biology question #1844



Tappar, a 22 year old female from New Delhi asks on January 18, 2004,

Q:

How did scientists conclude that a major part of our genome is junk? Did they search for open reading frames?

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the answer

David Baillie answered on January 22, 2004, A:

They are still not sure it is junk. What we do know is that the part we know makes proteins makes up about 1-2% and only about 3-5% is conserved (remains pretty much unchanged) between Mouse and Human.

So we think the remaining 95% is either doing something we don't understand or is not doing anything special (hence the term "junk").

Since the 95% does not seem to have much evolutionary constraint placed on it, the idea that it encodes important information seems unlikely.

Much of the "junk" is actually the remains of various types of genomic parasitic elements that seem to replicate on their own in our (and most organism's) genomes. We do not know of any role they play in our biology, but we might discover an important role some day.

In organisms less difficult to work with than humans (like flies and worms), people have talked about removing big chunks of the "junk" to see what happens. It is clear a small part of it may be involved in chromosome structure and behaviour but there is not much else known. We do know that similar types of animals or plants can exist with huge differences in the amount of "junk" they have. The puffer fish has about 5 times less DNA than the salmon, but both have almost the same number of genes. The difference seems to be mainly in the the absence of the parasitic elements in the pufferfish genome.

The human genome has about 1 million or more copies of one 300 base long element called the 'alu element' (because it has a diagnostic restriction enzyme cleavage site in it). Chimps and gorillas have the same number of alu elements, give or take 50,000 but when you get to mice and rats, they have not got the alu element. It seems to have been acquired relatively recently (within 100 million years). We are quite sure it has no role in normal human biology and think we could remove it all...but it's hard to do the experiment in people!

It looks like it came from an element that became capable of replicating and inserting itself into new sites in the genome, sometime after rodents and primates diverged.

Francis Crick once suggested to me that the excess DNA (the "junk") might act as a sink (as in heat sink) for mutation causing agents. Sort of like a decoy for the mutagens, reducing the damage they can do to the "important" part of the genome.

 

David Baillie answered on January 30, 2004, A:

Reader Aparna asks:
Could it be possible that this junk DNA codes for RNA using a promoter different from the classical promoters?

David Baillie responds:
Yes, there are many known RNA genes and we suspect there are more. Many people are looking at this possiblity. Go to Dr Sean Eddy's website at Washington University, St Louis for an approach to finding regulatory RNA genes. (Scroll down the page.)

One could also look at the genbank website under "Pubmed" for papers on regulatory RNA, (type in: let-7, lin-4, or Sean Eddy). This might lead to useful information.

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