Retrotransposon

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Retrotransposons are mobile genetic elements (mobile DNA) and are ubiquitous in the genomes of many eukaryotic organisms. They are particularly abundant in plants , where they are often a principal component of nuclear DNA. In maize 50-80% and in wheat up to 90% of the genome is made up of retrotransposons. They are a subclass of transposon.

Biological activity

The retrotransposons replicative mode of transposition increases the copy numbers of elements rapidly and thereby greatly increasing plant genome size. Like DNA transposable elements, they 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, 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.

Types of retrotransposons

Retrotransposons belong to the class I type of mobile elements, which consists 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 and the Ty3-gypsy 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, mostly located near the centromere . 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, 450,000 in number, make up approximately 8% of the human genome .

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) in plant species.

• LINEs (long interspersed elements) are long DNA sequences (>5kb) 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. .LINES are used to generate genetic fingerprints.
• SINEs (short interspersed elements) are short DNA sequences (<500 bases ) 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. . 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.

See also

• Transposon
• Genetics
• Alu sequence
• Interspersed repeat
• Retrotransposon_Markers, a powerful method of reconstructing phylogenies.
• Mobile DNA
• Horizontal gene transfer

Further reading

• Bennetzen, J. L., (2000) Transposable element contributions to plant gene and genome evolution. Plant Molecular Biology 42: 251–269, 2000.(Provides a comprehensive authoritative overview.)
• Lander ES, Linton LM, Birren B, Nusbaum C, et al.(2001) Initial sequencing and analysis of the human genome. Nature, 2001; 409(6822): 860-921
• Hansen RS.(2003) 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. (2005) 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. (2005) 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.