Transposable Genetic Elements

Transposable genetic elements (TEs) are segments of DNA that can be integrated into new chromosomal (genomic) locations either through direct DNA transfer (transposons), or via an RNA intermediate (retrotransposons). Pseudonyms for TEs include mobile elements, jumping genes, genomic parasites, and selfish DNA. TEs are known to be responsible for several human genetic diseases and may play a role in evolution in many species.

Early Evidence

Barbara McClintock originally theorized that unusual patterns of phenotypic variance (in corn kernels) could be explained by gene transposition. However, this explanation did not coincide with traditional Mendelian inheritance that genetic information was fixed within the genome , and her views were not widely accepted within the scientific community until the 1960s, when evidence of transposition began to accumulate.

McClintock was a cytogeneticist working on maize. She noted that, in maize, there was a pigment-bearing layer of the kernel, called the aleurone layer, that changed color from kernel to kernel and generation to generation. She also noted a baffling result that occurred when a homozygous plant for purple aleurone (CC) was crossed with a colorless aleurone homozygote (cc). About one-half of the kernels of offspring corn were solid purple, and one-half were purple with varying sizes of colorless spots, suggesting breakage (and loss) of the C locus. However, one of 4,000 analyzed kernels was colorless with purple spots, indicating a "gain-of-function" of the c locus. McClintock identified a locus (called Ds, which stands for dissociation) that induced nearby chromosome breakage only in the presence of another gene, which she called Ac (for activator). She concluded that the inactivation of pigment production is caused by insertion of the Ds gene into the C locus (disrupting pigment products and yielding the colorless background), and the eventual movement of the Ds out of the gene, restoring pigment production and yielding the purple spots. All of this could occur within a single kernel.

Further support for the mobility of the Ds and Ac genes was the inability to determine their chromosomal locations, which differed among plants. High mutational reversion rates have been subsequently identified in other organisms, with mobile elements now offering a plausible explanation.

TEs across the Evolutionary Tree

TEs are ubiquitous throughout the evolutionary tree from microorganisms to mammals. For instance, a bacterial virus called phage MuM (mutator) is characterized as a TE based on similarities with other transposons. Mu integration into the host bacterial chromosome is considered transposition because it can occur nearly anywhere, thereby inactivating host genes and generating insertions and deletions.

Transposons also occur naturally in bacterial genomes. The extensively studied species Escherichia coli (E. coli ) contains insertion sequences (IS) and transposons in its genome. IS elements are generally small, have inverted sequence repeats at their ends (important for their mobility), and contain an overlapping genetic region encoding a transposase and a repressor. Transposons are larger than IS elements, since they contain additional genes such as drug-resistance genes. These elements are flanked either by inverted repeats or by IS elements. Bacterial transposons undergo conservative transposition, in which the transposon is excised and pasted elsewhere, or replicative transposition, in which it is copied and the copy is inserted elsewhere.

Ty elements in yeast contain retroviral-related sequences (called gag and pol) and include long terminal repeats (LTRs); hence they are considered viral (or viral-like) retrotransposons or LTR retrotransposons. Their activity is replicative: An RNA is transcribed from the gene, reverse-transcribed to DNA (cDNA) and integrated elsewhere in the genome. Since Ty does not contain env genes, which code for encapsulating envelope proteins, it does not yield infectious particles. However, viruslike particles accumulate in cells in which retroposition has been induced.

The African Trypanosome, a parasitic protozoan, contains the ingi (non-LTR) retrotransposons. Ingi may therefore be referred to as a parasite's parasite. Full-length elements are 5.2 kilobase pairs long, have multiple adenine nucleotides at one end (called a "poly A tail"), and DNA sequences similar to reverse transcriptase genes and mammalian LINEs (discussed below). Among insects, the Drosophila genome contains a virtual cornucopia of TEs. Fruit fly transposons include mariner, hobo, and P elements, non-LTR-retrotransposons include I, F, and jockey elements, and LTR-retrotransposons such as gypsyM and copia-like elements. These eukaryotic transposons are similar to bacterial IS elements, but are generally larger due to the presence of introns (noncoding sequences of the genome).

The primary TEs in mammalian genomes include short and long interspersed repetitive elements (SINEs and LINEs, respectively). SINEs represent a group of small retrotransposons (75-500 base pairs ) and lack protein-coding sequences. In primates, Alu elements represent the predominant SINE family. More than 1 million copies of Alu are contained in the human genome, representing about 13 percent of the genome. This is truly impressive considering their lack of replicative autonomy. Alu elements are 300 base pairs in length, are rich in adenine sequences both internally and at the 3′ (downstream) end, and internal RNA polymerase III promoter sequences, allowing them to be replicated. L1 elements represent the predominant primate LINE family, contain two open reading frames , adenine-rich 3′ ends, and internal RNA polymerase II promoter sequences. They constitute approximately 20 percent of the human genome. A full-length LINE is about 6.5 kilobase pairs long, although most elements are truncated as a result of incomplete reverse transcription.

Transmission of TEs

TEs generally demonstrate vertical transmission, meaning that new incorporations are inheritable by offspring. Although transposons may excise from their genomic location and integrate elsewhere, retrotransposons form stable integrations, creating a molecular "fossil record" of past integration events.

Over 99 percent of human Alu elements are shared with the chimpanzee genome. Unlike Alu, L1 predates the origin of primates, with many integrations predating the origin of placental mammals. Most recent Alu and L1 integrations in the human genome generate insertion presence/absence variants that are referred to as dimorphisms.

Dimorphisms provide DNA markers useful in mapping studies, fingerprinting, and human population investigations. Retrotransposon integrations are also associated with human disorders. Examples include Alu integrations into NF1, factor IX, and BRCA2 genes yielding neurofibromatosis, hemophilia, and breast cancer, respectively, and L1 integrations into the c-myc, APC, and factor VIII genes cause breast cancer, colon cancer, and hemophilia, respectively.

Horizontal transfer of TEs, or the transmission between species, has also been implicated. General evidence involves the lack of phylogenetic correspondence between the TEs and their host organisms. For example, outside of the Drosophila melanogaster species group, jockey has been detected only in the distantly related D. funebris, suggesting that it was transferred between the two. P elements have also exhibited horizontal transfer, possibly from D. willistoni to D. melanogaster, but more importantly, strains of D. melanogaster are lacking the element, indicating recent spreading through populations. Additionally, insect-related mariner elements, characterized primarily by their transposase, have been identified in diverse organisms such as flatworms and hydra, yet are lacking in twenty other invertebrate species representing major phyla. These transfers are both ancient and relatively recent, as one element has 92 percent amino acid similarity between Hydra and a staphylinid beetle. Possible transmission vectors include parasites (such as mites) and viruses. Some evidence also exists for horizontal transfer of mammalian TEs, including the putative discovery of an Alu element in the malarial parasite Plasmodium vivax.

Transposition Mechanisms

Transposon mobility may be either nonreplicative or replicative. In nonreplicative mobility, the TE is cut out of its original position and integrated at a new location. In replicative mobility, transposition makes staggered cuts in donor and recipient sites, followed by a complex transfer, replication, and resealing operation.

SINE and LINE generation originates from "master genes": Only a few of the thousands to millions of copies are capable of serving as the source for new integrating elements. The proposed details of copy formation and integration differ between the two types of generation.

TEs and Species Evolution

Are TEs simply genomic parasites, or have they had a major impact on the evolution of species? Certainly, a TE integration could have an immediate detrimental impact on its host. However, specific and cumulative integrations may provide a mechanism for speciation. Drosophila P elements have been implicated in generating a reproductive barrier between strains. When females devoid of active elements are crossed with males of a strain with active elements, the TEs run rampant in developing germ-line cells, yielding various chromosomal anomalies and F₁ hybrid sterility. This may be an important mechanism in promoting the creation of new species from those strains.

Arguably, SINEs and LINEs may also drive species evolution through several mechanisms. They can disrupt or reset coordinated gene regulation, facilitate the pairing of homologous chromosomes, and possibly offer sites for genomic imprinting. In addition to individual integrations, LINEs have contributed to genomic diversity by delivering adjacent sequences, including whole genes, to new genomic locations. TEs also offer numerous sites for homologous unequal recombination.

Transposons as Molecular Biology Tools

Transposons can be used to facilitate cloning of genes, identify regulatory elements, and produce transgenic organisms. For example, transposon tagging involves inducing transposition of a TE, allowing for disruption of a gene that generates an organism with a mutant phenotype, and is followed by molecular techniques that allow for the identification of the gene. A variation of transposon tagging (enhancer trapping) uses P elements to identify DNA sequences that regulate the expression of genes. P elements can also be used to incorporate foreign genes into fruit flies (transgenics). In addition, transposon fossils have been useful for the isolation of species-specific DNA from complex sources such as using inter-Alu PCR for the isolation of human genomic DNA sequences.

see also DNA Libraries; Evolution of Genes; Imprinting; Mcclintock, Barbara; Repetitive DNA Elements; Retrovirus; Reverse Transcriptase; Yeast.

David H. Kass

and Mark A. Batzer

Bibliography

Batzer, Mark A., and Prescott L. Deininger. "Alu Repeats and Human Disease." Molecular Genetics and Metabolism 67, no. 3 (1999): 183-193.

Griffiths, Anthony J. F., et al. An Introduction to Genetic Analysis, 7th ed. New York:W. H. Freeman, 2000.

Kass, David H. "Impact of SINEs and LINEs on the Mammalian Genome." Current Genomics 2 (2001): 199-219.

Lander, Eric S., et. al. "Initial Sequencing and Analysis of the Human Genome." Nature 409 (2001): 860-921.

Lewin, Benjamin. Genes VII. New York: Oxford University Press, 2000.

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Watson, James D., et al. Recombinant DNA, 2nd ed. New York: W. H. Freeman, 1998.

Transposase is an enzyme that catalyzes transposition. It may be encoded in the transposon or may reside elsewhere.

Transposition

A transposition is a physical movement of genetic material (i.e., DNA ) within a genome or the movement of DNA across genomes (i.e., from one genome to another). Because these segments of genetic material contain genes, transpositions resulting in changes of the loci (location) or arrangements of genes are mutations . Transposition mutations occur in a wide range of organisms. Transposons occur in bacteria , and transposable elements have been demonstrated to operate in higher eukaryotic organisms, including mammalian systems.

Transposition mutations may only occur if the DNA being moved, termed the transposon, contains intact inverted repeats at its ends (terminus). In addition, functional tranposase enzymes must be present.

There are two types or mechanisms of transposition. Replicative transpositions involve the copying of the segment of section DNA to be moved (transposable element) before the segment is actually moved. Accordingly, with replicative transposition, the original section of DNA remains at its original location and only the copy is moved and inserted into its new position. In contrast, with conservative transpositions, the segment of DNA to be moved is physically cut from its original location and then inserted into a new location. The DNA from which the tranposon is removed is termed the donor DNA, and the DNA to which the transposon is added is termed the receptor DNA.

Transposons are not passive participants in transposition. Transposons carry the genes that code for the enzymes needed for transposition. In essence, they carry the mechanisms of transposition with them as they move or jump (hence Barbara McClintok's original designation of "jumping genes") throughout or across genomes. Transposons carry special insertion sequences (IS elements) that carry the genetic information to code for the enzyme transposase that is required to accomplish transposition mutations. One of the most important mechanisms of transposase is that they are the enzymes responsible for cutting the receptor DNA to allow the insertion of the transposon.

Transitions are a radical mutational mechanism. The physical removal of both DNA and genes can severely damage or impair the function of genes located in the transposons (especially those near either terminus). Correspondingly, the donor molecules suffer a deletion of material that may also render the remaining genes inoperative or highly impaired with regard to function.

McClintok's discovery of transposons, also termed "jumping genes" in the late 1940's (before the formation of the Waston-Crick model of DNA) resulted in her subsequent award of a Nobel Prize for Medicine or Physiology.

Transposition segments termed retrotransposons may also utilize an RNA intermediate complimentary copy to accomplish their transposition.

Transposition can radically and seriously affect phenotypic characteristics including transfer of antibiotic resistance in bacterium. Following insertion, transposed genetic elements usually generate multiple copies of the genes transferred, further increasing their disruption to both the genotype and phenotypic expression.

See also Antibiotics; Microbial genetics

trans·po·si·tion / ˌtranspəˈzishən/ • n. the action of transposing something: transposition of word order | a transposition of an old story into a contemporary context. ∎  a thing that has been produced by transposing something: in China, the dragon is a transposition of the serpent.DERIVATIVES: trans·po·si·tion·al / -shənl/ adj.

retrotransposon The product formed when a transposon is copied by RNA and is free within a cell. A retrotransposon can use reverse transcriptase to manufacture complementary DNA (thus copying the original transposon). Retroviruses are thought to have evolved from retrotransposons; these occur in most cells and are considered to be unhelpful and sometimes harmful (e.g. HIV).

retrotransposon A type of transposon found in the DNA of various organisms, including yeast, Drosophila, and mammals, that forms copies of itself using a mechanism similar to that of retroviruses. It undergoes transcription to RNA, then creates a DNA copy of the transcript with the aid of the enzyme reverse transcriptase. This DNA copy can then reintegrate into the cell's genome.