Retrotransposons

Kobayashi S, Goto-Yamamoto N and Hirochika H. 2004. Retrotransposon-induced mutations in grape skin color. Science 304 982. 

Vemeau, O., Catzeflis, F. and Furano, A. V. (1998) Determining and dating recent rodent speciation events by using LI (LINE-1) retrotransposons. Proc. Natl. Acad. Sd. U S A 95, 11284—9. 

Bachman N, Gelbart ME, Tsukiyama T, Boeke JD (2005) TFIIIB subunit Bdplp is required for periodic integration of the Tyl retrotransposon and targeting of isw2p to S. cerevisiae tDNAs. Genes Dev 19 955-964... 

Encoded by retrotransposons (residual viral genomes permanently maintained in human DNA) that play a role in amplifying certain repetitive sequences in DNA (see Chapter 7). 

Bourc his, D. and Bestor, T.H. (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature, 431, 96-99. 

Weichenrieder, O., Repanas, K. and Perrakis, A. (2004) Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon. Structure 12, 975-986. 

Kulkosky J, Jones KS, Katz RA, Mack JPG, Skalka AM. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol Cell Biol 1992 12 2331-2338. 

Some well-characterized eukaryotic DNA transposons from sources as diverse as yeast and fruit flies have a structure very similar to that of retroviruses these are sometimes called retrotransposons (Fig. 26-33). Retro-transposons encode an enzyme homologous to the retroviral reverse transcriptase, and their coding regions are flanked by LTR sequences. They transpose from one position to another in the cellular genome by means of an RNA intermediate, using reverse transcriptase to make a DNA copy of the RNA, followed by integration of the DNA at a new site. Most transposons in eukaryotes use this mechanism for transposition, distinguishing them from bacterial transposons, which move as DNA directly from one chromosomal location to another (see Fig. 25-43). 

Retrotransposons lack an env gene and so cannot form viral particles. They can be thought of as defective viruses, trapped in cells. Comparisons between retroviruses and eukaryotic transposons suggest that reverse transcriptase is an ancient enzyme that predates the evolution of multicellular organisms. 

Boeke, J.D. Devine, S.E. (1998) Yeast retrotransposons finding a nice, quiet neighborhood. Cell 93, 1087-1089. 

As described in Section B,l, mammalian DNA contains many retrotransposons (retroposons) that lie within short direct repeats characteristic of transposons. However, they contain a poly(A) tail at the 3 end, an indication of their relationship to RNA transcripts, and are discussed in Chapter 28. 

Transposition of DNA, which is discussed in Chapter 27, Section D,4, may seem to be a rare and relatively unimportant event in our body cells. However, transposon DNA accounts for 35% or more of the human genome740 and apparently plays a major role in evolution. Like other transposons, the DNA sequences known as retrotransposons also move about within DNA. However, they use an indirect mechanism that involves synthesis of mRNA and reverse transcription.740 741 The reverse transcribed complementary DNA may be inserted back into the genome at new locations. The necessary chemical reactions parallel those involved in the replication of retroviruses (Fig. 28-23, 28-24). Retrotransposens, truncated retrotransposons, and related sequences constitute as much as 16% of the human genome.741... 

There are two classes of retrotrotransposons those with long terminal repeats (LTRs) and those without (LTRs). The first group is closely related to retroviruses, but its members lack genes for envelope proteins. They do carry gag and pol genes similar to those of retroviruses (Fig. 28-3). Most retrotransposons are defective and do not move. Over evolutionary time they accumulate in the genome, sometimes to the extent that the genome size grows enormously. This... 

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

Bae, Y.A. and Kong, Y. (2003a) Divergent long-terminal-repeat retrotransposon families in the genome of Paragonimus westermani. Korean Journal of Parasitology 41, 221-231. 

Bae, Y.A., Moon, S.Y., Kong, Y., Cho, S.Y. and Rhyu, M.G. (2001) Csrnl, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retro-transposons. Molecular Biology and Evolution 1 8, 1474-1483. 

Copeland, C.S., Brindley, P.J., Heyers, O., Michael, S.F., Johnston, D.A., Williams, D.L., Ivens, A.C. and Kalinna, B.H. (2003) Boudicca, a retrovirus-like long terminal repeat retrotransposon from the genome of the human blood fluke Schistosoma mansoni. Journal of Virology 77, 6153-6166. 

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