Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination

Gene

Volumn 390, Issue 1-2, 2007, Pages 206-213

  Song, Mingzhou ^a   Boissinot, Stéphane ^b,c  

^a New Mexico State University   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

^c CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Genome evolution; Human; L1 LINE 1; Recombination; Retrotransposon

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE; GENE REPLICATION; GENETIC ANALYSIS; GENETIC RECOMBINATION; GENETICS; GENOMICS; HUMAN; LONG INTERSPERSED REPEAT; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; RETROPOSON;

CHROMOSOMES, HUMAN; EVOLUTION, MOLECULAR; FEMALE; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MALE; MODELS, GENETIC; RECOMBINATION, GENETIC; SELECTION (GENETICS);

MAMMALIA;

EID: 33846972640     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.09.033     Document Type: Article

References (45)

1. Bartolome C., Maside X., and Charlesworth B. On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol. Biol. Evol. 19 (2002) 926-937
2. Biemont C., Tsitrone A., Vieira C., and Hoogland C. Transposable element distribution in Drosophila. Genetics 147 (1997) 1997-1999
3. Boissinot S., Chevret P., and Furano A.V. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17 (2000) 915-928
4. Boissinot S., Entezam A., and Furano A.V. Selection against deleterious LINE-1-containing loci in the human lineage. Mol. Biol. Evol. 18 (2001) 926-935
5. Boissinot S., Entezam A., Young L., Munson P.J., and Furano A.V. The insertional history of an active family of L1 retrotransposons in humans. Genome Res. 14 (2004) 1221-1231
6. Boissinot S., Davis J., Entezam A., Petrov D., and Furano A.V. Fitness cost of LINE-1 (L1) activity in humans. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 9590-9594
7. Burwinkel B., and Kilimann M.W. Unequal homologous recombination between LINE-1 elements as a mutational mechanism in human genetic disease. J. Mol. Biol. 277 (1998) 513-517
8. Charlesworth B., and Charlesworth D. The population dynamics of transposable elements. Genet. Res. 42 (1983) 1-27
9. Charlesworth B., and Langley C.H. The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23 (1989) 251-287
10. Charlesworth B., Lapid A., and Canada D. The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution. Genet. Res. 60 (1992) 103-114
11. Charlesworth B., Lapid A., and Canada D. The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. II. Inferences on the nature of selection against elements. Genet. Res. 60 (1992) 115-130
12. Charlesworth B., Sniegowski P.D., and Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371 (1994) 215-220
13. Charlesworth B., Langley C.H., and Sniegowski P.D. Transposable element distributions in Drosophila. Genetics 147 (1997) 1993-1995
14. C.S.A.C. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 (2005) 69-87
15. Cooper D.M., Schimenti K.J., and Schimenti J.C. Factors affecting ectopic gene conversion in mice. Mamm. Genome 9 (1998) 355-360
16. Dasilva C., et al. Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 13636-13641
17. Felsenstein J. The evolutionary advantage of recombination. Genetics 78 (1974) 737-756
18. Finnegan D.J. Transposable elements. Curr. Opin. Genet. Dev. 2 (1992) 861-867
19. Fullerton S.M., Bernardo Carvalho A., and Clark A.G. Local rate of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18 (2001) 1139-1142
20. Furano A.V., Duvernell D., and Boissinot S. L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet. 20 (2004) 9-14
21. Gasior S.L., Wakeman T.P., Xu B., and Deininger P.L. The Human LINE-1 retrotransposon creates DNA double-strand breaks. J. Mol. Biol. 357 (2006) 1383-1393
22. Han J.S., and Boeke J.D. LINE-1 retrotransposons: Modulators of quantity and quality of mammalian gene expression?. BioEssays 27 (2005) 775-784
23. Han J.S., Szak S.T., and Boeke J.D. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429 (2004) 268-274
24. Hasty P., Rivera-Perez J., and Bradley A. The length of homology required for gene targeting in embryonic stem cells. Mol. Cell. Biol. 11 (1991) 5586-5591
25. Hill W.G., and Robertson A. The effect of linkage on the limit to artificial selection. Genet. Res. 8 (1966) 269-294
26. Hoogland C., and Biemont C. Chromosomal distribution of transposable elements in Drosophila melanogaster: test of the ectopic recombination model for maintenance of insertion site number. Genetics 144 (1996) 197-204
27. Kazazian H.H. Mobile elements: drivers of genome evolution. Science 303 (2004) 1626-1632
28. Khan H., Smit A., and Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 16 (2006) 78-87
29. Kong A., et al. A high-resolution recombination map of the human genome. Nat. Genet. 31 (2002) 241-247
30. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
31. Langley C.H., Montgomery E., Hudson R., Kaplan N., and Charlesworth B. On the role of unequal exchange in the containment of transposable element copy number. Genet. Res. 52 (1988) 223-235
32. Martin S.L., Li W.-H.P., Furano A.V., and Boissinot S. The structures of mouse and human L1 elements reflect their insertion mechanism. Cytogenet. Genome Res. 110 (2005) 223-228
33. Myers J.S., et al. A comprehensive analysis of recently integrated human Ta L1 elements. Am. J. Hum. Genet. 71 (2002) 312-326
34. Myers S., Bottolo L., Freeman C., McVean G., and Donnelly P. A fine-scale map of recombination rates and hotspots across the human genome. Science 310 (2005) 321-324
35. Neafsey D.E., Blumenstiel J.P., and Hartl D.L. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies. Mol. Biol. Evol. 21 (2004) 2310-2318
36. Nuzhdin S.V. Sure facts, speculations, and open questions about the evolution of transposable elements copy number. Genetica 107 (1999) 129-137
37. Ostertag E.M., and Kazazian Jr. H.H. Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35 (2001) 501-538
38. Pasyukova E.G., Nuzhdin S.V., Morozova T.V., and Mackay T.F. Accumulation of transposable elements in the genome of Drosophila melanogaster is associated with a decrease in fitness. J. Heredity 95 (2004) 284-290
39. Perepelitsa-Belancio V., and Deininger P.L. RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat. Genet. 35 (2003) 363-366
40. Petrov D., Aminetzach Y.T., Davis J.C., Bensasson D., and Hirsh A.E. Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol. Biol. Evol. 20 (2003) 880-892
41. Segal Y., et al. LINE-1 elements at the sites of molecular rearrangements in Alport syndrome-diffuse leiomyomatosis. Am. J. Hum. Genet. 64 (1999) 62-69
42. Song M., and Haralick R.M. Optimally quantized and smoothed histograms. Proceedings of the Joint Conference of Information Sciences, Durham, NC, 2002 (2002) 894-897
43. Song M., Boissinot S., Haralick R.M., and Phillips I.T. Estimating recombination rate distribution by optimal quantization. Proceesings of IEEE Computational Systems Bioinformatics Conference, 2003 (2003) 403-406
44. R Development Core Team, 2004. R: A language and environment for statistical computing. In: computing, R.F.f.s. (Ed.). Austria, Vienna, 2004.
45. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562