Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. Genetics (from Ancient Greek grc-Latn genetikos, “genitive” and that from grc-Latn genesis, “origin” a discipline of Biology, is In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex They are a subclass of transposon. Transposons are sequences of DNA that can move around to different positions within the Genome of a single cell, a process called transposition They are particularly abundant in plants, where they are often a principal component of nuclear DNA. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known In maize, 49-78% of the genome is made up of retrotransposons^[1]. Maize (ˈmeɪz ( Zea mays L. ssp mays) known as corn in some countries is a cereal grain domesticated in Mesoamerica In wheat, about 90% of the genome consists of repeated sequences and 68% of transposable elements^[2]. In mammals, almost half the genome (45% to 48%) comprises transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons while DNA transposons account for about 2-3%^[3].

Contents 1 Biological activity 2 Types of retrotransposons 2.1 LTR retrotransposons 2.1.1 Ty1-copia retrotransposons 2.1.2 Ty3-gypsy retrotransposons 2.2 Non-LTR retrotransposons 2.2.1 LINEs 2.2.2 SINEs 3 See also 4 References

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. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules Transposons are sequences of DNA that can move around to different positions within the Genome of a single cell, a process called transposition In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Like DNA transposable elements (class II transposons), retrotransposons can induce mutations by inserting near or within genes. 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 Nucleotide sequence of the Genetic material of an organism Genetic Insertion is the addition of one or more Nucleotide Base pairs into a genetic sequence Furthermore, retrotransposon-induced mutations are relatively stable, because the sequence at the insertion site is retained as they transpose via the replication mechanism.

Retrotransposons copy themselves to RNA and then, via reverse transcriptase, back to DNA. Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units In Biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase Enzyme that transcribes Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known 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.

Most retrotransposons are very old and through accumulated mutations, are no longer able to retrotranspose.

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. Transposons are sequences of DNA that can move around to different positions within the Genome of a single cell, a process called transposition Long terminal repeats ( LTRs) are found in retroviral DNA, flanking functional genes

LTR retrotransposons

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) , Ty3-gypsy-like (Metaviridae), and Pao-BEL-like groups based on both their degree of sequence similarity and the order of encoded gene products. The Pseudoviridae are a family of Viruses including the following genera Genus Pseudovirus; type species Saccharomyces Metaviridae are a family of Viruses which exist as Retrotransposons in a eukaryotic host’s genome 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 animals, fungi, protista, and plants with large genomes. "Haplo" redirects here For the fictional character see The Death Gate Cycle. In Cell biology, the nucleus (pl nuclei; from Latin la ''nucleus'' or la ''nuculeus'' "little nut" or kernel is a membrane-enclosed Pao-BEL like elements have so far only been found in animals^[4][5]. About 10% of the human genome and approximately 8% of the mouse genome are composed of the LTR transposons. [3]

Ty1-copia retrotransposons

are abundant in species ranging from single-cell algae to bryophytes, gymnosperms, and angiosperms. Algae ( sing. alga are a large and diverse group of simple typically Autotrophic organisms ranging from Unicellular to Multicellular forms Bryophytes are all Embryophytes ('land Plants) that are non-vascular: they have tissues and enclosed reproductive systems but they lack Vascular tissue Gymnosperm (Gymnospermae are a group of Spermatophyte seed-bearing Plants with Ovules on the edge or blade of an open Sporophyll, which are The flowering plants or angiosperms ( Angiospermae or Magnoliophyta) are the most widespread group

Ty3-gypsy retrotransposons

are also widely distributed, including both gymnosperms and angiosperms.

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) in the plant species.

LINEs

Long interspersed nuclear elements are long DNA sequences (>5kb^[6]) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase II into mRNA (messenger RNA to be translated into protein on ribosomes). RNA polymerase II (also called RNAP II and Pol II) is an enzyme found in eukaryotic cells Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that LINE elements code for 2 proteins; one that has the ability to bind single-stranded RNA, and another that has known reverse transcriptase and endonuclease activity, enabling them to copy both themselves and noncoding SINEs ,such as Alu elements (see below for more detail). In Communications a code is a rule for converting a piece of Information (for example a letter, Word, Phrase, or In Biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase Enzyme that transcribes Endonucleases are Enzymes that cleave the Phosphodiester bond within a Polynucleotide chain in contrast to Exonucleases which cleave Phosphodiester A typical LINE contains a 5' UTR (untranslated region), 2 ORFs (open reading frames), and a 3' UTR. The 5' UTR contains an internal polymerase II promoter sequence, while the 3' UTR contains a polyadenylation signal (AATAAA) and a poly-A tail. Polyadenylation is the synthesis of a poly(A tail a stretch of RNA where all the bases are Adenines at the end of an RNA molecule ^[7] 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. ^[8] LINEs are used to generate genetic fingerprints.

SINEs

Short interspersed nuclear elements are short DNA sequences (<500 bases^[6]) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, rRNA, and other small nuclear RNAs. 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 (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at Ribosomal RNA ( rRNA) is the central component of the Ribosome, the protein manufacturing machinery of all living cells. 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. An Alu sequence is a short stretch of DNA originally characterized by the action of the Alu restriction Endonuclease. Alu elements are 280 base pairs long, do not contain any coding sequences, and can be recognized by the restriction enzyme AluI (thus the name). A restriction enzyme (or restriction Endonuclease) is an Enzyme that cuts double-stranded DNA at specific recognition Nucleotide With about 1 million copies, SINEs make up about 13% of the human genome. ^[8] 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^[9]. 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. A retrovirus is any Virus belonging to the viral family Retroviridae. Human immunodeficiency virus ( HIV) is a Lentivirus (a member of the Retrovirus family that can lead to acquired immunodeficiency syndrome Human T-lymphotropic virus (HTLV is a Human, single-stranded RNA Retrovirus that causes T-cell Leukemia and T-cell Lymphoma Integrase is an enzyme produced by a Retrovirus (including HIV) that enables its genetic material to be integrated into the DNA of the infected cell The integrase is the retrotransposon equivalent of the transposase of DNA-transposons. Transposase is an Enzyme that binds to single-stranded DNA and can incorporate it into genomic DNA 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

• Endogenous retrovirus
• Transposon
• Genomic organization
• Interspersed repeat
• Retrotransposon markers, a powerful method of reconstructing phylogenies. Endogenous retroviruses are Retroviruses derived from ancient infections of Germ cells in Humans Mammals and other vertebrates as such their Transposons are sequences of DNA that can move around to different positions within the Genome of a single cell, a process called transposition Organisms have a vast array of ways in which their respective Genomes are organized Interspersed repetitive DNA is found in all eukaryotic Genomes. Retrotransposon markers are Retrotransposons that are used as cladistic markers

References

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