A bacterial DNA transposon
A transposable element (TE) is a DNA sequence that can change its position within the genome, sometimes creating mutations and altering the cell's genome size. Transposition often results in duplication of the TE. 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 generally considered "junk DNA". In Oxytricha, which has a unique genetic system, they play a critical role in development.[2] They are also very useful to researchers as a means to alter DNA inside a living organism.
|
Contents
- 1 Classification
- 2 Examples
- 3 In disease
- 4 Rate of transposition, induction and defense
- 5 Evolution
- 6 Applications
- 7 De novo repeat identification
- 8 See also
- 9 References
- 10 External links
|
Classification
Transposable elements (TEs) represent one of several types of mobile genetic elements. TEs are assigned to one of two classes according to their mechanism of transposition, which can be described as either copy and paste (class I TEs) or cut and paste (class II TEs).[3]
Class I (retrotransposons):
Class I TEs are copied in two stages: first they are transcribed from DNA to RNA, and the RNA produced is then reverse transcribed to DNA. This copied DNA is then inserted at a new position into the genome.[citation needed] The reverse transcription step is catalyzed by a reverse transcriptase, which is often encoded by the TE itself. The characteristics of retrotransposons are similar to retroviruses, such as HIV.[citation needed]
Retrotransposons are commonly grouped into three main orders:
- TEs with long terminal repeats (LTRs): encode reverse transcriptase, similar to retroviruses
- LINEs: encode reverse transcriptase, lack LTRs, and are transcribed by RNA polymerase II
- SINEs: do not encode reverse transcriptase and are transcribed by RNA polymerase III.
Retroviruses can also be considered TEs.[citation needed] For example, after entering a host cell and conversion of the retroviral RNA into DNA, the newly produced retroviral DNA is integrated into the genome of the host cell. These integrated DNAs represent a provirus of the retrovirus. The provirus is a specialized form of eukaryotic retrotransposon, which can produce RNA intermediates that may leave the host cell and infect other cells. The transposition cycle of retroviruses has similarities to that of prokaryotic TEs, suggesting a distant relationship between these two TEs types.[citation needed]
Class II (DNA transposons):
The cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. The transpositions are catalyzed by several transposase enzymes. Some transposases non-specifically bind to any target site in DNA, whereas others bind to specific DNA sequence targets. The transposase makes a staggered cut at the target site resulting in single-strand 5' or 3' DNA overhangs (sticky ends). This step cuts out the DNA transposon, which is then ligated it into a new target site; this process involves activity of a DNA polymerase that fills in gaps and of a DNA ligase that closes the sugar-phosphate backbone.[citation needed] This results in duplication of the target site. The insertion sites of DNA transposons may be identified by short direct repeats (created by the staggered cut in the target DNA and filling in by DNA polymerase) followed by a series of inverted repeats important for the TE excision by transposase. Cut-and-paste TEs may be duplicated if their transposition takes place during S phase of the cell cycle when a donor site has already been replicated, but a target site has not yet been replicated.[citation needed] Such 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 the cut-and-paste mechanism. In some cases, a replicative transposition is observed in which a transposon replicates itself to a new target site (e.g. Helitron (biology)).
Both classes of TEs may lose their ability to synthesise reverse transcriptase or transposase through mutation. However, such mutated TEs may continue to transpose through the genome if functional enzymes for the transposition are furnished by non-mutated TEs. Hence, transposition can be classified as either "autonomous" or "non-autonomous." For instance, for class II TEs, autonomous ones have an intact gene that encodes an active transposase enzyme; transposition of the TE does not require transposase activity from another TE. In contrast, non-autonomous elements encode defective polypeptides and therefore require transposase from a functional TE.[citation needed] 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 transposable element 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] The first mariner-element transposons outside of animals were found in Trichomonas vaginalis.[14] 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 [15]
- A helitron is a TE found in eukaryotes that are thought to replicate by a rolling-circle mechanism.
In disease
|
|
This section does not cite any references or sources. Please help improve this section by adding citations to reliable sources. Unsourced material may be challenged and removed. (October 2010) |
TEs are mutagens. They can damage the genome of their host cell in different ways:[16]
- 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.[17][18]
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.[19]
Cells defend against the proliferation of TEs in a number of ways. These include piRNAs and siRNAs[20] 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,[21] 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.[22] 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.[23] 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.[24]
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. There are over 40 antibiotic resistance genes identified on cassettes, also virulence genes.
Applications
Main article: Transposons 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 [25]
The Tc1/mariner-class of TEs Sleeping Beauty transposon system, awarded as the Molecule of the Year 2009[26] is active in mammalian cells and are being investigated for use in human gene therapy.[27][28][29]
De novo repeat identification
De novo repeat identification is an initial scan of sequence data that seeks to find the repetitive regions of the genome, and to classify these repeats. Many computer programs exist to perform de novo repeat identification, all operating under the same general principles. As short tandem repeats are generally 1-6 base pairs in length and are often consecutive, their identification is relatively simple.[30] Dispersed repetitive elements, on the other hand, are more challenging to identify, due to the fact that they are longer and have often acquired mutations. However, it is important to identify these repeats as they are often found to be transposable elements (TEs).[31]
De novo identification of transposons involves three steps: 1) find all repeats within the genome, 2) build a consensus of each family of sequences, and 3) classify these repeats (Makalowski et al. 2012). There are three groups of algorithms for the first step. One group is referred to as the k-mer approach, where a k-mer is a sequence of length k. In this approach, the genome is scanned for overrepresented k-mers; that is, k-mers that occur more often than is likely based on probability alone. The length k is determined by the type of transposon being searched for. The k-mer approach also allows mismatches, the number of which is determined by the analyst. Some k-mer approach programs use the k-mer as a base, and extend both ends of each repeated k-mer until there is no more similarity between them, indicating the ends of the repeats.[31] Another group of algorithms employs a method called sequence self-comparison. Sequence self-comparison programs use databases such as AB-BLAST to conduct an initial sequence alignment. As these programs find groups of elements that partially overlap, they are useful for finding highly diverged transposons, or transposons with only a small region copied into other parts of the genome.[32] Another group of algorithms follows the periodicity approach. These algorithms perform a Fourier transformation on the sequence data, identifying periodicities, regions that are repeated periodically, and are able to use peaks in the resultant spectrum to find candidate repetitive elements. This method works best for tandem repeats, but can be used for dispersed repeats as well. However, it is a slow process, making it an unlikely choice for genome scale analysis.[31]
The second step of de novo repeat identification involves building a consensus of each family of sequences. A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus is the one that occurred most often in the sequences being compared to make the consensus. For example, in a family of 50 repeats where 42 have a T base pair in the same position, the consensus sequence would have a T at this position as well, as the base pair is representative of the family as a whole at that particular position, and is most likely the base pair found in the family’s ancestor at that position.[31] Once a consensus sequence has been made for each family, it is then possible to move on to further analysis, such as TE classification and genome masking in order to quantify the overall TE content of the genome.
See also
- Insertion sequence
- Intragenomic conflict
- P element
- Tn3 Transposon
- 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 0-123-01463-8.
- Craig NL, Craigie R, Gellert M, and Lambowitz AM (ed.) (2002). Mobile DNA II. Washington, DC: ASM Press. ISBN 978-1-555-81209-6.
- Lewin B (2000). Genes VII. Oxford University Press. ISBN 978-0-198-79276-5.
Notes
- ^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1063197/.
- ^ "'Junk' DNA Has Important Role, Researchers Find". Science Daily. 21 May 2009. http://www.sciencedaily.com/releases/2009/05/090520140408.htm.
- ^ 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.
- ^ Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1.
- ^ 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.
- ^ Schnable et al. (November 2009). "The B73 maize genome: complexity, diversity, and dynamics". Science 326 (5956): 1112–1115. Bibcode 2009Sci...326.1112S. doi:10.1126/science.1178534. PMID 19965430. http://www.sciencemag.org/content/326/5956/1112.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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).
- ^ 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).
- ^ 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).
- ^ Mandal, P.K. & Kazazian, H.H., Jr. SnapShot: Vertebrate transposons. Cell 135, 192-192 e1 (2008).
- ^ Carlton, et al. (2007)Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis. Science 315 (5809): 207-212
- ^ 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.
- ^ 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
- ^ 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.
- ^ Kapitonov V.V., Pavlicek, A., Jurka, J. (2006). "Anthology of Human Repetitive DNA". Encyclopedia of Molecular Cell Biology and Molecular Medicine. doi:10.1002/3527600906.mcb.200300166.
- ^ Paquin CE, Williamson VM (5 October 1984). "Temperature Effects on the Rate of Ty Transposition". Science 226 (4670): 53–55. Bibcode 1984Sci...226...53P. doi:10.1126/science.226.4670.53. PMID 17815421.
- ^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2812477/.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ Ivics Z., Izsvak Z. (2006). "Transposons for gene therapy! Curr". Gene Ther. 6 (5): 593–607. doi:10.2174/156652306778520647.
- ^ 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.
- ^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2862530/.
- ^ Surya Saha, Susan Bridges, Zenaida V. Magbanua, Daniel G. Peterson. Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences. Tropical Plant Biol., 2008, 1:85–96
- ^ a b c d Wojciech Makałowski, Amit Pande, Valer Gotea, Izabela Makałowska. Tranposable Elements and Their Identification. Evolutionary Genomics: Statistical and Computational Methods, Volume 1. Methods in Molecular Biology, vol. 855, p. 337-359.
- ^ Surya Saha, Susan Bridges, Zenaida V. Magbanua, Daniel G. Peterson. Empirical comparison of ab initio repeat finding programs. Nucleic Acids Research, 2008, Vol. 36, No. 7
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
|
Genetics: repeated sequence
|
|
| Tandem repeats |
- Satellite DNA
- Variable number tandem repeat/Minisatellite
- Short tandem repeat/Microsatellite (Trinucleotide repeat disorders)
|
|
| Interspersed repeats |
|
Transposon
|
|
Retrotransposon
|
|
|
|
DNA transposon
|
|
|
|
|
| Genomic island |
|
|
|
Genetics: homologous recombination / mobile genetic elements
|
|
| Primarily prokaryotic |
- Conjugation
- Transduction
- Transformation
|
|
| Occurs in eukaryotes |
- Transfection
- Chromosomal crossover
- Gene conversion
- Fusion gene
- Horizontal gene transfer
- Sister chromatid exchange
- Transposon
|
|
|
B bsyn: dna (repl, cycl, reco, repr) · tscr (fact, tcrg, nucl, rnat, rept, ptts) · tltn (risu, pttl, nexn) · dnab, rnab/runp · stru (domn, 1°, 2°, 3°, 4°)
|
|
