"junk DNA" a useful term or not?

Not so much wrong as perhaps overstated. The HGP certainly identified a whole lot of Open reading frames which were likely candidates for protein coding, but it would be an exaggeration to suggest they have identified genes coding for every protein in the body. Those genes are bound to be there in the sequence but where and what they do are mostly unknown. Some genes previously identified as pseudogenes have subsequently been shown to have functions, such as one instance where an mRNA transcript was produced from a 'pseudogene' of Makorin1 which helped to stabilise Makorin1 mRNA. So even if a 'pseudogene' has clear elements showing it has lost its protein-coding function, say loss of an ATG sit, it may still have a function.TTFN,WK

mispost, sorry having trouble with the boardThis message has been edited by mick, 05-19-2005 11:54 AM

mispostThis message has been edited by mick, 05-19-2005 11:53 AM

Hi,I'm picking up a discussion that was taking place on the simple evidence for ID thread. AdminBen requested that the discussion be moved here. The discussion concerned repetitive elements and pseudogenes. Junk DNA replicates itself during cell division in the same way as any other DNA. But I guess you are asking how repetitive elements duplicate themselves and spread around the genome.There are some pictures of the process at the following locations:http://www.anselm.edu/...age/jpitocch/genbio/transposons.JPG
(I think the "transposon enzyme" must refer to reverse transcriptase)http://www.gmuender.org/bt/genetik/img046.gif
(This looks like a viral insertion)Here is a nice overview of the different types of repetitive element: Sticking with repetitive elements for a moment - there is a good way to tell that repetitive elements are of viral origin rather than degradation of old human genes. Each retrovirus contains a set of characteristic genes - these are called gag, pol and env. Gag is the gene that codes for the viral capsid (the outer shell of the virus), pol is the gene that codes for reverse transcriptase, and env is the gene that codes for proteins that stick out of the coat of the virus. When you look at the larger repetitive elements (like LINEs) you find that you can identify viral env genes within the nucleotide sequence. So the viral origin of these repetitive elements is clear.Moving to pseudogenes, you are right that these are old degraded genes. But they tend to be degraded duplicates of extant genes, not degraded ancestral genes. Usually, for every pseudogene you have, you also have a functional copy of the same gene. Pseudogenes tend to have a relatively recent origin in random gene duplication. When a gene (or part of a gene) is accidentally duplicated, the genetic control systems of that gene are usually not duplicated along with it. So the new duplicate never gets to be expressed.If you want to find some ancient remnants of ancestral genes, the best place to look is our housekeeping genes! We share many such genes with yeast, for example, and they are still functional and expressed. I suspect that ID would like to find a function for things like repetitive elements. But it's pretty clear that they have no function other than their own duplication, and hence are good evidence for Darwinian processes operating within the genome. They don't appear to have any biological function in the cell. If anything they impose a cost in terms of the rapidity with which a cell can divide. Pretty much the same goes for pseudogenes. Pseudogenes are coding genes that are never expressed - therefore they are genes that have LOST their function. The propogation of repetitive elements is probably consistent with your view, yes. Although the phylogenetic patterns implied by the distribution of repetitive elements in different species are not consistent with YEC.MickThis message has been edited by mick, 05-19-2005 12:13 PM

Hi DP, It's been a while since I've covered RNA splicing but I don't think that's a fair analogy. I think it's bound to confuse Faith anyway. You can get fully functioning genes without any introns in them at all.For Faith:Apologies if this is a bit brief, but I'm off down the pub at 5:30 and my typing speed is glacial. If I say something you don't understand, don't be affraid to ask. I also apologise if you know most of this.

Genes encoded in the DNA are 'transcribed' into messenger RNA (mRNA)

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mRNA is then read by the protein sythesis machinary in the cell and a functioning protein is made. This is known as 'translation'

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There are parts of the gene that are transcribed, but not translated. Some of these are stuck slap bang in the middle of the gene (introns) and are effectively looped out of the mRNA - in a process known as RNA splicing. Here's a diagram showing how that happens.

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Hope that helps.

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Now I'm sure one of the more experienced resident biologists will correct me

The only thing I would add is that there is evidence that (some) introns do actually have a function, and play a role in gene expression.First, some introns are self-splicing (they fold themselves up and remove themselves from the mrna autocatalytically, which is a function of a sort).Second, some of the intron-coded mrna can act as a transcription regulator for the gene of which it is a part, and for transcription in general (google snoRNA).Third, it is also possible that introns act as spacers that put the exons into positions accessible to transcription factors.Last, there is at least one example of a gene in which all the functional sequences are contained within the introns rather than exons (I think the introns all code for snoRNA, and the exons are destroyed without doing anything).While we can be pretty sure that repetitive elements (30-40% of the human genome) and pseudogenes are genuinely junk, the position on introns is less clear.MickThis message has been edited by mick, 05-19-2005 01:23 PM

quote:

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While we can be pretty sure that repetitive elements (30-40% of the human genome) and pseudogenes are genuinely junk, the position on introns is less clear.

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This may be too general a statement. There are HERVs that have known fucntion such as some of the the env genes of the HERV-W and HERV-FRD class HERVs (syncytin genes). There are hints that other HERVs have cellular functions i.e. shaping the developing immune system, but since it has not been intensively researched it would be premature to lump all repetitive DNA together as junk. SINES may be mostly junk and most LINEs as well...pseudogenes are also most likely totally functionless like mtDNA pseudogenes (Numts...unless you count totally messing up mtDNA phylogenies as a function). I think it is too early to really say what is junk and what is not..though some research on large scale deletions in mice suggest that large portions of the genome have no impact on fitness i.e. junk.

A quick thanks to everyone for for the corrections & clarifications...

I haven't read more than your post yet so I guess I'll find out along with you how right or wrong others say you are.Meanwhile thank you, it helps to have something to visualize. So the same basic stuff is there as in the rest of DNA but it doesn't make proteins for some reason?Introns don't look any different from the rest of the gene hm?Sorry it took so long to get over here. I was reluctant to switch because I'm trying to avoid the science forums for a while. May not stick around here either but I appreciate your info.

I'm glad something is consistent with my view. Thanks.OK, I now have a lot to consider in this thread. Thanks to all for the input.This message has been edited by Faith, 05-22-2005 03:32 AM

I am jealous. Here in Anerica, you can die of frustration trying to find a science program with any depth. And that's with 150 channels!

Yes, but the terminology was never useful, to answer your original question, and I guess I would argue the term should not be used in any context. 'Junk' implies a lack of function for a sequence (repetitive or otherwise) on the singular criterium that there has been no 'function' demonstrated for it - as yet. It is therefore a negatively defined 'catch all', waste bucket category that is delineated only by our substantial empirical limitations.

I think could possibly lead to the discovery of a new class of RNA. Not surprisingly this was discovered at Harvard .

I stumbled across this earlier, and reminded me of Faiths "What does it look like?" question. I haven't tried it myself yet.You will need:
Water
Salt
Washing-up liquid
Some strong booze (ie Gin)
Two glassesMethod:
Put the booze in the freezer until it's ice cold.
Put a teaspoon of washing-up liquid in one of the glasses, and add 3 teaspoons of water.
Mix up some salt water in the other glass.
Rinse your mouth with the salt water for 30 seconds. This will collect some cells from your mouth.
Spit it into the washing-up liquid glass and stir fow a few minutes. The detergent will break up the cell walls and release the DNA.
CAREFULLY pour a couple of teaspoons of gin down the side of the glass: It should form a seperate layer on top of the mix.
After a few minutes, you should see white clumps appear in the gin. That's your DNA.(Copied from New Scientist's "101 things to do before you die" book. Sadly, all I have in at the moment is Guinness, so it will have to wait 'til tommorow...)Enjoy...This message has been edited by Dead Parrot, 05-23-2005 07:47 PM

Its interesting that the article you choose to link to isn't actually about a new class of RNA at all. They clearly suggest that the mechanism is based on transcription of the SRG1 removing and inhibiting factors binding to the SER3 promoter. If it was an inhibitory form of RNA it would be unlikely to be novel given the wealth of current research material on RNAi, microRNAs and other inhibitory forms.TTFN,WK