Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are particularly abundant in plants, where they are often a principal component of nuclear DNA. In maize, 49-78%^[1] and in wheat up to 90%^{[citation needed]} of the genome is made up of retrotransposons. They are a subclass of transposon. Genetics (from the Greek genno γεννώ= give birth) is the science of genes, heredity, and the variation of organisms. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista An eukaryote (yoo-KAR-ee-ot) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the biological development of a cellular form of life or a virus. ... Binomial name Zea mays L. Maize (Zea mays ssp. ... Species T. aestivum T. boeoticum T. compactum T. dicoccoides T. dicoccon T. durum T. monococcum T. spelta T. sphaerococcum References:   ITIS 42236 2002-09-22 For the indie rock group see: Wheat (band). ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called transposition. ...

Biological activity

The retrotransposons' replicative mode of transposition through an RNA intermediate increases the copy numbers of elements rapidly and thereby can increase genome size. Like DNA transposable elements (class II transposons), retrotransposons can induce mutations by inserting near or within genes. Furthermore, retrotransposon-induced mutations are relatively stable, because the sequence at the insertion site is retained as they transpose via the replication mechanism. Replication may mean: In biology: Self-replication, when a molecule (or any other pattern) makes a copy of itself DNA replication, the act of copying the genetic material of a cell (DNA) to a daughter cell Semiconservative replication, mechanism of DNA replication Other: replication (computer science), the provision of redundant... Transposition is a method in genetics where a transposon is inserted into the studied gene to help identify the function or silence the selected gene. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called Transposition. ... In biology, mutations are changes to the genetic material (either DNA or RNA). ... An illustration of an insertion at chromosome level At DNA level, an insertion means the insertion of a few base pairs into a genetic sequence. ...

Retrotransposons copy themselves to RNA and then, via reverse transcriptase, back to DNA. Transposition and survival of retrotransposons within the host genome are possibly regulated both by retrotransposon- and host-encoded factors, to avoid deleterious effects on host and retrotransposon as well, in a relationship that has existed for many millions of years between retrotransposons and their plant hosts. The understanding of how retrotransposons and their hosts' genomes have co-evolved mechanisms to regulate transposition, insertion specificities, and mutational outcomes in order to optimize each other's survival is still in its infancy. Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the biological development of a cellular form of life or a virus. ...

Types of retrotransposons

Retrotransposons, also known as class I transposable elements, consist of two sub-types, the long terminal repeat (LTR) and the non-LTR retrotransposons. The LTR retrotransposons have direct LTRs that range from ~100 bp to over 5 kb in size. LTR retrotransposons are further sub-classified into the Ty1-copia-like (Pseudoviridae) and the Ty3-gypsy-like (Metaviridae) groups based on both their degree of sequence similarity and the order of encoded gene products. Ty1-copia and Ty3-gypsy groups of retrotransposons are commonly found in high copy number (up to a few million copies per haploid nucleus) in plants with large genomes. Ty1-copia retrotransposons are abundant in species ranging from single-cell algae to bryophytes, gymnosperms, and angiosperms. Ty3-gypsy retrotransposons are also widely distributed, including both gymnosperms and angiosperms. LTR retrotransposons make up approximately 8% of the human genome.^[2] The non-LTR retrotransposons, consists of two sub-types, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). They can also be found in high copy numbers (up to 250,000^{[citation needed]}) in the plant species. Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called Transposition. ... When HIV integrates its genetic sequence into a hosts DNA the Long Terminal Repeat or LTR is a DNA sequence found at the ends of this integrated sequence. ... Genera Pseudovirus Hemivirus The Pseudoviridae are a family of viruses, including the following genera: Genus Pseudovirus; type species: Saccharomyces cerevisiae Ty1 virus Genus Hemivirus; type species: Drosophila melanogaster copia virus Categories: Viruses | Virus stubs ... Genera Metavirus Errantivirus The Metaviridae are a family of viruses, including the following genera: Genus Metavirus; type species: Saccharomyces cerevisiae Ty3 virus Genus Errantivirus; type species: Drosophila melanogaster gypsy virus Categories: Viruses | Virus stubs ... Haploid (meaning simple in Greek) cells have only one copy of each chromosome. ... The eukaryotic cell nucleus. ... A seaweed (Laurencia) up close: the branches are multicellular and only about 1 mm thick. ... Bryophyte is a botanical term which refers to any member of the following divisions of the Plantae kingdom: Bryophyta (mosses) Anthocerophyta (hornworts) Hepatophyta (liverworts) Despite the similarity in name, a bryophyte does not exclusively imply a species of the division bryophyta. ... Gymnosperms are seed-bearing, vascular plants. ... Classes Magnoliopsida - Dicots Liliopsida - Monocots The flowering plants (also angiosperms or Magnoliophyta) are one of the major groups of modern plants, comprising those that produce seeds in specialized reproductive organs called flowers, where the ovulary or carpel is enclosed. ...

• LINEs (long interspersed nuclear elements) are long DNA sequences (>5kb^[3]) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase II into mRNA (messenger RNA to be translated into protein on ribosomes). LINE elements code for 2 genes, one of which has known reverse transcriptase and integrase activity, enabling them to copy both themselves and other, noncoding LINES such as AluI elements (see below for more detail). Because LINES move by copying themselves (instead of moving, like transposons do), they enlarge the genome. The human genome, for example, contains about 900,000 LINES, which is roughly 21% of the genome.^[4] LINES are used to generate genetic fingerprints.
• SINEs (short interspersed nuclear elements) are short DNA sequences (<500 bases ^[3]) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, rRNA, and other small nuclear RNAs. SINEs do not encode a functional reverse transcriptase protein and rely on other mobile elements for transposition. The most common SINES in primates are called Alu sequences. Alu elements are about 300 base pairs long, do not contain any coding sequences, and can be recognized by the restriction enzyme AluI (thus the name). With about 1 million copies, SINEs make up about 11% of the human genome.^[4] While previously believed to be "junk DNA", recent research suggests that both LINEs and SINEs have a significant role in gene evolution, structure and transcription levels. The distribution of these elements has been implicated in some genetic diseases and cancers.

Retroviruses, like HIV-1 or HTLV-1 behave like retrotransposons and contain both reverse transcriptase and integrase. The integrase is the retrotransposon equivalent of the transposase of DNA-transposons. RNA polymerase II (also called RNAP II and Pol II) transcribes DNA to synthesize precursors of mRNA and most snRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. ... The interaction of mRNA in a eukaryote cell. ... Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... In communications, a code is a rule for converting a piece of information (for example, a letter, word, or phrase) into another form or representation, not necessarily of the same type. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... Integrase is a protein produced by a virus that enables genetic material that is helpful to the virus, proviral DNA, to be integrated into the DNA of the infected cell. ... Genetic fingerprinting or DNA testing is a technique to distinguish between individuals of the same species using only samples of their DNA. Its invention by Sir Alec Jeffreys at the University of Leicester was announced in 1985. ... RNA polymerase III (also called Pol III) transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. ... Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. ... An Alu sequence is a short stretch of DNA characterized by the action of the Alu restriction endonuclease. ... A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the phosphate backbones of the double helix without damaging the bases. ... Genera Alpharetrovirus Betaretrovirus Gammaretrovirus Deltaretrovirus Epsilonretrovirus Lentivirus Spumavirus A retrovirus is any virus belonging to the viral family Retroviridae. ... Human immunodeficiency virus or HIV is a retrovirus that causes Acquired Immunodeficiency Syndrome (AIDS), a condition in which the immune system begins to fail, leading to life-threatening opportunistic infections. ... ... Integrase is a protein produced by a virus that enables genetic material that is helpful to the virus, proviral DNA, to be integrated into the DNA of the infected cell. ... Transposase is an enzyme that binds to single-stranded DNA and can incorporate it into genomic DNA. Class I transposons encode a transposase which allows them to enable transposons to be cut from genomic DNA and be inserted at another location. ... Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called transposition. ...

See also

• Transposon
• Genetics
• Alu sequence
• Interspersed repeat
• Retrotransposon markers, a powerful method of reconstructing phylogenies.

Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called transposition. ... Genetics (from the Greek genno γεννώ= give birth) is the science of genes, heredity, and the variation of organisms. ... An Alu sequence is a short stretch of DNA characterized by the action of the Alu restriction endonuclease. ... Interspersed repetitive DNA is found in all eukaryotic genomes. ... Retrotransposons as cladistic markers The analysis of SINEs – Short INterspersed Elements – LINEs – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular cladistic markers represents a particularly interesting complement to DNA sequence and morphological data. ...

References

• Lander ES, Linton LM, Birren B, Nusbaum C, et al. Initial sequencing and analysis of the human genome. Nature, 2001; 409(6822): 860-921
• Hansen RS. X inactivation-specific methylation of LINE-1 elements by DNMT3B: implications for the Lyon repeat hypothesis. Hum Mol Genet, 2003; 12(19): 2559-67.
• Teugels E, De Brakeleer S, Goelen G, Lissens W, Sermijn E, De Greve J. De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes. Hum Mutat. 2005 Sep;26(3):284.
• Han K, Sen SK, Wang J, Callinan PA, et al. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res, 2005; 33(13): published online July 20, 2005

McCarthy EM, McDonald JF. Long terminal repeat retrotransposons of Mus musculus. Genome Biology 2004, 5: R14. [2]

Notes

1. ^ SanMiguel, Phillip and Jeffrey L. Bennetzen (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotranposons. Annals of Botany 82 (supplement A): 37-44. [[1]]
2. ^ Lander ES, Linton LM, Birren B, Nusbaum C, et al. Initial sequencing and analysis of the human genome. Nature, 2001; 409(6822): 860-921
3. ^ ^a b King, Robert C. and William D. Stansfield (1997). A Dictionary of Genetics. Fifth Edition. Oxford University Press.
4. ^ ^a b Pierce, B. A. (2005). Genetics: A conceptual approach. Freeman. Page 311.