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Human codon usage

Fr. Des fatherdes at hotmail.com
Fri Sep 22 04:32:46 EST 2000


In article <cupton-2109001151130001 at hera.bioc.uvic.ca>,
  cupton at uvic.ca (Chris Upton) wrote:
>
> > >
> >
> > Hi James:  it works well for yeast and e.coli but NOT for humans.
> > Humans do not show increasing codon usage bias with gene expression
> > levels.  Local G+C content variation seems to be the dominant factor
in
> > different usage of codons in human genes.
> >
> > Des Higgins
> >
> >
> > Sent via Deja.com http://www.deja.com/
> > Before you buy.
>
> Hi,
>   Do you have any references for this observation?
> I've always wondered about it....   you see many AT rich viruses
> replicating very nicely in human cells!
>

I never suggested they should not.  There is no evidence that highly
expressed human genes look much different from ones with low expression
levels (unlike Drosophila, S.cerevis., many bacteria etc. where there
is a distinct trend for highly expressed genes to prefer certain
codons).  The references for the codon bias are numerous and start in
the 1980s with Gouy and Gautier and then Ikemura and many papers by
Paul Sharp (p.m.sharp).  I do not know the specific human reference.
There is a long series of paper by Giorgio Bernardi on analysis of human
 DNA variation around the genome (isochores) which is closely related.
There is one summary paper by Sharp and others from 1989 or 1990 in
Nucleic Acids research which summarises the human data and maybe gives a
reference.

Des Higgins

> Cheers,
>   Chris Upton
> --
> Dept Biochemistry and Microbiology
> University of Victoria
> Victoria BC
>


Sent via Deja.com http://www.deja.com/
Before you buy.







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