Are we genomic mosaics? Variations of the genome of somatic cells can contribute to diversify our phenotypes

Current Genomics

Volumn 11, Issue 6, 2010, Pages 379-386

  Astolfi, P A ^a   Salamini, F ^b   Sgaramella, V ^b  

^a UNIVERSITY OF PAVIA   (Italy)

^b PTP   (Italy)

Author keywords

Aneuploidy; Copy number variation; Epigenomics; Genomics; Retroposons; Transposons

Indexed keywords

ARTICLE; CELL FUNCTION; CELL NUCLEUS TRANSPLANTATION; CELL TRANSDIFFERENTIATION; CELL TRANSFER; CHROMATIN; COPY NUMBER VARIATION; DEVELOPMENTAL STAGE; DNA DETERMINATION; GENETIC VARIABILITY; GENOMICS; HUMAN; INHERITANCE; MOSAICISM; NUCLEIC ACID BASE SUBSTITUTION; PHENOTYPE; REGULATORY SEQUENCE; SOMATIC CELL;

EID: 78649990353     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920210793175949     Document Type: Article

References (68)

1. Schrödinger, E. What is Life - the Physical Aspect of the Living Cell. Cambridge University Press; 1944.
2. Abbott, A. Human genome at ten: The human race. Nature, 2010, 464(7289), 668-669
3. Ho, L.; Crabtree, G. R. Chromatin remodelling during development. Nature, 2010, 463, 474-484.
4. Ptashne, M.; Hobert, O.; Davidson, E. Questions over the scientific basis of epigenome project. Nature, 2010, 464(7288), 487.
5. Szyf, M. The early life environment and the epigenome. BBA, 2009, 1790, 878-885.
6. Margueron, R.; Reinberg, D. Chromatin structure and the inheritance of epigenetic information. Nat. Rev. Genet., 2010, 11, 285-296.
7. Perry, G.H.; Dominy, N.J.; Claw, K.G.; Lee, A.S.; Fiegler, H.; Redon, R.; Werner, J.; Villanea, F.A.; Mountain, J.L.; Misra, R.; Carter, N.P.; Lee, C.; Stone, A.C. Diet and evolution of human amylase gene copy number variations. Nat. Genet., 2007, 39, 1256-1260.
8. Turner, B. M. Epigenetic responses to environmental change and their evolutionary implications. Phil. Trans. Royal Soc., 2009, 364, 3403-3418.
9. Dear, D. H. Copy-number variation: the end of the genome? Trends Biotechnol., 2009, 27, 448-455.
10. Beetschen, J-C.; Fischer, J-L. Yves Delage (1854-1920) as a forerunner of modern nuclear transfer experiments. Int. J. Dev. Biol., 2004, 48, 607-612.
11. Beroukhim, R.; Mermel, C. H.; Porter, D.; Wei, G.; Raychaudhuri, S.; Donovan, J.; Barretina, J.; Boehm, J. S.; Dobson, J.; Urashima, M.; Mc Henry, K. T.; Pinchback, R. M.; Ligon, A. H.; Cho, Y. J.; Haery, L.; Greulich, H.; Reich, M.; Winckler, W.; Lawrence, M. S.; Weir, B. A.; Tanaka, K. E.; Chiang, D. Y.; Bass, A. J.; Loo, A.; Hoffman, C.; Prensner, J.; Liefeld, T.; Gao, Q.; Yecies, D.; Signoretti, S.; Maher, E.; Kaye, F, J.; Sasaki, H.; Tepper, J.E.; Fletcher, J. A.; Tabernero, J.; Baselga, J.; Tsao, M. S.; Demichelis, F.; Rubin, M. A.; Janne, P. A.; Daly, M. J.; Nucera, C.; Levine, R. L.; Ebert, B. L.; Gabriel, S.; Rustgi, A. K.; Antonescu, C. R.; Ladanyi, M.; Letai, A.; Garraway, L. A.; Loda, M.; Beer, D. G.; True, L. D.; Okamoto, A.; Pomeroy, S. L.; Singer, S.; Golub, T. R.; Lander, E. S.; Getz, G.; Sellers, W. R.; Meyerson, M. The landscape of somatic copy-number alteration across human cancers. Nature, 2010, 463, 899-905.
12. Temin, H. M. The DNA Provirus Hypothesis. The Establishment and Implications of RNA-Directed Synthesis. 1975, Nobel Lecture.
13. Griffith, D. J. Endogenous retroviruses in the human genome sequence. Genome Biol., 2001, 2(6), 1017.1-1017.5.
14. Gingeras, Th. Implications of non-cp-linear transcripts. Nature, 2010, 461, 206-211
15. McClintock. B. The significance of the response of the genome to challenge. 1983, Nobel Lecture.
16. Zeh, D.W.; Zeh, J.A.; Ishida, Y. Transposable elements and an epigenetic basis for punctuated equilibria. Bioessays, 2009, 31, 715-726.
17. Ostertag, E. M.; Kazazian, H. H. L1 integration in a transgenic mouse model. Nature, 2005, 435, 810-811.
18. Lee, J.A.; Lupski, J.R. Genomic rearrangements and gene copy number alterations as a cause of nervous system disorders. Neuron, 2006, 52, 103-121.
19. Storchova, Z.; Pellman, D. From polyploidy to aneuploidy, genome instability and cancer. Nat. Rev. Mol. Cell Biol., 2004, 5, 45-54.
20. Jackson, S.P.; Bartek, J. The DNA-damage response in human biology and disease. Nature, 2009, 461, 1071-1078.
21. Shapiro, J. A. Revisiting the Central Dogma in the 21st century. Ann. N. Y. Acad. Sci., 2009, 1178, 6-28.
22. Morgante, M. Plant genome organisation and diversity: the year of junk! Curr. Opin. Biotechnol., 2006, 17, 168-173.
23. Sgaramella, V.; Salamini, F. Gene paucity, genome instability, clonal development: has an individual genome the potential to encode for more than one brain? DNA Repair, 2006, 5, 531-533.
24. The Human Genome Variation Working Group. Completing the map of human genetic variation. Nature, 2007, 447, 161-165.
25. Gaubatz, J.W. Extrachromosomal circular DNAs and genomic sequences plasticity in eukaryotic cells. Mutat. Res., 1990, 237, 5-6.
26. Panelli, S.; Damiani, G.; Galli, C.; Sgaramella, V. Rearranged genomes of bovine blood cells can allow the development of clones till late stages; but rare unrearranged genomes have greater potential and lead to adulthood. Gene, 2004, 334, 99-103.
27. Tachibana, M.; Sparman, M.; Sritanaudomchai, H.; Ma, H.; Clepper, L.; Woodward, J.; Li, Y.; Ramsey, C.; Kolotushkina, O.; Mitalipov, S. Mitochondrial gene replacement in primate offspring and embryonic stem cells. Nature, 2009, 461, 367-372.
28. Garber, M.; Zody, M. C.; Arachchi, H. M.; Berlin, A.; Gnerre, S.; Green, L. M.; Lennon, N.; Nusbaum, C. Closing gaps in the human genome using sequencing by synthesis. Genome Biol., 2009, 10, RR60 (doi:10.1186/gb-2009-10-6-r60).
29. Drmanac, R.; Sparks, A. B.; Callow, M. J.; Halpern, A. L.; Burns, N. L.; Kermani, B. G.; Carnevali, P.; Nazarenko, I.; Nilsen, G. B.; Yeung, G.; Dahl, F.; Fernandez, A.; Staker, B.; Pant, K. P.; Baccash, J.; Borcherding, A. P.; Brownley, A.; Cedeno, R.; Chen, L.; Chernikoff, D.; Cheung, A.; Chirita, R.; Curson, B.; Ebert, J. C.; Hacker, C. R.; Hartlage, R.; Hauser, B.; Huang, S.; Jiang, Y.; Karpinchyk, V.; Koenig, M.; Kong, C.; Landers, T.; Le, C.; Liu, J.; McBride, C. E.; Morenzoni, M.; Morey, R. E.; Mutch, K.; Perazich, H.; Perry, K.; Peters, B. A.; Peterson, J.; Pethiyagoda, C. L.; Pothuraju, K.; Richter, C.; Rosenbaum, A. M.; Roy, S.; Shafto, J.; Sharanhovich, U.; Shannon, K. W.; Sheppy, C. G.; Sun, M.; Thakuria, J. V.; Tran, A.; Vu, D.; Zaranek, A. W.; Wu, X.; Drmanac, S.; Oliphant, A. R.; Banyai, W. C.; Martin, B.; Ballinger, D. G.; Church, G. M.; Reid, C. A. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science, 2010, 327, 78-81.
30. Rohlin, A.; Wernersson, J.; Engwall, Y.; Wiklund, L.; Björk, J.; Nordling, M. Parallel sequencing used in detection of mosaic mutations: comparisons with four diagnostic DNA screening techniques. Hum. Mutat., 2009, 30, 1012-1020.
31. Smith, J.J.; Antonacci, F.; Eichler, E.E.; Amemiya, C.T. Programmed loss of millions of base pairs from a vertebrate genome. PNAS, 2009, 106, 11212-11216.
32. Hilbricht, T.; Varotto, S.; Sgaramella, V.; Bartels, D.; Salamini, F.; Furini, A. Retrotransposons and siRNA have a role in the evolution of desiccation tolerance leading to resurrection of the plant Craterostigma plantagineum. New Phytol., 2008, 179, 877-887.
33. Martienssen, R. Great leap forward? Transposable elements, small interfering RNA and adaptive Lamarckian evolution. New Phytol., 2008, 179, 570-572.
34. Friedberg, E.C.; Walker, G.C.; Siede, W. DNA Repair and Mutagenesis. ASM, 1995.
35. Maksakova, I.A.; Mager, D.L.; Reiss, D. Keeping active endogenous retroviral-like elements in check: the epigenetic perspective. Cell. Mol. Life Sci., 2008, 65, 3329-3347.
36. Tam, O.H.; Aravin, A.A.; Stein, P.; Girard, A.; Murchison, E.P.; Cheloufi, S.; Hodges, E.; Anger, M.; Sachidanandam, R.; Schultz, R.M.; Hannon, G.J. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature, 2008, 453, 534-539.
37. Bock, R. The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci., 2009, 15, 11-15.
38. Vanneste, E.; Voet, T.; Le Caignec, C.; Ampe, M.; Konings, P.; Melotte, C.; Debrock, S.; Amyere, M.; Vikkula, M.; Schuit, F.; Fryns, J.P.; Verbeke, G.; D'Hooghe, T.; Moreau, Y.; Vermeesch, J. R. Chromosome instability is common in human cleavage-stage embryos. Nat. Med., 2008, 15, 577-583.
39. Ledbetter, D.H. Chaos in the embryo. Nat. Med., 2008, 15, 490-491.
40. Vorsanova, S.G.; Kolotii, A.D.; Iourov, I.Y.; Monakhov, V.V.; Kirillova, E.A.; Soloviev, I.V.; Yurov, Y.B. Evidence for high frequency of chromosomal mosaicism in spontaneous abortions revealed by interphase FISH analysis. J. Histochem. Cytochem., 2005, 53, 375-380.
41. Iourov, I. Y.; Vorsanova, S. G.; Liehr, T.; Kolotii, A. D.; Yurov, Y. B. Increased chromosome instability dramatically disrupts neural genome integrity and mediates cerebellar degeneration in the ataxia-telangiectasia brain. Hum. Mol. Genet., 2009, 18, 2656-2669.
42. Westra, J.W.; Peterson, S.E.; Yung, Y.C.; Mutoh, T.; Barral, S.; Chun, J. Aneuploid mosaicism in the developing and adult cerebellar cortex. J. Comparat. Neurol., 2008, 507, 1944-1951.
43. Sgaramella, V.; Astolfi, P. Somatic genome variations interact with environment, genome and epigenome in the determination of the phenotype: A paradigm shift in genomics? DNA Repair, 2010, 9, 470-473.
44. Conrad, D. F.; Pinto, D.; Redon, R.; Feuk, L.; Gokcumen, O.; Zhang, Y.; Aerts, J.; Andrews, T. D.; Barnes, C.; Campbell, P.; Fitzgerald, T.; Hu, M.; Ihm, C. H.; Kristiansson, K.; Macarthur, D. G.; Macdonald, J. R.; Onyiah, I.; Pang, A. W.; Robson, S.; Stirrups, K.; Valsesia, A.; Walter, K.; Wei J; Wellcome Trust Case Control Consortium, Tyler-Smith, C.; Carter, N. P.; Lee, C.; Scherer, S. W.; Hurles, M. E. Origins and functional impact of copy-umber variations in the human genome. Nature, 2009, 464, 704-712.
45. Vijg, J. Ageing of the genome. Oxford: Oxford University Press; 2007.
46. Iourov, I.Y.; Vorsanova, S.G.; Liehr, T.; Yurov, Y.B. Aneuploidy in the normal, Alzheimer's disease and ataxia-telangiectasia brain: differential expression and pathological meaning. Neurobiol. Dis., 2009, 34, 212-220.
47. Vega, F.; Medeiros, L.J. V(D)J recombination and staggered DNA breaks: guilty again. Blood, 2010, 115, 2121-2122.
48. Bacolla, A.; Wells, R. D. Non-B conformations as determinants of mutagenesis and human disease. Mol. Carcinog., 2009, 48, 273-285.
49. Motl, J. A.; Chalker, D. L. Subtraction by addition: domesticated transposases in programmed DNA elimination. Genes Dev., 2009, 23, 2455-2460.
50. Sen, S. K.; Han, K.; Wang, J.; Lee, J.; Wang, H.; Callinan, P.A.; Dyer, M.; Cordaux, R.; Liang, P.; Batzer, M.A. Human Genomic Deletions Mediated by Recombination between Alu Elements. Am. J. Hum. Genet., 2006, 79, 41-53.
51. Eichler, E.E. Widening the spectrum of human genetic variation. Nat. Genet., 2006, 38, 9-11.
52. Wakayama, T.; Perry, A.C.; Zuccotti, M.; Johnson, K.R.; Yanagimachi, R. Full-term development of mice from enucleated oocytes injected with cumulus cell nuclei. Nature, 1998, 394, 369-373.
53. Gurdon, J. Nuclear reprogramming in egg. Nat. Med., 2009, 15, 1141-1144.
54. Whitelaw, E.; Martin, D.K. Retroposons as epigenetic mediators of phenotypic variations in mammals. Nat. Genet., 2001, 27, 361-365.
55. Ossowski, S.; Schneeberger, K.; Lucas-Lledó, J.I.; Warthmann, N.; Clark, R.M.; Shaw, R.G.; Weigel, D.; Lynch, M. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science, 2010, 327, 92-96.
56. Waterston, R. H.; Lindblat-Toh, K.; Birney, E.; Rogers, J.; Abril, J.F.; Agarwal, P.; Agarwala, R.; Ainscough, R.; Alexandersson, M.; An, P.; Antonarakis, S.E.; Attwood, J.; Baertsch, R.; Bailey, J.; Barlow, K.; Beck, S.; Berry, E.; Birren, B.; Bloom, T.; Bork, P.; Botcherby, M.; Bray, N.; Brent, M.R.; Brown, D.G.; Brown, S.D.; Bult, C.; Burton, J.; Butler, J.; Campbell, R.D.; Carninci, P.; Cawley, S.; Chiaromonte, F.; Chinwalla, A.T.; Church, D.M.; Clamp, M.; Clee, C.; Collins, F.S.; Cook, L.L.; Copley, R.R.; Coulson, A.; Couronne, O.; Cuff, J.; Curwen, V.; Cutts, T.; Daly, M.; David, R.; Davies, J.; Delehaunty, K.D.; Deri, J.; Dermitzakis, E.T.; Dewey, C.; Dickens, N.J.; Diekhans, M.; Dodge, S.; Dubchak, I.; Dunn, D.M.; Eddy, S.R.; Elnitski, L.; Emes, R.D.; Eswara, P.; Eyras, E.; Felsenfeld, A.; Fewell, G.A.; Flicek, P.; Foley, K.; Frankel, W.N.; Fulton, L.A.; Fulton, R.S.; Furey, T.S.; Gage, D.; Gibbs, R.A.; Glusman, G.; Gnerre, S.; Goldman, N.; Goodstadt, L.; Grafham, D.; Graves, T.A.; Green, E.D.; Gregory, S.; Guigó, R.; Guyer, M.; Hardison, R.C.; Haussler, D.; Hayashizaki, Y.; Hillier, L.W.; Hinrichs, A.; Hlavina, W.; Holzer, T.; Hsu, F.; Hua, A.; Hubbard, T.; Hunt, A.; Jackson, I.; Jaffe, D.B.; Johnson, L.S.; Jones, M.; Jones, T.A.; Joy, A.; Kamal, M.; Karlsson, E.K.; Karolchik, D.; Kasprzyk, A.; Kawai, J.; Keibler, E.; Kells, C.; Kent, W.J.; Kirby, A.; Kolbe, D.L.; Korf, I.; Kucherlapati, R.S.; Kulbokas, E.J.; Kulp, D.; Landers, T.; Leger, J.P.; Leonard, S.; Letunic, I.; Levine, R.; Li, J.; Li, M.; Lloyd, C.; Lucas, S.; Ma, B.; Maglott, D.R.; Mardis, E.R.; Matthews, L.; Mauceli, E.; Mayer, J.H.; McCarthy, M.; McCombie, W.R.; McLaren, S.; McLay, K.; McPherson, J.D.; Meldrim, J.; Meredith, B.; Mesirov, J.P.; Miller, W.; Miner, T.L.; Mongin, E.; Montgomery, K.T.; Morgan, M.; Mott, R.; Mullikin, J.C.; Muzny, D.M.; Nash, W.E.; Nelson, J.O.; Nhan, M.N.; Nicol, R.; Ning, Z.; Nusbaum, C.; O'Connor, M.J.; Okazaki, Y.; Oliver, K.; Overton- Larty, E.; Pachter, L.; Parra, G.; Pepin, K.H.; Peterson, J.; Pevzner, P.; Plumb, R.; Pohl, C.S.; Poliakov, A.; Ponce, T.C.; Ponting, C.P.; Potter, S.; Quail, M.; Reymond, A.; Roe, B.A.; Roskin, K.M.; Rubin, E.M.; Rust, A.G.; Santos, R.; Sapojnikov, V.; Schultz, B.; Schultz, J.; Schwartz, M.S.; Schwartz, S.; Scott, C.; Seaman, S.; Searle, S.; Sharpe, T.; Sheridan, A.; Shownkeen, R.; Sims, S.; Singer, J.B.; Slater, G.; Smit, A.; Smith, D.R.; Spencer, B.; Stabenau, A.; Stange-Thomann, N.; Sugnet, C.; Suyama, M.; Tesler, G.; Thompson, J.; Torrents, D.; Trevaskis, E.; Tromp, J.; Ucla, C.; Ureta-Vidal, A.; Vinson, J.P.; Von Niederhausern, A.C.; Wade, C.M.; Wall, M.; Weber, R.J.; Weiss, R.B.; Wendl, M.C.; West, A.P.; Wetterstrand, K.; Wheeler, R.; Whelan, S.; Wierzbowski, J.; Willey, D.; Williams, S.; Wilson, R.K.; Winter, E.; Worley, K.C.; Wyman, D.; Yang, S.; Yang, S.P.; Zdobnov, E.M.; Zody, M.C.; Lander, E.S. Initial sequencing and comparative analysis of the mouse genome. Nature, 2002, 420, 520-565.
57. Panelli, S.; Damiani, G.; Espen, L.; Sgaramella, V. Ligation overcomes terminal underrepresentation in multiple displacement amplification of linear DNA. BioTechniques, 2005, 39, 174-179.
58. Sen, S. K.; Han, K.; Wang, J.; Lee, J.; Wang, H.; Callinan, P. A.; Dyer, M.; Cordaux, R.; Liang, P.; Batzer, M. A. Human genomic deletions mediated by recombination between Alu elements. Am. J. Hum. Genet., 2006, 79, 41-53.
59. Bovee, D.; Zhou, Y.; Haugen, E.; Wu, Z.; Hayden, H. S.; Gillett, W.; Cooper G. M.; Sampas, N.; Phelps, K.; Levy, R.; Morrison, V. A.; Sprague, J.; Jewett, D.; Buckely, D.; Subramaniam, S.; Chang, J.; Smith, D. R.; Olson, M. Z. V.; Eichler, E. E.; Kayl, R. Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nat. Genet., 2008, 40, 96-101;
60. Freeman, J. L.; Perry, G. H.; Feuk, L.; Redon, R.; McCarroll, S. A.; Altshuler, D. M.; Aburatani, H.; Jones, K. W.; Tyler-Smith, C.; Hurles, M. E.; Carter, N.P.; Scherer, S. W.; Lee, C. Copy number variation: New insights in genome diversity. Genome Res., 2006, 16, 949-961;
61. Innan, H.; Kondrashov, F. The evolution of gene duplication: classifying and distinguishing between models. Nat. Rev. Genet., 2010, 11, 97-107.
62. Zufall, R. A.; Robinson, T.; Katz, L. A. Evolution of developmentally regulated genome rearrangements in eukaryotes. J. Exp. Zool. B Mol. Dev. Evol., 2005, 304B, 448-455.
63. Lamarck, J-B. Philosophie zoologique, ou exposition des considerations relatives à l'histoire naturelle des animaux. 1809. Paris, Dent.
64. Robertson, M. Editorial: Gene regulation, evolvability, and the limits of genomics. J. Biol., 2009, 8, 94.
65. Koonin, E.; Wolf, Y.I. Is evolution Darwinian or Lamarckian? Biol. Direct, 2009, 4, 42-56.
66. Mattick, J. S.; Mehler, M. F. RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci., 2008, 31, 227-230.
67. Edelman, G.M.; Tononi, G. A Universe of Consciousness. How Matter Becomes Imagination. Basic Books, 2000.
68. Gross, C.G. Making sense of printed symbols. Review of the book "Reading in the brain", by S. Dehaene, Viking NY 2009. Science, 2010, 327, 524-525.