There was recently a research article describing the genome of the lone insect native to Antarctica - the university's press release on it is here: https://news.wsu.edu/2014/08/12/rese.../#.U_N7ZEtXrNY
The most unusual thing about the genome: very little repetitive DNA, very few transposable elements, and shorter introns. The net result is that this is the smallest insect genome yet sequenced. The authors think that the rough environmental conditions have selected for a streamlined genome, and as a result, a lot of the "junk DNA" has been deleted.
I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA, since a lot of people have lots of misconceptions regarding it. I'll provide a short discussion of what we know, and then i'd be happy to answer any questions people have. (I did about 20 years of research in biology before changing jobs.)
What is junk DNA? DNA that encodes proteins is not considered junk. DNA that regulates gene expression (which we've known about since the early 1960s) is also not considered junk, even though it doesn't encode a protein. Neither is structural DNA, like the centromere and telomeres, which help keep the chromosomes intact and split equally during cell division. So, discovering useful, non-coding DNA is not a surprise, and doesn't disprove the idea that junk DNA exists, even though many press reports have and continue to claim this.
Junk DNA is a subset of the following: disabled genes, disabled viruses, transposable elements, and repetitive DNA. A small subset of this DNA does have a function - for example, there was a recent estimate that a bit under 10% of the disabled genes in the human genome now make RNAs that perform regulatory functions without encoding a protein. But the majority of it performs no known function. And, accordingly, it's not conserved between species - while humans and chickens share many identical coding and regulatory DNA sequences, they share very little repetitive DNA.
How does junk DNA come about? Several known processes create DNA that performs no useful biological function. For example, many viruses insert into the genome as part of their normal lifestyle - behavior that's good for the virus, but not the owner of the genome. The normal process of copying DNA often makes mistakes when it comes to repetitive sequences (think 37 copies of "AT" in a row), adding to the number of copies. And duplications and deletions of DNA occur all the time (google "Copy Number Variations") and many people have them present in their own genome. All of these processes produce DNA that is not useful to their organism.
As a result, some amount of junk DNA is inevitable - processes we can observe create it all the time. So the big question is not whether it exists, but how much of it is there. Only two processes can get rid of it: modification into usefulness or deletion. The first has been known to happen; a number of genes in the human genome came about through the modification of pieces of virus DNA. But it appears to be rare; most viruses aren't anywhere near a gene. So the majority of the junk pruning takes place through deletion.
As a result, the amount of junk DNA in a genome is the balance between the creative processes and deletion of DNA.
In most cases, organisms seem to tolerate a lot of junk DNA. Pines, for example, all have 12 chromosomes, each of which is nearly as large as the entire human genome - the majority of the DNA is for transposable elements. In contrast, there are a few species, like this Antarctic insects, where conditions are harsh enough that any little bit helps with survival. As a result, these organisms have very little of the repetitive DNA.
Hopefully, this clarifies the situation somewhat. If there are things people want more details about, I'd love to have a discussion of it.
The most unusual thing about the genome: very little repetitive DNA, very few transposable elements, and shorter introns. The net result is that this is the smallest insect genome yet sequenced. The authors think that the rough environmental conditions have selected for a streamlined genome, and as a result, a lot of the "junk DNA" has been deleted.
I thought this might be a good opportunity to start a discussion of the science (rather than the metaphysical implications) of junk DNA, since a lot of people have lots of misconceptions regarding it. I'll provide a short discussion of what we know, and then i'd be happy to answer any questions people have. (I did about 20 years of research in biology before changing jobs.)
What is junk DNA? DNA that encodes proteins is not considered junk. DNA that regulates gene expression (which we've known about since the early 1960s) is also not considered junk, even though it doesn't encode a protein. Neither is structural DNA, like the centromere and telomeres, which help keep the chromosomes intact and split equally during cell division. So, discovering useful, non-coding DNA is not a surprise, and doesn't disprove the idea that junk DNA exists, even though many press reports have and continue to claim this.
Junk DNA is a subset of the following: disabled genes, disabled viruses, transposable elements, and repetitive DNA. A small subset of this DNA does have a function - for example, there was a recent estimate that a bit under 10% of the disabled genes in the human genome now make RNAs that perform regulatory functions without encoding a protein. But the majority of it performs no known function. And, accordingly, it's not conserved between species - while humans and chickens share many identical coding and regulatory DNA sequences, they share very little repetitive DNA.
How does junk DNA come about? Several known processes create DNA that performs no useful biological function. For example, many viruses insert into the genome as part of their normal lifestyle - behavior that's good for the virus, but not the owner of the genome. The normal process of copying DNA often makes mistakes when it comes to repetitive sequences (think 37 copies of "AT" in a row), adding to the number of copies. And duplications and deletions of DNA occur all the time (google "Copy Number Variations") and many people have them present in their own genome. All of these processes produce DNA that is not useful to their organism.
As a result, some amount of junk DNA is inevitable - processes we can observe create it all the time. So the big question is not whether it exists, but how much of it is there. Only two processes can get rid of it: modification into usefulness or deletion. The first has been known to happen; a number of genes in the human genome came about through the modification of pieces of virus DNA. But it appears to be rare; most viruses aren't anywhere near a gene. So the majority of the junk pruning takes place through deletion.
As a result, the amount of junk DNA in a genome is the balance between the creative processes and deletion of DNA.
In most cases, organisms seem to tolerate a lot of junk DNA. Pines, for example, all have 12 chromosomes, each of which is nearly as large as the entire human genome - the majority of the DNA is for transposable elements. In contrast, there are a few species, like this Antarctic insects, where conditions are harsh enough that any little bit helps with survival. As a result, these organisms have very little of the repetitive DNA.
Hopefully, this clarifies the situation somewhat. If there are things people want more details about, I'd love to have a discussion of it.
Comment