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Historical Background
Transposable elements were discovered by
Barbara McClintock through an analysis of genetic
instability in maize. She was studying maize
genetics and, in particular, was interested in
understanding a phenomenon of genetic instability
which was recognizable by the appearance of a
spotted phenotype in a somatic cell tissue by using
the ‘breakage–fusion–bridge’ strains to map genes.
She identified two interesting loci-Dissociator (Ds)
and Activator (Ac), which could transpose or
change positions on the chromosome. In one case,
she
observed
frequent
chromosome
break
occurring at the Ds locus on chromosome-9 in Acdependent manner. Interestingly, this Ds element
could move in the genome even to different
chromosomes. In another case, the Ds locus
seemed to regulate the expression of neighbouring
genes. The change in position of the Ds element
correlated with the expression of the C gene, and
resulted in variegation of the kernel colour. Based
on her observations, McClintock proposed that Ac
and Ds were ‘controlling elements’ that regulated
the expression of other genes. In the wake of the
discovery of Ac/Ds, few more transposable
element systems were identified in maize. In 1936,
Marcus Rhoades observed frequent mutability of
anthocyanin pigmentation in the aleurone of the
endosperm in Mexican Black corn, giving a dotted
phenotype. He determined that the unstable
phenotype of the a1 gene that was responsible for
the aleurone pigmentation was controlled by the
Dotted (Dt) gene.
The years following the discovery of the Ac/Ds
elements were marked by genetic characterization
of new transposons in maize. However, there was
an uncertainty among the biologists whether
transposons caused alteration in phenotype of
other genes because they disrupt other genes by
insertion or they cause alteration in phenotype by
their ‘controlling’ influence. When the limitations of
maize genetics to resolve this puzzle was clearly
felt, research in bacterial genetics was breaking
new grounds. In 1961, Jacob and Monod proposed
the operon model for regulation of expression of
the b-galactosidase gene in E. coli. Here the LacI
gene regulates the expression of the Lac operon.
Based on this observation, McClintock suggested a
parallel between regulation of gene expression in
bacteria and the effect of the ‘controlling elements’
in maize. In the following decade, more
transposable elements, including IS and Tn
elements in bacteria; Ty elements in yeast; and
copia-like elements, Foldback elements and P
elements in Drosophila were identified, mainly due
to their ability to cause mutations, rearrange the
genome, and regulate or modify the expression of
other genes. The power of genetics in these
systems, their simplicity and small size of genome,
coupled with the advantage of emerging molecular
techniques enabled the characterization of many
transposable elements at the genetic and
molecular level.
Introduction
Transposable elements are repetitive genomic
sequences that are able to move or transpose from
one chromosomal location to another. These
mobile elements have been variously called
jumping genes, mobile elements, insertion
sequences and transposons. The formal name for
this family of mobile genes is transposable
element,
and
their
movement
is
called
transposition. Transposition has also been called
illegimate recombination because it requires no
homology between sequences nor is it site-specific.
Consequently, it is relatively inefficient. The term
transposon was coined by Hedges and Jacob in
1974 for a DNA segment which could move from
one DNA molecule to other and usually disrupts
genetic function resulting in the phenotypic
variation.
The transposable elements often
replicate themselves. The replicative capacity of
transposable elements is essence of their
evolutionary
success
and
has
important
implications for the dynamics between elements
and their hosts.
The transposable elements are present in both
prokaryotic and eukaryotic chromosomes. These
are
even
more
prevalent
in
eukaryotic
chromosomes than in bacterial chromosomes. For
instance,
25%
to
40%
of
mammalian
chromosomes consist of transposable elements
that have accumulated in the course of evolution.
In addition, half of the spontaneous mutations
seen in Drosophila are attributed to the movement
and insertion of transposable elements. The
contribution of the transposable elements to
genome architecture and to the advent of genome
novelty is likely to be dependent, at least in part,
on the transposition mechanism, diversity, number
and rate of turnover of transposable elements in
the genome at any given time.
The transposable elements transpose by a
mechanism that involves DNA synthesis followed
by random integration at a new target site in the
genome. All transposable elements encode for
transposase, the special enzyme activity that helps
in the insertion of transposons at a new site and
most of them contain inverted repeats at their
ends. The major structural difference between
bacterial
transposable
elements
and
their
eukaryotic counterparts is the mechanism of
transposition. Only eukaryotic genomes contain a
special type of transposable elements, called
retroposons, which use reverse transcriptase to
transpose
through
an
RNA
intermediate.
Retroposons are more common than transposons.
They are either retroviral or nonviral. Viral
retroposons encode for the enzymes reverse
transcriptase and integrase and are flanked by
long terminal repeats (LTRs) in the same way as
retroviruses. Nonviral retroposons are the most
frequently encountered transposons in mammals.
The
typical
and
most
abundant
nonviral
retroposons are the short interspersed elements
(SINEs) and the long interspersed elements
(LINEs), which are usually repeated many times in
the mammalian genome. Both SINEs and LINEs
lack LTRs and are thought to transpose through
special retrotransposition mechanism that involves
transcription of one strand of the retroposon in to
RNA. This RNA undergoes conformation change
(looping) and provides a primer for the synthesis
of single-stranded cDNA. The cDNA later serves as
template for the synthesis of a double-stranded
DNA that is inserted in the genome by an unknown
mechanism.
Characteristics of Transposable Elements
1. The transposable elements were found to be
DNA sequences that code for enzymes which bring
about the insertion of an identical copy in to a new
DNA site.
2. Transposition events involve both recombination
and
replication
processes
which
frequently
generate two daughter copies of the original
transposable elements. One copy remains at the
parent site while the other appears at the target
site.
3. The insertion of transposable elements
invariably disrupts the integrity of their target
genes. For example, if an IS (insertion sequence)
becomes inserted in to an operon, it interrupts the
coding sequence and inactivates the expression of
the target gene in to which it inserts as well as any
gene downstream in that same operon. This is
because an IS contains transcription and/or
translation termination signals that block the
expression of other genes downstream in an
operon. This ‘one-way’ mutational effect or polarity
is referred to as polar mutation.
4. Since transposable elements carry signals for
the initiation for the initiation for RNA synthesis,
they sometimes activate previously dormant
genes.
5. A transposable element is not a replicon, thus,
it cannot replicate apart from the host
chromosome the way that plasmids and phage
can.
6. The frequency of transposition is low for most
transposons, in the range of one transposition per
104 to 107 cells per generation in prokaryotes.
7. Transposons can grow or diminish by
accumulating or losing DNA sequences that are in
addition to those necessary for transposition.
8. There exists no homology between the
transposon and the target site for its insertion.
Many transposons can insert at virtually any
position in the host chromosome or on to a
plasmid. Some transposons seem to be more likely
to insert at certain positions (hot-spots), but rarely
at base-specific target sites.
Classification of Transposable Elements in
Eukaryotes
Eukaryotic
transposable
elements
are
ubiquitous and widespread mobile genetic entities.
These elements often make up a substantial
fraction of the host genomes in which they reside.
For example, approximately 1/2 of the human
genome was recently shown to consist of
transposable element sequences. Transposable
elements are classified based upon
their
mechanism of transposition as well as by
comparison of their genomic structures and
sequences
Class 1
In Class 1 transposons, the transposon is
transcribed into RNA, which is reverse transcribed
by the transposable element encoded reverse
transcriptase. The cDNA is inserted at different loci
by the transposase. Class 1 elements are also
called
retrotransposons,
and
include
both
autonomous and non-autonomous elements.
Retrotransposons are further classified as LTR
elements and non-LTR elements, based on their
transposition mechanism and structure. LTRs are
named after the ‘Long Terminal Repeats’ in direct
orientation at either end of the transposon. The
LTRs bear structural similarity to retroviruses. The
autonomous elements encode at least two genes:
the gag gene encodes a capsid-like protein and the
pol gene encodes a polyprotein with various
activities,
including
protease,
reverse
transcriptase, RNaseH and integrase. LTR elements
are further classified into copia-like and gypsy-like
elements. The non-LTR retrotransposons lack the
long terminal repeats; instead they terminate by
simple sequence repeats. They are divided into
two: long interspersed nuclear elements (LINEs)
and short interspersed nuclear elements (SINEs).
Their coding regions include a gag-like protein, an
endonuclease and reverse transcriptase.
Class 2
The Class 2nd transposons transpose by direct
cut-and-paste mechanism without any RNA
intermediate. The transposase recognizes the
terminal inverted repeat sequences (TIRs) on
either ends of the transposable element, cuts it out
and inserts at a new site. The transposase makes
a staggered cut at the target site producing sticky
ends, cuts out the transposon and ligates it into
the target site. A DNA polymerase fills in the
resulting gaps from the sticky ends and DNA ligase
closes the sugar-phosphate backbone. This results
in target site duplication and the insertion sites of
DNA transposons may be identified by short direct
repeats followed by inverted repeats. The
duplications at the target site can result in gene
duplication, which plays an important role in
evolution.
DNA transposons are grouped into several
super families and families based on sequence
similarity, length of the TIRs, and length of the
TSD. hAT, CACTA, Mutator, PIF/Harbinger,
Tc1/mariner are well represented class 2
transposable element groups in eukaryotes.
Transposable elements in eukaryotes can be
classified in to four types on the basis of their
structure. The basis of their classification includes
the size and nature of the terminal repeats or
inverted repeats. The four types of transposons
are: (i) With long terminal direct repeats (e.g.
Copia in Drosophila, Ty in Yeast and IAP in mice);
(ii) with long terminal inverted repeats (e.g. FB, TE
in Drosophila); (iii) with short terminal inverted
repeats (e.g. P and I in Drosophila; Ac/Ds in
maize; TamI in snapdragon and TcI in
Coenorhabditis) and (iv) without terminal repeats
(e.g. Alu in mammals).
Transposable
Elements
in
Drosophila
melanogastere
The presence of transposable elements in D.
melanogaster was first inferred from observations
analogous to those that identified the first insertion
sequence in E.coli. These sequences include the
copia retroposon, the foldback (FB) family and the
P elements.
(a) Copia-like elements
Its name reflects the presence of a large
number of closely related sequences that code for
abundant mRNAs, as the name derives from the
Latin copia means abundance. The copia-like
elements of Drosophila constitute atleast seven
families, ranging in size from 5-8.5 kb. Members of
each family appear at 100-1000 positions in the
Drosophila genome. Each member carries a long,
direct, terminal repeat and a short, imperfect
inverted repeat. The number of copies of the
copia-like element depends on the strain of fly.
The members of the family are widely dispersed.
The locations of the copia elements show a
different (although overlapping) spectrum in each
strain of D. melanogaster. These differences have
developed over evolutionary periods.
The copia element is ~5000 bp long, with
identical direct terminal repeats of 276 bp. Each of
the direct repeats itself ends in related inverted
repeats. A direct repeat of 5 bp of targer DNA is
generated at the site of insertion. The divergence
between individual members of the copia family is
slight, at <5%; variations often contain small
deletions. All of these features are common to the
other copia-like families, although their individual
members display greater divergence.
Copia-like elements cause a duplication of a
characteristic number of base pairs of Drosophila
DNA on insertion. Certain classic Drosophila
mutations result from the insertion of copia-like
and other elements, e.g. the white apricot (wa)
mutation for eye colour is caused by the insertion
of an element from the copia family in to the white
locus.
(b) P elements
The P element in Drosophila is one of the best
examples
of
exploiting
the
properties
of
transposable elements in eukaryotes. This element
is 2907 bp long and features a 31 bp inverted
repeat at each end. The element encodes a
transposase. Although, the transposase is required
for transposition, it can be supplied by a second
element. Therefore, P element with internal
deletions can be mobilized and then remain fixed
in the new position in the absence of the second
element, thus the P element can serve as a
convenient marker. P elements do not utilize an
RNA intermediate during transposition and can
insert at many different positions in the Drosophila
chromosome. The transposition of a P element is
controlled by repressors encoded by the element.
When P elements are mobilized, they produce
a syndrome of traits known collectively as hybrid
dysgenesis. These traits include temperaturedependent sterility, elevated rates of mutation,
chromosome rearrangement and recombination.
The syndrome is usually seen only in the progeny
of males with autonomous P elements and females
that lack P elements. These two kinds of strains
are called ‘P’ and ‘M’ because they contribute
paternally and maternally respectively to hybrid
dysgenesis. The reciprocal cross P (female) × M
(male) yields hybrids in which the dysgenic traits
are much reduced, due to the maternal component
of P element regulation by cytotype. The dysgenic
traits can be explained largely by genomic changes
due to P element transposition and excision in
developing germ cells. The sterility is due to loss of
germ cells early in development. It is more
pronounced in females, where there are fewer
germ cells to spare than in males, and at
temperatures above 250C. The mutations come
about through several mechanisms, but are
primarily P insertions in to genes and imprecise
excision of P element near genes. Chromosome
rearrangements usually result from breakage at
the sites of two or more P element insertions,
followed by rejoining of the chromosome segments
in a different order. P-induced recombination
occurs preferentially in the genetic intervals
containing mobile P elements, and usually within 2
kb of the insertion site.
(b) Foldback (FB) elements
Foldback elements are transposable elements
found in many eukaryotic genomes. They are
thought to contribute significantly to genome
plasticity. These elements range from a few
hundred to few thousand base pairs and carry long
inverted repeats at the termini. The repeats may
be adjoining or may be separated, but can always
fold back to form stem and loop structures.
In D. melanogaster, foldback elements have
been shown to be involved in the transposition of
large chromosomal regions and in the genetic
instability of some alleles of the white gene. They
may cause mutations by insertion or by their effect
on gene expression due to their presence near a
control region.
Transposable Elements in Maize
The transposable elements in maize were
discovered by Marcus Rhoades and Barbara
McClintock. These genetic elements in maize were
found to be responsible for turning the expression
of genes ‘on’ or ‘off’ hence the name ‘controlling
elements’. These controlling elements when
located on maize chromosomes represented
specific sites for breakage and reunion of
chromosomes leading to gross changes in
chromosome structure. Some of the most popular
controlling elements found in maize are activatordissociation (Ac-Ds) system and suppressormutator (spm) system. The number, type and
location of these elements are characteristic of
each maize strain. These elements can be
classified in to two classes- (i) an autonomous
element, which have the ability to excise and
transpose, rendering sites of their insertion
mutable, and (ii) non-autonomous elements, which
do not transpose and are unstable and can be
derived from autonomous elements of the same
family. They become unstable only when an
autonomous member of the same family is present
elsewhere in the genome. When complemented by
an autonomous member of the same family, the
non-autonomous member may display properties
of the autonomous element including its ability to
transpose.
(a) Activator-Dissociation
(Ac-Ds)
system
Ac-Ds system is the most popular system and
was discovered in 1950 by Barbara McClintock,
when she found the presence of a genetic factor
Ds (dissociation) caused high tendency towards
chromosome breakage at the location, where it
appears. These breaks could be located either
cytologically at pachytene or genetically by
uncovering of recessive alleles in a heterozygote.
This property of Ds was dependent on another
unlinked genetic factor Ac (Activator). Thus, in
presence of Ac, Ds may undergo transposition or
may cause chromosome breaks and an increase in
the number of Ac element in the genome
decreases the frequency of transposition or
chromosome breaks by Ds.
The functionally autonomous element, Ac,
consists of 4563 nucleotide-pairs bounded by an 8
nucleotide-pair direct repeat. This direct repeat is
created at the time that the element inserts in to a
site on a chromosome. Other repeat sequences are
found within the element itself. The most
conspicuous of these are at the ends, where an 11
nucleotide-pair sequence at one end is repeated in
the opposite orientation at the other end. These
inverted terminal repeats are thought to play an
important role in transposition.
The Ds element shows considerable structural
heterogeneity. One class of Ds element is derived
from Ac element by deletion of internal sequences.
Another class possesses the characteristic inverted
terminal repeat sequences of Ac, as well as some
of the sub-terminal sequences, but the remainder
of the DNA is different. These unusual members of
the Ac/Ds family are called aberrant Ds elements.
A third class of Ds element is characterized by a
peculiar piggybacking arrangement. One Ds
element is inserted into another, but in an inverted
orientation. It has been shown that these double
Ds elements are responsible for chromosome
breakage.
The activating function of Ac elements is
associated with a protein that they synthesize.
Since this protein is involved in transposition, it is
sometimes called the transposase of the Ac/Ds
family. Deletion or mutations in the gene that
encode this protein abolish the activating signal
and explain why Ds elements, which have such
lesions, cannot activate themselves. However,
since this transposase is diffusible, a single Ac
element can provide it to all the Ac and Ds
elements in the genome. Therefore, we can say
that Ac/Ds transposase is trans-acting.
(b) Supressor-mutator
(spm-dSpm)
system
The suppressor-mutator family of maize
transposon was discovered by Barbara McClintock.
In this family, the autonomous element is called
Spm and the non-autonomous elements are called
dSpm (‘d’ stands for deleted or defective). Spm
elements are 8287 nucleotide-pairs long, including
13 nucleotide-pair inverted repeats. When they
insert in to a chromosome, they create 3
nucleotide-pair target site duplication. The dSpm
elements are smaller than the Spm elements
because part of the DNA sequence has been
deleted. These deletions disrupt the functioning of
a gene carried by complete Spm elements and
therefore prevent the synthesis of the gene’s
product. Since this product is necessary for
transposition, deleted dSpm elements are unable
to stimulate their own movement.
The Spm family was named because its
elements can suppress the function of genes in to
which they have transposed. This occurs when an
inserted dSpm element interacts with an Spm
element located elsewhere in the genome.
Although, the dSpm insertion reduces the
expression of the gene, it does not abolish it
completely. However, when an autonomous Spm
element is introduced in to the genome, the
expression of the pigmentation gene is completely
inhibited in most of the kernel. This indicates the
‘supressor’ action of the Spm element. In
addition, this element stimulates the excision of
the dSpm element in some of the cells, leading to
clones in which gene function is partially restored.
These clones, which are recognized by their
moderate to heavy pigmentation, demonstrate the
trans-acting, ‘mutator’ function of the Spm
element.
Transposable Elements in Yeast
The yeast Saccharomyces cerevisiae
carries transposable elements called Ty elements
which comprise a family of dispersed repetitive
DNA sequences that are found at different sites in
different strains of yeast. Ty is an abbreviation for
‘transposon yeast’. Ty elements are retroposons,
with a reverse transciptase activity, that transpose
via an RNA intermediate.
The frequency of Ty transposition is lower
than that of most bacterial transposons, ~10-7 to
10-8. There is considerable divergence between
individual Ty elements. Most elements fall into one
of two major classes, called Ty1 and Ty917. They
have the same general organization. Each element
is 6.3 kb long; the last 330 bp at each end
constitute direct repeats, called delta. Individual Ty
elements of each type have many changes from
the prototype of their class, including base pair
substitutions, insertions and deletions. There are
~30 copies of Ty1 and ~6 of the Ty917 type in a
typical yeast genome. In addition, there are ~100
independent delta elements called solo deltas. Not
all of the Ty elements in any yeast genome are
active. Most have lost the ability to transpose and
are analogous to insert endogenous proviruses.
These ‘dead’ elements retain the delta repeats,
though, and as a result they provide targets for
transposition in response to the proteins
synthesized by an active element.
A Ty element is altered by adding a promoter
that can be activated by the addition of galactose.
Activation
of
the
promoter
will
increase
transcription through the Ty element. Then an
intron from another gene is inserted into the Ty
element. Because the final product of transposition
contains no intron, the intron must have been
spliced out of an RNA transcript. This splicing must
have taken place, where the primary transcript
contains the intron but the final processed mRNA
does not. This RNA is then copied by reverse
transcriptase and integrated into the chromosomal
DNA. The addition of galactose greatly increases
the frequency of transposition of the altered Ty
element. This increased frequency suggests the
involvement of RNA, because galactose-stimulated
transcription begins at the galactose-sensitive
promoter. Because introns are excised only in the
course of RNA processing, the transposed Ty DNA
must have been copied from an RNA intermediate
transcribed from the original Ty element and then
processed by RNA splicing. The DNA copy of the
spliced mRNA is then integrated into the yeast
chromosome.
Significance of transposable elements
Transposons seem to play a role in evolution
and biology by promoting rearrangement and
restructuring of genes. Transposition may directly
cause both deletion and inversion mutagenesis.
They cause mutations by insertion into genes and
affect the regulation of genes by inserting near
promoters. They also provide substrates for
genetic rearrangements and thus act as agents of
genome evolution. Furthermore, transposable
elements mediate the movement of host DNA
sequences to new locations, enrich the genome
with identical sequences positioned at different
locations, and promote homologous recombination.
Such recombination may eventually result in
deletions, inversions and translocations.
Transposons usually influence the expression
of the proximity of their insertion sites. They are
therefore extensively used as tools to create
random insertion in bacteria, yeast and higher
eukaryotes. They are also used in large scale
genomic studies.
Transposable elements have played an
important
role
in
the
diversification
and
enrichment of mammalian transcriptomes through
various mechanisms such as exonization and
intronozation (the birth of new exons/introns from
previously intronic/exonic sequences respectively),
and insertion in to first and last exons.
Transposable elements may play a crucial and
essential role in evolution and could be the
‘missing link’ in our understanding of how
multicellular and vertebrate organisms arose. The
whole idea of transposons as purely selfish DNA is
beginning to crumble. It now appears that at least
some transposable elements may be essential to
the organisms in which they reside. Even more
interesting is the growing likelihood that
transposable elements have played an essential
role in the evolution of higher organisms, including
humans. Transposable elements have also been
used as vectors to transform the organisms
genetically.
In
prokaryotes,
the
antibioticresistance marker carried by different transposons
serves as a convenient marker.
Transposable elements have many potential
applications
in
genetic
research
including
insertional mutagenesis, gene mapping, gene
cloning, gene transfer within and between species,
and identification of genes expressed in specific
tissues at a particular time. All these genetic
approaches are important in the study of molecular
biology and evolution. As the number of known
transposable
elements
increases
and
their
properties are further documented, their utility as
genetic research tools will become greater.