1887

Chapter 49 : Origins and Evolution of Retrotransposons

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Origins and Evolution of Retrotransposons, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap49-1.gif /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap49-2.gif

Abstract:

This chapter summarizes the similarities and differences of retrotransposons, as well as the phylogenetic relationships of the various elements that have been characterized from each of the two classes of retrotransposons. It discusses what can be inferred about the ages and origins of retroelements and their relationship to other cellular components. In the most unusual group of long terminal repeat (LTR), retrotransposons, complete elements have unusual inverted or split terminal repeats and do not encode an integrase. One of the most interesting aspects of the evolution of the LTR retrotransposons is their close relationship to retroviruses, caulimoviruses, and hepadnaviruses. The simplicity of the target-primed reverse transcription (TPRT) mechanism for inserting new copies appears to permit considerable structural flexibility in the evolution of different non-LTR retrotransposons. The authors suggest that it is more likely that the LTR retrotransposons evolved from the same lineages of eubacterial sequences as all other retroelements. They have attempted in this chapter to provide an overview of the diversity and mode of evolution of eukaryotic retrotransposable elements and to trace their origins back to prokaryotic sequences.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49

Key Concept Ranking

Group II Introns
0.5155855
Circular Double-Stranded DNA
0.4102811
Linear Double-Stranded DNA
0.40974334
0.5155855
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1.
Figure 1.

Retrotransposition mechanism of retroviruses and most LTR retrotransposons. Only the basic steps of this reaction are shown for comparison to that of the non-LTR retrotransposition mechanism ( Fig. 7 ). Thick lines, flanking chromosomal sequences; thin lines, element sequences with long terminal repeats (LTRs) indicated as boxed triangles. The RNA template (wavy line) used for protein translation and reverse transcription begins and ends within the LTR sequences. The sequences within these terminal repeats that are used by the reverse transcriptase to template jump between ends are indicated with smaller boxed triangles. First-strand DNA synthesis is primed by a tRNA annealed near the 5′ terminal repeat of the RNA (clover leaf), while second-strand synthesis is primed by an RNase H-resistant RNA near the 3′ terminal repeat (not shown). After formation in the cytoplasm of a linear DNA intermediate, the element-encoded integrase binds to termini of the intermediate, migrates to the nucleus, cleaves a target site on chromosomal DNA, and inserts the DNA intermediate in a reaction similar to that of DNA transposons. Finally, DNA repair fills in the gaps that had been generated by the staggered cut in the chromosome, generating a target-site duplication of uniform length for each element (small open triangles).

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Phylogeny of the LTR retrotransposons and related viruses, based on their reverse transcriptase domain. The portion of the reverse transcriptase domain of each element used in this analysis (approximately 250 residues) includes the seven blocks of conserved residues found in the finger and palm regions of all retroelements ( ), as well as an eighth block corresponding to part of the thumb region ( ). The phylogram is a 50% consensus tree of the elements based on the neighbor joining distance algorithms ( ) and is rooted using non-LTR retrotransposon sequences (not shown). Numbers adjacent to branch points indicate bootstrap values (percentage from 1,000 trials). The name of each published element is shown at the right of each branch along with either the common name, well-known genus name, or complete species identification of the host in which the element was found. The names of the four major groups of LTR retrotransposons are shown to the right of the figure and correspond to one or more of the first elements identified in the group (see text). Several elements of the DIRS and BEL clade have been obtained directly from sequence databases and have not been named. The phylogeny does not include all available elements in each group; rather, it represents only the diversity of elements known to date. Accession numbers for each element sequence, as well as analyses involving more comprehensive sets of elements, can be found in several previous reports ( ).

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

ORF structure of representative elements from each major group of LTR retrotransposons and of related viruses. The multiple ORFs of each element are indicated by the rectangular boxes, with boxes on different levels indicating ORFs in different reading frames or separated by termination codons. The three consensus ORFs found in all retroviruses () are shown, but additional small ORFs encoded by HIV are not indicated. Shaded regions indicate the enzymatic domains associated with the gene: RT, reverse transcriptase; RH, RNase H; IN, integrase; PR, protease. Vertical black bars within some or -like ORFs represent cysteine-histidine motifs believed to be associated with nucleic-acid binding domains. For the Ty3/copia, BEL, and Ty3/gypsy groups, two elements are shown, one with an -like ORF and one without an -like ORF.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4.
Figure 4.

Phylogeny of the LTR retrotransposons and related viruses based on their RH domain. The RH domain of each element is approximately 140 residues in length ( ). The phylogram is based on the neighbor-joining distance algorithms and is rooted using cellular RH sequences of eubacteria. Seven eukaryotic and seven eubacterial sequences selected to represent the diversity in each kingdom were used in the analysis, but individual branches have not been shown to conserve space. Also to conserve space, only a subset of the LTR retrotransposons used in Fig. 2 is presented. The species used and accession numbers can be found in reference 91. Numbers adjacent to branch points indicate bootstrap values (percentage from 1,000 trials). Also included in the phylogram are the RH domains found in non-LTR retrotransposons of the I group ( Fig. 8 and 9 ). Only the name of each published element is shown at the right of each branch, since the host species can be found in either Fig. 2 or 9 .

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5.
Figure 5.

Comparison of the integrase (IN) domain of LTR retrotransposons. Representative elements were selected to show the diversity of structure in each group. Members of the DIRS, hepadnavirus, and caulimovirus groups of elements shown in Fig. 2 do not appear to contain an IN domain ( Fig. 3 ). The IN domain represents the end of the ORF in most elements; however, it is followed by the RT domain in theTy1/copia group and by an -like domain in Cer13. All IN domains contain a cysteine-histidine motif (HH-CC) at the N-terminal end and three conserved acidic residues (aspartic [D] or glutamic [E]), which form the active site of the catalytic domain. Spacing between these acidic residues is similar in retrovirus and gypsy/Ty3 groups but is different in the BEL and Ty1/copia groups. In the C-terminal direction from these common IN regions, the proteins differ between groups and even among elements of the same group. Regions with sequence identity between members of the same group are shaded gray. C-terminal protein regions that are poorly conserved within a group are not shaded. In the case of the Ty3/gypsy and retrovirus groups, sequence similarity between groups can also be detected. This similarity includes a short region found in all elements and a longer region (identified as GPY/F) found in only some elements of each group ( ). The C-terminal end of some members of the Ty3/gypsygroup contains a chromodomainor, in the case of Ty3, a modified chromodomain ( ).

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6.
Figure 6.

Schematic of LTR retrotransposon evolution showing the nine instances in which the lineage has given rise to viruses or potential viruses. The figure shows only a summary of the phylogenetic relationships derived from the reverse transcriptase sequences of the seven groups of elements (the detailed phylogeny is shown in Fig. 2 ). The length and height of each triangle represent, respectively, the presumed age (based on the diversity) and abundance of each group. The nine instances where an LTR-retrotransposon lineage (gray lines and triangles) can be proposed to have assumed viral-like properties are indicated in black. In only four instances (hepadnaviruses, caulimoviruses, retroviruses, and gypsy elements) have the elements directly been shown to be viruses. In the five other instances, the lineage is assumed to have viral-like properties because of the acquisition of an -like ORF. In four cases, the evolutionary origin of the protein that enables (or presumably enables) the element to leave a cell has been traced to the indicated viral source. Adapted from reference 95.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7.
Figure 7.

Target-primed reverse transcription (TPRT) model for the integration of non-LTR retrotransposons. Most elements end in an A-rich or poly(A) 3′ end. Transcription is usually mediated by an internal promoter, which initiates RNA synthesis upstream of itself. However, some elements appear to be expressed as cotranscripts with host genes. Most of the information concerning the TPRT reaction is based on in vitro studies with the protein encoded by the R2 element ( ). This TPRT accounts for many of the integration properties of other non-LTR retrotransposons, but the degree to which this mechanism reflects that used by these different elements is not known. In the initial step of the integration reaction, an element encoded endonuclease cleaves the first (primer) strand of the target site and uses the released 3′ hydroxyl of the terminal nucleotide to prime reverse transcription starting within the poly(A) tail. Cleavage of the second (non-primer) strand occurs after reverse transcription. Thick lines, DNA target sequences; wavy lines, element RNA sequences; thin lines, element DNA sequences. The mechanism by which the 5′ end of the newly made cDNA is attached to the upstream target sequences is unclear, but it appears to be functionally equivalent to the reverse transcriptase simply jumping from the RNA template onto the DNA target. If this jump occurs before the reverse transcriptase reaches the end of the RNA template, a 5′ truncated copy is generated. The process of 5′ attachment generates considerable sequence variation at the junction of the element with the target site, even in the absence of 5′ truncations. The means by which the RNA is removed and the second strand of the element synthesized is not known. Non-LTR retrotransposons differ in whether they generate a target-site duplication and in whether that duplication is of a defined length.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8.
Figure 8.

Diagram of the ORF structure of five non-LTR retrotransposons selected to represent the diversity of structures found in this class of elements. ORFs are represented by rectangular boxes, with boxes at different levels indicating ORFs in different reading frames or separated by termination codons. Shaded regions indicate identified enzymatic domains: RT, reverse transcriptase; RH, RNase H; APE, apurinic-apyrimidinic endonuclease; EN, endonuclease. Vertical black bars represent cysteine-histidine motifs believed to be associated with nucleic-acid binding domains. These elements represent the first element to be characterized from each of the five major groups of non-LTR retrotransposons identified in Fig. 9 and Table 1 .

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 9.
Figure 9.

Phylogeny of the non-LTR retrotransposons based on their reverse transcriptase domain. This domain corresponds to approximately 440 amino acid residues as defined by Malik et al. ( ). The phylogeny is a 50% consensus tree of the elements using the neighbor-joining algorithms and is rooted with the reverse transcriptase sequences of the group II introns (not shown). Numbers at each node indicate bootstrap values (percentage of 1,000 trials). The name of each element and the host organism from which it was isolated are given to the right. The elements can be divided into distinct clades, with each clade named after one of the earliest elements described from that clade (intermediate size names to the right). The tree is similar to that previously reported ( ) except the addition of 13 new elements has defined three new clades. Individual, well-resolved clades or several clades containing elements with the same ORF structure have been placed into five groups (large names to the right). The elements within each group are delineated by the dotted horizontal lines. The basic structure of the elements in each group is shown in Fig. 8 .

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 10.
Figure 10.

Alternative explanations as to why the phylogeny of a mobile element can violate the phylogeny of the host species. In scenario A, the mobile element lineage separates into two independent lineages (solid and broken lines) that are differentially maintained in the four extant species. Species A, C, and D each retain one lineage, while both lineages are lost in species B. The elements in species A and C represent an orthologous lineage, while the elements in species C and D represent paralogous lineages. In scenario B, a single lineage of the mobile element is lost from the ancestor of species A and B and retained in species C and D. A horizontal transfer of the element from species C introduces the elements into species A. Either series of events (panels A and B) can explain why the elements isolated from species C are more closely related to the elements from the distant species A, rather than to the elements from the related species D. The best means to differentiate between these two explanations is to estimate the rate of sequence evolution of the element and then to determine whether it is the divergence of elements in species A and D or the divergence of elements in species D and C that is most consistent with this rate of evolution.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 11.
Figure 11.

Plot of sequence divergence versus age estimates of non-LTR retrotransposons. Divergence calculations are based on the amino acid sequence of the RT domain. Circles, comparisons between arthropod elements; squares, comparisons between vertebrate elements. The clade from which each comparison is made ( Fig. 9 and Table 1 ) is shown immediately adjacent to each data point (J, Jockey clade). The curves are average rates of divergence in arthropods (solid line) based on data from the R1 and R2 clades and in vertebrates (dotted lines) based on data from the L1 clade ( ). Most divergences are based on the entire RT domain; however, in some cases the divergences are based on ∼50% of this domain corrected to the complete RT domain using several outgroup comparisons. Divergence time estimates are described in reference 91.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 12.
Figure 12.

Schematic diagram of the unrooted phylogenetic tree of eukaryotic and prokaryotic retroelements. The phylogram is derived from the amino acid sequence of their encoded reverse transcriptase domain. Each group of retroelements is represented by a triangle, with the length of that triangle related to the sequence diversity with the group. The phylogenetic analysis is similar to those used in previous reports ( ), except that the regions of conserved sequences were not forced into blocks and an additional conserved region (segment 2A, reference ) was included ( ). The extensive sequence changes have resulted in a long branch length leading to the LTR retrotransposon lineage, suggesting that its position on the phylogeny is in question (see text). The arrow indicates where the branch leading to the RNA-directed RNA polymerases would be located on this tree of retroelement sequences. As described in the text, utilization of these RNA polymerases only identifies the most divergent branch of the phylogeny (mid-point roots) and thus is of limited value.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 13.
Figure 13.

Mosaic origin of the LTR retrotransposons. All mobile elements in eukaryotes are assumed to have descended from bacterial elements. The structure and function of eukaryotic DNA transposons are virtually identical to those in bacteria ( ). Non-LTR retrotransposons are suggested to have descended from a bacterial retroelement, probably a mobile group II intron. The origin of the LTR retrotransposons is postulated to have resulted from the fusion of these two original classes of mobile elements. The reverse transcriptase, RNase H, and -like proteins were derived from a non-LTR retrotransposon, and the integrase was derived from a transposon. The only other protein component of LTR retrotransposons is a protease, presumably derived from the host genome. This model for the origin of the LTR retrotransposons suggests a change in the nomenclature. The originally termed non-LTR retrotransposons (or LINEs) are referred to simply as retroposons. This term faithfully reflects the original use of the term ( ) as elements which are simple reverse transcription products of an RNA. We suggest the originally termed LTR-retrotransposons continue to be referred to as posons. This term accurately reflects the mosaic nature of their structure and integration mechanism as part poson and part poson.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817954.chap49
1. Aksoy, S.,, S. Williams,, S. Chang,, and F. F. Richards. 1990. SLACS retrotransposon from Trypanosoma brucei gambiense is similar to mammalian LINEs. Nucleic Acids Res. 18:785792.
2. Anzai, T.,, H. Takahashi,, and H. Fujiwara. 2001. Sequencespecific recognition and cleavage of Telomeric Repeat (TTAGG)n by Endonuclease of Non-Long Terminal Repeat Retrotransposon TRAS1. Mol. Cell. Biol. 21:100108.
3. Bateman, A.,, E. Birney,, R. Durbin,, S. R. Eddy,, R. D. Finn,, and E. L. L. Sonnhammer. 1999. Pfam 3.1: 1313 multiple alignments match the majority of proteins. Nucleic Acids Res. 27:260262.
4. Besansky, N. J. 1990. A retrotransposable element from the mosquito Anopheles gambiae. Mol. Cell. Biol. 10:863871.
5. Blumenthal, T. 1998. Gene clusters and polycistronic transcription in eukaryotes. Bioessays 20:480487.
6. Boeke, J. D.,, and V. G. Corces. 1989. Transcription and reverse transcription of retrotransposons. Annu. Rev. Microbiol. 43:403434.
7. Boeke, J. D.,, and S. E. Devine. 1998. Yeast retrotransposons: finding a nice quiet neighborhood. Cell 93:10871089.
8. Boeke, J. D.,, T. H. Eickbush,, S. B. Sandmeyer,, and D. F. Voytas,. 2000. Pseudoviridae, p. 349357. In M. H. V. van Regenmortel et al. (ed.), Virus Taxonomy: VIIth Report of the ICTV. Springer-Verlag, New York, N.Y..
9. Boeke, J. D.,, T. H. Eickbush,, S. B. Sandmeyer,, and D. F. Voytas,. 1999. Metaviridae, p. 359367. In M. H. V. van Regenmortel et al. (ed.), Virus Taxonomy: VIIth Report of the ICTV. Springer-Verlag, New York, N.Y..
10. Boeke, J. D.,, C. A. Garfinkel,, A. Styles,, and G. R. Fink. 1985. Ty elements transpose through an RNA intermediate. Cell 40:491500.
11. Boeke, J. D.,, and J. P. Stoye,. 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements, p. 343435. In J. M. Coffin, S. H. Hughes,, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
12. Bowen, N. J.,, and J. F. McDonald. 1999. Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral- like elements. Genome Res. 9:924935.
13. Britt, W. J.,, and M. Mach. 1996. Human cytomegalovirus glycoproteins. Intervirology 39:401412.
14. Britten, R. J. 1995. Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 92:599601.
15. Bucheton, A. 1990. I transposable elements and I-R hybrid dysgenesis in Drosophila. Trends Genet. 6:1621.
16. Burke, W. D.,, C. C. Calalang,, and T. H. Eickbush. 1987. The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme. Mol. Cell. Biol. 7:22212230.
17. Burke, W. D.,, H. S. Malik,, J. P. Jones,, and T. H. Eickbush. 1999. The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol. Biol. Evol. 16:502511.
18. Burke, W. D.,, H. S. Malik,, W. C. Lathe,, and T. H. Eickbush. 1998. Are retrotransposons long term hitchhikers? Nature 239:141142.
19.Reference deleted.
20. Cappello, J.,, K. Handelsman,, and H. Lodish. 1985. Sequence of Dictyostelium DIRS-1: an apparent retrotransposon with inverted terminal repeats and an internal circle junction sequence. Cell 43:105115.
21. Capy, P.,, C. Basin,, D. Higuet,, and T. Langin. 1998. Dynamics and Evolution of Transposable Elements. Springer-Verlag, New York, N.Y..
22. Cavalier-Smith, T. 1991. Intron phylogeny: a new hypothesis. Trends Genet. 7:145148.
23. Charlesworth, B.,, and C. H. Langley. 1989. The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23:251287.
24. Chaboissier, M. C.,, D. Finnegan,, and A. Bucheton. 2000. Retrotransposition of the I factor, a non-long terminal repeat retrotransposon of Drosophila, generates tandem repeats at the 3' end. Nucleic Acids Res. 28:24672472.
25. Christensen, S.,, G. Pont-Kingdom,, and D. Carroll. 2000. Target specificity of the endonuclease from the Xenopus laevis non-long terminal repeat retrotransposon, Tx1L. Mol. Cell. Biol. 20:12191226.
26. Coffin, J. M.,, S.H. Hughes,, and H. E. Varmus. 1997. Retroviruses. Cold Spring Harbor Laboratory Press, New York, N.Y..
27. Cook, J. M.,, J. Martin,, A. Lewin,, R. E. Sinden,, and M. Tristem. 2000. Systematic screening of Anopheles mosquito genomes yields evidence for a major clade of Pao-like retrotransposons. Insect. Mol. Biol. 9:109117.
28. Cousineau, B.,, S. Lawrence,, D. Smith,, and M. Belfort. 2000. Retrotransposition of a bacterial group II intron. Nature 404: 10181021.
29. Cousineau, B.,, D. Smith,, S. Lawrence-Cavanagh,, J. E. Mueller,, J. Yang,, D. Mills,, D. Manias,, G. Dunny,, A. M. Lambowitz,, and M. Belfort. 1998. Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination. Cell 94:451462.
30. Craig, N. L. 1995. Unity in transposition reactions. Science 270:253254.
31. Cummings, M. 1994. Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer. Trends Ecol. Evol. 9:141145.
32. Davies, D. R.,, I. Y. Goryshin,, W. S. Reznikoff,, and I. Rayment. 2000. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289:7785.
33. Davis, P. S.,, and B. H. Judd. 1995. Nucleotide sequence of the transposable element BEL of Drosophila melanogaster. Drosoph. Inf. Ser. 76:134136.
34. de Chastonay, Y.,, H. Felder,, C. Link,, P. Aeby,, H. Tobler,, and F. Müller. 1992. Unusual features of the retroid element PATfrom the nematode Panagrellus redivivus. Nucleic Acids Res. 20:16231628.
35. Desset, S.,, C. Conte,, P. Dimitri,, V. Calco,, B. Dastugue,, and C. Vaury. 1999. Mobilization of two retroelements, ZAM and Idefix, in a novel unstable line of Drosophila melanogaster. Mol. Biol. Evol. 16:5466.
36. Doak, T. G.,, F. P. Doerder,, C. L. Jahn,, and G. Herrick. 1994. A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common “D35E” motif. Proc. Natl. Acad. Sci. USA 91:942946.
37. Doolittle, R. F.,, D. F. Feng,, M. S. Johnson,, and M. A. Mc- Clure. 1989. Origins and evolutionary relationships of retroviruses. Q. Rev. Biol. 64:130.
38. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:21242128.
39. Drew, A. C.,, and P. J. Brindley. 1997. A retrotransposon of the non-long terminal repeat class from the human blood fluke Schistosoma mansoni. Similarities with the chicken repeat 1-like elements from vertebrates. Mol. Biol. Evol. 14: 602610.
40. Eickbush, T. H. 1992. Transposing without ends: the non- LTR retrotransposable elements. New Biol. 4:430440.
41. Eickbush, T. H., 1994. Origin and evolutionary relationships of retroelements, p. 121157. In S. S. Morse (ed.), The Evolutionary Biology of Viruses. Raven Press, New York, N.Y..
42. Eickbush, T. H. 1997. Telomerase and retrotransposons: which came first? Science 277:911912.
43. Eickbush, D. G.,, and T. H. Eickbush. 1995. Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics 139:671684.
44. Eickbush, D. G.,, W. D. Lathe,, M. P. Francino,, and T. H. Eickbush. 1995. R1 and R2 retrotransposable elements of Drosophila evolve at rates similar to that of nuclear genes. Genetics 139:685695.
45. Engelman, A.,, A. B. Hickman,, and R. Craigie. 1994. The core and carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to nonspecific DNA binding. J. Virol. 68:59115917.
46.Eskes R., J. Yang, A. M. Lambowitz, and P. S. Perlman. 1997. Mobility of yeast mitochondrial group II introns: engineering a new site specificity and retrohoming via full reverse splicing. Cell 88:865874.
47. Esnault, C.,, J. Maestre,, and T. Heidmann. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24:363367.
48. Fawcett, D. H.,, C. K. Lister,, E. Kellett,, and D. J. Finnegan. 1986. Transposable elements controlling I-R hybrid dysgenesis in D. melanogaster are similar to mammalian LINEs. Cell 47:10071015.
49. Fayet, O.,, P. Raymond,, P. Polard,, M. F. Prere,, and M. Chandler. 1990. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? Mol. Microbiol. 4:17711777.
50. Felder, H.,, A. Herzceg,, Y. de Chastonay,, P. Aeby,, H. Tobler,, and F. Müller. 1994. Tas, a retrotransposon from the parasitic nematode Ascaris lumbricoides. Gene 149:219225.
51. Feng, Q.,, J. V. Moran,, H. H. Kazazian,, and J. D. Boeke. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87:905916.
52. Feng, Q.,, G. Schumann,, and J. D. Boeke. 1998. Retrotransposon R1Bm endonuclease cleaves the target sequence. Proc. Natl. Acad. Sci. USA 95:20832088.
53. Finnegan, D. J., 1989. The I factor and I-R hybrid dysgenesis in Drosophila melanogaster, p. 503517. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C..
54. Flavell, A. J.,, V. Jackson,, M. P. Iqbal,, I. Riach,, and S. Waddell. 1995. Ty1-copia group retrotransposon sequences in amphibia and reptilia. Mol. Gen. Genet. 246:6571.
55. Friesen, P. D.,, and M. S. Nissen. 1990. Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome. Mol. Cell. Biol. 10: 30673077.
56. Gabriel, A.,, T. J. Yen,, D. C. Schwartz,, C. L. Smith,, J. D. Boeke,, B. Sollner-Webb,, and D. W. Cleveland. 1990. A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata. Mol. Cell. Biol. 10:615624.
57. Ganem, D.,, and H. E. Varmus. 1987. The molecular biology of the hepatitis B viruses. Annu. Rev. Biochem. 56:651693.
58. Garfinkel, D. J.,, J. D. Boeke,, and G. R. Fink. 1985. Ty element transposition: reverse transcriptase and virus-like particles. Cell 42:507517.
59. Garrett, J.,, D. S. Knutzon,, and D. Carroll. 1989. Composite transposable elements in the Xenopus laevis genome. Mol. Cell. Biol. 9:30183027.
60. Gonzalez, P.,, and H. A. Lessios. 1999. Evolution of sea urchin retroviral-like (SURL) elements: evidence from 40 echinoid species. Mol. Biol. Evol. 16:938952.
61. Gorbalenya, A. E. 1994. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci. 3:11171120.
62. Hansen, L. J.,, D. L. Chalker,, and S. B. Sandmeyer. 1988. Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses. Mol. Cell. Biol. 8: 52455256.
63. Hansen, J. L.,, A. M. Long,, and S. C. Schultz. 1997. Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:11091122.
64. Hardies, S. C.,, C. H. Martin,, C. F. Voliva,, C. A. Hutchinson,, and M. H. Edgell. 1986. An analysis of replacement and synonymous changes in the rodent L1 repeat family. Mol. Biol. Evol. 3:109125.
65. Hartl, D. L.,, A. R. Lohe,, and E. R. Lozovskya. 1997. Modern thoughts on an ancyent marinere: function, evolution, regulation. Annu. Rev. Genet. 31:337358.
66. Hattori, M.,, S. Kuhara,, O. Takenaka,, and Y. Sakaki. 1986. L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein. Nature 321:625628.
67. Higashiyama, T.,, Y. Noutoshi,, M. Fujie,, and T. Yamada. 1997. Zepp, a LINE-like retrotransposon accumulated in the Chorella telomeric region. EMBO J. 16:37153723.
68. Hohjoh, H.,, and M. F. Singer. 1997. Sequence-specific single-stranded RNA binding protein encoded by the human LINE- 1 protein and RNA. EMBO J. 15:630639.
69. Inouye, S.,, and M. Inouye. 1993. The retron: a bacterial retroelement required for the synthesis of msDNA. Curr. Opin. Genet. Dev. 3:713718.
70. Jensen, S.,, and T. Heidmann. 1991. An indicator gene for detection of germline retrotransposition in transgenic Drosophila demonstrates RNA-mediated transposition of the LINE I element. EMBO J. 10:19271937.
71. Jordan, I. K.,, L. V. Matyunia,, and J. F. McDonald. 1999. Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proc. Natl. Acad. Sci. USA 96: 1262112625.
72. Kajikawa, M.,, K. Ohshima,, and N. Okada. 1997. Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. Mol. Biol. Evol. 14:12061217.
73. Kazazian, H. H.,, and J. V. Moran. 1998. The impact of L1 retrotransposition on the human genome. Nat. Genet. 19: 1924.
74. Khan, E.,, J. P. Mack,, R. A. Katz,, J. Kulkosky,, and A. M. Skalka. 1991. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res. 19:851860.
75. Kim, J. M.,, S. Vanguri,, J. D. Boeke,, A. Gabriel,, and D. F. Voytas. 1998. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8:464478.
76. Kimmel, B. E.,, O. K. Ole-Moiyoi,, and J. R. Young. 1987. Ingi, a 5.2-kilobase dispersed sequence element from Trypanosoma brucei that carries half a smaller mobile element at their end and has homology with mammalian LINEs. Mol. Cell. Biol. 7:14651475.
77. Kohlstaedt, L. A.,, J. Wang,, J. M. Friedman,, P. A. Rice,, and T. A. Steitz. 1992. Crystal structure at 3.5 angstrom resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:17831790.
78. Koonin, E. V.,, A. R. Mushegian,, E. V. Ryabov,, and V. V. Dolja. 1991. Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity. J. Gen. Virol. 72:28952903.
79. Kordis, D.,, and F. Gusenbek. 1998. Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc. Natl. Acad. Sci. USA 95: 1070410709.
80. Kulkosky, J.,, K. S. Jones,, R. A. Katz,, J. P. G. Mack,, and A. M. Skalka. 1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and the bacterial insertion sequence transposases. Mol. Cell. Biol. 12:23312338.
81. Kuzio, J.,, M. N. Pearson,, S. H. Harwood,, C. J. Funk,, J. T. Evans,, J. M. Slavicek,, and G. F. Rohrmann. 1999. Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology 253:1734.
82. Lambowitz, A. M.,, M. G. Caprara,, S. Zimmerly,, and P. S. Perlman. 1999. Group I and group II ribozymes as RNPs: clues to the past and guides to the future, p. 451485. The RNA World II. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y..
83. Laten, H. M.,, A. Majumdar,, and E. A. Gaucher. 1998. SIRE- 1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein. Proc. Natl. Acad. Sci. USA 95: 68976902.
84. Lathe, W. C.,, W. D. Burke,, and T. H. Eickbush. 1995. Evolutionary stability of the R1 retrotransposable element in the genus Drosophila. Mol. Biol. Evol. 12:10941105.
85. Lathe, W. C., III, and T. H. Eickbush. 1997. A single lineage of R2 retrotransposable elements is an active, evolutionarily stable component of the Drosophila rDNA locus. Mol. Biol. Evol. 14:12321241.
86. Lerat, E.,, and P. Capy. 1999. Retrotransposons and retroviruses: analysis of the envelope gene. Mol. Biol. Evol. 16: 11981207.
87. Li, W. H. 1993. So, what about the molecular clock hypothesis? Curr. Opin. Genet. Dev. 3:896901.
88. Lockhart, B. E.,, J. Menke,, G. Dahal,, and N. E. Olszewski. 2000. Characterization and genomic analysis of tobacco vein clearing virus, a plant pararetrovirus that is transmitted vertically and related to sequences integrated in the host genome. J. Gen. Virol. 81:15791585.
89. Loeb, D. D.,, R. W. Padgett,, S. C. Hardies,, W. R. Shehee,, M. B. Comer,, M. H. Edgell,, and C. A. Hutchison III. 1986. The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons. Mol. Cell. Biol. 6:168182.
90. Luan, D. D.,, and T. H. Eickbush. 1995. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol. Cell. Biol. 15: 38823891.
91. Luan, D. D.,, and T. H. Eickbush. 1996. Downstream 28S gene sequences on the RNA template affect the choice of primer and the accuracy of initiation by the R2 reverse transcriptase. Mol. Cell. Biol. 16:47264734.
92. Luan, D. D.,, M. H. Korman,, J. L. Jakubczak,, and T. H. Eickbush. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72:595605.
93. Malik, H. S.,, W. D. Burke,, and T. H. Eickbush. 1999. The age and evolution of non-LTR retrotransposable elements. Mol. Biol. Evol. 16:793805.
94. Malik, H. S.,, and T. H. Eickbush. 1999. The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol. Biol. Evol. 15: 11231134.
95. Malik, H. S.,, and T. H. Eickbush. 1999. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J. Virol. 73:51865190.
96. Malik, H. S.,, and T. H. Eickbush. 2000. NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans. Genetics 154:193203.
97. Malik, H. S.,, and T. H. Eickbush. 2001. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 11:11871197.
98. Malik, H. S.,, S. Henikoff,, and T. H. Eickbush. 2000. Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res. 10:13071318.
99. Marin, I.,, and C. Llorens. 2000. Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol. Biol. Evol. 17:10401049.
100. Marin, I.,, P. Plata-Rengifo,, M. Labrador,, and A. Fontdevila. 1998. Evolutionary relationships among the members of an ancient class on non-LTR retrotransposons found in the nematode Caenorhabditis elegans. Mol. Biol. Evol. 15: 13901402.
101. Marlor, R.,, S. Parkhurst,, and V. Corces. 1986. The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins. Mol. Cell. Biol. 6:11291134.
102. Martin, F.,, C. Maranon,, M. Olivares,, C. Alonso,, and M. C. Lopez. 1995. Characterization of a non-long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: homology of the first ORF with the Ape family of DNA repair enzymes. J. Mol. Biol. 247:4959.
103. Martin, S. L. 1991. LINEs. Curr. Opin. Genet. Dev. 1: 505508.
104. McClure, M. A. 1991. Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol. Biol. Evol. 8: 835856.
105. Michel, F.,, and J.-L. Ferat. 1995. Structure and activities of group II introns. Annu. Rev. Biochem. 64:435461.
106. Mizrokhi, L. J.,, S. G. Georgieva,, and Y. V. Ilyin. 1988. Jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promoter by RNA polymerase II. Cell 54:685691.
107. Mizrokhi, L. J.,, and A. M. Mazo. 1990. Evidence for horizontal transmission of the mobile element jockey between distant Drosophila species. Proc. Natl. Acad. Sci. USA 86: 92169220.
108. Mizuuchi, K. 1992. Transpositional recombination: mechanistic insights from studies of mu and other elements. Annu. Rev. Biochem. 61:10111051.
109. Moran, J. V.,, S. E. Holmes,, T. P. Naas,, R. J. DeBerardinis,, J. D. Boeke,, and H. H. Kazazian. 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87:917927.
110. Mount, S. M.,, and G. M. Rubin. 1985. Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol. Cell. Biol. 5:16301638.
111. Nakamura, T. M.,, and T. R. Cech. 1998. Reversing time: origin of telomerase. Cell 92:587600.
112. Nakamura, T. M.,, G. B. Morin,, K. B. Chapman,, S. L. Weinrich,, W. H. Andrews,, L. Lingner,, C. B. Harley,, and T. R. Cech. 1997. Telomerase catalytic subunit homologs from fission yeast and human. Science 277:955959.
113. Okada, N.,, and M. Hamada. 1997. The 3' ends of tRNA-derived SINEs originated from the 3' ends of LINEs: a example from the bovine genome. J. Mol. Evol. 44:S52S56.
114. Okada, N.,, M. Hamada,, I. Ogiwara,, and K. Ohshima. 1997. SINEs and LINEs share common 3' sequences: a review. Gene 205:229243.
115. Okazaki, S.,, H. Ishikawa,, and H. Fujiwara. 1995. Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori. Mol. Cell. Biol. 15:45454552.
116. Palmer, J. D.,, and J. M. Logsdon, Jr. 1991. The recent origins of introns. Curr. Opin. Genet. Dev. 1:470477.
117. Pantazidis, A.,, M. Labrador,, and A. Fontdevila. 1999. The retrotransposon Osvaldo from Drosophila buzzatii displays all structural features of a functional retrovirus. Mol. Biol. Evol. 16:909921.
118. Pelisson, A.,, D. J. Finnegan,, and A. Bucheton. 1991. Evidence for retrotransposition of the I factor, a LINE element of Dro sophila melanogaster. Proc. Natl. Acad. Sci. USA 88: 49074910.
119. Peterson-Burch, B. D.,, D. A. Wright,, H. M. Laten,, and D. F. Voytas. 2000. Retroviruses in plants? Trends Genet. 14: 151152.
120. Petrov, D. A.,, E. L. Lozovskaya,, and D. L. Hartl. 1996. High intrinsic rate of DNA loss in Drosophila. Nature 384: 346349.
121. Pfeiffer, P.,, and T. Hohn. 1983. Involvement of reverse transcription in the replication of cauliflower mosaic virus: a detailed model and test of some aspects. Cell 33:781789.
122. Richert-Poggeler, K. R.,, and R. J. Shepherd. 1997. Petunia vein-clearing virus: a plant pararetrovirus with the core sequences for an integrase function. Virology 236:137146.
123. Robertson, H. M. 1993. The mariner transposable element is widespread in insects. Nature 362:241245.
124. Rogers, J. 1985. The origin and evolution of retroposons. Int. Rev. Cytol. 93:187279.
125. SanMiguel, P.,, B. S. Gaut,, A. Tiknonov,, Y. Nakajima,, and J. L. Bennetzen. 1998. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20:4345.
126. Saitou, N.,, and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406425.
127. Schwarz-Sommer, Z.,, L. Leclercq,, E. Gobel,, and H. Saedler. 1987. Cin4, an insert altering the structure of the A1 gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 6:38733880.
128. Shub, D. A.,, H. Goodrich-Blair,, and S. R. Eddy. 1994. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci. 19:402406.
129. Seleme, M.-D. C.,, I. Busseau,, S. Malinsky,, A. Bucheton,, and D. Teninges. 1999. High-frequency retrotransposition of a marked I factor in Drosophila melanogaster correlates with a dynamic expression pattern of the ORF1 protein in the cytoplasm of oocytes. Genetics 151:761771.
130. Sheen, F. M.,, and R. W. Levis. 1994. Transposition of the LINE-like retrotransposon TART to Drosophila chromosome termini. Proc. Natl. Acad. Sci. USA 91:1251012514.
131. Shiba, T.,, and K. Saigo. 1983. Retrovirus-like particles containing RNA homologous to the transposable element copia in Drosophila melanogaster. Nature 302:119124.
132. Singer, M. F.,, and J. Skowronski. 1985. Making sense out of LINEs: long interspersed repeat sequences in mammalian genomes. Trends Biochem. Sci. 10:119122.
133. Smit, A. F. 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6:743748.
134. Smit, A. F. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9:657663.
135. Song, S. U.,, T. Gerasimova,, M. Kurkulos,, J. D. Boeke,, and V. G. Corces. 1994. An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes Dev. 8:20462057.
136. Springer, M. S.,, N. A. Tusneem,, E. H. Davidson,, and R. J. Britten. 1995. Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer. Mol. Biol. Evol. 12:219230.
137. Swergold, G. D. 1990. Identification, characterization, and cell specificity of a human LINE-1 promoter. Mol. Cell. Biol. 10:67186729.
138. Szafranski, K.,, G. Glockner,, T. Dingermann,, K. Dannat,, A. A. Noegel,, L. Eichinger,, A. Rosenthal,, and T. Winckler. 1999. Non-LTR retrotransposons with unique integration preferences downstream of Dictyostelium discoideum tRNA genes. Mol. Gen. Genet. 262:772780.
139. Szemraj, J.,, G. Plucienniczak,, J. Jaworski,, and A. Plucienniczak. 1995. Bovine Alu-like sequences mediate transposition of a new site-specific retroelement. Gene 152:261264.
140. Takahashi, H.,, S. Okazaki,, and H. Fujiwara. 1997. A new family of site-specific retrotransposons, SART1, is inserted into telomeric repeats of the silkworm, Bombyx mori. Nucleic Acids Res. 25:15781584.
141. Takeya, T.,, H. Hanafusa,, R. P. Junghans,, G. Ju,, and A. M. Skalka. 1981. Comparison between the viral transforming gene (src) of recovered avian sarcoma virus and its cellular homolog. Mol. Cell. Biol. 1:10241037.
142. Temin, H. M. 1989. Retrons in bacteria. Nature 339: 254255.
143. Terzian, C.,, C. Ferraz,, J. Demaille,, and A. Bucheton. 2000. Evolution of the Gypsy endogenous retrovirus in the Drosophila melanogaster subgroup. Mol. Biol. Evol. 17:908914.
144.Tessier L. H., M. Keller, R. L. Chan, R. Fournier, J. H. Weil, and P. Imbault. 1991. Short leader sequences may be transferred from small RNAs to pre-mature mRNAs by trans-splicing in Euglena. EMBO J. 10:26212625.
145. Trelogan, S. A.,, and S. L. Martin. 1995. Tightly regulated, developmentally specific expression of the first open reading frame from LINE-1 during mouse embryogenesis. Proc. Natl. Acad. Sci. USA 92:15201524.
146. Usdin, K.,, P. Chevret,, F. M. Catzeflis,, R. Verona,, and A. V. Furano. 1995. L1 (LINE-1) retrotransposable elements provide a “fossil” record of the phylogenetic history of murid rodents. Mol. Biol. Evol. 12:7382.
147. Varmus, H.,, and P. Brown,. 1989. Retroviruses, p. 53108. In D. E. Berg, and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C..
148. Vazquez-Manrique, R. P.,, M. Hernandez,, M. J. Martinez- Sebastian,, and R. de Frutos. 2000. Evolution of gypsy endogenous retroviruses in the Drosophila obscura species group. Mol. Biol. Evol. 17:11851193.
149. Verneau, O.,, F. Catzeflis,, and A. V. Furano. 1998. Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons. Proc. Natl. Acad. Sci. USA 95: 1128411289.
150. Volff, J.-N.,, C. Korting,, and M. Schartl. 2000. Multiple lineages of the non-LTR retrotransposon Rex1 with various success in invading fish genomes. Mol. Biol. Evol. 17: 16731684.
151. Voliva, C. F.,, S. L. Martin,, C. A. Hutchison III,, and M. H. Edgell. 1984. Dispersal process associated with the L1 family of interspersed repetitive DNA sequences. J. Mol. Biol. 178: 795813.
152. Voytas, D. F.,, and F. M. Ausubel. 1988. A copia-like transposable element family in Arabidopsis thaliana. Nature 336: 242244.
153. Wang, G.-H.,, and C. Seeger. 1992. The reverse transcriptase of hepatitis B virus acts as a primer for viral DNA synthesis. Cell 71:663670.
154. Wang, H.,, and A. M. Lambowitz. 1993. The Mauriceville plasmid reverse transcriptase can initiate cDNA synthesis de novo and may be related to reverse transcriptase and DNA polymerase progenitor. Cell 75:10711081.
155. Wank, H.,, J. SanFilippo,, R. N. Singh,, M. Matsuura,, and A. M. Lambowitz. 1999. A reverse-transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA. Mol. Cell. 4:239250.
156. Wei, W.,, N. Gilbert,, S. L. Ooi,, J. F. Lawler,, E. M. Ostertag,, H. H. Kazazian,, J. D. Boeke,, and J. V. Moran. 2001. Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 21:14291439.
157. Weiner, A. M.,, P. L. Deininger,, and A. Efstratiadis. 1986. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55:631661.
158. Wright, D. A.,, and D. F. Voytas. 1998. Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. Genetics 149:703715.
159. Xiong, Y.,, and T. H. Eickbush. 1988. Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol. Biol. Evol. 5: 675690.
160. Xiong, Y.,, and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9:33533362.
161. Xiong, Y.,, W. D. Burke,, and T. H. Eickbush. 1993. Pao, a highly divergent retrotransposable element from Bombyx mori containing long terminal repeats with tandem copies of the putative R region. Nucleic Acids Res. 21:21172123.
162. Xiong, Y.,, and T. H. Eickbush. 1993. Dong, a new non-long terminal repeat (non-LTR) retrotransposable element from Bombyx mori. Nucleic Acids Res. 21:1318.
163. Yang, J.,, and T. H. Eickbush. 1998. RNA-induced changes in the activity of the endonuclease encoded by the R2 retrotransposable element. Mol. Cell. Biol. 18:34553465.
164. Yang, J.,, H. S. Malik,, and T. H. Eickbush. 1999. Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc. Natl. Acad. Sci. USA 96:78477852.
165. Yang, J.,, G. Mohr,, P. S. Perlman,, and A. M. Lambowitz. 1998. Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity in aI1 and reverse splicing into DNA transposition sites in vitro. J. Mol. Biol. 282:505523.
166. Zimmerly, S.,, H. Guo,, P. S. Perlman,, and A. M. Lambowitz. 1995. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82:110.
167. Zimmerly, S.,, H. Guo,, R. Eskes,, J. Yang,, P. S. Perlman,, and A. M. Lambowitz. 1995. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83:529538.

Tables

Generic image for table
Table 1.

Classification of non-LTR retrotransposons

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error