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Mark D. Garfinkel garfinkl at iitmax.iit.edu
Mon Jan 31 11:32:58 EST 1994

pkeeling at ac.dal.ca (Patrick Keeling) writes:

>[I restore attribution to me, garfinkl at iitmax.acc.iit.edu]
>>         *Also, let's remember that a significant portion of human
>> repetitive DNA, namely the Alu repeats, code for the 7SL RNA [...]
>> Not all "complex" repetitive
>> DNA is retrotransposon or other selfish DNA, or "mysterious" in some way.
>I may well be mistaken, but I think it is incorrect to say that the
>Alu element IS a 7S RNA. It is my understanding that the Alu sequence
>was originally derrived from a "renegade" 7S gene [...]
        *I was wrong in my assertion about the relationship between 7SL
RNA and Alu repeats. PK is correct that Alu sequences are *related* to
7SL genes, but do not code for functional 7SL RNA. Or at least the Darnell,
Lodish & Baltimore textbook gives me that impression.

>Also, I believe that you are wrong in your assertion that Alu is not a
>retro-element, it has an RNA pol III promoter, and appears to undertake
>RNA mediated transposition.
        *Correct on both counts. But does it not have a PolIII promoter
due to its ancestry?
>Lastly, I would like to know why you would think that a retro-element
>present in the genome 500,000 times is "mysterious", while an
>equal number of genes for the 7S RNA is not.
        *Contribution to phenotype. By definition (punning, here),
"mysterious" DNAs either do not contribute to phenotype, or they do so
in ways we don't know about. Either way, it's hard at present to
understand why a genome would carry 500K of them. In contrast, if
a hypothetical organism contained 500K 7SL RNA genes, and there were a
stage in the life cycle when 7SL RNA gene transcription is maxed-out,
i.e., all 500K copies are fully laden with RNA polymerases, then there'd
be experimental evidence that the organism required all the copies; it
would make experimental sense & I'd be happy.

	There are a number of cases in other vertebrate species & in
invertebrates where oogenesis is a particularly intensive biosynthetic
period & parts of the genome are transcribed at full-throttle, making use
of all members of a repeated gene family to maximum effect.

	Now if our hypothetical organism with 500K 7SL genes *never*
made maximum transcriptional use of them, I'd be no more comprehending of
the surfeit of gene copies than I am of the abundance of Alu repeats.

	Hope this makes better sense.

Mark D. Garfinkel
e-mail: garfinkl at iitmax.acc.iit.edu

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