IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

Genome Length

Keith Robison robison at mito.harvard.edu
Sat Oct 21 16:09:33 EST 1995


Michael Coyne (mcoyne at argo.net) wrote:
: Agschultz wrote:
: > 
: > On October 6, 1995, Mary Kuhner writes,
: > 
: > > In many organisms another substantial portion of the junk (DNA) consists
: > of
: > > thousands of copies of sequences which have the ability to duplicate
: > > themselves.  These may or may not be useful in some way to the organism;
: > > they could survive even if they are not useful, as a sort of genetic
: > > parasite, because of that copying ability.

: Okay, now I'm confused.  By what critera is DNA classified as "junk"?  I would 
: have assumed that junk DNA would imply DNA which, when examined at the sequence 
: level, shows no evidence of a function.  

Your confusion is understandable; there is no rigorous definition of
"junk" DNA.  Nor is there any trivial way to prove that a segment
of DNA does not have biological function -- the label "junk DNA"
is as much (or more) an expression of our ignorance than a useful
definition.


: Even this is not enough of a 
: definition, since many (most?) eucaryotic genes have exons, 
: which are "useless" 

Definition point: you have things backwards:  
	INtrons are INbetween the EXpressed EXons.

: bits of DNA (in as much as they don't code for anything) but still perform a 
: vital function as "spacers", if you will.  DNA which has the ability to 
: duplicate itself (presumably unlinked to the replication of the chromosome) 
: must therefore have some genes and therefore is not junk.  How does this DNA 
: duplicate itself (most DNA codes for proteins, which in turn do the work)?  If 
: these pieces of DNA excise themselves and form replicons which then 
: re-integrate into the chromosome, they are behaving much like plasmids or 
: viruses, and therefore probably were introduced to the genome by outside 
: acquision.  These pieces of DNA could be integrated viruses or plasmids, and 
: could serve as a source of plasticity to the genome by adding a mechanism of 
: introducing mutations.


Things frequently labeled as junk (not necessarily non-overlapping categories):
	introns
	dead retroviruses
	pseudogenes (relics of genes with obvious defects)
	transposons (retro- and DNA-based)
	simple sequence repeats (e.g. (CAG)20 )



Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 





More information about the Mol-evol mailing list

Send comments to us at biosci-help [At] net.bio.net