[HAPS-L] Mutations - well, maybe- repeated sequences?

["Carl Shuster" <CShuster@xxxxxxxxxxxxxxx>]

Does anyone know how much of the "95-98% non-coding" is actually repeated sequences?  I seem to recall that the human genome can contain some sequences that have been repeated as many as 1,000,000 times (!!!).  I also seem to recall that repeated sequences do account for a suprising number of genetic diseases in humans, including Huntingtons disease.

Carl Shuster
Biology
Madison Area Technical College
(608) 246-6203
CShuster@xxxxxxxxxxxxxxx


>>> "Rawding, Robert S" <RAWDING001@xxxxxxxxxx> 02/18/07 10:43 AM >>>
Ken and others,
 
The "98% of the DNA ...(as),, 'non-coding'" may not be entirely correct.   There are more than 1,000 reports of evident to the contrary in diverse organisms.   
 
Perhaps it is better to state that the "98%" (other sources say 95%) 'non-coding' is simply '98%' with unknown function.  Here are some of the contrary evidence - there are quite a few studies that show that these so-called 'junk DNA' regions may be (1) physically blocking transcription of adjacent genes, (2) regulating gene expression during development, (3) enhancers for transcription of proximal genes, and (4) regulating translation of proteins.  
 
There are also interspersed nuclear elements (L1 elements) which may be responsible for the plasticity of the genome, which are likely jumping genes.  There may be 50-60 of these in the human genome - certain sequences resemble similar sequences in bacteria.   For a nice discussion of the possibilities that these 'non coding' DNA sections may actually be some kind of language, see a nice article by F. Flam - "Hints of a language in junk DNA", Science 266:1320, 1994.
 
If you also take a look at the genetic code, there are six codons for arginine alone, which suggests that if one of the bases in the middle of the codon was erroneous, it wouldn't matter during transcription - arginine is still going to become part of the peptide chain.     So the redundancy of the code itself for some amino acids may offset some of these mutations.    More critical would be amino acids that have only two codons, where it would make sense that erroneous base duplications or substitutions here would have a higher probability for the appearance of a mutation.
 
It also makes sense that the appearance of a developmental mutation later rather than earlier in embryonic development is likely to have a greater effect on the descendent cells versus mutations that might occur in our post-natal cells.
 
I'm not certain that I'd want to categorically admonish the 'deleterious' effects of mutations - even 'some' of the time, rather than 'most' of the time.   I don't think anyone really has a good handle on mutation rates in general in the absence of mutagenic substances, given the nature of the 'self-correction' that occurs in nuclear enzymes that are guarding against such mutations, such as excision of thymine-thymine dimers, and so on.   
 
Surely there is abundant evidence that UV light and nasty stuff like benzene 'up' these rates (and we'll never know for sure how many of us were 'poisoned' by the aniline dye in ditto copies we received in school - and now I'm really dating myself!!!).
 
It may very well be true that the 'non-coding' regions that show mutations have no observable effect.   But maybe reserving judgement on such is the most prudent way to proceed.
 
Bob
 

Robert S. Rawding, Ph.D.
Assistant Professor
Department of Biology
Gannon University
109 University Square 
Erie, PA 16541

Phone: (814) 871-5872
FAX: (814) 871-5757 






From: HAPS-L-owner@xxxxxxxxxxx on behalf of Ken Saladin
Sent: Sat 2/17/07 6:00 PM
To: HAPS-L@xxxxxxxxxxx 
Subject: [HAPS-L] Mutations



The conventional wisdom is that most mutations are deleterious. But if 98% 
of the DNA is noncoding (and with certain other assumptions that seem of 
only peripheral relevance), wouldn't it be more accurate to say that a 
considerable majority of mutations are harmless? 
Just a bit of food for thought. 
Ken 

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