Not so much junk in the DNA trunk
Date: November 14, 2008 | Author: Bob NovellaCategory: General Science, Myths and Misconceptions, Science and Medicine | Comments: 6 » | Tags: junk dna, transposons
For decades now we’ve known that the 3 billion base pairs that make up human dna contain vast wastelands of genetic code that do not code for proteins. No function could be found for much of this apparent useless 97% of our genome. In 1972, late geneticist Susumu Ohno coined the term “junk dna”.
This designation has always been controversial and many scientists considered the term provisional until some function could be found for at least some if it. Over the years, theories have been proposed and tantalizing clues have been revealed that show that much of this “dark matter of the genome” is not junk at all.
The Journal of Genome Research published recently an article from scientists at the Genome Institute of Singapore who claim that much of the so-called junk dna is not only useful, it’s one of the key ingredients that distinguishes people from other animals.
In their paper, the scientists describe how these long stretches of repeated base pairs in our dna are important for determining which genes turn on, when they turn on, and how much they turn on. These repeats are also shown to jump around the genome changing how genes are expressed which could obviously then change the course of evolution.
I’m a little confused about what’s new about the jumping gene part. So-called transposons or mobile genetic elements were discovered decades ago. Geneticist Barbara McClintlock even won a Nobel prize for discovering them in 1983. The article mentions that the genetic elements can be “explosively distributed” throughout the genome. Perhaps this is the new twist that the scientists at the Genome Institute of Singapore discovered.
Any who…have you ever wondered why successful experimental trials on animals so often fail to translate to successful human trials even though they have almost identical genes to humans.
University of California, San Francisco neurologist Raymond White said:
“…I anticipate that as our knowledge of these events grows, we will begin to understand much more how and why the rat differs so dramatically from the monkey, even though they share essentially the same complement of genes and proteins.”
It appears then that the erstwhile junk dna, by affecting the activity of gene expression is one of the key distinguishing factors between closely related species.
Dr. Raymond White continues…
“The findings by Dr. Bourque and his colleagues at the GIS are very exciting and represent what may be one of the major discoveries in the biology of evolution and gene regulation of the decade,”
6 Responses to “Not so much junk in the DNA trunk”
By SkepGeek on Nov 14, 2008 | Reply
I wonder if this has any affect on molecular clock techniques used to determine when two species had the most recent ancestor. Don’t they make assumptions about the part of the DNA they use being junk?
By Adrian on Nov 14, 2008 | Reply
It seems really chic to say that Junk DNA isn’t Junk and I wonder how much Bob and even the Science Daily has succumbed.
To be clear, even the strongest claim in the article does nothing to argue that Junk DNA isn’t junk:
This research also shows that these repeats are anything but “junk DNA,” since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species.
That first sentence is nonsense and it contradicts itself. The sequences inserted by viruses and long blocks of repeating, noncoding segments are junk. That’s the very definition of junk. It is because these segments are junk that they can mutate and change without any impediment and be the “source of evolutionary variability” they talk about.
It’s yet another science writer trying to play up a controversy and to build up hope that our DNA was designed instead of looking like an evolved, well, junk pile.
By Bob Novella on Nov 14, 2008 | Reply
Thanks for the comment Adrian
I should have been clearer that genomes do indeed contain many segments that can only be described as junk. I agree that even if they may have some future utility it doesn’t detract from their current junkiness.
My take-away from my research was that a subset of this junk isn’t really junk since it plays a key role in gene regulation.
I did see one article that claimed that the research shows there is no junk in dna since god doesn’t make junk. This of course is nonsense but the vast majority of articles I came across did not take this position.
By springer.adam on Nov 14, 2008 | Reply
The term “junk DNA” also refers to introns which are segments of DNA that are found in between exons which are coding segments of DNA. After transcription the mRNA is rid of said introns by way of splicosomes. The separated introns then float away and the newly connected exons are then translated into proteins. Although it is not known what introns are used for if anything at all, they are different from the 97% of DNA you spoke of.
By rachelwells on Nov 15, 2008 | Reply
I’m confused… and agree with you about not knowing what is the new finding of this piece. I might go and read the original article but interesting blog either way. So thanks!
I think molecular clocks are typically proteins like hemoglobin or cytochrome c- conserved function, but slight changes in DNA sequence that may or may not change the amino acid sequence. I’m unsure how repeditive junk DNA (e.g. minisatellites) could be used as a measure for divergence between species seeing as they are highly recombinant regions. They would be useful for other things such as telling the difference between two people (who committed the crime for example), because they are highly variable between individuals.
I vaguely remember that the specific sequences within an intron of one gene can actually act as enhancers of transcription up to 50kbp away from another gene that is developmentally regulated. So gene A (bystander gene) has an intron that acts as an enhancer for gene B (target developmental gene). That’s one possible role of introns. Gene A and gene B would need to interact however, via proteins known as ‘architectural’ proteins. These regions of the chromosome are a.k.a genomic regulatory blocks (GRBs).
Junk DNA may also be mistaken as older damaged genes that have mutated to such an extent that they have typically lost their introns and promoters. These are called pseudogenes, and arise long after gene duplication and subsequent loss of selective pressure to maintain the 2nd copy of the gene. They may be difficult to distinguish from junk DNA because gene searching programmes use promoter sequences etc to identify genes.
Also, junk DNA is often called junk until it’s found to be ‘RNA only coding’ DNA…that is, it does not go that step further to make the protein. This area of research is referred to as RNA interference and I urge anyone interested in genetics to look up the early purple petunia experiments that lead to the discovery of RNA interference. I get excited thinking about it. It’s awesome
By IPVlazy on Nov 15, 2008 | Reply
I’m more into physics than biology so I don’t know much about this but it sounds very interesting, and it sounds like a biologists “dark matter” as you noted, so I am guessing that this is quite an important discovery… so since I have no clue where I am going with this comment.. I hope they continue to do well in this research.