Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Streva, Vincent A ^a,e   Jordan, Vallmer E ^b   Linker, Sara ^c   Hedges, Dale J ^d   Batzer, Mark A ^b   Deininger, Prescott L ^a  

^a TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^d OHIO STATE UNIVERSITY   (United States)

^e BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

High throughput sequencing; LINE1; Polymorphism; Retrotransposon

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE IDENTIFICATION; GENE INSERTION; GENE LIBRARY; GENE MAPPING; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMIC INSTABILITY; HUMAN; LONG INTERSPERSED REPEAT; MUTAGENESIS; NEXT GENERATION SEQUENCING; POLYMERASE CHAIN REACTION; RETROPOSON; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; VALIDATION PROCESS; ALLELE; CELL LINE; CHROMOSOMAL MAPPING; DNA SEQUENCE; FIBROBLAST; GENETIC ASSOCIATION STUDY; GENETIC POLYMORPHISM; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; METABOLISM; PROCEDURES;

ALLELES; CELL LINE; CHROMOSOME MAPPING; FIBROBLASTS; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84925869415     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1374-y     Document Type: Article

References (41)

1. de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011;7(12):e1002384.
2. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.
3. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110(1-4):462-7.
4. Boissinot S, Chevret P, Furano AV. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol. 2000;17(6):915-28.
5. Boissinot S, Furano AV. Adaptive evolution in LINE-1 retrotransposons. Mol Biol Evol. 2001;18(12):2186-94.
6. 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(1):78-87.
7. Kazazian Jr HH, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature. 1988;332(6160):164-6.
8. Skowronski J, Fanning TG, Singer MF. Unit-length line-1 transcripts in human teratocarcinoma cells. Mol Cell Biol. 1988;8(4):1385-97.
9. Salem AH, Myers JS, Otieno AC, Watkins WS, Jorde LB, Batzer MA. LINE-1 preTa elements in the human genome. J Mol Biol. 2003;326(4):1127-46.
10. Ovchinnikov I, Rubin A, Swergold GD. Tracing the LINEs of human evolution. Proc Natl Acad Sci U S A. 2002;99(16):10522-7.
11. Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, et al. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A. 2003;100(9):5280-5.
12. Myers JS, Vincent BJ, Udall H, Watkins WS, Morrish TA, Kilroy GE, et al. A comprehensive analysis of recently integrated human Ta L1 elements. Am J Hum Genet. 2002;71(2):312-26.
13. Lutz SM, Vincent BJ, Kazazian Jr HH, Batzer MA, Moran JV. Allelic heterogeneity in LINE-1 retrotransposition activity. Am J Hum Genet. 2003;73(6):1431-7.
14. Beck CR, Garcia-Perez JL, Badge RM, Moran JV. LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet. 2011;12:187-215.
15. Feng Q, Moran JV, Kazazian Jr HH, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell. 1996;87(5):905-16.
16. Mathias SL, Scott AF, Kazazian Jr HH, Boeke JD, Gabriel A. Reverse transcriptase encoded by a human transposable element. Science. 1991;254(5039):1808-10.
17. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell. 1993;72(4):595-605.
18. Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, et al. Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol. 2001;21(4):1429-39.
19. Scott AF, Schmeckpeper BJ, Abdelrazik M, Comey CT, O'Hara B, Rossiter JP, et al. Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence. Genomics. 1987;1(2):113-25.
20. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian Jr HH. High frequency retrotransposition in cultured mammalian cells. Cell. 1996;87(5):917-27.
21. Hardies SC, Martin SL, Voliva CF, Hutchison 3rd CA, Edgell MH. An analysis of replacement and synonymous changes in the rodent L1 repeat family. Mol Biol Evol. 1986;3(2):109-25.
22. Pascale E, Liu C, Valle E, Usdin K, Furano AV. The evolution of long interspersed repeated DNA (L1, LINE 1) as revealed by the analysis of an ancient rodent L1 DNA family. J Mol Evol. 1993;36(1):9-20.
23. Voliva CF, Jahn CL, Comer MB, Hutchison 3rd CA, Edgell MH. The L1Md long interspersed repeat family in the mouse: almost all examples are truncated at one end. Nucleic Acids Res. 1983;11(24):8847-59.
24. Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, et al. Somatic retrotransposition alters the genetic landscape of the human brain. Nature. 2011;479(7374):534-7.
25. Ewing AD, Kazazian Jr HH. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res. 2010;20(9):1262-70.
26. Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, et al. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell. 2010;141(7):1253-61.
27. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette 3rd LJ, et al. Landscape of Somatic Retrotransposition in Human Cancers. Science. 2012;337(6097):967-71.
28. Helman E, Lawrence ML, Stewart C, Sougnez C, Getz G, Meyerson M. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res. 2014;24(7):1053-63.
29. Pitkanen E, Cajuso T, Katainen R, Kaasinen E, Valimaki N, Palin K, et al. Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer. Oncotarget. 2014;5(3):853-9.
30. Tubio JM, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, et al. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014;345(6196):1251343.
31. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, et al. LINE-1 retrotransposition activity in human genomes. Cell. 2010;141(7):1159-70.
32. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods. 2008;5(12):1005-10.
33. Yuanxin Y, Chengcai A, Li L, Jiayu G, Guihong T, Zhangliang C. T-linker-specific ligation PCR (T-linker PCR): an advanced PCR technique for chromosome walking or for isolation of tagged DNA ends. Nucleic Acids Res. 2003;31(12):e68.
34. Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P. dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat. 2006;27(4):323-9.
35. Ewing AD, Kazazian Jr HH. Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. Genome Res. 2011;21(6):985-90.
36. Gilbert N, Lutz S, Morrish TA, Moran JV. Multiple fates of L1 retrotransposition intermediates in cultured human cells. Mol Cell Biol. 2005;25(17):7780-95.
37. Gilbert N, Lutz-Prigge S, Moran JV. Genomic deletions created upon LINE-1 retrotransposition. Cell. 2002;110(3):315-25.
38. Seleme MC, Vetter MR, Cordaux R, Bastone L, Batzer MA, Kazazian Jr HH. Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. Proc Natl Acad Sci U S A. 2006;103(17):6611-6.
39. Shukla R, Upton KR, Munoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell. 2013;153(1):101-11.
40. Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, et al. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res. 2012;22(12):2328-38.
41. Konkel MK, Wang J, Liang P, Batzer MA. Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene. 2007;390(1-2):28-38.