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

["David Evans" <devans@xxxxxxx>]

Right about the HD Carl. 

-----Original Message-----
From: HAPS-L-owner@xxxxxxxxxxx [mailto:HAPS-L-owner@xxxxxxxxxxx] On
Behalf Of Carl Shuster
Sent: Tuesday, February 20, 2007 3:12 PM
To: HAPS-L@xxxxxxxxxxx
Subject: [HAPS-L] Mutations - well, maybe- repeated sequences?

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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