Alu distribution and mutation types of cancer genes

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Zhang, Wensheng ^a   Edwards, Andrea ^a   Fan, Wei ^b   Deininger, Prescott ^c   Zhang, Kun ^a  

^a XAVIER UNIVERSITY OF LOUISIANA   (United States)

^b IBM T J WATSON RESEARCH CENTER   (United States)

^c TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALU SEQUENCE; ARTICLE; CARCINOGENESIS; EXON; GENE INSERTION SEQUENCE; GENE MUTATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC MODEL; INTRON; MULTIVARIATE ANALYSIS; REGRESSION ANALYSIS; TUMOR GENE; CLUSTER ANALYSIS; GENETICS; HUMAN; HUMAN GENOME; METHODOLOGY; MUTATION; NEOPLASM; NUCLEOTIDE SEQUENCE; RECESSIVE GENE; STATISTICAL MODEL;

ALU ELEMENTS; CLUSTER ANALYSIS; DNA MUTATIONAL ANALYSIS; EXONS; GENES, NEOPLASM; GENES, RECESSIVE; GENOME, HUMAN; HUMANS; INTRONS; MODELS, STATISTICAL; MUTATION; NEOPLASMS; REGRESSION ANALYSIS;

EID: 79953108463     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-157     Document Type: Article

References (54)

1. Novick GE, Batzer MA, Deininger PL, Herrera RJ. The Mobile Genetic Element "Alu" in the Human Genome. BioScience 1996, 46(1):32-41.
2. Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV. Duplication, coclustering, and selection of human Alu retrotransposons. Proc Natl Acad Sci USA 2004, 101(5):1268-1272. 10.1073/pnas.0308084100, 337042, 14736919.
3. Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002, 3(5):370-379. 10.1038/nrg798, 11988762.
4. Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 1997, 94(5):1872-1877. 10.1073/pnas.94.5.1872, 20010, 9050872.
5. Jurka J. Evolutionary impact of human Alu repetitive elements. Curr Opin Genet Dev 2004, 14(6):603-608. 10.1016/j.gde.2004.08.008, 15531153.
6. Abrusan G, Krambeck HJ. The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model. J Mol Evol 2006, 63(4):484-492. 10.1007/s00239-005-0275-0, 16955238.
7. Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res 2004, 14(4):517-527. 10.1101/gr.1984404, 383295, 15059992.
8. Zhang K, Fan W, Deininger P, Edwards A, Xu Z, Zhu D. Breaking the computational barrier: a divide-conquer and aggregate based approach for Alu insertion site characterisation. Int J Comput Biol Drug Des 2009, 2(4):302-322. 10.1504/IJCBDD.2009.030763, 2922064, 20090173.
9. Kvikstad EM, Makova KD. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res 2010, 20(5):600-613. 10.1101/gr.099044.109, 2860162, 20219940.
10. Wang J, Song L, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms. Gene 2006, 365:11-20. 10.1016/j.gene.2005.09.031, 1847407, 16376498.
11. Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G. Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol 2007, 8(6):R127. 10.1186/gb-2007-8-6-r127, 2394776, 17594509.
12. Levy A, Sela N, Ast G. TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res 2008, (36 Database):D47-52. 2238949, 17986453.
13. Gu TJ, Yi X, Zhao XW, Zhao Y, Yin JQ. Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics 2009, 10:563. 10.1186/1471-2164-10-563, 19943974.
14. Stenger JE, Lobachev KS, Gordenin D, Darden TA, Jurka J, Resnick MA. Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. Genome Res 2001, 11(1):12-27. 10.1101/gr.158801, 11156612.
15. Deininger PL, Batzer MA. Alu repeats and human disease. Mol Genet Metab 1999, 67(3):183-193. 10.1006/mgme.1999.2864, 10381326.
16. Belancio VP, Roy-Engel AM, Deininger PL. All y'all need to know 'bout retroelements in cancer. Semin Cancer Biol 2010, 20(4):200-210. 10.1016/j.semcancer.2010.06.001, 20600922.
17. Strout MP, Marcucci G, Bloomfield CD, Caligiuri MA. The partial tandem duplication of ALL1 (MLL) is consistently generated by Alu-mediated homologous recombination in acute myeloid leukemia. Proc Natl Acad Sci USA 1998, 95(5):2390-2395. 10.1073/pnas.95.5.2390, 19353, 9482895.
18. Viel A, Petronzelli F, Della Puppa L, Lucci-Cordisco E, Fornasarig M, Pucciarelli S, Rovella V, Quaia M, Ponz de Leon M, Boiocchi M, et al. Different molecular mechanisms underlie genomic deletions in the MLH1 Gene. Hum Mutat 2002, 20(5):368-374. 10.1002/humu.10138, 12402334.
19. Hsieh SY, Chen WY, Yeh TS, Sheen IS, Huang SF. High-frequency Alu-mediated genomic recombination/deletion within the caspase-activated DNase gene in human hepatoma. Oncogene 2005, 24(43):6584-6589.
20. van der Klift H, Wijnen J, Wagner A, Verkuilen P, Tops C, Otway R, Kohonen-Corish M, Vasen H, Oliani C, Barana D, et al. Molecular characterization of the spectrum of genomic deletions in the mismatch repair genes MSH2, MLH1, MSH6, and PMS2 responsible for hereditary nonpolyposis colorectal cancer (HNPCC). Genes Chromosomes Cancer 2005, 44(2):123-138. 10.1002/gcc.20219, 15942939.
21. O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser RS, Wong KK, Li W, McKenna K, Liu XS, Feng B, et al. Alu elements mediate MYB gene tandem duplication in human T-ALL. J Exp Med 2007, 204(13):3059-3066. 2150982, 18070937.
22. Franke G, Bausch B, Hoffmann MM, Cybulla M, Wilhelm C, Kohlhase J, Scherer G, Neumann HP. Alu-Alu recombination underlies the vast majority of large VHL germline deletions: Molecular characterization and genotype-phenotype correlations in VHL patients. Hum Mutat 2009, 30(5):776-786. 10.1002/humu.20948, 19280651.
23. Teugels E, De Greve J. About the c.156_157insAlu BRCA2 breast cancer predisposing mutation. Breast Cancer Res Treat 2009, 116(3):621-622. 10.1007/s10549-008-0188-x, 18807268.
24. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nat Rev Cancer 2004, 4(3):177-183. 10.1038/nrc1299, 2665285, 14993899.
25. http://www.sanger.ac.uk/genetics/CGP/cosmic/
26. Korenberg JR, Rykowski MC. Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell 1988, 53(3):391-400. 10.1016/0092-8674(88)90159-6, 3365767.
27. Medstrand P, van de Lagemaat LN, Mager DL. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res 2002, 12(10):1483-1495. 10.1101/gr.388902, 187529, 12368240.
28. Grover D, Majumder PP, C BR, Brahmachari SK, Mukerji M. Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. Mol Biol Evol 2003, 20(9):1420-1424. 10.1093/molbev/msg153, 12832639.
29. Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet 2008, 4(10):e1000225. 10.1371/journal.pgen.1000225, 2562518, 18841251.
30. Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, Ast G. Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol 2009, 5(3):e1000300. 10.1371/journal.pcbi.1000300, 2639721, 19266014.
31. Sellis D, Provata A, Almirantis Y. Alu and LINE1 distributions in the human chromosomes: evidence of global genomic organization expressed in the form of power laws. Mol Biol Evol 2007, 24(11):2385-2399. 10.1093/molbev/msm181, 17728280.
32. Benjamini Y, Hochberg Y. Controlling the false discover rate - A practical and powerful approach to multiple testing. J ROY STAT SOC B MET 1995, 75:289-300.
33. Hu RJ, Lee MP, Connors TD, Johnson LA, Burn TC, Su K, Landes GM, Feinberg AP. A 2.5-Mb transcript map of a tumor-suppressing subchromosomal transferable fragment from 11p15.5, and isolation and sequence analysis of three novel genes. Genomics 1997, 46(1):9-17. 10.1006/geno.1997.4981, 9403053.
34. Casella G, Berger RL. Statistical inference. 2001, Thmoson Learning, 2.
35. McCoy MW, Allen AP, Gillooly JF. The random nature of genome architecture: predicting open reading frame distributions. PLoS One 2009, 4(7):e6456. 10.1371/journal.pone.0006456, 2714469, 19649247.
36. Dennis B, Patil GP. The gamma distribution and weighted multimodal gamma distributions as models of population abundance. Mathematical Biosciences 1984, 68:187-212.
37. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc 2009, 4(1):44-57.
38. Tsirigos A, Rigoutsos I. Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput Biol 2009, 5(12):e1000610. 10.1371/journal.pcbi.1000610, 2784220, 20019790.
39. Gilbert N, Lutz-Prigge S, Moran JV. Genomic deletions created upon LINE-1 retrotransposition. Cell 2002, 110(3):315-325. 10.1016/S0092-8674(02)00828-0, 12176319.
40. Morrish TA, Gilbert N, Myers JS, Vincent BJ, Stamato TD, Taccioli GE, Batzer MA, Moran JV. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet 2002, 31(2):159-165. 10.1038/ng898, 12006980.
41. Callinan PA, Wang J, Herke SW, Garber RK, Liang P, Batzer MA. Alu retrotransposition-mediated deletion. J Mol Biol 2005, 348(4):791-800. 10.1016/j.jmb.2005.02.043, 15843013.
42. Sen SK, Huang CT, Han K, Batzer MA. Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome. Nucleic Acids Res 2007, 35(11):3741-3751. 10.1093/nar/gkm317, 1920257, 17517773.
43. Srikanta D, Sen SK, Huang CT, Conlin EM, Rhodes RM, Batzer MA. An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. Genomics 2009, 93(3):205-212. 10.1016/j.ygeno.2008.09.016, 2672417, 18951971.
44. Sen SK, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA. Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet 2006, 79(1):41-53. 10.1086/504600, 1474114, 16773564.
45. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. A fine-scale map of recombination rates and hotspots across the human genome. Science 2005, 310(5746):321-324. 10.1126/science.1117196, 16224025.
46. http://www.ncrna.org
47. Debacker K, Kooy RF. Fragile sites and human disease. Hum Mol Genet 2007, 16(Spec No. 2):R150-158. 10.1093/hmg/ddm136, 17567780.
48. Baker SJ, Markowitz S, Fearon ER, Willson JK, Vogelstein B. Suppression of human colorectal carcinoma cell growth by wild-type p53. Science 1990, 249(4971):912-915. 10.1126/science.2144057, 2144057.
49. Volinia S, Mascellani N, Marchesini J, Veronese A, Ormondroyd E, Alder H, Palatini J, Negrini M, Croce CM. Genome wide identification of recessive cancer genes by combinatorial mutation analysis. PLoS One 2008, 3(10):e3380. 10.1371/journal.pone.0003380, 2557123, 18846217.
50. Dagan T, Sorek R, Sharon E, Ast G, Graur D. AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res 2004, (32 Database):D489-492. 10.1093/nar/gkh132, 308866, 14681464.
51. http://transpogene.tau.ac.il
52. http://ftp.genome.washington.edu
53. Ricci V. Fitting distributions with R 2005,
54. Nagelkerke NJD. A note on a general definition of the coefficient of determination. Biometrika 1991, (78):691-692.