It takes two transposons to tango

Personal view of the genome project
45 Goffeau, A. et al. (1997) The Yeast Genome Directory. Nature
387, 1–105
46 The C. elegans Sequencing Consortium (1998) Genome
sequence of the nematode C. elegans: a platform for
investigating biology. Science 282, 2012–2018
47 Adams, M.D. et al. (2000) The genome sequence of
Drosophila melanogaster. Science 287, 2185–2195
48 Leversha, M.A. et al. (1999) A molecular cytogenetic clone
resource for chromosome 22. Chromosome Res. 7, 571–573
49 Kirsch, I.R. et al. (2000) A systematic, high-resolution
linkage of the cytogenetic and physical maps of the human
genome. Nat. Genet. 24, 339–340
50 Pinkel, D. et al. (1998) High resolution analysis of DNA copy
number variation using comparative genomic hybridization
to microarrays. Nat. Genet. 20, 207–211
51 Lockhart, D.J. and Winzeler, E.A. (2000) Genomics, gene
expression and DNA arrays. Nature 405, 827–836
52 Pandey, A. and Mann, M. (2000) Proteomics to study genes
and genomes. Nature 405, 837–846
53 Risch, N.J. (2000) Searching for genetic determinants in the
new millennium. Nature 405, 847–856
It takes two transposons
to tango
transposable-element-mediated chromosomal
Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more
specifically, than other cellular processes1–3. One explanation of such events is homologous recombination
between multiple copies of a TE present in a genome. Although this does occur, strong evidence from a number
of TE systems in bacteria, plants and animals suggests that another mechanism – alternative transposition –
induces a large proportion of TE-associated chromosomal rearrangements. This paper reviews evidence for
alternative transposition from a number of unrelated but structurally similar TEs. The similarities between
alternative transposition and V(D)J recombination are also discussed, as is the use of alternative transposition
as a genetic tool.
ince the first description of mobile genetic elements4,5,
transposable elements (TEs) have been found to be
associated with chromosomal rearrangements such as
deletions, duplications, inversions, the formation of acentric fragments and dicentric chromosomes, translocations
and recombination of host genomes. This aspect of transposable element function has implications for evolution2,6
and for understanding several human genomic disorders7,8
and, because of this, the mechanisms involved in transposon-mediated chromosomal rearrangements warrant
thorough investigation.
TEs are classified by their sequence structure and transposition mechanisms1,3,6. Class I TEs – retroposons and
retrotransposons – transpose by an RNA intermediate.
Retroposons have a structure similar to mRNA; retrotransposons are structurally similar to retroviruses and are
bounded by long terminal repeats (LTR). Class II TEs –
insertion sequences (IS elements, Box 1) and transposons –
transpose by a DNA intermediate catalysed by a transposase enzyme. IS elements and transposons are bounded
by terminal inverted repeats (TIR). In addition to the TIR,
additional sequences differentiate the two ends and are
necessary for transposition. In prokaryotes, IS elements
contain sequences encoding transposase, and transposons
0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S0168-9525(00)02104-1
are TEs that contain sequences encoding other genes in
addition to transposase, such as genes encoding enzymes
responsible for antibiotic resistance. In eukaryotes, all TEs
that transpose by a DNA intermediate are classified as
transposons. Some Class II TEs, such as IS10, IS50, Ac/Ds
(Box 1), Tam3, P, hobo and mariner, encode a single
transposase gene. Other Class II TEs, such as Tn7, Phage
Mu, Mutator and En/Spm, encode multiple proteins that
catalyse and regulate transposition.
Two possible mechanisms by which TE-associated
chromosomal rearrangements can occur are: (i) indirectly
by homologous recombination or (ii) directly by an alternative transposition process.
The indirect action of TEs promotes chromosomal
rearrangements by presenting the genome with multiple
similar, if not identical, sequences between which strand
transfer can occur. This may occur by recombination of
the homologous sequences or by faulty repair of doublestrand breaks formed during transposable element
excision using ectopic homologous sequences as a repair
Not all the rearrangements observed can be explained
by homologous recombination between elements at different locations. For instance, rearrangements have been
TIG October 2000, volume 16, No. 10
Yasmine H.M. Gray
Molecular Genetics and
Evolution Group,
Research School of
Biological Sciences,
Australian National
University, Canberra,
ACT 2601, Australia.
Transposons and chromosomal rearrangements
FIGURE 1. Chromosomal rearrangements caused by homologous recombination
trends in Genetics
Homologous recombination between repetitive sequences, such as TEs, can result in chromosomal rearrangement such as deletions, duplications and inversions. Each line represents a DNA
double helix. The two sister chromatids of each of the homologous chromosomes are shown. Black ovals denote the centromere. TEs are represented by the thick black line bounded by open
and closed arrows, indicating relative orientation of the element. The TE insertion sites are illustrated by open circles or boxes, with each shape representing distinct insertion sites on the
chromosome and the equivalent sites on the chromosome(s) without a TE at that site. Homologous recombination requires a minimum of two copies of the repetitive sequence, one at each
breakpoint, and is denoted by an ‘X’ in this figure. (a) TEs in same relative orientation on homologous chromosomes result in the formation of chromosomes containing either a deletion or a
duplication of the intervening sequence. Both rearrangements are associated with recombination between two homologues. (b) TEs in opposite relative orientation on homologous
chromosomes result in the formation of a dicentric chromosome and an acentric fragment. (c) TEs in same relative orientation on one chromosome result in the formation of chromosomes
containing either a deletion or a duplication of the intervening sequence, differing from events in A by the lack of recombination between homologues and the net increase or decrease of the
TE number. (d) TEs in opposite relative orientation on one chromosome can result in the formation of an inversion between the two TEs. If caused by homologous recombination, deletions and
duplications can only be formed by TEs in the same relative orientation and inversions can only be formed by TEs in opposite relative orientation. Another mechanism must be invoked to
explain inversions between TEs in the same relative orientation, deletions and duplications between TEs in opposite relative orientations, and all chromosomal rearrangements when a TE is
present at only one of the rearrangement breakpoints.
described where an element was found at only one of
the rearrangement breakpoints in the parental chromosome9,10. Some rearrangements described are inconsistent
with the orientation of the elements present in the chromosome prior to rearrangement11, such as duplications
between inverted copies of a TE or inversions between TEs
in the same relative orientation (Fig. 1). Also, because
recombination does not normally occur in Drosophila
melanogaster males12, rearrangements mediated by TEs
such as P and hobo must occur by another mechanism in
the male germ line of Drosophila.
The direct action of TEs in promoting chromosomal
rearrangements is one mechanism that can account for
rearrangements not caused by homologous recombination. TEs induce chromosomal rearrangements directly
by an alternative version of the traditional transposition
reaction where the TE ends involved come from separate
elements rather than a single element (Fig. 2b). Evidence
for similar events has been described for several families of
TEs, including the IS10/Tn10 elements in bacteria13,14,
Ac/Ds elements in maize and tobacco11,15,16, Tam3 in
Antirrhinum majus (snapdragon)9,10,17–20 and P elements in
Rearrangements associated with different TE systems
have previously been examined separately. Here, published data from several different systems are reviewed in
order to emphasize the fact that the transposon-induced
rearrangements first described a decade ago in prokaryotes occur by the same mechanism in many eukaryotic TE
systems. The mechanism is an alternative to the normal
transposition reaction in each system. Furthermore, the
TIG October 2000, volume 16, No. 10
repair of the double-strand breaks produced during
alternative transposition is analogous to V(D)J recombination
and provides additional evidence supporting the theory
that V(D)J recombination is derived from a so-called RAG
TEs – a common resource for genome plasticity
In order to comprehend complex chromosomal rearrangements induced by alternative transposition of TEs, one
must first understand the basics of traditional transposition. The TEs inducing rearrangements described in this
review are all Class II TEs encoding a single transposase
and include prokaryotic IS elements and both prokaryotic
and eukaryotic transposons. Functionally, these TEs share
a common conservative transposition mechanism, known
as cut-and-paste, where the first step of transposition is
the synapsis of complementary left- and right-TE ends,
followed by excision of the ends, target site capture and
strand transfer1,3. Insertion of the TE into the target molecule can occur in either orientation relative to the original
element, resulting in a simple insertion (Fig. 2a). Repair of
the double-strand break occurs and can result in formation of an excision footprint, regeneration of the TE
using the sister chromatid as a template, gene conversion,
or recombination.
Chromosomal rearrangements more complex than simple insertions result from alternative transposition events
where complementary ends from separate TEs synapse
rather than the traditional synapsis of complementary ends
from a single TE9–11,13–24. The synapsis of TE ends from separate molecules has been demonstrated in vitro and is referred
Transposons and chromosomal rearrangements
to as bimolecular synapsis (Box 1)14,24. Figure 2b depicts an
alternative transposition event, in steps equivalent to those
depicted in Figure 2a for traditional transposition.
Once the hybrid element is formed (Box 1), the chemical steps of the alternative transposition reaction are identical to those of a normal transposition reaction. Excision
of the hybrid element forms two double-strand breaks.
The ‘excised’ hybrid element may reinsert into the
genome. The remaining double-strand breaks at the site of
hybrid element excision may be repaired. Transposase is
required for alternative transposition to occur. However,
in contrast to the excision of an intact TE, one end of each
of the TEs in a hybrid element remains covalently bound
to a large chromosomal fragment.
The type of rearrangements produced by alternative
transposition depends on the type of DNA molecules
involved – either linear or circular – for both donor and
target, and on the location of the target site relative to
the ends involved in alternative synapsis. The types of
rearrangements observed depend on the viability of the
resulting chromosome structure in the species being examined. Detailed examples of various types of rearrangements can be found in the original publications9–11,13–24.
Figure 2b examines an alternative transposition event
where the complementary ends involved are from homologous elements on sister chromatids, with an insertion
target site located on the same chromosome arm on the
homologue as the element ends forming the hybrid
element. This scenario results in the formation either of
an acentric fragment and a dicentric chromosome or of
recombinant chromosomes with recombinants containing
a reciprocal deletion/duplication. Most of the reported
chromosomal rearrangements (Box 1) consistent with
alternative transposition are of deletions, duplications
and inversions. Such a bias in the types of observed
events could be due to higher frequency of occurrence or
While Figure 2b details one type of rearrangement that
can be formed by alternative transposition, Figure 3
contains a schematic summary of sixteen possible classes
of rearrangement caused by alternative transposition.
Notably, an inversion is produced if the hybrid element
inserts into one of the chromosome arms involved in formation of the hybrid element (Classes 29 and 39 in Fig. 3).
Inversions formed by alternative transposition will contain
both copies of the target site duplication on a single chromosome. One of the target site duplications is located
within the inverted segment and, therefore, the duplicated
target sites are in inverse complementary orientation,
rather than the direct orientation found flanking normal
transposon insertions. The experimental determination of
a number of independent inversion events containing the
predicted structure, including the target site duplication
typical of TE insertion events, was instrumental in demonstrating that alternative transposition does occur in
eukaryotes22. An animated diagram of the formation of an
inversion caused by alternative transposition can be found
A translocation event could result if the insertion target
site is on a different chromosome from that which the
TE ends forming the hybrid element originate (Fig. 4).
Specifically, precise reciprocal translocations result when
caused by alternative transposition. Translocations were
amongst the first observed TE-mediated chromosomal
FIGURE 2. Traditional versus alternative transposition
trends in Genetics
The basic steps of transposition are shown as discrete steps for illustration purposes. Each line
represents a DNA double helix. The two sister chromatids of each of the homologous chromosomes are
shown. Black ovals denote the centromere. Complementary left- and right-ends of the TE are shown as
open or closed triangles, respectively. The original target site duplications are shown as open circles.
The new target site duplications are shown as open boxes. Asterisks denote the double-strand breaks
that are repaired and can result in formation of an excision footprint, regeneration of the TE using the
sister chromatid as a template, gene conversion or recombination. (a) Traditional cut-and-paste
transposition – complementary TE ends from an intact element synapse, excise and reinsert into a new
target site. The TE can insert in either of two orientations relative to the directionality of the original
insertion. In the case of traditional transposition, either insertion orientation results in a simple
insertion. (b) Alternative transposition – the first step in alternative transposition is the synapsis of
complementary TE ends from seperate TEs to form a hybrid element. In the case illustrated here, the
complementary TE ends are derived from homologous elements on sister chromatids. Once bimolecular
synapsis occurs, excision, insertion of the hybrid element into the new target site and repair of the
double-strand breaks occurs by the same mechanisms as in traditional transposition. Because the
hybrid element remains covalently bound to the chromosome, different insertion orientations result in
different types of chromosomal rearrangements. In the example shown here, one insertion orientation
results in formation of an acentric fragment and a dicentric chromosome, while the other insertion
orientation results in the formation of recombinant chromosomes. Note that the recombinant
chromosomes in this example also contain a reciprocal deletion or duplication of the genomic segment
between the original and new target sites. All chromosomal rearrangements resulting from alternative
transposition have two distinctive structures consistent with a TE insertion event. First, one of the
breakpoints in the rearrangement should be at the terminus of a functional TE end. Second, a target site
duplication should be produced. The two copies of the target site duplication will be situated on two
different chromosomes in many of the resulting rearrangements.
TIG October 2000, volume 16, No. 10
Transposons and chromosomal rearrangements
FIGURE 3. Many types of chromosomal rearrangement can result from a single TE insertion
iii 1
trends in Genetics
Alternative transposition results in sixteen classes of rearrangement when the
insertion target site is on the same chromosome arm as the TEs involved in
forming the hybrid element. The diversity of possible rearrangements formed by
alternative transposition is in contrast to the specificity of rearrangements
formed by homologous recombination (Fig. 1). The basic steps, (i)–(vi), of
traditional and alternative transposition as shown in Figure 2 are repeated here
illustrating the process and outcomes of alternative transposition for target sites
in the eight zones possible relative to the TEs involved in forming the hybrid
element. Each line represents a DNA double helix. The two sister chromatids of
each of the homologous chromosomes are shown. Black ovals denote the
centromere. Complementary left- and right-ends of the TE are shown as open or
closed triangles, respectively. The original target site duplications are shown as
open circles. The new target site is shown as open boxes. Asterisks denote the
double-strand breaks that are repaired and can result in formation of an excision
footprint, regeneration of the TE using the sister chromatid as a template, gene
conversion, or recombination. Symbols: D = deletion, S = duplication.
TIG October 2000, volume 16, No. 10
rearrangements25 but have not featured prominently in the
recent literature. The paucity of reports describing TEinduced translocations could be due to restriction of target
site choice by the physical constraints of the hybrid element being tethered to chromosome arms. Alternatively,
even if the translocation event occurs readily, gametes produced are not likely to be viable unless the complementing
translocated chromosomes segregate together.
The transposition of non-TE genomic sequences could
result if complementary ends from two different elements
on the same chromosome arm separated by the exogenous
sequence combine to form a hybrid element (Fig. 5). Such
events are known to occur readily in prokaryotic systems.
For instance, compound transposons such as Tn10 are
formed when two copies of an IS element, IS10 in the
case of Tn10, transpose as a unit with the intervening
sequence. Evidence for similar events involving closely
linked Ac/Ds elements in plants has been published11,26,27.
Recently, successful excision and transposition of a
macrotransposon has been observed in Drosophila consisting of two mariner elements (Box 1) surrounding
exogenous sequences. The inner ends of each mariner
element had been mutated and were no longer able to
serve as substrates for transposase (Lozovskaya and Hartl,
personal communication). Such eukaryotic macrotransposons might be regarded as analogous to bacterial transposons. Several more complex rearrangements could be
envisioned and probably do occur, although more complex rearrangements are also more likely to be non-viable.
Given that alternative transposition events are expected
to undergo the same molecular reactions as occur during
classical transposition, one would expect that the doublestrand breaks created during hybrid element excision
would also undergo repair, as does the double-strand
break formed by the excision of an intact TE. Rearranged
chromosomes result from this process, referred to as
Hybrid-element Excision Repair (HER) in the P element
system22,28,29. Strong evidence is available from Ac/Ds in
maize and tobacco where excision footprints have been
found at the rearrangement breakpoint of complex
rearrangements shown to have been mediated by alternative transposition11,15,16.
The many examples of transposase-dependent excision
and insertion events involving hybrid elements, as well
as repair of double-strand breaks formed by the excision
of hybrid elements, strongly support the occurrence of
Transposons and chromosomal rearrangements
alternative transposition. The only difference between traditional and alternative transposition is the choice of TE
ends to synapse.
Bimolecular synapsis cannot explain all TE-mediated
rearrangements not explained by homologous recombination. True one-ended transpositions and adjacent
inverted duplications reported in snapdragon18,30,31 and
Drosophila32 are just some of the rearrangements fitting
this description. The purpose of this review is to demonstrate the ubiquity of alternative transposition in a number
of TE systems, without diminishing the role other mechanisms in TE-mediated genome rearrangement.
Regulation of alternative transposition
In addition to similarities in structure and transposition
mechanism, described above, the IS10, hAT elements –
such as Ac/Ds and Tam3 – and P elements show other
similarities that must be considered in the context of their
effects on alternative transposition, including regulation
mechanisms, choice of insertion site and complexity of TE
Regulation of transposition is similar in P elements, the
hAT superfamily (Box 1) and IS10, although not all regulatory mechanisms have been demonstrated for all the elements examined1,3. Relevant to alternative transposition is
the regulation of transposition by the methylation state of
the element. Both traditional and alternative transpositions of IS10 and Ac/Ds elements have been shown to
be regulated by methylation16,27,33. Only hemi-methylated
sequences at the transposase binding sites are recognized
by transposase, thus restricting transposition to immediately after passage of a DNA replication fork27,33 and providing an additional regulation mechanism in the recognition of TE end complementarity16. D. melanogaster does
not display obvious differential methylation12 and this
regulation mechanism is therefore unlikely to affect P or
other elements in Drosophila.
Another important factor affecting the types of chromosome rearrangements caused by alternative transposition is the location of hybrid element insertion. Here, the
issue of physical constraint of the hybrid element should
be considered. Deletions extending over at least 100 kb
have been described23. It is therefore reasonable to expect
that duplications or inversions of over 100 kb are also
formed. No absolute limit has yet been established for the
distance between the locations of hybrid element excision
and insertion, so the possibility remains that alternative
transposition is not physically constrained by the covalent
tether between the hybrid element and the remaining
chromosome arms. This supports the possibility of hybrid
element insertion into a separate chromosome, resulting in
the formation of exact reciprocal translocations (Fig. 4).
In terms of preference of the insertion distance, both P
and Ac/Ds elements have been shown to transpose to
closely linked sites and to sites in close proximity of other
P and Ac/Ds elements more often than if insertion sites
were chosen at random27,34. The preference for insertion
into nearby target sites would decrease the possibility of
large deletions and duplications, as well as translocations
– an aspect that may be crucial to the viability of alternative transpositions. Also, the choice of a target site close
to an existing element may explain the number of
rearranged chromosomes derived from progenitor chromosomes containing elements at both rearrangement
FIGURE 4. Formation of precise reciprocal translocations
trends in Genetics
Insertion of a hybrid element into a separate chromosome results in the formation of exact reciprocal
translocations, regardless of the target site. A viable zygote could result if the reciprocal products of
hybrid-element-mediated translocation segregated into the same germ cell and no deleterious gene
interruption occurred at the breakpoints.
In terms of TE structures that promote alternative
transposition, an inverse correlation between the complexity of element structure and the formation of chromosomal rearrangements has been established for Ac/Ds and P
elements21,27. Ac elements and State-II Ds elements, which
are simple deletion derivatives of Ac, produce high rates
of transposition. Conversely, State-I Ds elements have
complicated structures and produce high levels of
chromosome breakage with very little transposition27.
Chromosomal rearrangements associated with alternative
transposition of P elements have also been shown to be
more likely to occur with more complex presentation of
functional element ends21. One explanation is that, unlike
intact elements that can undergo either traditional or
alternative transposition, disjointed element ends may
be recognized by transposase only as part of a hybrid
Clearly, intact TEs undergo traditional transposition
more frequently than alternative transposition. However,
intact TEs do participate in the formation of hybrid elements that then undergo alternative transposition. The
relative frequency of traditional versus alternative transposition can be determined by examining systems in which
TIG October 2000, volume 16, No. 10
Transposons and chromosomal rearrangements
BOX 1. Glossary of terms
FIGURE 5. Compound transposons (prokaryotes) and
macrotransposons (eukaryotes)
Ac/Ds – family of transposons first described in the 1940s by
Barbara McClintock in maize. Originally described as two
separate elements, Activator (Ac) and Dissociation (Ds),
molecular analysis has subsequently revealed that Ds
elements are, in fact, derivatives of Ac elements.
Bimolecular synapsis – synapsis of complementary TE ends
from separate molecules.
Chromosomal rearrangement – rearrangement of the linear
sequence of chromosomes including transposition, duplication, deletion, inversion or translocation of nucleic acid segments.
hAT superfamily – group of eukaryotic transposons that have
related transposase genes. The superfamily name is
derived from the hobo, Ac/Ds and Tam3 elements, which
were the first ‘members’ of this superfamily recognized to
have similar transposases. The level of protein similarity
ranges between 20 and 60%. The superfamily now includes
a number of other transposons, including Ascot-1 (from the
fungus Ascobolus immersus) hermes (first described in the
housefly Musca domestica), hermit (first described in
Queensland fruit fly, Bactrocera tryoni ), hopper (from the
oriental fruit fly, Bactrocera dorsalis), restless (first
described in fungus Tolypocladium inflatum) and Tfo1 (from
the fungus Fusarium oxysporum).
* *
* *
Hybrid element – the unit of DNA consisting of complementary TE ends from separate elements that have synapsed
and can undergo excision, target site capture and insertion
by the same mechanism as normal transposition.
Insertion sequence (IS) – prokaryotic TEs that transpose by a
DNA intermediate and contain only sequences necessary
for transposition (termini and transposase gene). Some IS
elements can form the termini of prokaryotic transposons,
such as IS10 forming the ends of Tn10 or IS50 forming the
ends of Tn5.
trends in Genetics
Ends from two copies of a TE in the same chromosome arm can associate to form a compound
transposon (e.g. with IS10/Tn10 ). Similar structures have been called macrotransposons when Ac/Ds
elements are involved. The resulting structure allows intervening ectopic sequences to be placed in a
new genomic context. This figure illustrates that transposition of the macrotransposon to the
homologous chromosome can result in duplication of the sequences between the two TEs. In the case of
Tn10, a tetracycline resistance gene is contained in the ectopic sequence. Similar structures have been
constructed using mariner elements with the inner inverted repeats mutated. These ‘mariner
sandwiches’ have been shown to excise and transpose (E. Lozovskaya and D. Hartl, pers. commun.).
an intact TE is also known to participate in the formation
of a hybrid element. The IS10/Tn10 elements constitute
one convenient system for this analysis. An IS10 element
transposes about once per 103 cell generations.
Rearrangements associated with alternative association of
the ends from the two IS10 elements that form the Tn10
termini13 occur about once per 105 cell generations35.
When compared with IS10 transposition and complex
rearrangements consistent with alternative transposition,
Tn10 transposition, which occurs about once every 107
cell generations35, may be viewed as a specific result of
aberrant synapsis of IS10 ends. Because Tn10 contains
sequences conferring antibiotic resistance between the two
TIG October 2000, volume 16, No. 10
mariner – transposon first isolated from Drosophila and
since shown to exist in a number of species, including
humans. All mariner elements duplicate the 2bp sequence,
TA, upon insertion and contain a D,D, (35) D catalytic triad,
rather than the D, D, (35) E motif shared by most other
transposases. Several subfamilies of mariner have been
described, with each subfamily containing elements with
highly conserved transposase proteins.
RAG transposon – proposed structure from which originated
the signal ends and RAG1/RAG2 proteins involved in V(D)J
recombination. For further discussion on the model for evolution of V(D)J recombination from a transposon insertion
event, see Reference 40.
V(D)J recombination – the process by which V, D and J coding segments are spliced together in somatic cells of the
immune system to produce a diverse range of antibodies.
IS10 elements, Tn10 also confers an evolutionary advantage to the bacterial cell in which it is located.
An extended superfamily of TEs consisting of elements
that transpose by a cut-and-paste mechanism, and which
may also undergo alternative transposition-induced
rearrangements, could be an appropriate category for TEs
such as IS1 and IS50. These TEs have demonstrated
cut-and-paste transposition as well as cointegrate formation36–38 that can now be understood as aberrant transposition events rather than a true cointegrate. In fact, an
inversion resulting in replication of the 9bp IS1 target site
and IS1 elements at the rearrangement breakpoints39
corresponds exactly with the sequence structure predicted
by the alternative transposition model.
Transposons and chromosomal rearrangements
Aberrant transposition and evolution
Many TEs were discovered because of the mutations they
cause. In some cases this was due to simple insertion or
excision of the element. In other cases complex traits were
observed, such as chromosome breakage-fusion-bridge
cycles due to Ac/Ds elements in maize and hybrid dysgenesis due to P elements in D. melanogaster, which can now
be explained by the alternative transposition mechanism
reviewed here.
The deleterious effects of alternative transposition are
balanced by the evolutionary advantages conferred by the
ability to rearrange genomic information. Mobility of TEs
is thought to increase in times of environmental and
genomic stress. Increases in traditional transposition
are likely to be accompanied by increases in alternative
transposition, as occurs during P-M hybrid dysgenesis.
Although the majority of chromosomal rearrangements
would be deleterious, occasional genome shuffling may
result in increased fitness. Could the increased capacity for
genome evolution constitute a selective advantage allowing TEs to persist? Such a process may be particularly relevant when the survival of a species is challenged, and
could be the evolutionary basis for increased TE mobility
under stressful conditions.
Similarities with V(D)J recombination
Several parallels have been observed between transposition and V(D)J recombination40–42. The coding joints
formed between V, D and J segments have structures similar to the footprints found at TE excision repair sites40.
Also, the finding that the signal end fragment can transpose and create a 5bp target site duplication upon insertion further supports the concept of a RAG transposon
(Box 1)41,42. Furthermore, and most important in respect
to parallels with alternative transposition, the 12/23 signal
end pairing rule is reminiscent of the TE end specificity,
with complementary left- and right-TE ends required for
synapsis, end cleavage and transposition40.
Some of the chromosomal rearrangements induced by
alternative transposition – specifically, repair after hybrid
element excision – are analogous to those occurring
during V(D)J recombination (Box 1). Just as the complementary TE ends involved in alternative synapsis form a
hybrid element, the complementary 12-signal and 23signal ends of the RAG transposon can synapse in any
number of combinations, regardless of linearity on
the chromosome. In V(D)J recombination, excision of
the hybrid element – the signal ends – is repaired to form
the coding joint, providing for a diverse and flexible
immune system. The following question is then raised.
Why does V(D)J recombination (repair of alternative
transposition) occur much more frequently than transposition of the intact RAG transposon or rearrangements in
which the signal ends reinsert into the genome?
The same question could be asked from another perspective. Why do some transposons undergo alternative
transposition far less frequently than others? The apReferences
1 Berg, D.E. and Howe, M.M. (1989) Mobile DNA, American
Society For Microbiology
2 Lim, J.K. and Simmons, M.J. (1994) Gross chromosome
rearrangements mediated by transposable elements in
Drosophila melanogaster. BioEssays 16, 269–275
3 Saedler, H. and Gierl, A. (1996) Transposable Elements,
preciation of the parallels between V(D)J recombination
and alternative transposition will hopefully result in
experiments that will elucidate the factors controlling
the balance between transposition and chromosomal
Alternative transposition as a genetic tool
Several genetic tools have been developed using TEs,
including transposon tagging and transposon-mediated
transformation. Here, alternative transposition is
proposed as an additional method in the repertoire of
TE-based genetic manipulation.
Alternative transposition can be used to delete regions of
chromatin adjacent to the TE both in vitro and in vivo (Fig.
2b). In prokaryotes, TE-induced deletions are a well-established technique. Recently, the EZ::TN™, KAN-2 insertion
kit has been commercialized by Epicentre Technologies.
This kit is based upon in vitro transposition of Tn5 elements
(with IS50 ends) and can be used to created deletions and
inversions adjacent to the Tn5 element43,44.
In eukaryotes, deletions have been induced adjacent to
intact Tam3 elements in snapdragon and P elements in
Drosophila in vivo23,34,45–47. The advantage of this method
over traditional mutagenesis techniques, such as use of the
mutagen ethyl methanesulfonate (EMS), is that only the
targeted gene is affected. The advantage over current TE
imprecise excision techniques is that one endpoint of the
deletion is defined. Isolation of deletion events and the
direction of the deletion are easily accomplished by screening for recombinant phenotypes. Nested deletions from a
few basepairs to several hundred kilobases in length, with
the breakpoint at the TE end being constant, can be isolated and the resulting differences in gene expression and
protein function examined.
The usefulness of this method in D. melanogaster is a
direct result of the availability of the P element insertion
libraries and techniques using a stable transposase source
to control target P element activity34,48–52. Available
through the Berkeley Drosophila Genome Project (BDGP),
the libraries are a collection of stocks, each containing a
single P element insertion. A large proportion of D.
melanogaster genes have been disrupted, not all producing
visible phenotypes. Insertion libraries of Ac/Ds and
En/Spm elements exist in the plant model organism,
Arabidopsis thaliana53,54. TE insertion libraries are also
being developed in other genomes and could be used for
the rapid isolation of deletions by similar methods.
I am grateful to J.A. Sved, M.M. Tanaka, W.R. Engels,
J.D.G. Jones and G.J. Cost for the insights that contributed to this work. J. Gibson, D. Jones, N. McCarthy,
B. Dixon, E. Tchoubrieva and three anonymous reviewers
provided valuable and much appreciated review of the
manuscript. I thank D. Hartl and E. Lozovskaya for permission to mention unpublished results. Y.H.M.G. is supported by the Australian Research Council.
4 McClintock, B. (1947) Cytogenetic studies of maize and
neurospora. Carnegie Institute of Washington Year Book 46,
5 McClintock, B. (1948) Mutable loci in maize. Carnegie
Institute of Washington Year Book 47, 155–169
6 Finnegan, D.J. (1989) Eukaryotic transposable elements and
genome evolution. Trends Genet. 5, 103–107
7 Schwartz, R.S. (1995) Molecular medicine: jumping genes.
New Engl. J. Med. 332, 941–944
8 Lupski, J.R. (1998) Genomic disorders: structural features of
the genome can lead to DNA rearrangements and human
disease traits. Trends Genet. 14, 417–422
9 Lister, C. and Martin, C. (1989) Molecular analysis of a
transposon-induced deletion of the nivea locus in Antirrhinum
majus. Genetics 123, 417–425
10 Lister, C. et al. (1993) Transposon-induced inversion in
TIG October 2000, volume 16, No. 10
Transposons and chromosomal rearrangements
Antirrhinum modifies nivea gene expression to give a novel
flower color pattern under the control of cycloidearadialis. Plant
Cell 5, 1541–1553
Weil, C.F. and Wessler, S.R. (1993) Molecular evidence that
chromosome breakage by Ds elements is caused by aberrant
transposition. Plant Cell 5, 515–522
Ashburner, M. (1989) Drosophila: A Laboratory Handbook, Cold
Spring Harbor Laboratory Press
Roberts, D.E. et al. (1991) IS10 promotes adjacent deletions at
low frequency. Genetics 128, 37–44
Chalmers, R.M. and Kleckner, N. (1996) IS10/Tn10 transposition
efficiently accommodates diverse transposon end
configurations. EMBO J. 15, 5112–5122
English, J. et al. (1993) A genetic analysis of DNA sequence
requirements for Dissociation state I activity in tobacco. Plant
Cell 5, 501–514
English, J.J. et al. (1995) Aberrant transpositions of maize
double Ds-like elements usually involve Ds ends on sister
chromatids. Plant Cell 7, 1235–1247
Martin, C. et al. (1988) Large-scale chromosomal restructuring
is induced by the transposable element Tam3 at the nivea locus
of Antirrhinum majus. Genetics 119, 171–184
Martin, C. and Lister, C. (1989) Genome juggling by
transposons: Tam3-induced rearrangements in Antirrhinum
majus. Dev. Genet. 10, 438–451
Coen, E.S. et al. (1986) Transposable elements generate novel
spatial patterns of gene expression in Antirrhinum majus. Cell
47, 285–296
Robbins, T.P. et al. (1989) A chromosome rearrangement
suggests that donor and recipient sites are associated during
Tam3 transposition in Antirrhinum majus. EMBO J. 8, 5–13
Svoboda, Y.H.M. et al. (1995) P-element-induced male
recombination can be produced in Drosophila melanogaster by
combining end-deficient elements in trans. Genetics 139,
Gray, Y.H.M. et al. (1996) P-element-induced recombination in
Drosophila melanogaster: Hybrid element insertion. Genetics
144, 1601–1610
Preston, C.R. et al. (1996) Flanking duplications and deletions
associated with P-induced male recombination in Drosophila.
Genetics 144, 1623–1638
Beall, E.L. and Rio, D.C. (1997) Drosophila P-element
transposase is a novel site-specific endonuclease. Genes Dev.
11, 2137–2151
25 McClintock, B. (1950) Mutable loci in maize. Carnegie Institute
of Washington Year Book 49, 157–167
26 Ralston, E. et al. (1989) Chromosome-breaking structure in
maize involving a fractured Ac element. Proc. Natl. Acad. Sci. U.
S. A. 86, 9451–9455
27 Kunze, R. (1996) The maize transposable element Activator (Ac).
In Transposable Elements (Saedler, H. and Gierl, A., eds.), pp.
161–194, Springer-Verlag
28 Gloor, G.B. and Lankenau, D.H. (1998) Gene conversion in
mitotically dividing cells: a view from Drosophila. Trends Genet.
14, 43–46
29 Lankenau, D.H. and Gloor, G.B. (1998) In vivo gap repair in
Drosophila: a one-way street with many destinations. BioEssays
20, 317–327
30 Martin, C. et al. (1988) Large-scale chromosomal restructuring
is induced by the transposable element Tam3 at the nivea locus
of Antirrhinum majus. Genetics 119, 171–184
31 Coen, E.S. and Carpenter, R. (1988) A semi-dominant allele, niv525, acts in trans to inhibit expression of its wild-type
homologue in Antirrhinum majus. EMBO J. 7, 877–883
32 Delattre, M. et al. (1995) Prevalence of localized rearrangements
vs. transpositions among events induced by Drosophila P
element transposase on a P transgene. Genetics 141,
33 Kleckner, N. et al. (1996) Tn10 and IS10 transposition and
chromosome rearrangements: mechanism and regulation in vivo
and in vitro. In Transposable elements (Saedler, H. and Gierl, A.,
eds.), pp. 49–82, Springer-Verlag
34 Engels, W.R. (1996) P elements in Drosophila. In Transposable
Elements (Saedler, H. and Gierl, A., eds), pp. 103–124, SpringerVerlag
35 Kleckner, N. (1990) Regulating Tn10 and IS10 transposition.
Genetics 124, 449–454
36 Tomcsanyi, T. et al. (1990) Intramolecular transposition by a
synthetic IS50 (Tn5) derivative. J. Bacteriol. 172, 6348–6354
37 Turlan, C. and Chandler, M. (1995) IS1-mediated intramolecular
rearrangements: formation of excised transposon circles and
replicative deletions. EMBO J. 14, 5410–5421
38 Lichens-Park, A. and Syvanen, M. (1988) Cointegrate formation
by IS50 requires multiple donor molecules. Mol. Gen. Genet. 211,
39 Badía, J. et al. (1998) A rare 920-kilobase chromosomal
inversion mediated by IS1 transposition causes constitutive
expression of the yiaK-S operon for carbohydrate utilization in
Escherichia coli. J. Biol. Chem. 273, 8376–8381
40 Fugmann, S.D. et al. (2000) The RAG proteins and V(D)J
recombination: Complexes, ends, and transposition. Annu. Rev.
Immunol. 18, 495–527
41 Agrawal, A. et al. (1998) Transposition mediated by RAG1 and
RAG2 and its implications for the evolution of the immune
system. Nature 394, 744–751
42 Hiom, K. et al. (1998) DNA transposition by the RAG1 and RAG2
proteins: a possible source of oncogenic translocations. Cell 94,
43 Goryshin, I.Y. and Reznikoff, W.S. (1998) Tn5 in vitro
transposition. J. Biol. Chem. 273, 7367–7374
44 York, D. et al. (1998) Simple and efficient generation in vitro of
nested deletions and inversions: Tn5 intramolecular
transposition. Nucleic Acids Res. 26, 1927–1933
45 Ingram, G.C. et al. (1998) The Antirrhinum ERG gene encodes a
protein related to bacterial small GTPases and is required for
embryonic viability. Curr. Biol. 8, 1079–1082
46 Ingram, G.C. et al. (1997) Dual role for fimbriata in regulating
floral homeotic genes and cell division in Antirrhinum. EMBO J.
16, 6521–6534
47 Gray, Y.H.M. et al. (1998) Structure and associated mutational
effects of the cysteine proteinase (CP1) gene of Drosophila
melanogaster. Insect Mol. Biol. 7, 291–293
48 Rørth, P. (1996) A modular misexpression screen in Drosophila
detecting tissue-specific phenotypes. Proc. Natl. Acad. Sci. U. S.
A. 93, 12418–12422
49 Rørth, P. et al. (1998) Systematic gain-of-function genetics in
Drosophila. Development 125, 1049–1057
50 Rubin, G.M. (1998) The Drosophila genome project: a progress
report. Trends Genet. 14, 340–343
51 Spradling, A.C. et al. (1999) The BDGP gene disruption project:
single P-element insertions mutating 25% of vital Drosophila
genes. Genetics 153, 135–177
52 Spradling, A.C. et al. (1995) Gene disruptions using P
transposable elements: an integral component of the
Drosophila genome project. Proc. Natl. Acad. Sci. U. S. A. 92,
53 Parinov, S. et al. (1999) Analysis of flanking sequences from
Dissociation insertion lines: A database for reverse genetics in
Arabidopsis. Plant Cell 11, 2263–2270
54 Tissier, A.F. et al. (1999) Multiple independent defective
suppressor-mutator transposon insertions in Arabidopsis: a
tool for functional genomics. Plant Cell 11, 1841–1852
Antibacterial responses in Drosophila are the focus of several recent studies. The caspase encoding gene dredd, functions in
an antibacterial pathway probably with imd and relish1,2. This conclusion is supported by results from Stöven et al., who show
that Relish processing and activation requires a functional dredd gene3. Two members of a Drosophila IkB kinase complex, the
kinase DmIKKb and the structural factor DmIKKg,`` are required for antibacterial gene induction by LPS, regulate Relish
phosphorylation and processing but are not required for Toll-mediated antifungal gene expression4. Mutations in the DmIKKg
gene block Relish-dependent immune induction of the genes encoding antibacterial peptides after infection5. Dredd, DmIKKb,
DmIKKg, Imd and Relish may define a pathway that mediates Drosophila antibacterial responses. Finally, recent results show
that the Jak–Stat signalling cascade regulates the expression of complement-like proteins in the Drosophila fat body after
Elrod-Erickson, M. et al. (2000) Interactions between the cellular and humoral immune responses in Drosophila. Curr. Biol. 10 (13), 781–784
Leulier, F. et al. The Drosophila caspase Dredd is required to resist Gram-negative bacterial infection. EMBO R. (in press)
Stöven, S. et al. Activation of the Drosophila NF-kB factor Relish by rapid endoproteolytic cleavage. EMBO R. (in press)
Silverman, N. et al. (2000) A Drosophila IkB kinase complex required for Relish cleavage and antibacterial immunity. Genes Dev. (in press)
Rutschmann, S. et al. Role of Drosophila IKKg in a Toll-independent antibacterial immune response. Nat. Immun. (in press)
Lagueux, M. et al. (2000) Constitutive expression of a novel complement like protein in Toll and Jak gain-of-function mutants of Drosophila. Proc. Natl. Acad. Sci. U. S. A. (in
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