From Wikipedia,
the free encyclopedia.
Retrotransposons are
mobile
genetic elements and are
ubiquitous in the
genomes of many
eukaryotic organisms. They are
particularly abundant in plants,
where they are often a principal
component of nuclear
DNA. In
maize 50-80% and in
wheat up to 90% of the
genome is made up of
retrotransposons.
Biological activity
The retrotransposons
replicative mode of
transposition increases the
copy numbers of elements rapidly
and thereby greatly increasing
plant
genome size. Like DNA
transposable elements, they
can induce
mutations by
inserting near or within
genes. Furthermore,
retrotransposon induced mutations
are relatively stable; because the
sequence at the insertion site is
retained as they transpose via
replication mechanism.
Retrotransposons copy
themselves to
RNA and then, via
reverse transcriptase, back to
DNA.
Transposition and survival of
retrotransposons within the host
genome are possibly regulated both
by retrotransposon- and
host-encoded factors, to avoid
deleterious effects on host and
retrotransposon as well, in a
relationship that has existed for
many millions of years between
retrotransposons and their plant
hosts. The understanding of how
retrotransposons and their hosts’
genomes have co-evolved mechanisms
to regulate transposition,
insertion specificities, and
mutational outcomes in order to
optimize each other's survival is
still in its infancy.
Types of retrotransposons
Retrotransposons belong to
class I type of mobile elements,
consists of two sub-types, the
long terminal repeat (LTR) and the
non-LTR retrotransposons. The LTR
retrotransposons have direct LTRs
that range from ~100 bp to over 5
kb in size. LTR retrotransposons
are further sub-classified into
the Ty1-copia and the Ty3-gypsy
groups based on both their degree
of sequence similarity and the
order of encoded gene products.
Ty1-copia and Ty3-gypsy groups of
retrotransposons are commonly
found in high copy number (up to a
few million copies per
haploid
nucleus) in plants with large
genomes. Ty1-copia
retrotransposons are abundant in
species ranging from single-cell
algae to
bryophytes,
gymnosperms, and
angiosperms. Ty3-gypsy
retrotransposons are also widely
distributed, including both
gymnosperms and angiosperms. LTR
retrotransposons make up
approximately 8% of the human
genome.
The non-LTR retrotransposons,
consists of two sub-types, long
interspersed nuclear elements (LINEs)
and short interspersed nuclear
elements (SINEs). They can also be
found in high copy numbers (up to
250,000) in the plant species.
- LINES (long interspersed
elements) are long DNA sequences
that represent
reverse-transcribed RNA
molecules originally transcribed
by
RNA polymerase II into
mRNA (messenger RNA to be
translated into
protein on
ribosomes). Also called
pseudogenes, they do not
contain
introns or
promoters, but can
code for
reverse transcriptase or
integrase, enabling them to
copy both themselves and other,
noncoding LINES. Because LINES
move by copying themselves
(instead of moving, like
transposons do), they enlarge
the genome. The human genome,
for example, contains about
500,000 LINES, which is roughly
21% of the genome. LINES are
used to generate
genetic fingerprints.
- SINES (short interspersed
elements) are short DNA
sequences that represent
reverse-transcribed RNA
molecules originally transcribed
by
RNA polymerase III into
tRNA,
rRNA, and other small
nuclear RNAs. SINEs do not
encode a functional reverse
transcriptase protein and rely
on other mobile elements for
transposition. The most common
SINES are called
Alu sequences. Alu elements
are about 300 base pairs long,
do not contain any coding
sequences, and can be recognized
by the
restriction enzyme AluI
(thus the name). With about 1
million copies, they make up
about 11% of the human genome.
Both LINES and SINES are also
called "selfish DNA" or "junk
DNA", because they do not
serve any known purpose. SINEs
make up 13.5% of the human
genome.
Several
viruses, like
HIV-1 or
HTLV-1 behave like retroposons
and contain both reverse
transcriptase and
integrase, the retroposon
equivalent of
transposase.
See also
