Mobile Genetic Elements [Methods In Molec Bio, Książki, Biochemia
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METHODS IN MOLECULAR BIOLOGY
TM
Volume 260
Mobile Genetic
Elements
Protocols and Genomic
Applications
Edited by
Wolfgang J. Miller
Pierre Capy
METHODS IN MOLECULAR BIOLOGY
TM
Mobile Genetic
Elements
Protocols and Genomic
Applications
Edited by
Wolfgang J. Miller
Pierre Capy
TEs as Natural Molecular Tools
1
1
Mobile Genetic Elements
as Natural Tools for Genome Evolution
Wolfgang J. Miller and Pierre Capy
Summary
Transposable elements (TEs) are ubiquitous components of all living organisms, and in the
course of their coexistence with their respective host genomes, these parasitic DNAs have
played important roles in the evolution of complex genetic networks. The interaction between
mobile DNAs and their host genomes are quite diverse, ranging from modifications of gene
structure and regulation to alterations in general genome architecture. Thus over evolutionary
time these elements can be regarded as natural molecular tools in shaping the organization,
structure, and function of eukaryotic genes and genomes. Based on their intrinsic properties
and features, mobile DNAs are widely applied at present as a technical “toolbox,” essential for
studying a diverse spectrum of biological questions. In this chapter we aim to review both the
evolutionary impact of TEs on genome evolution and their valuable and diverse methodologi-
cal applications as the molecular tools presented in this book.
Key Words:
Transposable elements; selfish DNAs; genome evolution; neogene formation;
heterochromatin; stress induction; molecular tools.
1. Introduction
Many organisms contain far more repetitive DNA sequences than single-
copy sequences. Repetitive sequences include mobile genetic DNAs that are
universal components of all living genomes. Transposable elements (TEs) are
gene-sized segments of DNA with the special ability to move between differ-
ent chromosomal locations in their hosts’ genome. Today the genomes of vir-
tually all eukaryotic and prokaryotic species are known to contain significant
numbers of TEs.
1.1. Occurrence and Classification
In some bacterial species, up to 10% of the genome is composed of insertion
sequences (IS elements), while in eukaryotes these elements can make up more
From: Methods in Molecular Biology, vol. 260: Mobile Genetic Elements
Edited by: W. J. Miller and P. Capy © Humana Press Inc., Totowa, NJ
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Miller and Capy
than 50%. In genetic model systems like
Drosophila melanogaster
,
in silico
analyses have recently indicated that approx 22% of its genome is built up by
TEs and their remnants
(1)
. Even in humans, about half of the genome is
derived from transposable elements—in particular, long interspersed elements
(LINEs), short interspersed elements (SINEs), LTR retrotransposons, and DNA
transposons
(2)
.
When compared to the genomes of other eukaryotic organisms such as
mouse, fly, worm, and mustard weed, the human genome has a much higher
density of TEs in the euchromatin. This difference is based on the finding that
the vast majority of TEs in humans seem to be more ancient and mainly
transpositionally inactive, while in the model organisms mentioned above
mobile DNAs are younger and thus still more active
(2)
.
TEs are classified into two major groups based on their transposition mecha-
nism
(3)
. Class I elements, such as LTR-retrotranposons and LINEs, are char-
acterized by DNA sequences with homology to reverse transcriptase, and they
are often referred to as retroelements or retrovirus-like elements. Their mobil-
ity is achieved through an RNA intermediate that is reverse-transcribed prior
to reinsertion, thus mediating a “copy-and-paste” mechanism. This group also
includes the SINE elements that use the reverse transcriptase of LINEs.
Class II elements are characterized by terminal inverted repeats (TIRs), and
they use DNA as a direct-transposition intermediate. They are therefore called
DNA transposons and move by a conservative “cut-and-paste” mechanism
catalyzed by a transposase. This enzyme is element-encoded in the auto-
nomous DNA transposons and is provided
in trans
for internally deleted,
nonautonomous elements.
1.2. Historical Overview
In the course of the twentieth century, our vision of the genome dramatically
evolved from that of a stable and almost fixed structure to that of a highly
flexible and dynamic information storage system. In the first half of the last
century, the genome was basically considered as a stable chain of genes located
in a head-to-tail organization along chromosomes, slowly evolving by the
accumulation of random mutations at constant frequencies. Today such a con-
ception is outdated, but it took more than 30 yr to change this dogma
(4)
.
Based on her pioneering work on chromosome breakage in maize in the
early 1940s, Barbara McClintock provided the first direct experimental evi-
dence suggesting that genomes are not static but highly plastic entities
(5)
.
Elements involved in these phenomena were initially called “controlling ele-
ments.” Based on her observations that some breakage events were always
observed at the same chromosomal region, McClintock assumed that these
events were due to a particular genetic element named
Ds
for “Dissociation.”
TEs as Natural Molecular Tools
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In later work she deduced that the instability of
Ds
elements causing chromo-
somal breakage is dependent on the presence of another type of element desig-
nated as
Ac
for “Activator.” Later on in the 1980s, molecular techniques
revealed that the
Ac–Ds
system is composed of autonomous (
Ac
) and non-
autonomous (
Ds
) copies, whereas only
Ac
encodes the functional transposase
enzyme required for the mobility of both elements
(6)
. Although McClintock’s
genetic work was the first clear indication of the existence of mobile DNA
elements serving as a major genetic source for genome plasticity, it took more
than 30 years before her concept of a dynamic genome became generally
accepted
(7–9)
.
Between the 1960s and 1970s the following observations paved the way for
the discovery and the molecular characterization of mobile DNAs in prokary-
otes (
reviewed in
ref.
4
): The discovery of the bacteriophage
Mu
(10)
; and the
elucidation of IS elements
(11–13)
as causative agents of mutations, along with
their capacity for transmitting antibiotic resistance
(14
,
15)
. As soon as appro-
priate molecular tools were developed for eukaryotic systems in the early
1980s, TEs were recognized immediately as universal components of all living
organisms.
Two types of theories have been suggested to explain the ubiquitous pres-
ence of TEs as well as their high genomic proportions. Soon after the initial
discoveries regarding TEs, researchers influenced by the “phenotypic para-
digm” of the neo-Darwinian theory broadly speculated that mobile DNAs pro-
vide a direct selective advantage to their host organisms. Alternatively, in the
light of the emergence of the neutral theory at the end of the 1970s and early
1980s, mobile DNAs were classified as “selfish DNAs” or “ultimate parasites”
(16
,
17)
. The authors of both classic papers pointed out that the presence and
spread of mobile DNAs could be explained solely by their ability to over-
replicate the genes of the host genome without invoking a positive selection
advantage at the level of the individual organism. As dogmatically stated by
Dawkins
(18)
, mobile DNAs are “…genes or genetic material which spread by
forming additional copies of itself within the host genome and do not contrib-
ute to the phenotype. …”
During the last two decades, detailed molecular analyses of transposable
elements, focusing on their dynamics and evolution within the host genomes,
have modified our perception. Although it is generally accepted at present that
mobile DNAs can be regarded as genomic parasites producing mainly neutral
and deleterious effects, some of their induced mutations and genomic changes
have made significant contributions to the evolution of their hosts
(19–21)
.
In this respect these elements can be regarded as a useful genetic load or even
as useful parasites
(22)
.
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Miller and Capy
Today, it seems increasingly obvious that genomes can profit from the pres-
ence and action of mobile DNAs at various levels bringing about acceleration
of genome evolution, as will be detailed in the sections that follow. Of course,
mobile DNAs are not the only factor driving genome evolution, but it seems
that they could be present at the origin of important events. Therefore, mobile
DNAs can be regarded as evolution accelerators, particularly when genomes
are facing population and/or environmental stresses
(23)
.
In general, TEs are found in all kinds of genomic compartments, such as
pericentromeric heterochromatin, telomeres, regulatory regions, exons, and
introns.
A priori
, they can move everywhere in a genome, because their actual
genomic target sites consist of a few base pairs only. However, they are not
randomly distributed since they are frequently observed in heterochromatin
and in regulatory regions. It remains difficult to demonstrate whether they pref-
erentially target such regions by target sequence specificity or chromatin
accessibility, or instead integrate randomly in the genome with natural selection
then retaining and accumulating insertions at particular genomic compartments.
In the following sections, we discuss several aspects of the dynamics and
evolution of TEs and their interactions with the host genome. Extensive reviews
have been published recently covering in detail the broad spectrum of TE–host
interactions and their evolutionary consequences
(9
,
19–21)
. Thus we will first
review briefly some of the most important impacts of TEs acting as natural
tools on host genome evolution, so that we may then introduce their technical
applications as molecular tools and molecular marker systems in modern biology.
2. The Role of TEs as Natural Tools for Shaping Genome Evolution
2.1. Heterochromatin: Only a Wasteland for Transposable Elements?
The evolutionary relationship between TEs and heterochromatin is still con-
troversial. In general, TEs and their derivatives are found as highly enriched
clusters in genomic regions close to the centromere and telomere, and along
the chromosomal arms within the intercalary heterochromatin. Obviously TE
insertions in heterochromatin are less deleterious than euchromatic insertions,
and their concentration in these regions of low gene density might be mainly
due to selection against ectopic recombination
(24)
. Indeed, theoretical models
have implied that TEs should accumulate in regions with low rates of recombi-
nation, such as in the heterochromatin
(25
,
26)
. Recent experimental data
obtained from
Drosophila
, however, have provided no sufficient support for
the hypothesis that the primary reason for the accumulation of mobile DNAs in
the heterochromatin is selection against TEs in the euchromatin
(27
,
28)
.
As suggested by Dimitri and Junakovic, “Their accumulation in heterochroma-
tin does not seem to be related to intrinsic properties of transposon families …
[but could be] determined by some sort of interaction between each transposon
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