Genetic and epigenetic variations contributed by Alu retrotransposition

BMC Genomics

Volumn 12, Issue , 2011, Pages

  de Andrade, Alexandre ^a   Wang, Min ^a,b   Bonaldo, Maria F ^a,b   Xie, Hehuang ^a,b   Soares, Marcelo B ^a,b  

^a CHILDREN S MEMORIAL RESEARCH CENTER   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; CPG DINUCLEOTIDE; DINUCLEOTIDE; ORF2P PROTEIN; PROTEIN; TRANSLOCASE OF THE OUTER MITOCHONDRIAL MEMBRANE 5; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ALU SEQUENCE; ARTICLE; AT RICH SEQUENCE; CPG ISLAND; DNA FLANKING REGION; DNA METHYLATION; EPIGENETICS; GENE; GENE DUPLICATION; GENE INSERTION; GENE LOCUS; GENETIC VARIABILITY; HEMIZYGOSITY; HIGH THROUGHPUT BISULFITE SEQUENCING; HIGH THROUGHPUT SEQUENCING; HUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RETROPOSON; SEQUENCE ANALYSIS; TOMM5 GENE; GENETIC EPIGENESIS;

ALU ELEMENTS; BASE SEQUENCE; DNA METHYLATION; EPIGENESIS, GENETIC; GENETIC VARIATION; RETROELEMENTS;

EID: 83655197845     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-617     Document Type: Article

References (48)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921. 10.1038/35057062, 11237011.
2. Paolella G, Lucero MA, Murphy MH, Baralle FE. The Alu family repeat promoter has a tRNA-like bipartite structure. EMBO J 1983, 2(5):691-696. 555171, 16453450.
3. Weiner AM. An abundant cytoplasmic 7 S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 1980, 22(1 Pt 1):209-218.
4. Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die?. Genome Res 2009, 19(4):545-555. 10.1101/gr.089789.108, 2665774, 19273617.
5. Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 2003, 35(1):41-48. 10.1038/ng1223, 12897783.
6. Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. Comparative analysis of Alu repeats in primate genomes. Genome Res 2009, 19(5):876-885. 10.1101/gr.083972.108, 2675976, 19411604.
7. Batzer MA, Deininger PL, Hellmann-Blumberg U, Jurka J, Labuda D, Rubin CM, Schmid CW, Zietkiewicz E, Zuckerkandl E. Standardized nomenclature for Alu repeats. J Mol Evol 1996, 42(1):3-6. 10.1007/BF00163204, 8576960.
8. Chen JM, Stenson PD, Cooper DN, Ferec C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 2005, 117(5):411-427. 10.1007/s00439-005-1321-0, 15983781.
9. Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002, 3(5):370-379. 10.1038/nrg798, 11988762.
10. Roy AM, Carroll ML, Kass DH, Nguyen SV, Salem AH, Batzer MA, Deininger PL. Recently integrated human Alu repeats: finding needles in the haystack. Genetica 1999, 107(1-3):149-161.
11. Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD, Hoppens CL, Deininger PL. Structure and variability of recently inserted Alu family members. Nucleic Acids Res 1990, 18(23):6793-6798. 10.1093/nar/18.23.6793, 332733, 2175877.
12. Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. Active Alu retrotransposons in the human genome. Genome Res 2008, 18(12):1875-1883. 10.1101/gr.081737.108, 2593586, 18836035.
13. Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 2010, 141(7):1253-1261. 10.1016/j.cell.2010.05.020, 2943760, 20603005.
14. Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, Glass JL, Attreed M, Avner P, Wutz A, Barillot E, et al. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 2010, 141(6):956-969. 10.1016/j.cell.2010.04.042, 20550932.
15. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV. LINE-1 retrotransposition activity in human genomes. Cell 2010, 141(7):1159-1170. 10.1016/j.cell.2010.05.021, 3013285, 20602998.
16. Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, et al. Mobile elements create structural variation: analysis of a complete human genome. Genome Res 2009, 19(9):1516-1526. 10.1101/gr.091827.109, 2752133, 19439515.
17. Deininger PL, Batzer MA. Alu repeats and human disease. Mol Genet Metab 1999, 67(3):183-193. 10.1006/mgme.1999.2864, 10381326.
18. Kolomietz E, Meyn MS, Pandita A, Squire JA. The role of Alu repeat clusters as mediators of recurrent chromosomal aberrations in tumors. "Genes, Chromosomes and Cancer" 2002, 35(2):97-112.
19. Roy-Engel AM, El-Sawy M, Farooq L, Odom GL, Perepelitsa-Belancio V, Bruch H, Oyeniran OO, Deininger PL. Human retroelements may introduce intragenic polyadenylation signals. Cytogenet Genome Res 2005, 110(1-4):365-371. 10.1159/000084968, 16093688.
20. Callinan PA, Batzer MA. Retrotransposable elements and human disease. Genome Dyn 2006, 1:104-115.
21. Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M. Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet 2009, 25(2):63-66. 10.1016/j.tig.2008.11.005, 19101055.
22. Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N, Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, et al. Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci USA 2008, 105(11):4220-4225. 10.1073/pnas.0709398105, 2393765, 18334644.
23. Hewitt SM, Fraizer GC, Saunders GF. Transcriptional silencer of the Wilms' tumor gene WT1 contains an Alu repeat. J Biol Chem 1995, 270(30):17908-17912. 10.1074/jbc.270.30.17908, 7629096.
24. Wu J, Grindlay GJ, Bushel P, Mendelsohn L, Allan M. Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element. Mol Cell Biol 1990, 10(3):1209-1216. 360999, 2304465.
25. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008, 29(4):499-509. 10.1016/j.molcel.2007.12.013, 18313387.
26. Chu WM, Ballard R, Carpick BW, Williams BR, Schmid CW. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol 1998, 18(1):58-68. 121451, 9418853.
27. Tufarelli C, Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG, Higgs DR. Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet 2003, 34(2):157-165. 10.1038/ng1157, 12730694.
28. Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 1997, 13(8):335-340. 10.1016/S0168-9525(97)01181-5, 9260521.
29. Rodriguez J, Vives L, Jorda M, Morales C, Munoz M, Vendrell E, Peinado MA. Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells. Nucleic Acids Res 2008, 36(3):770-784. 2241897, 18084025.
30. Kochanek S, Renz D, Doerfler W. Transcriptional silencing of human Alu sequences and inhibition of protein binding in the box B regulatory elements by 5'-CG-3' methylation. FEBS Lett 1995, 360(2):115-120. 10.1016/0014-5793(95)00068-K, 7875314.
31. Xie H, Wang M, Bonaldo Mde F, Rajaram V, Stellpflug W, Smith C, Arndt K, Goldman S, Tomita T, Soares MB. Epigenomic analysis of Alu repeats in human ependymomas. Proc Natl Acad Sci USA 2010, 107(15):6952-6957. 10.1073/pnas.0913836107, 2872440, 20351280.
32. Xie H, Wang M, Bonaldo Mde F, Smith C, Rajaram V, Goldman S, Tomita T, Soares MB. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res 2009, 37(13):4331-4340. 10.1093/nar/gkp393, 2715246, 19458156.
33. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29(1):308-311. 10.1093/nar/29.1.308, 29783, 11125122.
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):323-329. 10.1002/humu.20307, 1855216, 16511833.
35. Roy-Engel AM, Salem AH, Oyeniran OO, Deininger L, Hedges DJ, Kilroy GE, Batzer MA, Deininger PL. Active Alu element "A-tails": size does matter. Genome Res 2002, 12(9):1333-1344. 10.1101/gr.384802, 186649, 12213770.
36. Feng Q, Moran JV, Kazazian HH, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 1996, 87(5):905-916. 10.1016/S0092-8674(00)81997-2, 8945517.
37. El-Sawy M, Deininger P. Tandem insertions of Alu elements. Cytogenet Genome Res 2005, 108(1-3):58-62. 10.1159/000080802, 15545716.
38. Hagan CR, Sheffield RF, Rudin CM. Human Alu element retrotransposition induced by genotoxic stress. Nat Genet 2003, 35(3):219-220. 10.1038/ng1259, 14578886.
39. Liu WM, Maraia RJ, Rubin CM, Schmid CW. Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res 1994, 22(6):1087-1095. 10.1093/nar/22.6.1087, 307934, 7512262.
40. Perez-Stable C, Shen CK. Competitive and cooperative functioning of the anterior and posterior promoter elements of an Alu family repeat. Mol Cell Biol 1986, 6(6):2041-2052. 367744, 3023916.
41. Lupski JR. Retrotransposition and structural variation in the human genome. Cell 2010, 141(7):1110-1112. 10.1016/j.cell.2010.06.014, 20602993.
42. Grover D, Mukerji M, Bhatnagar P, Kannan K, Brahmachari SK. Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics 2004, 20(6):813-817. 10.1093/bioinformatics/bth005, 14751968.
43. Deng G, Nguyen A, Tanaka H, Matsuzaki K, Bell I, Mehta KR, Terdiman JP, Waldman FM, Kakar S, Gum J, et al. Regional hypermethylation and global hypomethylation are associated with altered chromatin conformation and histone acetylation in colorectal cancer. Int J Cancer 2006, 118(12):2999-3005. 10.1002/ijc.21740, 16425274.
44. Roman-Gomez J, Jimenez-Velasco A, Agirre X, Castillejo JA, Navarro G, Garate L, Jose-Eneriz ES, Cordeu L, Barrios M, Prosper F, et al. Promoter hypermethylation and global hypomethylation are independent epigenetic events in lymphoid leukemogenesis with opposing effects on clinical outcome. Leukemia 2006, 20(8):1445-1448. 10.1038/sj.leu.2404257, 16688225.
45. Daskalos A, Nikolaidis G, Xinarianos G, Savvari P, Cassidy A, Zakopoulou R, Kotsinas A, Gorgoulis V, Field JK, Liloglou T. Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer. Int J Cancer 2009, 124(1):81-87. 10.1002/ijc.23849, 18823011.
46. Englander EW, Howard BH. Nucleosome positioning by human Alu elements in chromatin. J Biol Chem 1995, 270(17):10091-10096. 10.1074/jbc.270.17.10091, 7730313.
47. Tanaka Y, Yamashita R, Suzuki Y, Nakai K. Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics 11:309.
48. Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, et al. The UCSC genome browser database: update 2007. Nucleic Acids Res 2007, (35 Database):D668-673.