euL1db: The European database of L1HS retrotransposon insertions in humans

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D43-D47

  Mir, Ashfaq A ^a   Philippe, Claude ^a   Cristofari, Gäel ^a  

^a UNIVERSITY OF NICE SOPHIA ANTIPOLIS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; DATA BASE; DNA SEQUENCE; EUL1DB DATABASE; GENE INSERTION; GENETIC POLYMORPHISM; PHENOTYPE; PRIORITY JOURNAL; RETROPOSON; SEQUENCE ANALYSIS; DISEASES; GENETICS; HUMAN; LONG INTERSPERSED REPEAT; NUCLEIC ACID DATABASE;

DATABASES, NUCLEIC ACID; DISEASE; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; PHENOTYPE; POLYMORPHISM, GENETIC;

EID: 84941135612     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1043     Document Type: Article

References (43)

1. Brouha, B., Schustak, J., Badge, R. M., Lutz-Prigge, S., Farley, A. H., Moran, J. V. and Kazazian, H. H. J. (2003) Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl. Acad. Sci. U. S. A., 100, 5280-5285.
2. Burns, K. H. and Boeke, J. D. (2012) Human transposon tectonics. Cell, 149, 740-752.
3. Hancks, D. C. and Kazazian, H. H. (2012) Active human retrotransposons: variation and disease. Curr. Opin. Genet. Dev., 22, 191-203.
4. Beck, C. R., Garcia-Perez, J. L., Badge, R. M. and Moran, J. V. (2011) LINE-1 elements in structural variation and disease. Annu. Rev. Genomics Hum. Genet., 12, 187-215.
5. Hohjoh, H. and Singer, M. F. (1997) Sequence-specific single-strand RNA binding protein encoded by the human LINE-1 retrotransposon. EMBO J., 16, 6034-6043.
6. Mathias, S. L., Scott, A. F., Kazazian, H. H., Boeke, J. D. and Gabriel, A. (1991) Reverse transcriptase encoded by a human transposable element. Science, 254, 1808-1810.
7. Feng, Q., Moran, J. V., Kazazian, H. H. and Boeke, J. D. (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell, 87, 905-916.
8. Kulpa, D. A. and Moran, J. V. (2006) Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat. Struct. Mol. Biol., 13, 655-660.
9. Doucet, A. J., Hulme, A. E., Sahinovic, E., Kulpa, D. A., Moldovan, J. B., Kopera, H. C., Athanikar, J. N., Hasnaoui, M., Bucheton, A. et al. (2010) Characterization of LINE-1 ribonucleoprotein particles. PLoS Genet., 6, e1001150.
10. Luan, D. D., Korman, M. H., Jakubczak, J. L. and Eickbush, T. H. (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell, 72, 595-605.
11. Cost, G. J., Feng, Q., Jacquier, A. and Boeke, J. D. (2002) Human L1 element target-primed reverse transcription in vitro. EMBO J., 21, 5899-5910.
12. Gilbert, N., Lutz-Prigge, S. and Moran, J. V. (2002) Genomic deletions created upon LINE-1 retrotransposition. Cell, 110, 315-325.
13. Symer, D. E., Connelly, C., Szak, S. T., Caputo, E. M., Cost, G. J., Parmigiani, G. and Boeke, J. D. (2002) Human l1 retrotransposition is associated with genetic instability in vivo. Cell, 110, 327-338.
14. Ostertag, E. M. and Kazazian, H. H. (2001) Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res., 11, 2059-2065.
15. Moran, J. V., De Berardinis, R. J. and Kazazian, H. H. J. (1999) Exon shuffling by L1 retrotransposition. Science, 283, 1530-1534.
16. Goodier, J. L., Ostertag, E. M. and Kazazian, H. H. (2000) Transduction of 3'-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet., 9, 653-657.
17. Repanas, K., Zingler, N., Layer, L. E., Schumann, G. G., Perrakis, A. and Weichenrieder, O. (2007) Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease. Nucleic Acids Res., 35, 4914-4926.
18. Monot, C., Kuciak, M., Viollet, S., Mir, A. A., Gabus, C., Darlix, J. L. and Cristofari, G. (2013) The specificity and flexibility of L1 reverse transcription priming at imperfect T-tracts. PLoS Genet., 9, e1003499.
19. Viollet, S., Monot, C. and Cristofari, G. (2014) L1 retrotransposition: the snap-velcro model and its consequences. Mob. Genet. Elem., 4, e28907.
20. O'Donnell, K. A. and Burns, K. H. (2010) Mobilizing diversity: transposable element insertions in genetic variation and disease. Mob. DNA, 1, 21.
21. Ray, D. A. and Batzer, M. A. (2011) Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res., 21, 813-820.
22. Ewing, A. D. and Kazazian, H. H. (2011) Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. Genome Res., 21, 985-990.
23. Stewart, C., Kural, D., Strömberg, M. P., Walker, J. A., Konkel, M. K., Stütz, A. M., Urban, A. E., Grubert, F., Lam, H. Y., Lee, W. P. et al. (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet., 7, e1002236.
24. Beck, C. R., Collier, P., Macfarlane, C., Malig, M., Kidd, J. M., Eichler, E. E., Badge, R. M. and Moran, J. V. (2010) LINE-1 retrotransposition activity in human genomes. Cell, 141, 1159-1170.
25. Huang, C. R., Schneider, A. M., Lu, Y., Niranjan, T., Shen, P., Robinson, M. A., Steranka, J. P., Valle, D., Civin, C. I., Wang, T. et al. (2010) Mobile interspersed repeats are major structural variants in the human genome. Cell, 141, 1171-1182.
26. Iskow, R. C., McCabe, M. T., Mills, R. E., Torene, S., Pittard, W. S., Neuwald, A. F., Van Meir, E. G., Vertino, P. M. and Devine, S. E. (2010) Natural mutagenesis of human genomes by endogenous retrotransposons. Cell, 141, 1253-1261.
27. Ewing, A. D. and Kazazian, H. H. (2010) High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res., 20, 1262-1270.
28. Kazazian, H. H., Wong, C., Youssoufian, H., Scott, A. F., Phillips, D. G. and Antonarakis, S. E. (1988) Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature, 332, 164-166.
29. Kaer, K. and Speek, M. (2013) Retroelements in human disease. Gene, 518, 231-241.
30. Coufal, N. G., Garcia-Perez, J. L., Peng, G. E., Yeo, G. W., Mu, Y., Lovci, M. T., Morell, M., O'Shea, K. S., Moran, J. V. and Gage, F. H. (2009) L1 retrotransposition in human neural progenitor cells. Nature, 460, 1127-1131.
31. Baillie, J. K., Barnett, M. W., Upton, K. R., Gerhardt, D. J., Richmond, T. A., De Sapio, F., Brennan, P. M., Rizzu, P., Smith, S., Fell, M. et al. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 479, 534-537.
32. Evrony, G. D., Cai, X., Lee, E., Hills, L. B., Elhosary, P. C., Lehmann, H. S., Parker, J. J., Atabay, K. D., Gilmore, E. C., Poduri, A. et al. (2012) Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell, 151, 483-496.
33. Shukla, R., Upton, K. R., Muñoz-Lopez, M., Gerhardt, D. J., Fisher, M. E., Nguyen, T., Brennan, P. M., Baillie, J. K., Collino, A., Ghisletti, S. et al. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell, 153, 101-111.
34. Solyom, S., Ewing, A. D., Rahrmann, E. P., Doucet, T., Nelson, H. H., Burns, M. B., Harris, R. S., Sigmon, D. F., Casella, A., Erlanger, B. et al. (2012) Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res., 22, 2328-2338.
35. Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J., Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K. et al. (2012) Landscape of somatic retrotransposition in human cancers. Science, 337, 967-971.
36. Miki, Y., Nishisho, I., Horii, A., Miyoshi, Y., Utsunomiya, J., Kinzler, K. W., Vogelstein, B. and Nakamura, Y. (1992) Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res., 52, 643-645.
37. Rodić, N. and Burns, K. H. (2013) Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms? PLoS Genet., 9, e1003402.
38. Goodier, J. L. (2014) Retrotransposition in tumors and brains. Mob. DNA, 5, 11.
39. Helman, E., Lawrence, M. S., Stewart, C., Sougnez, C., Getz, G. and Meyerson, M. (2014) Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res., 24, 1053-1063.
40. Karolchik, D., Barber, G. P., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) The UCSC genome browser database: 2014 update. Nucleic Acids Res., 42, D764-D770.
41. Lappalainen, I., Lopez, J., Skipper, L., Hefferon, T., Spalding, J. D., Garner, J., Chen, C., Maguire, M., Corbett, M., Zhou, G. et al. (2013) DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res., 41, D936-D941.
42. Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O. and Walichiewicz, J. (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res., 110, 462-467.
43. Wang, J., Song, L., Grover, D., Azrak, S., Batzer, M. A. and Liang, P. (2006) dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum. Mutat., 27, 323-329.