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transition bias

Brian Foley brianf at med.uvm.edu
Sat Jul 23 15:48:26 EST 1994

Jonathan F Wendel (jfw at iastate.edu) wrote:

: Most of us have had reason to encounter, at one time or another,
: transition/transversion biases.  I am wondering, though, whether there is
: any information on biases WITHIN transitions.  Specifically, are there data
: on AG versus CT transition frequencies in either plants, fungi, or animal
: nuclear or organellar genomes?

	Is this a trick question?  I always thought that an A -> G transition
on one strand of DNA was accompanied by a T -> C transition on the other
strand.  So A -> G must equal T -> C and visa versa.
	There is a lot of data on strand asymetry in DNA damage and 
repair.  The basic finding is that DNA which is frequently trranscribed 
is repaired faster than non-transcribed DNA, and that the repair process 
favors the transcribed strand that is serving as template.  It seems most 
likley that stalled polymerases (both DNA polymerase and Transcriptase) 
signal the repair machinery to come and fix the damage.

	If you really want to see mutational bias, look at the mutation 
frequencies of dinucleotides.  You will find that in eukaryotes, CG 
dinucleotides mutate to TG or CA at a very high rate, compared to other 
mutations.  This is due to methylation of C, followed by deamination of 
5-methyl cytosine.  Deaminated 5-methyl cytosine is thymidine.

	CG dinucleotides are rare in human DNA because of this.  Instead 
of the 1/16 proportion of this dinucleotide sequence we would find in 
random DNA, it is present at about 1/320, or 20-fold less than expected.
Despite it's rareness in human DNA, mutations in CG dinucleotides account 
for about 30% of human inheritable mutations.

: Please respond to me by email.  I will synthesize the remarks I receive and
: post them.  Thanks.
: -- 
:                    Jonathan F Wendel
:        Department of Botany, Iowa State University
:                     Ames, Iowa 50011
:       Email: JFW at IASTATE.EDU  Phone: (515) 294-7172

*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *

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