BIOL 200 Lecture Notes - Alternative Splicing, Dna Ligase, Pseudogene

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6 Apr 2012
Naveen Sooknanan McGill Fall 2011
LTR retrotransposons, LINEs and SINEs:
While DNA Transposons move using a “cut and paste mechanism”, LTR retrotransposons move
through and RNA intermediate, much like retroviruses.
In fact, retrotransposons use a reverse transcriptase enzyme in order to reincorporate
themselves into the genome, which can use RNA or DNA as a template
They have a very small gene length, approximately 6-11 kbp (although they can be
considerably larger), and have a very high copy number, almost half a million
LTR retrotransposons can be found in small number in the human genome, but are much
more predominant in plant genomes like wheat and flowers
The structure of an LTR is almost identical to that of a retrovirus in its proviral form.
They both have noncoding target-site direct
repeats at the very ends of the transposon
(which are part of the normal genome)
They both also have a protein coding region,
although they proteins for which they code are
slightly different
They both also contain an LTR region
The protein coding region of the retroviral ORF contains a series of exons coding for 5 different
The gag region codes for a group specific antigen
The pol region codes for a polymerase regions which synthesizes various enzymes
involved in the transcription process
o Within this region, PR codes for protease, RT for reverse transcriptase and IN for
o This region form one long mRNA molecule involving all of these polypeptides
but are then cleaved post transcriptionally in order to separate the polypeptide
chain into functional proteins
The env region codes for an envelope which allows the retrovirus to escape the cell and
complete its life cycle
The ORF order of an LTR retrotransposon are almost the same as the proviral ORF, except that
they have no env region. This means that the LTR retrotransposon is not allowed to leave the cell
(i.e. it is not infectious like a retrovirus).
Due to the vast similarities between these two species, there is a debate as to which came first in
the evolutionary process: LTR retrotransposons or retroviruses.
One argument states that the retroviruses could have entered the host cell (which is
possible as there are many retroviruses littering the genome) and lost their env region
disabling their infectious properties
The counterargument involves the capturing of an LTR retrotransposon by a host cell
(which is not uncommon) and somehow gained an env region from the host cell, thus
gaining retroviral properties
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