Effects of genome-wide copy number variation on expression in mammalian cells

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Wang, Richard T ^a   Ahn, Sangtae ^b,d   Park, Christopher C ^a   Khan, Arshad H ^a   Lange, Kenneth ^a,c   Smith, Desmond J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of Southern California   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d GE GLOBAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; UNTRANSLATED RNA;

ANIMAL CELL; ARTICLE; CENTROMERE; CHROMATIN IMMUNOPRECIPITATION; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LOCUS; GENE MAPPING; GENE NUMBER; GENOTYPE; HAMSTER; HUMAN; MAMMAL CELL; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; QUANTITATIVE TRAIT LOCUS; RADIATION HYBRID MAPPING; RNA EXTRACTION; X CHROMOSOME; ANIMAL; GENE EXPRESSION PROFILING; GENETIC LINKAGE; GENETICS; GENOME; GLIOBLASTOMA; HYBRID CELL;

CRICETINAE; MAMMALIA;

ANIMALS; CHROMOSOMES, HUMAN, X; CRICETINAE; DNA COPY NUMBER VARIATIONS; DOSAGE COMPENSATION, GENETIC; GENE EXPRESSION PROFILING; GENETIC LINKAGE; GENOME; GLIOBLASTOMA; HUMANS; HYBRID CELLS; MICE; QUANTITATIVE TRAIT LOCI;

EID: 81055149799     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-562     Document Type: Article

References (63)

1. Goss SJ, Harris H. New method for mapping genes in human chromosomes. Nature 1975, 255(5511):680-684.
2. Cox DR, Burmeister M, Price ER, Kim S, Myers RM. Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 1990, 250(4978):245-250.
3. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, et al. Large-Scale Copy Number Polymorphism in the Human Genome. Science 2004, 305(5683):525-528.
4. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. Global variation in copy number in the human genome. Nature 2006, 444(7118):444-454.
5. Lee JA, Madrid RE, Sperle K, Ritterson CM, Hobson GM, Garbern J, Lupski JR, Inoue K. Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect. Ann Neurol 2006, 59(2):398-403.
6. Cahan P, Li Y, Izumi M, Graubert TA. The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nat Genet 2009, 41(4):430-437.
7. Deeb SS. The molecular basis of variation in human color vision. Clin Genet 2005, 67(5):369-377.
8. Park CC, Ahn S, Bloom JS, Lin A, Wang RT, Wu T, Sekar A, Khan AH, Farr CJ, Lusis AJ, et al. Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids. Nat Genet 2008, 40:(4):421-429.
9. Stewart EA, McKusick KB, Aggarwal A, Bajorek E, Brady S, Chu A, Fang N, Hadley D, Harris M, Hussain S, et al. An STS-based radiation hybrid map of the human genome. Genome Res 1997, 7(5):422-433.
10. Figueroa J, Pendon C, Valdivia M. Molecular cloning and sequence analysis of hamster CENP-A cDNA. BMC Genomics 2002, 3(1):11.
11. Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Royal Stat Soc, Series B 1995, 57(1):289-300.
12. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat 2001, 29:1165-1188.
13. Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 2002, 296(5568):752-755.
14. Dennis G, Sherman B, Hosack D, Yang J, Gao W, Lane H, Lempicki R. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biology 2003, 4(9):R60.
15. Williams BR, Prabhu VR, Hunter KE, Glazier CM, Whittaker CA, Housman DE, Amon A. Aneuploidy Affects Proliferation and Spontaneous Immortalization in Mammalian Cells. Science (New York, NY) 2008, 322(5902):703-709.
16. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 2003, 35(1):57-64.
17. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(43):15545-15550.
18. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP. The microRNAs of Caenorhabditis elegans. Genes and Development 2003, 17(8):991-1008.
19. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628.
20. Guttman M, Amit I, Garber M, French C, Lin M, Feldser D, Huarte M, Zuk O, Carey B, Cassady J, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458(7235):223-227.
21. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved Elements in the Human Genome. Science 2004, 304(5675):1321-1325.
22. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101(16):6062-6067.
23. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Project G, et al. Diversity of Human Copy Number Variation and Multicopy Genes. Science 2010, 330(6004):641-646.
24. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, et al. Origins and functional impact of copy number variation in the human genome. Nature 2009, 464(7289):704-712.
25. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, et al. Mapping and sequencing of structural variation from eight human genomes. Nature 2008, 453(7191):56-64.
26. Henrichsen CN, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, Schutz F, Ruedi M, Kaessmann H, Reymond A. Segmental copy number variation shapes tissue transcriptomes. Nat Genet 2009, 41(4):424-429.
27. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315:848-853.
28. Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ. Copy number variation influences gene expression and metabolic traits in mice. Human Molecular Genetics 2009, 18(21):4118-4129.
29. Rasko JE, Battini JL, Gottschalk RJ, Mazo I, Miller AD. The RD114/simian type D retrovirus receptor is a neutral amino acid transporter. Proc Natl Acad Sci USA 1999, 96(5):2129-2134.
30. Rai SK, Duh FM, Vigdorovich V, Danilkovitch-Miagkova A, Lerman MI, Miller AD. Candidate tumor suppressor HYAL2 is a glycosylphosphatidylinositol (GPI)-anchored cell-surface receptor for jaagsiekte sheep retrovirus, the envelope protein of which mediates oncogenic transformation. Proc Natl Acad Sci USA 2001, 98(8):4443-4448.
31. Miller AD. Identification of Hyal2 as the cell-surface receptor for jaagsiekte sheep retrovirus and ovine nasal adenocarcinoma virus. Curr Top Microbiol Immunol 2003, 275:179-199.
32. Miller AD, Bergholz U, Ziegler M, Stocking C. Identification of the myelin protein plasmolipin as the cell entry receptor for Mus caroli endogenous retrovirus. J Virol 2008, 82(14):6862-6868.
33. Kantardjieff A, Nissom PM, Chuah SH, Yusufi F, Jacob NM, Mulukutla BC, Yap M, Hu W-S. Developing genomic platforms for Chinese hamster ovary cells. Biotechnology Advances 2009, 27(6):1028-1035.
34. Ahn S, Wang RT, Park CC, Lin A, Leahy RM, Lange K, Smith DJ. Directed Mammalian Gene Regulatory Networks Using Expression and Comparative Genomic Hybridization Microarray Data from Radiation Hybrids. PLoS Comput Biol 2009, 5(6):e1000407.
35. Kim PM, Korbel JO, Gerstein MB. Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context. Proceedings of the National Academy of Sciences 2007, 104(51):20274-20279.
36. Chow JC, Yen Z, Ziesche SM, Brown CJ. Silencing of the mammalian × chromosome. Annu Rev Genomics Hum Genet 2005, 6:69-92.
37. Chaumeil J, Le Baccon P, Wutz A, Heard E. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev 2006, 20(16):2223-2237.
38. Clemson CM, Hall LL, Byron M, McNeil J, Lawrence JB. The × chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc Natl Acad Sci USA 2006, 103(20):7688-7693.
39. Wutz A, Rasmussen TP, Jaenisch R. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 2002, 30(2):167-174.
40. Lucchesi JC, Kelly WG, Panning B. Chromatin remodeling in dosage compensation. Annu Rev Genet 2005, 39:615-651.
41. Fackelmayer FO. A stable proteinaceous structure in the territory of inactive × chromosomes. J Biol Chem 2005, 280(3):1720-1723.
42. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y. Role of histone H3 lysine 27 methylation in × inactivation. Science 2003, 300(5616):131-135.
43. Lucchesi JC, Manning JE. Gene dosage compensation in Drosophila melanogaster. Adv Genet 1987, 24:371-429.
44. Meyer BJ, Casson LP. Caenorhabditis elegans compensates for the difference in × chromosome dosage between the sexes by regulating transcript levels. Cell 1986, 47(6):871-881.
45. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003, 422(6929):297-302.
46. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, Cheung VG. Genetic analysis of genome-wide variation in human gene expression. Nature 2004, 430(7001):743-747.
47. Kang HM, Ye C, Eskin E. Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics 2008, 180(4):1909-1925.
48. Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, et al. Genetical genomics: spotlight on QTL hotspots. PLoS Genet 2008, 4(10):e1000232.
49. Wu C, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, et al. Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet 2008, 4(5):e1000070.
50. Perez-Enciso M, Quevedo JR, Bahamonde A. Genetical genomics: use all data. BMC Genomics 2007, 8:69.
51. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 2005, 37(7):766-770.
52. Laurent P, Schibler L, Vaiman A, Laubier J, Delcros C, Cosseddu G, Vaiman D, Cribiu EP, Yerle M. A 12 000-rad whole-genome radiation hybrid panel in sheep: application to the study of the ovine chromosome 18 region containing a QTL for scrapie susceptibility. Anim Genet 2007, 38(4):358-363.
53. Rink A, Eyer K, Roelofs B, Priest KJ, Sharkey-Brockmeier KJ, Lekhong S, Karajusuf EK, Bang J, Yerle M, Milan D, et al. Radiation hybrid map of the porcine genome comprising 2035 EST loci. Mamm Genome 2006, 17(8):878-885.
54. Womack JE, Johnson JS, Owens EK, Rexroad CE, Schlapfer J, Yang YP. A whole-genome radiation hybrid panel for bovine gene mapping. Mamm Genome 1997, 8(11):854-856.
55. Itoh T, Watanabe T, Ihara N, Mariani P, Beattie CW, Sugimoto Y, Takasuga A. A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci. Genomics 2005, 85(4):413-424.
56. McCarthy LC, Bihoreau MT, Kiguwa SL, Browne J, Watanabe TK, Hishigaki H, Tsuji A, Kiel S, Webber C, Davis ME, et al. A whole-genome radiation hybrid panel and framework map of the rat genome. Mamm Genome 2000, 11(9):791-795.
57. Hitte C, Madeoy J, Kirkness EF, Priat C, Lorentzen TD, Senger F, Thomas D, Derrien T, Ramirez C, Scott C, et al. Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping. Nat Rev Genet 2005, 6(8):643-648.
58. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America 2003, 100(20):11484-11489.
59. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human Mouse Alignments with BLASTZ. Genome Research 2003, 13(1):103-107.
60. Hofacker IL, Fekete M, Flamm C, Huynen MA, Rauscher S, Stolorz PE, Stadler PF. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucl Acids Res 1998, 26(16):3825-3836.
61. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly 1994, 125(2):167-188.
62. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, et al. The Bioperl Toolkit: Perl Modules for the Life Sciences. Genome Research 2002, 12(10):1611-1618.
63. Kent WJ. BLAT - The BLAST-Like Alignment Tool. Genome Research 2002, 12(4):656-664.