HAT transposon

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hAT transposons are a superfamily of DNA transposons, or Class II transposable elements, that are common in the genomes of plants, animals, and fungi. [1] [2] [3]

Contents

Nomenclature and classification

Superfamilies are identified by shared DNA sequence and ability to respond to the same transposase. [1] Common features of hAT transposons include a size of 2.5-5 kilobases with short terminal inverted repeats and short flanking target site duplications generated during the transposition process. [3]

The hAT superfamily's name derives from three of its members: the hobo element from Drosophila melanogaster , the Activator or Ac element from Zea mays , and the Tam3 element from Antirrhinum majus . [4] The superfamily has been divided based on bioinformatics analysis into at least two clusters defined by their phylogenetic relationships: the Ac family and the Buster family. [1] More recently, a third group called Tip has been described. [3]

Family members

The hAT transposon superfamily includes the first transposon discovered, Ac from Zea mays (maize), first reported by Barbara McClintock. [1] [5] McClintock was awarded the Nobel Prize in Physiology or Medicine in 1983 for this discovery. [6] The family also includes a subgroup known as space invaders or SPIN elements, which have very high copy numbers in some genomes and which are among the most efficient known transposons. Although no extant active example is known, laboratory-generated consensus sequences of active SPIN elements are able to generate high copy numbers when introduced to cells from a wide range of species. [1] [7]

Distribution

hAT transposons are widely distributed across eukaryotic genomes, but are not active in all organisms. Inactive hAT transposon sequences are present in mammal genomes, including the human genome; [1] they are among the transposon families believed to have been present in the ancestral vertebrate genome. [8] Among mammals, the genome of the little brown bat Myotis lucifugus is notable for its relatively high and recently acquired number of inactive hAT transposons. [1]

The distribution of SPIN elements is patchy and does not relate well to known phylogenetic relationships, prompting suggestions that these elements may have spread through horizontal gene transfer. [1] [7]

Domestication

Transposons are said to be exapted or "domesticated" when they have acquired functional roles in the host genome. Several sequences evolutionarily related to the hAT family have been exapted in diverse organisms, including Homo sapiens . [1] An example is the ZBED gene family, which encode a group of zinc finger-containing regulatory proteins. [9]

Related Research Articles

Transposable element Semiparasitic DNA sequence

A transposable element is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983.

Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules. Other functions of non-coding DNA include the transcriptional and translational regulation of protein-coding sequences, scaffold attachment regions, origins of DNA replication, centromeres and telomeres. Its RNA counterpart is non-coding RNA.

Selfish genetic elements are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no positive or a net negative effect on organismal fitness. Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are vulnerable to selfish behaviour by their parts.

Barbara McClintock American scientist and cytogeneticist

Barbara McClintock was an American scientist and cytogeneticist who was awarded the 1983 Nobel Prize in Physiology or Medicine. McClintock received her PhD in botany from Cornell University in 1927. There she started her career as the leader in the development of maize cytogenetics, the focus of her research for the rest of her life. From the late 1920s, McClintock studied chromosomes and how they change during reproduction in maize. She developed the technique for visualizing Maize chromosomes and used microscopic analysis to demonstrate many fundamental genetic ideas. One of those ideas was the notion of genetic recombination by crossing-over during meiosis—a mechanism by which chromosomes exchange information. She produced the first genetic map for maize, linking regions of the chromosome to physical traits. She demonstrated the role of the telomere and centromere, regions of the chromosome that are important in the conservation of genetic information. She was recognized as among the best in the field, awarded prestigious fellowships, and elected a member of the National Academy of Sciences in 1944.

Chromosomal crossover Cellular process

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

Horizontal gene transfer Type of nonhereditary genetic change involving swapping of DNA or RNA other than from parent to offspring

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms.

Retrotransposon

Retrotransposons are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the process reverse transcription using an RNA transposition intermediate.

Transposase is an enzyme that binds to the end of a transposon and catalyses its movement to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism. The word "transposase" was first coined by the individuals who cloned the enzyme required for transposition of the Tn3 transposon. The existence of transposons was postulated in the late 1940s by Barbara McClintock, who was studying the inheritance of maize, but the actual molecular basis for transposition was described by later groups. McClintock discovered that pieces of the chromosomes changed their position, jumping from one chromosome to another. The repositioning of these transposons allowed other genes for pigment to be expressed. Transposition in maize causes changes in color; however, in other organisms, such as bacteria, it can cause antibiotic resistance. Transposition is also important in creating genetic diversity within species and adaptability to changing living conditions. During the course of human evolution, as much as 40% of the human genome has moved around via methods such as transposition of transposons.

Mobilome

The mobilome is the entire set of mobile genetic elements in a genome. Mobilomes are found in eukaryotes, prokaryotes, and viruses. The compositions of mobilomes differ among lineages of life, with transposable elements being the major mobile elements in eukaryotes, and plasmids and prophages being the major types in prokaryotes. Virophages contribute to the viral mobilome.

Transposon mutagenesis, or transposition mutagenesis, is a biological process that allows genes to be transferred to a host organism's chromosome, interrupting or modifying the function of an extant gene on the chromosome and causing mutation. Transposon mutagenesis is much more effective than chemical mutagenesis, with a higher mutation frequency and a lower chance of killing the organism. Other advantages include being able to induce single hit mutations, being able to incorporate selectable markers in strain construction, and being able to recover genes after mutagenesis. Disadvantages include the low frequency of transposition in living systems, and the inaccuracy of most transposition systems.

Helitrons are one of the three groups of eukaryotic class 2 transposable elements (TEs) so far described. They are the eukaryotic rolling-circle transposable elements which are hypothesized to transpose by a rolling circle replication mechanism via a single-stranded DNA intermediate. They were first discovered in plants and in the nematode Caenorhabditis elegans, and now they have been identified in a diverse range of species, from protists to mammals. Helitrons make up a substantial fraction of many genomes where non-autonomous elements frequently outnumber the putative autonomous partner. Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which can evolve into novel host genes or become essential for Helitron transposition.

The Sleeping Beauty transposon system is a synthetic DNA transposon designed to introduce precisely defined DNA sequences into the chromosomes of vertebrate animals for the purposes of introducing new traits and to discover new genes and their functions. It is a Tc1/mariner-type system, with the transposase resurrected from multiple inactive fish sequences.

Miniature Inverted-repeat Transposable Elements (MITEs) are a group of non-autonomous Class II transposable elements. Being non-autonomous, MITEs cannot code for their own transposase. They exist within the genomes of animals, plants, fungi and bacteria. MITEs are generally short elements with terminal inverted repeats and two flanking target site duplications (TSDs). Like other transposons, MITEs are inserted predominantly in gene-rich regions and this can be a reason that they affect gene expression and play important roles in accelerating eukaryotic evolution. Their high copy number in spite of small sizes has been a topic of interest.

The PiggyBac (PB) transposon is a mobile genetic element that efficiently transposes between vectors and chromosomes via a "cut and paste" mechanism. During transposition, the PB transposase recognizes transposon-specific inverted terminal repeat sequences (ITRs) located on both ends of the transposon vector and efficiently moves the contents from the original sites and integrates them into TTAA chromosomal sites. The powerful activity of the PiggyBac transposon system enables genes of interest between the two ITRs in the PB vector to be easily mobilized into target genomes. The TTAA-specific transposon piggyBac is rapidly becoming a highly useful transposon for genetic engineering of a wide variety of species, particularly insects. They were discovered in 1989 by Malcolm Fraser at the University of Notre Dame.

Transposon silencing is a form of transcriptional gene silencing targeting transposons. Transcriptional gene silencing is a product of histone modifications that prevent the transcription of a particular area of DNA. Transcriptional silencing of transposons is crucial to the maintenance of a genome. The “jumping” of transposons generates genomic instability and can cause extremely deleterious mutations. Transposable element insertions have been linked to many diseases including hemophilia, severe combined immunodeficiency, and predisposition to cancer. The silencing of transposons is therefore extremely critical in the germline in order to stop transposon mutations from developing and being passed on to the next generation. Additionally, these epigenetic defenses against transposons can be heritable. Studies in Drosophila, Arabidopsis thaliana, and mice all indicate that small interfering RNAs are responsible for transposon silencing. In animals, these siRNAS and piRNAs are most active in the gonads.

Ac/Ds transposable controlling elements was the first transposable element system recognized in maize. The Ac Activator element is autonomous, whereas the Ds Dissociation element requires an Activator element to transpose. Ac was initially discovered as enabling a Ds element to break chromosomes. Both Ac and Ds can also insert into genes, causing mutants that may revert to normal on excision of the element. The phenotypic consequence of Ac/Ds transposable element includes mosaic colors in kernels and leaves in maize.

DNA transposons are DNA sequences, sometimes referred to "jumping genes", that can move and integrate to different locations within the genome. They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I TEs, retrotransposons, that move through an RNA intermediate. DNA transposons can move in the DNA of an organism via a single-or double-stranded DNA intermediate. DNA transposons have been found in both prokaryotic and eukaryotic organisms. They can make up a significant portion of an organism's genome, particularly in eukaryotes. In prokaryotes, TE's can facilitate the horizontal transfer of antibiotic resistance or other genes associated with virulence. After replicating and propagating in a host, all transposon copies become inactivated and are lost unless the transposon passes to a genome by starting a new life cycle with horizontal transfer. It is important to note that DNA transposons do not randomly insert themselves into the genome, but rather show preference for specific sites.

Polintons are large DNA transposons which contain genes with homology to viral proteins and which are often found in eukaryotic genomes. They were first discovered in the mid-2000s and are the largest and most complex known DNA transposons. Polintons encode up to 10 individual proteins and derive their name from two key proteins, a DNA polymerase and a retroviral-like integrase.

Tc1/mariner is a class and superfamily of interspersed repeats DNA transposons. The elements of this class are found in all animals, including humans. They can also be found in protists and bacteria.

Transib is a superfamily of interspersed repeats DNA transposons. It was named after the Trans-Siberian Express. It is similar to EnSpm/CACTA.

References

  1. 1 2 3 4 5 6 7 8 9 Arensburger, Peter; Hice, Robert H.; Zhou, Liqin; Smith, Ryan C.; Tom, Ariane C.; Wright, Jennifer A.; Knapp, Joshua; O'Brochta, David A.; Craig, Nancy L.; Atkinson, Peter W. (May 2011). "Phylogenetic and Functional Characterization of the Transposon Superfamily". Genetics. 188 (1): 45–57. doi:10.1534/genetics.111.126813. PMC   3120152 . PMID   21368277.
  2. ↑ Kempken, F; Windhofer, F (April 2001). "The hAT family: a versatile transposon group common to plants, fungi, animals, and man". Chromosoma. 110 (1): 1–9. doi:10.1007/s004120000118. PMID   11398971. S2CID   1925295.
  3. 1 2 3 Rossato, Dirleane Ottonelli; Ludwig, Adriana; Deprá, Maríndia; Loreto, Elgion L. S.; Ruiz, Alfredo; Valente, Vera L. S. (February 2014). "BuT2 Is a Member of the Third Major Group of hAT Transposons and Is Involved in Horizontal Transfer Events in the Genus Drosophila". Genome Biology and Evolution. 6 (2): 352–365. doi:10.1093/gbe/evu017. PMC   3942097 . PMID   24459285.
  4. ↑ Rubin, E; Lithwick, G; Levy, AA (July 2001). "Structure and evolution of the hAT transposon superfamily". Genetics. 158 (3): 949–57. doi:10.1093/genetics/158.3.949. PMC   1461711 . PMID   11454746.
  5. ↑ McCLINTOCK, B (June 1950). "The origin and behavior of mutable loci in maize". Proceedings of the National Academy of Sciences of the United States of America. 36 (6): 344–55. Bibcode:1950PNAS...36..344M. doi: 10.1073/pnas.36.6.344 . PMC   1063197 . PMID   15430309.
  6. ↑ "The Nobel Prize in Physiology or Medicine 1983". Nobelprize.org. Retrieved 8 September 2018.
  7. 1 2 Li, X.; Ewis, H.; Hice, R. H.; Malani, N.; Parker, N.; Zhou, L.; Feschotte, C.; Bushman, F. D.; Atkinson, P. W.; Craig, N. L. (22 October 2012). "A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture". Proceedings of the National Academy of Sciences. 110 (6): E478–E487. doi: 10.1073/pnas.1121543109 . PMC   3568352 . PMID   23091042.
  8. ↑ Chalopin, Domitille; Naville, Magali; Plard, Floriane; Galiana, Delphine; Volff, Jean-Nicolas (February 2015). "Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates". Genome Biology and Evolution. 7 (2): 567–580. doi: 10.1093/gbe/evv005 . PMC   4350176 . PMID   25577199.
  9. ↑ Hayward, Alexander; Ghazal, Awaisa; Andersson, Göran; Andersson, Leif; Jern, Patric; Robinson-Rechavi, Marc (22 March 2013). "ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions". PLOS ONE. 8 (3): e59940. Bibcode:2013PLoSO...859940H. doi: 10.1371/journal.pone.0059940 . PMC   3606216 . PMID   23533661.
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