Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1)

Gene

Volumn 465, Issue 1-2, 2010, Pages 9-16

  Bao, Weidong ^a   Jurka, Jerzy ^a  

^a Genetic Information Research Institute   (United States)

Author keywords

Evolution; HAL1; LINE 1; Non LTR retrotransposon

Indexed keywords

ARTICLE; DNA STRUCTURE; EVOLUTIONARY RATE; GENETIC CODE; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOME ANALYSIS; GUINEA PIG; LONG INTERSPERSED ELEMENT 1; MAMMALIAN GENETICS; MOLECULAR EVOLUTION; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; RETROPOSON;

ANIMALS; EVOLUTION, MOLECULAR; GUINEA PIGS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; OPEN READING FRAMES; PHYLOGENY; RETROELEMENTS; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

CAVIA; EUTHERIA; MAMMALIA; METATHERIA;

EID: 77955573664     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2010.06.005     Document Type: Article

References (41)

1. Adey N.B., Schichman S.A., Graham D.K., Peterson S.N., Edgell M.H., Hutchison C.A. Rodent L1 evolution has been driven by a single dominant lineage that has repeatedly acquired new transcriptional regulatory sequences. Mol. Biol. Evol. 1994, 11:778-789.
2. Bao Z., Eddy S.R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002, 12:1269-1276.
3. Basame S., Wai-lun Li P., Howard G., Branciforte D., Keller D., Martin S.L. Spatial assembly and RNA binding stoichiometry of a LINE-1 protein essential for retrotransposition. J. Mol. Biol. 2006, 357:351-357.
4. Belancio V.P., Hedges D.J., Deininger P. LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Res. 2006, 34:1512-1521.
5. Boissinot S., Furano A.V. Adaptive evolution in LINE-1 retrotransposons. Mol. Biol. Evol. 2001, 18:2186-2194.
6. Buzdin A., et al. The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic Acids Res. 2003, 31:4385-4390.
7. Buzdin A., Ustyugova S., Gogvadze E., Vinogradova T., Lebedev Y., Sverdlov E. A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3' terminus of l1. Genomics 2002, 80:402-406.
8. Dewannieux M., Esnault C., Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 2003, 35:41-48.
9. Esnault C., Maestre J., Heidmann T. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 2000, 24:363-367.
10. Feng Q., Moran J.V., Kazazian H.H., Boeke J.D. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 1996, 87:905-916.
11. Fieldhouse D., Yazdani F., Golding G.B. Substitution rate variation in closely related rodent species. Heredity 1997, 78(Pt 1):21-31.
12. Garcia-Perez J.L., Doucet A.J., Bucheton A., Moran J.V., Gilbert N. Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. Genome Res. 2007, 17:602-611.
13. Gilbert N., Lutz S., Morrish T.A., Moran J.V. Multiple fates of L1 retrotransposition intermediates in cultured human cells. Mol. Cell. Biol. 2005, 25:7780-7795.
14. Goodier J.L., Ostertag E.M., Du K., Kazazian H.H. A novel active L1 retrotransposon subfamily in the mouse. Genome Res. 2001, 11:1677-1685.
15. Hayward B.E., Zavanelli M., Furano A.V. Recombination creates novel L1 (LINE-1) elements in Rattus norvegicus. Genetics 1997, 146:641-654.
16. Hohjoh H., Singer M.F. Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. EMBO J. 1996, 15:630-639.
17. Hulme A.E., Bogerd H.P., Cullen B.R., Moran J.V. Selective inhibition of Alu retrotransposition by APOBEC3G. Gene 2007, 390:199-205.
18. Januszyk K., et al. Identification and solution structure of a highly conserved C-terminal domain within ORF1p required for retrotransposition of long interspersed nuclear element-1. J. Biol. Chem. 2007, 282:24893-24904.
19. Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:1872-1877.
20. Jurka J., Kapitonov V.V. Sectorial mutagenesis by transposable elements. Genetica 1999, 107:239-248.
21. Jurka J., Kapitonov V.V., Pavlicek A., Klonowski P., Kohany O., Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 2005, 110:462-467.
22. Kapitonov V.V., Tempel S., Jurka J. Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene 2009.
23. Khan H., Smit A., Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006, 16:78-87.
24. Khazina E., Weichenrieder O. Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:731-736.
25. Kulpa D.A., Moran J.V. Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition. Hum. Mol. Genet. 2005, 14:3237-3248.
26. Kulpa D.A., Moran J.V. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat. Struct. Mol. Biol. 2006, 13:655-660.
27. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
28. Larkin M.A., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
29. Luan D.D., Korman M.H., Jakubczak J.L., Eickbush T.H. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 1993, 72:595-605.
30. Martin S.L., et al. A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity. Nucleic Acids Res. 2008, 36:5845-5854.
31. Martin S.L., Bushman F.D. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol. Cell. Biol. 2001, 21:467-475.
32. Mathias S.L., Scott A.F., Kazazian H.H., Boeke J.D., Gabriel A. Reverse transcriptase encoded by a human transposable element. Science 1991, 254:1808-1810.
33. Moran J.V., Holmes S.E., Naas T.P., DeBerardinis R.J., Boeke J.D., Kazazian H.H. High frequency retrotransposition in cultured mammalian cells. Cell 1996, 87:917-927.
34. Naas T.P., et al. An actively retrotransposing, novel subfamily of mouse L1 elements. EMBO J. 1998, 17:590-597.
35. Ostertag E.M., Kazazian H.H. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res. 2001, 11:2059-2065.
36. Smit A.F. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 1999, 9:657-663.
37. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
38. Wallace N., Wagstaff B.J., Deininger P.L., Roy-Engel A.M. LINE-1 ORF1 protein enhances Alu SINE retrotransposition. Gene 2008, 419:1-6.
39. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
40. Wei W., et al. Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 2001, 21:1429-1439.
41. Zhang Z., Li J., Zhao X.Q., Wang J., Wong G.K., Yu J. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinform. 2006, 4:259-263.