The genomics of gene expression

Genomics

Volumn 84, Issue 3, 2004, Pages 449-457

  Stamatoyannopoulos, John A ^a  

^a Canal View Bldg 551 N 34th S ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANS ACTING FACTOR;

ALLELE; DISEASE ASSOCIATION; DNA MICROARRAY; DNA POLYMORPHISM; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HERITABILITY; HUMAN; MAMMAL; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REVIEW; SPECIES DIFFERENCE; TRANSCRIPTION REGULATION;

ANIMALS; GENE EXPRESSION REGULATION; GENES, REGULATOR; GENOMICS; MAMMALS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

VERTEBRATA;

EID: 3843151605     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2004.05.002     Document Type: Review

References (62)

1. Pilpel Y., Sudarsanam P., Church G.M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29:2001;153-159
2. Segal E., Shapira M., Regev A., Pe'er D., Botstein D., Koller D., Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34:2003;166-176
3. Markstein M., Markstein P., Markstein V., Levine M.S. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. USA. 99:2002;763-768
4. Berman B.P., Nibu Y., Pfeiffer B.D., Tomancak P., Celniker S.E., Levine M., Rubin G.M., Eisen M.B. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. USA. 99:2002;757-762
5. Stathopoulos A., Van Drenth M., Erives A., Markstein M., Levine M. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell. 111:2002;687-701
6. Rebeiz M., Reeves N.L., Posakony J.W. SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data: site clustering over random expectation. Proc. Natl. Acad. Sci. USA. 99:2002;9888-9893
7. Halfon M.S., Grad Y., Church G.M., Michelson A.M. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12:2002;1019-1028
8. Ureta-Vidal A., Ettwiller L., Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4:2003;251-262
9. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:2002;520-562
10. Elnitski L., Hardison R.C., Li J., Yang S., Kolbe D., et al. Distinguishing regulatory DNA from neutral sites. Genome Res. 13:2003;64-72
11. Dermitzakis E.T., Reymond A., Lyle R., Scamuffa N., Ucla C., et al. Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature. 420:2002;578-582
12. 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
13. Loots G.G., Ovcharenko I., Pachter L., Dubchak I., Rubin E.M. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 12:2002;832-839
14. Mortlock D.P., Guenther C., Kingsley D.M. A general approach for identifying distant regulatory elements applied to the Gdf6 gene. Genome Res. 13:2003;2069-2081
15. Trinklein N.D., Aldred S.J., Saldanha A.J., Myers R.M. Identification and functional analysis of human transcriptional promoters. Genome Res. 13:2003;308-312
16. Jansen R.C., Nap J.P. Genetical genomics: the added value from segregation. Trends Genet. 17:2001;388-391
17. King M.C., Wilson A.C. Evolution at two levels in humans and chimpanzees. Science. 188:1975;107-116
18. Jin W., Riley R.M., Wolfinger R.D., White K.P., Passador-Gurgel G., Gibson G. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet. 29:2001;389-395
19. Sandberg R., Yasuda R., Pankratz D.G., Carter T.A., Del Rio J.A., Wodicka L., Mayford M., Lockhart D.J., Barlow C. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl. Acad. Sci. USA. 97:2000;11038-11043
20. Brem R.B., Yvert G., Clinton R., Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science. 296:2002;752-755
21. Oleksiak M.F., Churchill G.A., Crawford D.L. Variation in gene expression within and among natural populations. Nat. Genet. 32:2002;261-266
22. Schadt E.E., Monks S.A., Drake T.A., Lusis A.J., Che N., Colinayo V., Ruff T.G., Milligan S.B., Lamb J.R., Cavet G., Linsley P.S., Mao M., Stoughton R.B., Friend S.H. Genetics of gene expression surveyed in maize, mouse and man. Nature. 422:2003;297-302
23. Whitney A.R., Diehn M., Popper S.J., Alizadeh A.A., Boldrick J.C., Relman D.A., Brown P.O. Individuality and variation in gene expression patterns in human blood. Proc. Natl. Acad. Sci. USA. 100:2003;1896-1901
24. Cheung V.G., Conlin L.K., Weber T.M., Arcaro M., Jen K.Y., Morley M., Spielman R.S. Natural variation in human gene expression assessed in lymphoblastoid cells. Nat. Genet. 33:2003;422-425
25. Yvert G., Brem R.B., Whittle J., Akey J.M., Foss E., Smith E.N., Mackelprang R., Kruglyak L. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35:2003;57-64
26. Lahr G., Starzinski-Powitz A., Mayer A. Analysis of specific gene expression. Methods Enzymol. 356:2002;271-281
27. Cowles C.R., Hirschhorn J.N., Altshuler D., Lander E.S. Detection of regulatory variation in mouse genes. Nat. Genet. 32:2002;432-437
28. Yan H., Yuan W., Velculescu V.E., Vogelstein B., Kinzler K.W. Allelic variation in human gene expression. Science. 297(5584):2002;1143
29. Bray N.J., Buckland P.R., Owen M.J., O'Donovan M.C. Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet. 113:2003;149-153
30. Pastinen T., Sladek R., Gurd S., Sammak A., Ge B., Lepage P., Lavergne K., Villeneuve A., Gaudin T., Brandstrom H., Beck A., Verner A., Kingsley J., Harmsen E., Labuda D., Morgan K., Vohl M.C., Naumova A.K., Sinnett D., Hudson T.J. A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genom. 2003;. In press
31. Lo H.S., Wang Z., Hu Y., Yang H.H., Gere S., Buetow K.H., Lee M.P. Allelic variation in gene expression is common in the human genome. Genome Res. 13(8):2003;1855-1862
32. Ferguson-Smith A.C., Surani M.A. Imprinting and the epigenetic asymmetry between parental genomes. Science. 293:2001;1086-1089
33. Sakatani T., Wei M., Katoh M., Okita C., Wada D., Mitsuya K., Meguro M., Ikeguchi M., Ito H., Tycko B., Oshimura M. Epigenetic heterogeneity at imprinted loci in normal populations. Biochem. Biophys. Res. Commun. 283:2001;1124-1130
34. Watanabe D., Barlow D.P. Random and imprinted monoallelic expression. Genes Cells. 1:1996;795-802
35. Jeong S., Lee Y.J., Jang J.S., Park C.W., Chung J.H., Seong J.K., Lee K.K., Yu D.Y. A novel epigenetic control operating on Vme1+ locus leads to variegated monoallelic expression. Biochem. Biophys. Res. Commun. 279:2000;884-890
36. Khodursky A.B., Bernstein J.A. Life after transcription - revisiting the fate of messenger RNA. Trends Genet. 19(3):2003;113-115
37. Sleutels F., Barlow D.P. The uniqueness of the imprinting mechanism. Curr. Opin. Genet. Dev. 10:2000;229-233
38. Felsenfeld G., Groudine M. Controlling the double helix. Nature. 421:2003;448-453
39. Butler J.E., Kadonaga J.T. The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 16:2002;2583-2592
40. van Driel R., Fransz P.F., Verschure P.J. The eukaryotic genome: a system regulated at different hierarchical levels. J. Cell Sci. 116:2003;4067-4075
41. Li Q., Peterson K.R., Fang X., Stamatoyannopoulos G. Locus control regions. Blood. 100:2002;3077-3086
42. Hardison R.C. New views of evolution and regulation of vertebrate beta-like globin gene clusters from an orphaned gene in marsupials. Proc. Natl. Acad. Sci. USA. 98:2001;1327-1329
43. Dillon N. Gene autonomy: positions, please... Nature. 425:2003;457
44. Spitz F., Gonzalez F., Duboule D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell. 113:2003;405-417
45. Blom van Assendelft G., Hanscombe O., Grosveld F., Greaves D.R. The beta-globin dominant control region activates homologous and heterologous promoters in a tissue-specific manner. Cell. 56:1989;969-977
46. Heckman C.A., Cao T., Somsouk L., Duan H., Mehew J.W., Zhang C.Y., Boxer L.M. Critical elements of the immunoglobulin heavy chain gene enhancers for deregulated expression of bcl-2. Cancer Res. 63:2003;6666-6673
47. Santagati F., Abe K., Schmidt V., Schmitt-John T., Suzuki M., Yamamura K., Imai K. Identification of cis-regulatory elements in the mouse Pax9/Nkx2-9 genomic region: implication for evolutionary conserved synteny. Genetics. 165:2003;235-242
48. Nobrega M.A., Ovcharenko I., Afzal V., Rubin E.M. Scanning human gene deserts for long-range enhancers. Science. 302:2003;413
49. Cohen B.A., Mitra R.D., Hughes J.D., Church G.M. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet. 26:2000;183-186
50. Lercher M.J., Urrutia A.O., Hurst L.D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31:2002;180-183
51. Blumenthal T., et al. A global analysis of Caenorhabditis elegans operons. Nature. 417:2002;851-854
52. Spellman P.T., Rubin G.M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1:2002;5
53. Lercher M.J., Blumenthal T., Hurst L.D. Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res. 13:2003;238-243
54. Rockman M.V., Wray G.A. Abundant raw material for cis-regulatory evolution in humans. Mol. Biol. Evol. 19:2002;1991-2004
55. Doerge R.W. Mapping and analysis of quantitative trait loci in experimental populations. Nat. Rev. Genet. 3(1):2002 (Jan);43-52
56. Mitchell S.M., Frayling T.M. The role of transcription factors in maturity-onset diabetes of the young. Mol. Genet. Metab. 77:2002;35-43
57. Stride A., Hattersley A.T. Different genes, different diabetes: lessons from maturity-onset diabetes of the young. Ann. Med. 34:2002;207-216
58. Yan H., Dobbie Z., Gruber S.B., Markowitz S., Romans K., Giardiello F.M., Kinzler K.W., Vogelstein B. Small changes in expression affect predisposition to tumorigenesis. Nat. Genet. 30:2002;25-26
59. Crawford D.L., Powers D.A. Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. Proc. Natl. Acad. Sci. USA. 86:1989;9365-9369
60. Ramalho A.S., Beck S., Meyer M., Penque D., Cutting G.R., Amaral M.D. Five percent of normal cystic fibrosis transmembrane conductance regulator mRNA ameliorates the severity of pulmonary disease in cystic fibrosis. Am. J. Respir. Cell. Mol. Biol. 27:2002;619-627
61. Rave-Harel N., Kerem E., Nissim-Rafinia M., Madjar I., Goshen R., Augarten A., Rahat A., Hurwitz A., Darvasi A., Kerem B. The molecular basis of partial penetrance of splicing mutations in cystic fibrosis. Am. J. Hum. Genet. 60:1997;87-94
62. Sabo P.J., Humbert R., Hawrylycz M., Wallace J.C., Dorschner M.O., McArthur M., Stamatoyannopoulos J.A. Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc. Natl. Acad. Sci. USA. 101:2004;4537-4542