In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading

Nature Genetics

Volumn 33, Issue 4, 2003, Pages 469-475

  Knight, Julian C ^a,b   Keating, Brendan J ^a   Rockett, Kirk A ^a   Kwiatkowski, Dominic P ^a,c  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b HARVARD UNIVERSITY   (United States)

^c JOHN RADCLIFFE HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II;

ALLELE; ANALYTIC METHOD; ARTICLE; ENZYME PHOSPHORYLATION; GENE CONTROL; GENE EXPRESSION; GENE LOCUS; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; HAPLOTYPE SPECIFIC CHROMATIN IMMUNOPRECIPITATION; IMMUNOPRECIPITATION; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DNA BINDING; REGULATORY MECHANISM;

ALLELES; AUTOANTIGENS; CELL LINE; CHROMATIN; GENETIC TECHNIQUES; GENOMIC IMPRINTING; GENOTYPE; HAPLOTYPES; HUMANS; MASS SCREENING; MASS SPECTROMETRY; MODELS, GENETIC; PHOSPHORYLATION; POLYMORPHISM, GENETIC; PRECIPITIN TESTS; PROTEIN BINDING; RIBONUCLEOPROTEINS, SMALL NUCLEAR; RNA POLYMERASE II; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 0037381011     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1124     Document Type: Article

References (41)

1. Bartholomew, B., Dahmus, M.E. & Meares, C.F. RNA contacts subunits IIo and IIc in HeLa RNA polymerase II transcription complexes. J. Biol. Chem. 261, 14226-14231 (1986).
2. Laybourn, P.J. & Dahmus, M.E. Transcription-dependent structural changes in the C-terminal domain of mammalian RNA polymerase subunit IIa/o. J. Biol. Chem. 264, 6693-6698 (1989).
3. O'Brien, T., Hardin, S., Greenleaf, A. & Lis, J.T. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature 370, 75-77 (1994).
4. Komarnitsky, P., Cho, E.J. & Buratowski, S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452-2460 (2000).
5. Dahmus, M.E. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271, 19009-19012 (1996).
6. Schroeder, S.C., Schwer, B., Shuman, S. & Bentley, D. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14, 2435-2440 (2000).
7. Yamamoto, S. et al. Studies of nematode TFIIE function reveal a link between Ser5 phosphorylation of RNA polymerase II and the transition from transcription initiation to elongation. Mol. Cell. Biol. 21, 1-15 (2001).
8. Cho, E.J., Kobor, M.S., Kim, M., Greenblatt, J. & Buratowski, S. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 15, 3319-3329 (2001).
9. Cadena, D.L. & Dahmus, M.E. Messenger RNA synthesis in mammalian cells is catalyzed by the phosphorylated form of RNA polymerase II. J. Biol. Chem. 262, 12468-12474 (1987).
10. Weeks, J.R., Hardin, S.E., Shen, J., Lee, J.M. & Greenleaf, A.L. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. Genes Dev. 7, 2329-2344 (1993).
11. Nissen, R.M. & Yamamoto, K.R. The glucocorticoid receptor inhibits NFKB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 14, 2314-2329 (2000).
12. Ozcelik, T. et al. Small nuclear ribonucleoprotein polypeptide N (SNRPN), an expressed gene in the Prader-Willi syndrome critical region. Nat. Genet. 2, 265-269 (1992).
13. Reed, M.L. & Leff, S.E. Maternal imprinting of human SNRPN, a gene deleted in Prader-Willi syndrome. Nat. Genet. 6, 163-167 (1994).
14. Patturajan, M. et al. Growth-related changes in phosphorylation of yeast RNA polymerase II. J. Biol. Chem. 273, 4689-4694 (1998).
15. Li, E., Beard, C. & Jaenisch, R. Role for DNA methylation in genomic imprinting. Nature 366, 362-365 (1993).
16. Feil, R. & Khosla, S. Genomic imprinting in mammals: an interplay between chromatin and DNA methylation? Trends Genet. 15, 431-435 (1999).
17. Hu, J.F., Oruganti, H., Vu, T.H. & Hoffman, A.R. The role of histone acetylation in the allelic expression of the imprinted human insulin-like growth factor II gene. Biochem. Biophys. Res. Commun. 251, 403-408 (1998).
18. Saitoh, S. & Wada, T. Parent-of-origin specific histone acetylation and reactivation of a key imprinted gene locus in Prader-Willi syndrome. Am. J. Hum. Genet. 66, 1958-1962 (2000).
19. Braun, A., Little, D.P. & Koster, H. Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. Clin. Chem. 43, 1151-1158 (1997).
20. Jurinke, C., van den Boom, D., Cantor, C.R. & Koster, H. Automated genotyping using the DNA MassArray technology. Methods Mol. Biol. 170, 103-116 (2001).
21. Griffin, T.J. & Smith, L.M. Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry. Trends Biotechnol. 18, 77-84 (2000).
22. McGuire, W., Hill, A.V.S., Allsopp, C.E.M., Greenwood, B.M. & Kwiatkowski, D. Variation in the TNF-α promoter region associated with susceptibility to cerebral malaria. Nature 371, 508-511 (1994).
23. Cabrera, M. et al. Polymorphism in tumor necrosis factor genes associated with mucocutaneous leishmaniasis. J. Exp. Med. 182, 1259-1264 (1995).
24. Moffatt, M.F. & Cookson, W.O. Tumour necrosis factor haplotypes and asthma. Hum. Mol. Genet. 6, 551-554 (1997).
25. Shaw, M.A. et al. Association and linkage of leprosy phenotypes with HLA class II and tumour necrosis factor genes. Genes Immun. 2, 196-204 (2001).
26. Wilson, A.G., Symons, J.A., McDowell, T.L., McDevitt, H.O. & Duff, G.W. Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc. Natl. Acad. Sci. USA 94, 3195-3199 (1997).
27. Brinkman, B.M.N., Zuijdgeest, D., Kaigzel, E.L., Breedveld, F.C. & Verweij, C.L. Relevance of the tumor necrosis factor α-308 promoter polymorphism in TNFα gene regulation. J. Inflamm. 46, 32-41 (1996).
28. Dausset, J. et al. Centre d'etude du polymorphisme humain (CEPH): collaborative genetic mapping of the human genome. Genomics 6, 575-577 (1990).
29. Nedwin, G.E. et al. Human lymphotoxin and tumor necrosis factor genes: structure, homology and chromosomal location. Nucleic Acids Res. 13, 6361-6373 (1985).
30. Paul, N.L. & Ruddle, N.H. Lymphotoxin. Annu. Rev. Immunol. 6, 407-438 (1988).
31. Roach, D.R. et al. Secreted lymphotoxin-α is essential for the control of an intracellular bacterial infection. J. Exp. Med. 193, 239-246 (2001).
32. Engwerda, C.R. et al. Locally up-regulated lymphotoxin-α, not systemic tumor necrosis factor α, is the principle mediator of murine cerebral malaria. J. Exp. Med. 195, 1371-1377 (2002).
33. Ozaki, K. et al. Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction. Nat. Genet. 32, 650-654 (2002).
34. Messer, G. et al. Polymorphic structure of the tumor necrosis factor (TNF) locus: an Ncol polymorphism in the first intron of the human TNF-β gene correlates with a variant amino acid in position 26 and a reduced level of TNF-β production. J. Exp. Med. 173, 209-219 (1991).
35. Whichelow, C.E., Hitman, G.A., Raafat, I., Bottazzo, G.F. & Sachs, J.A. The effect of TNFB gene polymorphism on TNF-α and -β secretion levels in patients with insulin-dependent diabetes mellitus and healthy controls. Eur. J. Immunogenet. 23, 425-435 (1996).
36. Gabriel, S.B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225-2229 (2002).
37. Kwiatkowski, D. et al. TNF concentration in fatal cerebral, non-fatal cerebral, and uncomplicated Plasmodium falciparum malaria. Lancet 336, 1201-1204 (1990).
38. Sakatani, T. et al. Epigenetic heterogeneity at imprinted loci in normal populations. Biochem. Biophys. Res. Commun. 283, 1124-1130 (2001).
39. Richardson, A. et al. Nucleotide diversity of the TNF gene region in an African village. Genes Immun. 2, 343-348 (2001).
40. Takahashi, Y., Rayman, J.B. & Dynlacht, B.D. Analysis of promoter binding by the E2F and pRB families in vivo: distinct E2F proteins mediate activation and repression. Genes Dev. 14, 804-816 (2000).
41. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).