Transposable Elements and Genome Evolution (eBook)

Pierre Capy, Aur lie Hua-Van (Herausgeber)

eBook Download: EPUB

2024 | 1. Auflage
304 Seiten
Wiley (Verlag)
978-1-394-31245-0 (ISBN)

Infos

Since their discovery by Barbara McClintock in the mid-20th century, the importance of transposable elements in shaping the architecture, function and evolution of genomes has gradually been unveiled.

These DNA sequences populate nearly all genomes and are viewed as genomic parasites. They are mobile, capable of proliferating within genomes and also commonly travel between species.

These elements are mutagenic and are responsible for several human genetic disorders, but they also constitute a major source of genetic diversity. Some insertions have beneficial effects for the host and are selected for, giving rise to significant evolutionary innovations. Their dynamics within genomes are intricate, as are their interactions with other genome components. To limit their proliferation, the genome has evolved sophisticated defense mechanisms.

While researchers commonly use these elements as genetic tools, their identification in newly sequenced genomes remains a challenge due not only to their extensive diversity, but also their large copy numbers.

Aurélie Hua-Van is Professor of Biology at Paris-Saclay University, France. She teaches in various domains such as genetics, evolution, life origin and bioinformatics. Her research focuses on eukaryotic transposable elements evolution and dynamics, through experimental evolution and genomics.

Pierre Capy is a former Professor of Biology at Paris-Saclay University, France. He taught evolutionary biology, quantitative genetics and genome plasticity, and always tried to create bridges between ecology and molecular biology. It is within this context that his research on transposable elements is placed.

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Introduction

Aurélie HUA-VAN and Pierre CAPY

Évolution, Génomes, Comportement et Écologie (EGCE), CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France

Any biologist interested in the genetic material which is occupying the cells of their preferred species has been or will be confronted one day to transposable elements (TEs). They can represent an important part of the genome, although their raison d’être is not to participate in the core genetic program necessary for the cell survival.

TE activities are the causative agent of numerous major scientific discoveries in genetics and evolution, and the basis of important technological advances in Life Science research. They are passively used by our species in its effort for diversifying the most important supplies it needs (like all heterotrophic species), that is to say food. More importantly, they are responsible for some spectacular evolutionary key innovations, but also for many diseases that affect our species. Some examples are shown in Figure I.1.

Discovery of the genetics laws: Gregor Mendel, the father of genetics, formalized in 1865 the basic laws that govern the transmission of phenotypic characters under the control of a single gene. Rediscovered simultaneously by several authors at the beginning of the 20th century, these laws still stand true. One of Mendel’s models was the transmission of the wrinkled phenotype of pea seeds (Figure I.1). In 1999, it was found that the wrinkled phenotype is due the insertion of a TE in the promoter of a gene (Bhattacharyya et al. 1990).

Figure I.1. Famous examples of TE insertions that affect phenotypes or participate to evolution. By crossing smooth and wrinkled peas, Mendel discovered dominance/recessivity between alleles. Strong environmental pressure triggered rapid shift in morphotype in the pepper moth. Insertion of a TE in the promoter of a gene and subsequent rearrangement may change the color of grape. The programmed recombination process triggering diversity of immunoglobulin chains chains is mediated by an enzyme originating from a TE.

Illustration of natural selection acting in real-time: industrial melanism is a textbook example of rapid evolution and adaptation by natural selection. During the industrial revolution in England (mid-1800s), the peppered moth Biston betularia was known for having quickly shifted from a predominant light colored wings morphotype to a blackened one (Figure I.1). This species rests on trees such as birches during the day, and its color serves as camouflage, preventing the moth from being preyed on by birds. The darkening of trunks due to the pollution may have favored the expansion of the dark morphotype, as supported by the famous capture-mark-recapture experiment of Kettlewell (1955). In this species, wings color is determined by a single gene. The mutated allele responsible for wing darkening has recently been characterized (Van’t Hof et al. 2016). The mutation is due to an insertion originating from a TE. More examples concerning the involvement or TEs in adaptation to environmental stress are given in Chapter 5.

Input in biotechnology: as soon as TEs have been characterized, they have proven useful for researchers, as polymorphic markers, for typing strains, or for genome engineering, ranging from mutagenesis to gene therapy. Some examples of recent use of TEs in biotechnology and research are illustrated in Chapter 10.

Input in agronomy amelioration: artificial selection has been performed by human since the neolithic period and the start of domestication in order to improve quality and quantities of our supplies. Human-directed selection is still widely used nowadays, for examples, in agriculture and horticulture to create different varieties. Notably, the color diversity or variegation in color in cultivated flowers is often due to the activity of TEs, of which are also responsible for the diversity of the grape color (Figure I.1) or the varieties of blood oranges (Lisch 2013).

Example of evolutionary innovations: besides the genetic diversity of food and flowers enjoyed by humans, some TEs insertions have been naturally selected in the past to give rise to important genetic novelties contributing to species success, such as adaptive immunity by V(D)J recombination in jawed vertebrates (Figure I.1). Some famous examples of this phenomenon, called molecular domestication, will be illustrated in Chapter 6.

Input in human health: in eukaryotes, TEs are generally silenced by epigenetic mechanisms. The silencing is not perfect and low transposition activity may be observed, which can increase when epigenetic marks are altered. In humans, de novo insertions and recombination between the huge number of TE insertions are sometimes involved in diseases and cancers. Numerous examples are given in Chapter 3.

I.1. Almost 80 years of research on transposable elements

The existence of mobile genetic factors in eukaryotic genomes was suspected as early as 1944 when Barbara McClintock, a maize cytogeneticist, observed strange phenomena such as phenotypic variegation and phenotypic alterations to various degrees, sometimes associated with a precise timing or reversibility in plants having suffered some chromosome breakage-and-fusion cycles. At the chromosomal level, she observed rearrangements, modification of the locus size and transposition of the locus to another place, so she called it Ds (for dissociation). She realized that all of these were due to some controlling elements that could move (transpose) throughout the genome, modify the expression of nearby genes and cause chromosomal rearrangements. The system she described was bipartite, the effect of the Ds locus being only observed in the presence of the Ac (for Activator) locus, itself transposable (McClintock 1950).

Later on, at the beginning of the 1970s, puzzling observations such as male recombination (normally not occurring in Drosophila), sterility and high mutation rates were discovered in Drosophila melanogaster in some particular crosses between natural and laboratory strains, leading to the notion of hybrid dysgenesis. At about the same time, the first mobile insertion sequences (ISs), which are TEs in bacteria, were molecularly identified in Escherichia coli. Similar mobile sequences, the P element and the I factor, were finally found to be responsible for the hybrid dysgenesis phenomenon in Drosophila. It soon appeared that numerous TEs existed in Drosophila and that some of them transposed through a RNA intermediate.

TEs were then discovered in more and more species, after cloning of loci responsible for phenotypic changes. It became clear that most visible mutations in plants and animals were due to TE activities, in particular induced mutations (UV, X-rays, etc.), or selected ones. The noticeable effects are as follows (visible on multicellullar organisms): variegation (somatic transposition), reversibility (sometimes) and mild phenotypic effects. It appeared later on that the middle repetitive fraction of eukaryotic genomes was mainly composed of TEs (repeativeness of the genome could be measured by denaturation followed by slow renaturation, three compartments were detected, highly repeated sequences are the ones that renature very quickly, while it takes much more time for unique sequences to find the complementary strand). We now know that all eukaryotic genomes carry TEs, including unicellular eukaryotes. For most TEs, we have deciphered their transposition mechanisms and how they are regulated. We know their mutagenic consequences and their impact on genome evolution both at the functional and structural level. At the genomic era, a new challenge is to efficiently identify these TEs in new sequenced genomes (Chapter 11).

I.2. What is exactly a transposable element?

We can give a very minimal definition of transposable elements (TEs): a DNA sequence, able to move and replicate in the genome of a single cell. That is, TEs are mobile, repeated and dispersed in the genome. Although theoretically not false, this definition is too poor to encompass the extraordinary properties of such sequences.

Figure I.2. TEs identification: historical timeline. TEs have two properties: they are mobile and repeated. Their discoveries has first relied on the phenotypic changes associated with their mobility, mainly on model organisms. Since 20 years now, at the genomic era, new TEs are primarily identified in non-model organisms sequenced genomes because of their repeated nature. In between, the golden age of molecular biology has permitted a deep understanding of their biology and their impact on the genome. First identifications of main groups of eukaryotic TEs are indicated.

Alternatively, you will often hear them described as junk DNA, parasitic elements, selfish DNA, jumping genes and mobile genetic elements. We will first try to define and distinguish all of these terms and determine how they fit into TEs.

Mobile genetic elements (MGEs): MGEs correspond to any nucleic acid sequence which is not permanently embedded into the genome of its host cell and able to replicate independently from the genome replication. TEs are part of the large group referred to as the MGEs that also includes viruses and plasmids. This group encompasses all nonliving genetic entities that spent some or all of their time outside the genomes of their...

Produkt-Details

• Erscheint lt. Verlag: 15.8.2024
• Reihe/Serie: ISTE Consignment
• Sprache: englisch
• Themenwelt: Literatur ► Biografien / Erfahrungsberichte
• Themenwelt: Naturwissenschaften ► Biologie
• Schlagworte: DNA Sequences • Genetic disorders • genetic diversity • Genomes • genomic parasites • Transposable elements
• ISBN-10: 1-394-31245-8 / 1394312458
• ISBN-13: 978-1-394-31245-0 / 9781394312450