ALU repeats: is there any function?

Juergen Brosius RNA.world at uni-muenster.de
Mon Sep 25 12:17:40 EST 1995

In article <DFGtt9.AuG at cc.umontreal.ca>, "Benot Grondin from MONTREAL"
<GrondiB at IRCM.UMontreal.CA> wrote:

> Does anyone have an idea of alu repeat function?

Plenty - Alus, like many other SINEs (short interspersed repetitive
elements) and portions of retroelements (e.g. LTRs) are loaded with short
DNA stretches that provide regulatory sequences.  They contain, for
example, sequences that are being recognized by DNA binding proteins which
can act to enhance or supress transcriptional activity in adjacent genes. 
They can contribute promoter elements such as a CAAT box.  They introduce
new splice sites into genes.  As a result, novel exons can be recruited
from intronic material.  Even the Alus themselves can contribute novel
amino acid codons to protein coding regions.  Other SINEs (e.g. B1, the
rodent monomeric Alu analogue) provide poly(A) addition signals or may
modulate the stability of mRNAs when integrated into the 5 prime or 3 prime
untranslated regions.  Alus - due to their high G/C content can influence
the methylation state of sequences surrounding genes and thus influence
their expression.  Alus may influence nucleosome positioning etc. etc.

I can recommended a new book edited by Richard Maraia entitled *The impact
of short interspersed elements (SINEs) on the host genome* (1995) R.G.
Landes, Austin TX.

Of course, Alus did not evolve for those purposes and when integrated into
the wrong position they can have detrimental effects.  They are just highly
efficient retrogenes derived from one or a few master copies, whose
function is not known yet.  Nevertheless, Nature takes the opportunity to
recruit, co-opt or exapt [Brosius and Gould (1992) PNAS 89,10706] such
sequences into novel tasks. 

Since they are so numerous and can integrate into many different genomic
locations, SINEs including Alus are among the mediators of genomic
plasticity and a driving force of evolution.  They keep the genomic dating
game going - wedding existing genes to new regulatory elements.

Alus can also give rise to novel RNA coding genes, such as the neural BC200
RNA gene in primates.

Regards,											Juergen

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