as one. The researchers have done some good initial work but it will take some extra research to really nail down that all 60 are genes being used by the cell. Don't come away thinking that genes can’t form this way just because these particular researchers don't have solid proof of it happening for all 60 human genes. Genes can and do appear from scratch. One of the best examples is from baker's yeast.

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Spontaneous Gene Formation
As stated earlier, genes that are made from scratch are identified by comparing closely related species and finding spots where there is a gene in one species that is missing in another. Scientists must also be able to tell that this new gene sprang from the DNA that was already there. A great example of one of these genes is the BSC4 gene from baker's yeast. To see why BSC4 almost certainly formed from the DNA that was already in some ancestral yeast from long ago, it helps to understand what a gene looks like. And how one is put together.

T's are replaced with U's
because RNA has U instead of T.
Click here for why that might be.
A gene is really the set of instructions for making a protein. That protein then goes on to do a specific job in a cell. These instructions are written with just four letters: A, G, C, and T. All the words in the instructions are three letters long meaning that the DNA language consists of the 64 different three letter words to the right. One of these words, ATG, tells the cell to start making a protein at that ATG. Three different words, TAG, TGA, and TAA, tell the cell that a gene ends there. This is pretty much all there is to a gene. Note the "pretty much." There have to be 50 or 100 three letter words between the start and stop codons (as genetic words are called). And they have to spell out something useful. And the cell has to know that the ATG that starts the whole thing off is a gene and not just a random ATG (they are obviously common). A key step, though, is to get an ATG at one end, a TAG, TGA, or TAA at the other and 50-100 codons in between. Once you have that, natural selection can start to work on the gene and its protein so something useful is made. The BSC4 gene is an excellent place to start to understand how many changes need to happen to get the ball rolling on new gene formation. Here is the sequence of the new yeast gene in its entirety: As you can see, it starts with an ATG and ends with a TGA and has no TAG's, TGA's or TAA's in between. It is a nice sized, perfectly well behaved gene. Here is what that same stretch of DNA looks like in a related yeast: The five trouble spots have been highlighted in blue, lower case letters. Just changing one letter in each of these five words turns this DNA sequence into a gene. Not the same gene but a stretch of DNA that can evolve into a useful protein. And this is exactly what has happened in this case. BSC4 is an important protein in baker's yeast. Scientists think that it helps the yeast fix its broken DNA. And they know that if you get rid of it under certain conditions, the yeast dies. So this looks to be a definite case where a gene has appeared where there wasn't one before. The 60 in this study are not so clear cut because the scientists don't have as high quality data that cells read and use these genes in a human cell. But scientists will now get to work seeing which bits of DNA are actually genes. BSC4 Region from Four Different Yeast Species This image is taken from here. It has been included for people who want to delve more deeply into the DNA of all four yeast species to see the sorts of changes that have happened over time. The gray shaded boxes are DNA letters shared by all four yeast species at that position. Enjoy!