Transposable element

A bacterial DNA transposon

Transposable elements (TEs) are sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutations and alter the cell's genome size. Barbara McClintock's discovery of these jumping genes early in her career earned her a Nobel prize in 1983.^[1]

TEs make up a large fraction of the C-value of eukaryotic cells. They are often considered "junk DNA". In Oxytricha, which has a unique genetic system, they play a critical role in its development.^[2] They are also very useful to researchers as a means to alter DNA inside a living organism.

Classification

Transposable elements are only one of several types of mobile genetic elements. They are assigned to one of two classes according to their mechanism of transposition, which can be described as either "copy and paste" (for class I TEs) or "cut and paste" (for class II TEs).^[3]

Class I (Retrotransposons): They copy themselves in two stages, first from DNA to RNA by transcription, then from RNA back to DNA by reverse transcription. The DNA copy is then inserted into the genome in a new position. Reverse transcription is catalyzed by a reverse transcriptase, which is often coded by the TE itself. Retrotransposons behave very similarly to retroviruses, such as HIV.

There are three main orders of retrotransposons (other orders are less abundant):

• those with LTRs: encode reverse transcriptase, have long terminal repeats (LTRs), similar to retroviruses;
• LINEs: encode reverse transcriptase, lack LTRs, transcribed by RNA polymerase II;
• SINEs: do not code for reverse transcriptase, transcribed by RNA polymerase III.

Retroviruses can be considered as TEs. Indeed, after entering a host cell and converting their RNA into DNA, retroviruses integrate this DNA into the DNA of the host cell. The integrated DNA form (provirus) of the retrovirus is viewed as a particularly specialized form of eukaryotic retrotransposon, which is able to encode RNA intermediates that usually can leave the host cells and infect other cells. The transposition cycle of retroviruses also has similarities to that of prokaryotic TEs. The similarities suggest a distant familial relationship between these two TEs types.

Class II (DNA transposons): By contrast, the cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. The transpositions are catalyzed by various types of transposase enzymes. Some transposases can bind non-specifically to any target site, while others bind to specific sequence targets. The transposase makes a staggered cut at the target site producing sticky ends, cuts out the DNA 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 (a staggered cut in the target DNA filled by DNA polymerase) followed by inverted repeats (which are important for the TE excision by transposase). The duplications at the target site can result in gene duplication, which plays an important role in evolution^[4]:284.

Not all DNA transposons transpose through a cut-and-paste mechanism. In some cases a replicative transposition is observed in which transposon replicates itself to a new target site (e.g. Helitron (biology)).

Cut-and-paste TEs may be duplicated if transposition takes place during S phase of the cell cycle when the "donor" site has already been replicated, but the "target" site has not.

Both classes of TEs may lose their ability to synthesise reverse transcriptase or transposase through mutation, yet continue to jump through the genome because other TEs are still producing the necessary enzymes. Hence, they can be classified as either "autonomous" or "non-autonomous". For instance for the class II TEs, the autonomous ones have an intact gene that encodes an active transposase enzyme; the TE does not need another source of transposase for its transposition. In contrast, non-autonomous elements encode defective polypeptides and accordingly require transposase from another source. When a TE is used as a genetic tool, the transposase is supplied by the investigator, often from an expression cassette within a plasmid.^[5]

Examples

• The first TEs were discovered in maize (Zea mays), by Barbara McClintock in 1948, for which she was awarded a Nobel Prize in 1983. She noticed insertions, deletions, and translocations, caused by these elements. These changes in the genome could, for example, lead to a change in the color of corn kernels. About 85% of the genome of maize consists in TEs.^[6] The Ac/Ds system described by McClintock are class II TEs. Transposition of Ac in tobacco has been demonstrated by B. Baker (Plant Transposable Elements, pp 161-174, 1988, Plenum Publishing Corp., ed. Nelson).

• One family of TEs in the fruit fly Drosophila melanogaster are called P elements. They seem to have first appeared in the species only in the middle of the twentieth century. Within 50 years, they have spread through every population of the species. Gerald M. Rubin and Allan C. Spradling pioneered technology to use artificial P elements to insert genes into Drosophila by injecting the embryo.^[7][8][9]

• Transposons in bacteria usually carry an additional gene for function other than transposition---often for antibiotic resistance. In bacteria, transposons can jump from chromosomal DNA to plasmid DNA and back, allowing for the transfer and permanent addition of genes such as those encoding antibiotic resistance (multi-antibiotic resistant bacterial strains can be generated in this way). Bacterial transposons of this type belong to the Tn family. When the transposable elements lack additional genes, they are known as insertion sequences.

• The most common form of transposon in humans is the Alu sequence. It is approximately 300 bases long and can be found between 300,000 and a million times in the human genome.

• Mariner-like elements are another prominent class of transposons found in multiple species including humans. The Mariner transposon was first discovered by Jacobson and Hartl in Drosophila.^[10] This Class II transposable element is known for its uncanny ability to be transmitted horizontally in many species.^[11][12] There are an estimated 14 thousand copies of Mariner in the human genome comprising 2.6 million base pairs.^[13] These characteristics of the Mariner transposon have inspired the science fiction novel titled, "The Mariner Project".

• Mu phage transposition is the best known example of replicative transposition. Its transposition mechanism is somewhat similar to a homologous recombination.

• The five distinct yeast (Saccharomyces cerevisiae) retrotransposon families: Ty1, Ty2, Ty3, Ty4 and Ty5 ^[14]

• A helitron is a TE found in eukaryotes that are thought to replicate by a rolling-circle mechanism.

In disease

TEs are mutagens. They can damage the genome of their host cell in different ways ^[15]:

• a transposon or a retroposon that inserts itself into a functional gene will most likely disable that gene;
• after a DNA transposon leaves a gene, the resulting gap will probably not be repaired correctly;
• multiple copies of the same sequence, such as Alu sequences can hinder precise chromosomal pairing during mitosis and meiosis, resulting in unequal crossovers, one of the main reasons for chromosome duplication.

Diseases that are often caused by TEs include hemophilia A and B, severe combined immunodeficiency, porphyria, predisposition to cancer, and Duchenne muscular dystrophy.^[16][17]

Additionally, many TEs contain promoters which drive transcription of their own transposase. These promoters can cause aberrant expression of linked genes, causing disease or mutant phenotypes.

Rate of transposition, induction and defense

One study estimated the rate of transposition of a particular retrotransposon, the Ty1 element in Saccharomyces cerevisiae. Using several assumptions, the rate of successful transposition event per single Ty1 element came out to be about once every few months to once every few years.^[18]

Cells defend against the proliferation of TEs in a number of ways. These include piRNAs and siRNAs^[19] which silence TEs after they have been transcribed.

Some TEs contain heat-shock like promoters and their rate of transposition increases if the cell is subjected to stress,^[20] thus increasing the mutation rate under these conditions, which might be beneficial to the cell.

Evolution

The evolution of TEs and their effect on genome evolution is currently a dynamic field of study.

TEs are found in many major branches of life. They may have originated in the last universal common ancestor, or arisen independently multiple times, or perhaps arisen once and then spread to other kingdoms by horizontal gene transfer.^[21] While some TEs may confer benefits on their hosts, most are regarded as selfish DNA parasites. In this way, they are similar to viruses. Various viruses and TEs also share features in their genome structures and biochemical abilities, leading to speculation that they share a common ancestor.

Since excessive TE activity can destroy a genome, many organisms have developed mechanisms to inhibit this activity. Bacteria may undergo high rates of gene deletion as part of a mechanism to remove TEs and viruses from their genomes while eukaryotic organisms use RNA interference (RNAi) to inhibit TE activity. Nevertheless, some TEs generated large families often associated with speciation events.

Evolution has been particularly harsh on DNA transposons. In vertebrate animal cells nearly all >100,000 DNA transposons per genome have genes that encode inactive transposase polypeptides.^[22] In humans, all of the Tc1-like transposons are inactive. As a result the first DNA transposon used as a tool for genetic purposes, the Sleeping Beauty transposon system, was a Tc1/mariner-like transposon that was resurrected from a long evolutionary sleep.^[23]

Interspersed Repeats within genomes are created by transposition events accumulating over evolutionary time. Because interspersed repeats block gene conversion, they protect novel gene sequences from being overwritten by similar gene sequences and thereby facilitate the development of new genes.

TEs may have been co-opted by the vertebrate immune system as a means of producing antibody diversity: The V(D)J recombination system operates by a mechanism similar to that of some TEs.

TEs contain many type of genes- including those conferring antibiotic resistance and ability to transpose to conjugative plasmid. Some TEs also contain integrons(genetic elements that can capture and express genes from other sources) that contain integrase enzyme which can integrate gene cassettes. over 40 antibiotic resistance genes identified on cassettes: also virulance genes.

Applications

Main article: Transposable elements as a genetic tool

The first TE was discovered in the plant maize (Zea mays, corn species), and is named dissociator (Ds). Likewise, the first TE to be molecularly isolated was from a plant (Snapdragon). Appropriately, TEs have been an especially useful tool in plant molecular biology. Researchers use them as a means of mutagenesis. In this context, a TE jumps into a gene and produces a mutation. The presence of such a TE provides a straightforward means of identifying the mutant allele, relative to chemical mutagenesis methods.

Sometimes the insertion of a TE into a gene can disrupt that gene's function in a reversible manner, in a process called insertional mutagenesis; transposase-mediated excision of the DNA transposon restores gene function. This produces plants in which neighboring cells have different genotypes. This feature allows researchers to distinguish between genes that must be present inside of a cell in order to function (cell-autonomous) and genes that produce observable effects in cells other than those where the gene is expressed.

TEs are also a widely used tool for mutagenesis of most experimentally tractable organisms. The Sleeping Beauty transposon system has been used extensively as an insertional tag for identifying cancer genes ^[24]

The Tc1/mariner-class of TEs Sleeping Beauty transposon system, awarded as the Molecule of the Year 2009^[25] is active in mammalian cells and are being investigated for use in human gene therapy.^[26][27][28]

See also

• Insertion sequence
• Intragenomic conflict
• P element
• Tn10
• Signature tagged mutagenesis
• Evolution of sexual reproduction

References

• Kidwell, M.G. (2005). "Transposable elements". In ed. T.R. Gregory. The Evolution of the Genome. San Diego: Elsevier. pp. 165–221. ISBN 0-12-301463-8. 
• Craig NL, Craigie R, Gellert M, and Lambowitz AM (ed.) (2002). Mobile DNA II. Washington, DC: ASM Press. ISBN 978-1555812096. 
• Lewin B (2000). Genes VII. Oxford University Press. ISBN 978-0198792765. 

Notes

1. ^ McClintock, B. (June 1950). "The origin and behavior of mutable loci in maize". Proc Natl Acad Sci U S A. 36 (6): 344–355. Bibcode 1950PNAS...36..344M. doi:10.1073/pnas.36.6.344. PMC 1063197. PMID 15430309. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1063197. 
2. ^ "'Junk' DNA Has Important Role, Researchers Find". Science Daily. 21 May 2009. http://www.sciencedaily.com/releases/2009/05/090520140408.htm. 
3. ^ Wicker et al. (December 2007). "A unified classification system for eukaryotic transposable elements". Nature Reviews. Genetics 8 (12): 973–982. doi:10.1038/nrg2165. PMID 17984973. 
4. ^ Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1. 
5. ^ Ivics Z., Izsvak Z. (2005). "A whole lotta jumpin' goin' on: new transposon tools for vertebrate functional genomics". Trends Genet 21 (1): 8–11. doi:10.1016/j.tig.2004.11.008. PMID 15680506. 
6. ^ Schnable et al. (November 2009). "The B73 maize genome: complexity, diversity, and dynamics". Science 326 (5956): 1112–1115. doi:10.1126/science.1178534. PMID 19965430. http://www.sciencemag.org/content/326/5956/1112. 
7. ^ Spradling AC, Rubin GM (October 1982). "Transposition of cloned P elements into Drosophila germ line chromosomes". Science 218 (4570): 341–347. Bibcode 1982Sci...218..341S. doi:10.1126/science.6289435. PMID 6289435. 
8. ^ Rubin GM, Spradling AC (October 1982). "Genetic transformation of Drosophila with transposable element vectors". Science 218 (4570): 348–353. Bibcode 1982Sci...218..348R. doi:10.1126/science.6289436. PMID 6289436. 
9. ^ Cesari F (15 October 2007). "Milestones in Nature: Milestone 9: Transformers, Elements in Disguise". Nature. doi:10.1038/nrg2254. http://www.nature.com/milestones/miledna/full/miledna09.html. 
10. ^ Jacobson, J.W., Medhora, M.M. & Hartl, D.L. Molecular structure of a somatically unstable transposable element in Drosophila. Proc Natl Acad Sci U S A 83, 8684-8 (1986).
11. ^ Lohe, A.R., Moriyama, E.N., Lidholm, D.A. & Hartl, D.L. Horizontal transmission, vertical inactivation, and stochastic loss of mariner-like transposable elements. Mol Biol Evol 12, 62-72 (1995).
12. ^ Lampe, D.J., Witherspoon, D.J., Soto-Adames, F.N. & Robertson, H.M. Recent horizontal transfer of mellifera subfamily mariner transposons into insect lineages representing four different orders shows that selection acts only during horizontal transfer. Mol Biol Evol 20, 554-62 (2003).
13. ^ Mandal, P.K. & Kazazian, H.H., Jr. SnapShot: Vertebrate transposons. Cell 135, 192-192 e1 (2008).
14. ^ Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF (May 1998). "Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence". Genome Res. 8 (5): 464–78. doi:10.1101/gr.8.5.464. PMID 9582191. http://genome.cshlp.org/content/8/5/464.full. 
15. ^ Belancio, V.P., Hedges, D.J. and Deininger, P., Genome Res., 2008, 18, 343-358, Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
16. ^ Kazazian H.H., Goodier J.L. (2002). "LINE drive: retrotransposition and genome instability". Cell 110 (3): 277–80. doi:10.1016/S0092-8674(02)00868-1. PMID 12176313. 
17. ^ Kapitonov V.V., Pavlicek, A., Jurka, J. (2006). "Anthology of Human Repetitive DNA". Encyclopedia of Molecular Cell Biology and Molecular Medicine. 
18. ^ Paquin CE, Williamson VM (5 October 1984). "Temperature Effects on the Rate of Ty Transposition". Science 226 (4670): 53–55. doi:10.1126/science.226.4670.53. PMID 17815421. 
19. ^ Wei-Jen Chung,Katsutomo Okamura,Raquel Martin, Eric C. Lai (3 June 2008). "Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons". Current Biology 18 (11): 795–802. doi:10.1016/j.cub.2008.05.006. PMC 2812477. PMID 18501606. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2812477. 
20. ^ Dennis J. Strand, John F. McDonald (1985). "Copia is transcriptionally responsive to environmental stress". Nucleic Acids Research 13 (12): 4401–4410. doi:10.1093/nar/13.12.4401. PMC 321795. PMID 2409535. http://nar.oxfordjournals.org/cgi/content/abstract/13/12/4401. 
21. ^ Kidwell, M.G. (1992). "Horizontal transfer of P elements and other short inverted repeat transposons". Genetica 86 (1): 275–286. doi:10.1007/BF00133726. PMID 1334912. 
22. ^ Plasterk R.H.A., Izsvák Z., Ivics Z. (1999). "Resident aliens: the Tc1/mariner superfamily of transposable elements". Trends Genet 15 (8): 326–32. doi:10.1016/S0168-9525(99)01777-1. PMID 10431195. 
23. ^ Ivics Z., Hackett P.B., Plasterk R.H., Izsvak Z. (1997). "Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells". Cell 91 (4): 501–10. doi:10.1016/S0092-8674(00)80436-5. PMID 9390559. 
24. ^ Carlson C.M., Largaespada D.A. (2005). "Insertional mutagenesis in mice: new perspectives and tools". Nat. Rev. Genet 6 (7): 568–80. doi:10.1038/nrg1638. PMID 15995698. 
25. ^ Luft FC (May 2010). "Sleeping Beauty jumps to new heights". Mol. Med 88 (7): 641–643. doi:10.1007/s00109-010-0626-1. PMID 20467721. 
26. ^ Ivics Z., Izsvak Z. (2006). "Transposons for gene therapy! Curr". Gene Ther. 6 (5): 593–607. doi:10.2174/156652306778520647. 
27. ^ Wilson MH, Coates CJ, George AL (January 2007). "PiggyBac transposon-mediated gene transfer in human cells". Mol. Ther. 15 (1): 139–145. doi:10.1038/sj.mt.6300028. PMID 17164785. 
28. ^ Hackett P.B., Largaespada D.A., Cooper L.J.N. (2010). "A transposon and transposase system for human application". Mol. Ther. 18 (4): 674–83. doi:10.1038/mt.2010.2. PMC 2862530. PMID 20104209. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2862530. 

External links

• Kimball's Biology Pages: Transposons
• A possible connection between aberrant reinsertions and lymphoma - New Scientist
• GMO Safety: Transposons - research projects and basic infos
• A wiki specially dedicated to transposable elements and their classification
• Repbase - a database of transposable element sequences
• RepeatMasker - a computer program used by computational biologists to annotate transposons in DNA sequences
• Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells