How bioinformatics can help reverse engineer human aging

Ageing Research Reviews

Volumn 3, Issue 2, 2004, Pages 125-141

  De Magalhães, João Pedro ^a   Toussaint, Olivier ^a  

^a UNIVERSITY OF NAMUR   (Belgium)

Author keywords

Aging; Bioinformatics; Computational biology; Gerontology; Systems biology

Indexed keywords

BIOINFORMATICS; COMPUTER MODEL; DNA MICROARRAY; GENE IDENTIFICATION; GENETIC ALGORITHM; GENOMICS; GERONTOLOGY; HUMAN; IMAGE RECONSTRUCTION; PHYLOGENETIC TREE; PROTEOMICS; REVIEW; SENESCENCE; TISSUE ENGINEERING; TRANSCRIPTION REGULATION;

EID: 1242315665     PISSN: 15681637     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.arr.2003.08.006     Document Type: Review

References (101)

1. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., Watson, J.D., 1994. Molecular Biology of the Cell, third ed. Garland Publishing, New York/London.
2. Aravind L., Walker D.R., Koonin E.V. Conserved domains in DNA repair proteins and evolution of repair systems. Nucl. Acids Res. 27:1999;1223-1242.
3. Arnone M.I., Davidson E.H. The hardwiring of development: organization and function of genomic regulatory systems. Development. 124:1997;1851-1864.
4. Austad S.N. Comparative aging and life histories in mammals. Exp. Gerontol. 32:1997;23-38.
5. Bronikowski A.M., Alberts S.C., Altmann J., Packer C., Carey K.D., Tatar M. The aging baboon: comparative demography in a non-human primate. Proc. Natl. Acad. Sci. U.S.A. 99:2002;9591-9595.
6. Brown-Borg H.M., Borg K.E., Meliska C.J., Bartke A. Dwarf mice and the ageing process. Nature. 384:1996;33.
7. Cao S.X., Dhahbi J.M., Mote P.L., Spindler S.R. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc. Natl. Acad. Sci. U.S.A. 98:2001;10630-10635.
8. Case C.C. Transcriptional tools for aging research. Mech. Ageing Dev. 124:2003;103-108.
9. Chikofsky E.J., Cross J.H. II Reverse engineering and design recovery: a taxonomy. IEEE Software. 7:1990;13-17.
10. Chu S., DeRisi J., Eisen M., Mulholland J., Botstein D., Brown P.O., Herskowitz I. The transcriptional program of sporulation in budding yeast. Science. 282:1998;699-705.
11. Comfort, A., 1964. Ageing: The Biology of Senescence. Routledge & Kegan Paul, London.
12. Coschigano K.T., Clemmons D., Bellush L.L., Kopchick J.J. Assessment of growth parameters and life span of GHR/BP gene-disrupted mice. Endocrinology. 141:2000;2608-2613.
13. D'Haeseleer P., Liang S., Somogyi R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics. 16:2000;707-726.
14. de Boer J., Andressoo J.O., de Wit J., Huijmans J., Beems R.B., van Steeg H., Weeda G., van der Horst G.T., van Leeuwen W., Themmen A.P., Meradji M., Hoeijmakers J.H. Premature aging in mice deficient in DNA repair and transcription. Science. 296:2002;1276-1279.
15. de la Fuente A., Brazhnik P., Mendes P. Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet. 18:2002;395-398.
16. de Magalhaes J.P., Toussaint O. The evolution of mammalian aging. Exp. Gerontol. 37:2002;769-775.
17. de Magalhaes J.P. Is mammalian aging genetically controlled? Biogerontology. 4:2003;119-120.
18. Dermitzakis E.T., Clark A.G. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19:2002;1114-1121.
19. Enard W., Khaitovich P., Klose J., Zollner S., Heissig F., Giavalisco P., Nieselt-Struwe K., Muchmore E., Varki A., Ravid R., Doxiadis G.M., Bontrop R.E., Paabo S. Intra- and inter-specific variation in primate gene expression patterns. Science. 296:2002;340-343.
20. Eriksson M., Brown W.T., Gordon L.B., Glynn M.W., Singer J., Scott L., Erdos M.R., Robbins C.M., Moses T.Y., Berglund P., Dutra A., Pak E., Durkin S., Csoka A.B., Boehnke M., Glover T.W., Collins F.S. Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature. 423:2003;293-298.
21. Fickett J.W., Wasserman W.W. Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol. 11:2000;19-24.
22. Finch, C.E., 1990. Longevity, Senescence, and the Genome. The University of Chicago Press, Chicago/London.
23. Flurkey K., Papaconstantinou J., Miller R.A., Harrison D.E. Lifespan extension and delayed immune and collagen aging in mutant mice with defects in growth hormone production. Proc. Natl. Acad. Sci. U.S.A. 98:2001;6736-6741.
24. George J.C., Bada J., WZeh J., Brown S.E., O'Hara T., Suydam R. Age and growth estimates of bowhead whales (Balaena mysticetus) via aspartic acid racemization. Can. J. Zool. 77:1999;571-580.
25. Gottgens B., Barton L.M., Gilbert J.G., Bench A.J., Sanchez M.J., Bahn S., Mistry S., Grafham D., McMurray A., Vaudin M., Amaya E., Bentley D.R., Green A.R., Sinclair A.M. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol. 18:2000;181-186.
26. Gygi S.P., Rochon Y., Franza B.R., Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19:1999;1720-1730.
27. Hardison R.C., Oeltjen J., Miller W. Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res. 7:1997;959-966.
28. Hekimi S., Guarente L. Genetics and the specificity of the aging process. Science. 299:2003;1351-1354.
29. Henning K.A., Li L., Iyer N., McDaniel L.D., Reagan M.S., Legerski R., Schultz R.A., Stefanini M., Lehmann A.R., Mayne L.V.et al. The Cockayne syndrome group A gene encodes a WD repeat protein that interacts with CSB protein and a subunit of RNA polymerase II TFIIH. Cell. 82:1995;555-564.
30. Hofer S.M., Sliwinski M.J. Understanding ageing: an evaluation of research designs for assessing the interdependence of ageing-related changes. Gerontology. 47:2001;341-352.
31. Holzenberger M., Dupont J., Ducos B., Leneuve P., Geloen A., Even P.C., Cervera P., Le Bouc Y. IGF-1 receptor regulates lifespan and resistance to oxidative stress in mice. Nature. 421:2003;182-187.
32. Hood L., Galas D. The digital code of DNA. Nature. 421:2003;444-448.
33. Hood L. Systems biology: integrating technology, biology, and computation. Mech. Ageing Dev. 124:2003;9-16.
34. Ideker T., Galitski T., Hood L. A new approach to decoding life: systems biology. Annu. Rev. Genom. Hum. Genet. 2:2001a;343-372.
35. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:2001b;929-934.
36. Jazwinski S.M. Biological aging research today: potential, peeves, and problems. Exp. Gerontol. 37:2002;1141-1146.
37. Jennings E.G., Young R.A. Genome expression on the World Wide Web. Trends Genet. 15:1999;202-204.
38. Jiang C.H., Tsien J.Z., Schultz P.G., Hu Y. The effects of aging on gene expression in the hypothalamus and cortex of mice. Proc. Natl. Acad. Sci. U.S.A. 98:2001;1930-1934.
39. Kauffman, S.A., 1993. The Origins of Order, Self-Organization and Selection in Evolution. Oxford University Press, New York.
40. Kayo T., Allison D.B., Weindruch R., Prolla T.A. Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys. Proc. Natl. Acad. Sci. U.S.A. 98:2001;5093-5098.
41. Kirkwood T.B., Boys R.J., Gillespie C.S., Proctor C.J., Shanley D.P., Wilkinson D.J. Towards an e-biology of ageing: integrating theory and data. Nat. Rev. Mol. Cell Biol. 4:2003;243-249.
42. Kitano H. Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology. Curr. Genet. 41:2002a;1-10.
43. Kitano H. Computational systems biology. Nature. 420:2002b;206-210.
44. Krupa B. On the number of experiments required to find the causal structure of complex systems. J. Theor. Biol. 219:2002;257-267.
45. Kuro-o M., Matsumura Y., Aizawa H., Kawaguchi H., Suga T., Utsugi T., Ohyama Y., Kurabayashi M., Kaname T., Kume E., Iwasaki H., Iida A., Shiraki-Iida T., Nishikawa S., Nagai R., Nabeshima Y.I. Mutation of the mouse klotho gene leads to a syndrome resembling ageing. Nature. 390:1997;45-51.
46. Lander E.S.et al. Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium. Nature. 409:2001;860-921.
47. Lavrovsky Y., Chatterjee B., Clark R.A., Roy A.K. Role of redox-regulated transcription factors in inflammation, aging and age-related diseases. Exp. Gerontol. 35:2000;521-532.
48. Lee C.K., Klopp R.G., Weindruch R., Prolla T.A. Gene expression profile of aging and its retardation by caloric restriction. Science. 285:1999;1390-1393.
49. Levine M., Tjian R. Transcription regulation and animal diversity. Nature. 424:2003;147-151.
50. Levy S., Hannenhalli S. Identification of transcription factor binding sites in the human genome sequence. Mamm. Genome. 13:2002;510-514.
51. Lockhart D.J., Winzeler E.A. Genomics, gene expression and DNA arrays. Nature. 405:2000;827-836.
52. Lombard D.B., Beard C., Johnson B., Marciniak R.A., Dausman J., Bronson R., Buhlmann J.E., Lipman R., Curry R., Sharpe A., Jaenisch R., Guarente L. Mutations in the WRN gene in mice accelerate mortality in a p53-null background. Mol. Cell Biol. 20:2000;3286-3291.
53. Loots G.G., Locksley R.M., Blankespoor C.M., Wang Z.E., Miller W., Rubin E.M., Frazer K.A. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science. 288:2000;136-140.
54. Lund J., Tedesco P., Duke K., Wang J., Kim S.K., Johnson T.E. Transcriptional profile of aging in C. elegans. Curr. Biol. 12:2002;1566-1573.
55. Luscombe N.M., Greenbaum D., Gerstein M. What is bioinformatics? A proposed definition and overview of the field. Methods Inform. Med. 40:2001;346-358.
56. MacBeath G. Protein microarrays and proteomics. Nat. Genet. 32(Suppl.):2002;526-532.
57. Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999a;751-753.
58. Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature. 402:1999b;83-86.
59. Medawar, P., 1955. The definition and measurement of senescence, vol. I. In: Wolstenholme, G.E.W. (Ed.), Ciba Foundation Colloquia on Ageing. J. & A. Churchill, London, pp. 4-15.
60. shc adaptor protein controls oxidative stress response and life span in mammals. Nature. 402:1999;309-313.
61. Miller R.A. Kleemeier award lecture: are there genes for aging? J. Gerontol. A: Biol. Sci. Med. Sci. 54:1999;B297-B307.
62. Miller R.A., Chang Y., Galecki A.T., Al-Regaiey K., Kopchick J.J., Bartke A. Gene expression patterns in calorically restricted mice: partial overlap with long-lived mutant mice. Mol. Endocrinol. 16:2002;2657-2666.
63. Miskin R., Masos T. Transgenic mice overexpressing urokinase-type plasminogen activator in the brain exhibit reduced food consumption, body weight and size, and increased longevity. J. Gerontol. A: Biol. Sci. Med. Sci. 52:1997;B118-B124.
64. Mitnitski A.B., Graham J.E., Mogilner A.J., Rockwood K. Frailty, fitness and late-life mortality in relation to chronological and biological age. BMC Geriatr. 2:2002;1.
65. Nielsen J. Metabolic engineering: techniques for analysis of targets for genetic manipulations. Biotechnol. Bioeng. 58:1998;125-132.
66. Ohler U., Niemann H. Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet. 17:2001;56-60.
67. Pandey A., Mann M. Proteomics to study genes and genomes. Nature. 405:2000;837-846.
68. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A. 96:1999;4285-4288.
69. Pennacchio L.A., Rubin E.M. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2:2001;100-109.
70. Pilpel Y., Sudarsanam P., Church G.M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29:2001;153-159.
71. Reinke V. Functional exploration of the C. elegans genome using DNA microarrays. Nat. Genet. 32(Suppl.):2002;541-546.
72. Ren B., Cam H., Takahashi Y., Volkert T., Terragni J., Young R.A., Dynlacht B.D. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev. 16:2002;245-256.
73. Risch N.J. Searching for genetic determinants in the new millennium. Nature. 405:2000;847-856.
74. Roy A.K., Oh T., Rivera O., Mubiru J., Song C.S., Chatterjee B. Impacts of transcriptional regulation on aging and senescence. Ageing Res. Rev. 1:2002;367-380.
75. Schwaenen C., Wessendorf S., Kestler H.A., Dohner H., Lichter P., Bentz M. DNA microarray analysis in malignant lymphomas. Ann. Hematol. 82:2003;323-332.
76. Selinger D.W., Wright M.A., Church G.M. On the complete determination of biological systems. Trends Biotechnol. 21:2003;251-254.
77. Sherlock G., Hernandez-Boussard T., Kasarskis A., Binkley G., Matese J.C., Dwight S.S., Kaloper M., Weng S., Jin H., Ball C.A., Eisen M.B., Spellman P.T., Brown P.O., Botstein D., Cherry J.M. The Stanford Microarray Database. Nucl. Acids Res. 29:2001;152-155.
78. Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics. 16:2000;16-23.
79. Strohman R. Maneuvering in the complex path from genotype to phenotype. Science. 296:2002;701-703.
80. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
81. Toussaint O., Raes M., Remacle J. Aging as a multi-step process characterized by a lowering of entropy production leading the cell to a sequence of defined stages. Mech. Ageing Dev. 61:1991;45-64.
82. Tower J. Transgenic methods for increasing Drosophila life span. Mech. Ageing Dev. 118:2000;1-14.
83. Tyner S.D., Venkatachalam S., Choi J., Jones S., Ghebranious N., Igelmann H., Lu X., Soron G., Cooper B., Brayton C., Hee Park S., Thompson T., Karsenty G., Bradley A., Donehower L.A. p53 mutant mice that display early ageing-associated phenotypes. Nature. 415:2002;45-53.
84. Ureta-Vidal A., Ettwiller L., Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4:2003;251-262.
85. Venter J.C.et al. The sequence of the human genome. Science. 291:2001;1304-1351.
86. Wade, N., 2001. Life Script: How the Human Genome Discoveries Will Transform Medicine and Enhance Health. Simon & Schuster, London.
87. Wagner A. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics. 15:1999;776-784.
88. Wagner A. How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps. Bioinformatics. 17:2001;1183-1197.
89. Wahde M., Hertz J. Coarse-grained reverse engineering of genetic regulatory networks. Biosystems. 55:2000;129-136.
90. Wang L., Ogburn C.E., Ware C.B., Ladiges W.C., Youssoufian H., Martin G.M., Oshima J. Cellular Werner phenotypes in mice expressing a putative dominant-negative human WRN gene. Genetics. 154:2000;357-362.
91. Waterston R.H.et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:2002;520-562.
92. Wei L., Liu Y., Dubchak I., Shon J., Park J. Comparative genomics approaches to study organism similarities and differences. J. Biomed. Inform. 35:2002;142-150.
93. Weindruch, R., Walford, R.L., 1988. The Retardation of Aging and Disease by Dietary Restriction. C.C. Thomas, Springfield.
94. Weindruch R., Kayo T., Lee C.K., Prolla T.A. Gene expression profiling of aging using DNA microarrays. Mech. Ageing Dev. 123:2002;177-193.
95. Wong K.K., Maser R.S., Bachoo R.M., Menon J., Carrasco D.R., Gu Y., Alt F.W., DePinho R.A. Telomere dysfunction and Atm deficiency compromises organ homeostasis and accelerates ageing. Nature. 421:2003;643-648.
96. Wyrick J.J., Young R.A. Deciphering gene expression regulatory networks. Curr. Opin. Genet. Dev. 12:2002;130-136.
97. Yaspo M.L. Taking a functional genomics approach in molecular medicine. Trends Mol. Med. 7:2001;494-501.
98. Yeung M.K., Tegner J., Collins J.J. Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl. Acad. Sci. U.S.A. 99:2002;6163-6168.
99. Yu C.E., Oshima J., Fu Y.H., Wijsman E.M., Hisama F., Alisch R., Matthews S., Nakura J., Miki T., Ouais S., Martin G.M., Mulligan J., Schellenberg G.D. Positional cloning of the Werner's syndrome gene. Science. 272:1996;258-262.
100. Zhang H., Pan K.H., Cohen S.N. Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci. Proc. Natl. Acad. Sci. U.S.A. 100:2003;3251-3256.
101. Zou S., Meadows S., Sharp L., Jan L.Y., Jan Y.N. Genome-wide study of aging and oxidative stress response in Drosophila melanogaster. Proc. Natl. Acad. Sci. U.S.A. 97:2000;13726-13731.