Beyond expression profiling: Next generation uses of high density oligonucleotide arrays

Briefings in Functional Genomics and Proteomics

Volumn 2, Issue 1, 2003, Pages 47-56

  Kapranov, Philipp ^a   Sementchenko, Victor I ^a   Gingeras, Thomas R ^a  

^a Thermo Fisher Scientific   (United States)

Author keywords

ChIP; DNA methylation; Microarrays; Origins of replication; Transcriptome

Indexed keywords

COMPLEMENTARY DNA; RNA;

DNA MICROARRAY; DNA REPLICATION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; HUMAN; INSTRUMENTATION; METHODOLOGY; REVIEW;

DNA REPLICATION; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA; TRANSCRIPTION, GENETIC;

EID: 3242766188     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/2.1.47     Document Type: Article

References (53)

1. Lander, E. S., Linton, L. M., Birren, B. et al. (2001), 'Initial sequencing and analysis of the human genome', Nature, Vol. 409, pp. 860-921.
2. Venter, J. C, Adams, M.D., Myers, E. W. et al. (2001), 'The sequence of the human genome', Science, Vol. 291, pp. 1304-1351.
3. Waterston, R. H., Lindblad-Toh, K., Birney, E. et al. (2002), 'Initial sequencing and comparative analysis of the mouse genome', Nature, Vol. 420, pp. 520-562.
4. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Rapp, B. A. and Wheeler, D. L. (2002), 'GenBank', Nucleic Acids Res., Vol. 30, pp. 17-20.
5. Boguski, M. S., Lowe, T. M. and Tolstoshev, C. M. (1993), 'dbEST - database for "expressed sequence tags" ', Nat. Genet., Vol. 4, pp. 332-333.
6. Fodor, S. P., Read, J. L., Pirrung, M. C, Stryer, L., Lu, A. T. and Solas, D. (1991), 'Light-directed, spatially addressable parallel chemical synthesis', Science, Vol. 251, pp. 767-773.
7. Chee, M, Yang, R., Hubbell, E. et al. (1996), 'Accessing genetic information with high-density DNA arrays', Science, Vol. 274, pp. 610-614.
8. Lipshutz, R. J., Fodor, S. P., Gingeras, T. R. and Lockhart, D.J. (1999), 'High density synthetic oligonucleotide arrays', Nat. Genet., Vol. 21(1 Suppl), pp. 20-24.
9. McGall, G. H. and Christians, F. C. (2002), 'High-density genechip oligonucleotide probe arrays', Adv. Biochem. Eng. Biotechnol., Vol. 77, pp. 21-42.
10. Kapranov, P., Cawley, S. E., Drenkow, J. et al. (2002), 'Large-scale transcriptional activity in chromosomes 21 and 22', Science, Vol. 296, pp. 916-919.
11. Chen, J., Sun, M., Lee, S., Zhou, G., Rowley, J. D. and Wang, S. M. (2002), 'Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags', Proc. Natl. Acad. Sci. USA, Vol. 99, pp. 12257-12262.
12. Okazaki, Y., Furuno, M., Kasukawa, T. et al. (2002), 'Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs', Nature, Vol. 420, pp. 563-573.
13. Dermitzakis, E. T., Reymond, A., Lyle, R. et al. (2002), 'Numerous potentially functional but non-genic conserved sequences on human chromosome 21', Nature, Vol. 420, pp. 578-582.
14. Shoemaker, D. D., Schadt, E. E., Armour, C. D. et al. (2001), 'Experimental annotation of the human genome using microarray technology', Nature, Vol. 409, pp. 922-927.
15. Collins, J. E., Goward, M. E., Cole, C.G. et al. (2003), 'Reevaluating human gene annotation: A second-generation analysis of chromosome 22', Genome Res., Vol. 13, pp. 27-36.
16. Wheeler, D. L., Church, D. M., Federhen, S. et al. (2003), 'Database resources of the National Center for Biotechnology', Nucleic Acids Res., Vol. 31, pp. 28-33.
17. Ren, B., Robert, F., Wynck, J. J. et al. (2000), 'Genome-wide location and function of DNA binding proteins', Science, Vol. 290, pp. 2306-2309.
18. Wyrick, J.J., Aparicio, J. G., Chen, T. et al. (2001), 'Genome-wide distribution of ORC and MCM proteins in S. cereuisiae: High-resolution mapping of replication origins', Science, Vol. 294, pp. 2357-2360.
19. Shannon, M. F. and Rao, S. (2002), 'Transcription. Of chips and ChIPs'. Science, Vol. 296, pp. 666-669.
20. Orlando, V. (2000), 'Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation', Trends Biochem. Sci., Vol. 25, pp. 99-104.
21. Iyer, V. R., Horak, C. E., Scafe, C. S., Botstein, D., Snyder, M. and Brown, P. O. (2001), 'Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF', Nature, Vol. 409, pp. 533-538.
22. Horak, C. E. and Snyder, M. (2002), 'ChIP-chip: A genomic approach for identifying transcription factor binding sites', Methods Enzymol., Vol. 350, pp. 469-483.
23. Lee, T. I., Rinaldi, N.J., Robert, F. et al. (2002), 'Transcriptional regulatory networks in Saccharomyces cerevisiae, Science, Vol. 298, pp. 799-804.
24. Li, Q., Peterson, K. R., Fang, X. and Stamatoyannopoulos, G. (2002), 'Locus control regions', Blood, Vol. 100, pp. 3077-3086.
25. Soutto, M., Zhou, W. and Aune, T. M. (2002), 'Cutting edge: Distal regulatory elements are required to achieve selective expression of IFN-gamma in Th1/Tc1 effector cells', J. Immunol, Vol. 169, pp. 6664-6667.
26. Li, Q., Harju, S. and Peterson, K. R. (1999), 'Locus control regions: Coming of age at a decade plus', Trends Genet., Vol. 15, pp. 403-408.
27. Okuno, Y., Huettner, C. S., Radomska, H. S. et al. (2002), 'Distal elements are critical for human CD34 expression in vivo'. Blood, Vol. 100, pp. 4420-4426.
28. Majewski, J. and Ott, J. (2002), 'Distribution and characterization of regulatory elements in the human genome', Genome Res., Vol. 12, pp. 1827-1836.
29. Morishita, M., Kishino, T., Furukawa, K. et al. (2001), 'A 30-base-pair element in the first intron of SOX9 acts as an enhancer in ATDC5', Biochem. Biophp. Res. Commun., Vol. 288, pp. 347-355.
30. Stark, K., Kirk, D. L. and Schmitt, R. (2001), 'Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri', Genes Dev., Vol. 15, pp. 1449-1460.
31. Kuwahara, K., Saito, Y. and Ogawa, E. (2001), 'The neuron-restrictive silencer element-neuron-restrictive silencer factor system regulates basal and endothelin 1-inducible atrial natriuretic peptide gene expression in ventricular myocytes', Mol. Cell Biol., Vol. 21, pp. 2085-2097.
32. Hyder, S. M., Nawaz, Z., Chiappetta, C. and Stancel, G. M. (2000), 'Identification of functional estrogen response elements in the gene coding for the potent angiogenic factor vascular endothelial growth factor', Cancer Res., Vol. 60, pp. 3183-3190.
33. Pettersson, S., Cook, G. P., Bruggemann, M., Williams, G. T. and Neuberger, M. S. (1990), 'A second B cell-specific enhancer 3' of the immunoglobulin heavy-chain locus', Nature, Vol. 344, pp. 165-168.
34. Solymar, D. C, Agarwal, S., Bassing, C. H., Alt, F. W. and Rao, A. (2002), 'A 3' enhancer in the IL-4 gene regulates cytokine production by Th2 cells and mast cells', Immunity, Vol. 17, pp. 41-50.
35. Ayoubi, T. A. and Van De Ven, W. J. (1996), 'Regulation of gene expression by alternative promoters', Faseh J., Vol. 10, pp. 453-460.
36. Chiu, I. M., Touhalisky, K. and Baran, C. (2001), 'Multiple controlling mechanisms of FGF1 gene expression through multiple tissue-specific promoters', Prog. Nucleic Acid Res. Mol. Biol., Vol. 70, pp. 55-74.
37. Lewis, H. A., Musunuru, K., Jensen, K. B. et al. (2000), 'Sequence-specific RNA binding by a Nova KH domain: Implications for paraneoplastic disease and the fragile X syndrome', Cell, Vol. 100, pp. 323-332.
38. Tenenbaum, S. A., Carson, C. C Lager, P.J. and Keene, J. D. (2000), 'Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays', Proc. Natl. Acad. Sci. USA, Vol. 97, pp. 14085-14090.
39. Brown, V., Jin, P., Ceman, S. et al. (2001), 'Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome', Cell, Vol. 107, pp. 477-487.
40. Tenenbaum, S. A., Lager, P. J., Carson, C. C. and Keene, J. D. (2002), 'Ribonomics: Identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays', Methods, Vol. 26, pp. 191-198.
41. Diehn, M., Eisen, M. B., Botstein, D. and Brown, P. O. (2000), 'Large-scale identification of secreted and membrane-associated gene products using DNA microarrays', Nat. Genet., Vol. 25, pp. 58-62.
42. Ng, H. H. and Bird, A. (1999), 'DNA methylation and chromatin modification', Curr. Opin. Genet. Dev., Vol. 9, pp. 158-163.
43. Robertson, K. D. (2002), 'DNA methylation and chromatin - unraveling the tangled web', Oncogene, Vol. 21, pp. 5361-5379.
44. Robertson, K. D. (2001), 'DNA methylation, methyltransferases, and cancer', Oncogene, Vol. 20, pp. 3139-3155.
45. Turker, M. S. (2002), 'Gene silencing in mammalian cells and the spread of DNA methylation' Oncogene, Vol. 21, pp. 5388-5393.
46. Jones, P. A. (2002), 'DNA methylation and cancer', Oncogene, Vol. 21, pp. 5358-5360.
47. Pollack, J. R. and Iyer, V. R. (2002), 'Characterizing the physical genome', Nat. Genet., Vol. 32(Suppl 2), pp. 515-521.
48. Tompa, R., McCallum, C. M, Delrow, J., Henikoff J. G., van Steensel, B. and Henikoff, S. (2002), 'Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3', Curr. Biol., Vol. 12, pp. 65-68.
49. Vu, T. H., Li, T., Nguyen, D. et al. (2000), 'Symmetric and asymmetric DNA methylation in the human IGF2-H19 imprinted region', Genomics, Vol. 64, pp. 132-143.
50. Plass, C. and Soloway, P. D. (2002), 'DNA methylation, imprinting and cancer', Eur. J. Hum. Genet., Vol, 10, pp. 6-16.
51. Raghuraman, M. K., Winzeler, E. A., Collingwood, D. et al (2001), 'Replication dynamics of the yeast genome', Science, Vol. 294, pp. 115-121.
52. Schubeler, D., Scalzo, D., Kooperberg, C., van Steensel, B., Delrow, J. and Groudine, M. (2002), 'Genome-wide DNA replication profile for Drosophila melanogaster. A link between transcription and replication timing', Nat. Genet., Vol. 32, pp. 438-442.
53. Tupler, R., Perini, G. and Green, M. R. (2001), 'Expressing the human genome', Nature, Vol. 409, pp. 832-833.