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. They are one of the two subclasses of transposon, where the other is DNA transposon, which does not involve an RNA intermediate. They are particularly abundant in plants, where they are often a principal component of nuclear DNA. In maize, 49-78% of the genome is made up of retrotransposons. In wheat, about 90% of the genome consists of repeated sequences and 68% of transposable elements. In mammals, almost half the genome (45% to 48%) is transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons, while DNA transposons account for about 2-3%.
The retrotransposons' replicative mode of transposition by means of an RNA intermediate rapidly increases the copy numbers of elements 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.
Retrotransposons copy themselves to RNA and then back to DNA that may integrate back to the genome. The second step of forming DNA may be carried out by a reverse transcriptase, which the retrotransposon encodes. 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 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.
Because of accumulated mutations, most retrotransposons are no longer able to retrotranspose.
Types of 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 BEL-Pao-like 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 animals, fungi, protista, and plants genomes. BEL-Pao like elements have so far only been found in animals. Although Retroviruses are often classified separately, they share many features with LTR retrotransposons. A major difference with Ty1-copeia and Ty3-gypsy retrotransposons is that Retroviruses have an Envelope protein (ENV). A retrovirus can be transformed into an LTR retrotransposon through inactivation or deletion of the domains that enable extracellular mobility. If such a retrovirus infects and subsequently inserts itself in the genome in germ line cells, it may become transmitted vertically and become an Endogenous Retrovirus (ERV). Endogenous retroviruses make up about 8% of the human genome and approximately 10% of the mouse genome.
Are also widely distributed, including both gymnosperms and angiosperms.
Endogenous retroviruses (ERV)
Endogenous retroviruses are the most important LTR retrotransposons in mammals, including human where the Human ERVs make up 8% of the genome.
Non-LTR retrotransposons consist of two sub-types, long interspersed elements (LINEs) and short interspersed elements (SINEs). They can also be found in high copy numbers (up to 250,000) in the plant species. Non-long terminal repeat (LTR) retroposons are widespread in eukaryotic genomes. LINEs possess two ORFs, which encode all the functions needed for retrotransposition. These functions include reverse transcriptase and endonuclease activities, in addition to a nucleic acid-binding property needed to form a ribonucleoprotein particle. SINEs, on the other hand, co-opt the LINE machinery and function as nonautonomous retroelements.
Long Interspersed Elements (LINE-1 or L1) are a group of genetic elements that are found in large numbers in eukaryotic genomes, composing 17% of the human genome (99.9% of which is no longer capable of mobilization). Human coding L1 begins with an untranslated region (UTR) that includes an RNA polymerase II promoter, two non-overlapping open reading frames (ORF1 and ORF2), and ends with another UTR. ORF1 encodes an RNA binding protein and ORF2 encodes a protein having an endonuclease (e.g. RNase H) as well as a reverse transcriptase. The reverse transcriptase has a higher specificity for the LINE RNA than other RNA, and makes a DNA copy of the RNA that can be integrated into the genome at a new site. The endonuclease encoded by non-LTR retroposons may be AP (Apurinic/Pyrimidinic) type or REL (Restriction Endonuclease Like) type. R2 group of elements have REL type endonuclease which shows site specificity in insertion.
The 5' UTR contains the promoter sequence, while the 3' UTR contains a polyadenylation signal (AATAAA) and a poly-A tail. Because LINEs (and other class I transposons, e.g. LTR retrotransposons and SINEs) move by copying themselves (instead of moving by a cut and paste like mechanism, as class II transposons do), they enlarge the genome. The human genome, for example, contains about 500,000 LINEs, which is roughly 17% of the genome. Of these, approximately 7,000 are full-length, a small subset of which are capable of retrotransposition.
Interestingly, it was recently found that specific LINE-1 retroposons in the human genome are actively transcribed and the associated LINE-1 RNAs are tightly bound to nucleosomes and essential in the establishment of local chromatin environment.
Short Interspersed Elements are short DNA sequences (<500 bases) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, 5S ribosomal RNA, and other small nuclear RNAs. The mechanism of retrotransposition of these elements are more complicated than LINEs, and less dependent solely on the actual elements that they encode. SINEs do not encode a functional reverse transcriptase protein and rely on other mobile elements for transposition. In some cases they may have their own endonuclease that will allow them to cleave their way onto genome, but the majority of SINEs integrate at chromosomal breaks by using random DNA breaks to prime reverse transcriptase.
The most common SINEs in primates are called Alu sequences. Alu elements are approximately 350 base pairs long, do not contain any coding sequences, and can be recognized by the restriction enzyme AluI (hence the name). With about 1,500,000 copies, SINEs make up about 11% of the human genome. While historically viewed as "junk DNA", recent research suggests that, in some rare cases, both LINEs and SINEs were incorporated into novel genes so as to evolve new functionality. The distribution of these elements has been implicated in some genetic diseases and cancers. Although sequence analysis of human Alu subfamilies shows the existence of mosaic (recombinant) elements, experimental evidence is lacking. In the primitive eukaryote Entamoeba histolytica, the frequent exchange of sequence during retrotransposition has been reported; this results in a mosaic pattern in its SINE sequences.
- Endogenous retrovirus
- Insertion sequences
- Copy-number variation
- Genomic organization
- Interspersed repeat
- Retrotransposon markers, a powerful method of reconstructing phylogenies.
- SanMiguel P, Bennetzen JL (1998). "Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotranposons" (PDF). Annals of Botany 82 (Suppl A): 37–44. doi:10.1006/anbo.1998.0746.
- Li W, Zhang P, Fellers JP, Friebe B, Gill BS (November 2004). "Sequence composition, organization, and evolution of the core Triticeae genome". Plant J. 40 (4): 500–11. doi:10.1111/j.1365-313X.2004.02228.x. PMID 15500466.
- Lander ES, Linton LM, Birren B et al. (February 2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011.
- Dombroski BA, Feng Q, Mathias SL et al. (July 1994). "An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae". Mol. Cell. Biol. 14 (7): 4485–92. PMC 358820. PMID 7516468.
- Copeland CS, Mann VH, Morales ME, Kalinna BH, Brindley PJ (2005). "The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements". BMC Evol. Biol. 5 (1): 20. doi:10.1186/1471-2148-5-20. PMC 554778. PMID 15725362.
- Wicker T, Sabot F, Hua-Van A et al. (December 2007). "A unified classification system for eukaryotic transposable elements". Nat. Rev. Genet. 8 (12): 973–82. doi:10.1038/nrg2165. PMID 17984973.
- McCarthy EM, McDonald JF (2004). "Long terminal repeat retrotransposons of Mus musculus". Genome Biol. 5 (3): R14. doi:10.1186/gb-2004-5-3-r14. PMC 395764. PMID 15003117.
- Yadav, VP; Mandal, PK, Rao, DN, Bhattacharya, S (December 2009). "Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retroposon EhLINE1". The FEBS journal 276 (23): 7070–82. doi:10.1111/j.1742-4658.2009.07419.x. PMID 19878305.
- Singer MF (March 1982). "SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes". Cell 28 (3): 433–4. doi:10.1016/0092-8674(82)90194-5. PMID 6280868.
- Doucet AJ, Hulme AE, Sahinovic E, Kulpa DA, Moldovan JB, Kopera HC, Athanikar JN, Hasnaoui M, Bucheton A, Moran JV, Gilbert N (October 7, 2010). "Characterization of LINE-1 ribonucleoprotein particles". PLOS Genetics 6 (10): e1001150. doi:10.1371/journal.pgen.1001150. PMC 2951350. PMID 20949108.
- Ohshima K, Okada N (2005). "SINEs and LINEs: symbionts of eukaryotic genomes with a common tail". Cytogenet. Genome Res. 110 (1–4): 475–90. doi:10.1159/000084981. PMID 16093701.
- Yadav, VP; Mandal, PK, Rao, DN, Bhattacharya, S (December 2009). "Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retrotransposon EhLINE1". The FEBS journal 276 (23): 7070–82. doi:10.1111/j.1742-4658.2009.07419.x. PMID 19878305.
- Deininger PL, Batzer MA (October 2002). "Mammalian retroelements". Genome Res. 12 (10): 1455–65. doi:10.1101/gr.282402. PMID 12368238.
- Richard Cordaux and Mark Batzer (October 2009). "The impact of retrotransposons on human genome evolution". Nature Reviews Genetics 10 (10): 691–703. doi:10.1038/nrg2640. PMC 2884099. PMID 19763152.
- Griffiths, Anthony J. (2008). Introduction to genetic analysis (9th ed.). New York: W.H. Freeman. p. 505. ISBN 0-7167-6887-9.
- Rangwala S, Kazazian HH (2009). "Many LINE1 elements contribute to the transcriptome of human somatic cells". Genome Biology 10 (9): R100. doi:10.1186/gb-2009-10-9-r100. PMC 2768975. PMID 19772661.
- Chueh, A.C.; Northrop, Emma L.; Brettingham-Moore, Kate H.; Choo, K. H. Andy; Wong, Lee H. (Jan 2009). Bickmore, Wendy A., ed. "LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin". PLoS Genetics 5 (1): e1000354. doi:10.1371/journal.pgen.1000354. PMC 2625447. PMID 19180186.
- Stansfield, William D.; King, Robert C. (1997). A dictionary of genetics (5th ed.). Oxford [Oxfordshire]: Oxford University Press. ISBN 0-19-509441-7.
- Santangelo, Andrea; de Souza, Flavio; Franchini, Lucia; Bumaschny, Viviana; Low, Malcolm; Rubinstein,Marcelo (October 2007). "Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene". PLoS Genetics (Public Library of Science) 3 (10): 1813–26. doi:10.1371/journal.pgen.0030166. PMC 2000970. PMID 17922573. Retrieved 2007-12-31.
- Liang, Kung-Hao; Yeh, Chau-Ting. "A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger RNAs.". BMC Genomics. doi:10.1186/1471-2164-14-325. PMC 3655826. PMID 23663499. Retrieved 2013-05-11.
- Yadav, Vijay Pal; Mandal, Prabhat Kumar; Bhattacharya, Alok; Bhattacharya, Sudha (21 May 2012). "Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo". Nature Communications 3: 854. doi:10.1038/ncomms1855.