Epigenetic regulation and nucleosome positioning in the human TATA-less IL-1α promoter

Genes and Immunity

Volumn 9, Issue 7, 2008, Pages 582-590

  van Rietschoten, J G I ^a,b   Gal Yam, E N ^b   Jeong, S ^b   Cortez, C C ^b   Verweij, C L ^a   Jones, P A ^b  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTERLEUKIN 1ALPHA; MESSENGER RNA; METHYL CPG BINDING PROTEIN;

ARTICLE; CELL TYPE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; CONTROLLED STUDY; CYTOKINE RELEASE; DNA METHYLATION; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC EPIGENESIS; HUMAN; HUMAN CELL; IMMUNOREGULATION; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN LOCALIZATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TATA BOX; TRANSCRIPTION REGULATION;

CELL LINE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; HUMANS; INTERLEUKIN-1ALPHA; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; TATA BOX;

EID: 67651160569     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/gene.2008.53     Document Type: Article

References (29)

1. Lee GR, Kim ST, Spilianakis CG, Fields PE, Flavell RA. T helper cell differentiation: Regulation by cis elements and epigenetics. Immunity 2006; 24: 369-379.
2. Combarros O, Sanchez-Guerra M, Infante J, Llorca J, Berciano J. Gene dose-dependent association of interleukin-1A [-889] allele 2 polymorphism with Alzheimer's disease. J Neurol 2002; 249: 1242-1245.
3. Grone A. Keratinocytes and cytokines. Vet Immunol Immunopathol 2002; 88: 1-12.
4. Huang TT, Vinci JM, Lan L, Jeffrey JJ, Wilcox BD. Serotonin-inducible transcription of interleukin-1alpha in uterine smooth muscle cells requires an AP-1 site: Cloning and partial characterization of the rat IL-1alpha promoter. Mol Cell Endocrinol 1999; 152: 21-35.
5. Dinarello CA. Biologic basis for interleukin-1 in disease. Blood 1996; 87: 2095-2147.
6. Zaldivar F, Nugent DJ, Imfeld K, Berman MA. Identification of a novel regulatory element in the human interleukin 1 alpha (IL-1alpha) gene promoter. Cytokine 2002; 20: 130-135.
7. McDowell TL, Symons JA, Duff GW. Human interleukin-1 alpha gene expression is regulated by Sp1 and a transcriptional repressor. Cytokine 2005; 30: 141-153.
8. van Rietschoten JG, Verzijlbergen KF, Gringhuis SI, van der Pouw Kraan TC, Bayley JP, Wierenga EA et al. Differentially methylated alleles in a distinct region of the human interleukin-1alpha promoter are associated with allele-specific expression of IL-1alpha in CD4+ T cells. Blood 2006; 108: 2143-2149.
9. Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007; 128: 707-719.
10. Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet 2008; 9: 15-26.
11. Gal-Yam EN, Jeong S, Tanay A, Egger G, Lee AS, Jones PA. Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genet 2006; 2 e160.
12. Lin JC, Jeong S, Liang G, Takai D, Fatemi M, Tsai YC et al. Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell 2007; 12: 432-444.
13. Chen X, Wang J, Woltring D, Gerondakis S, Shannon MF. Histone dynamics on the interleukin-2 gene in response to T-cell activation. Mol Cell Biol 2005; 25: 3209-3219.
14. Bert AG, Johnson BV, Baxter EW, Cockerill PN. A modular enhancer is differentially regulated by GATA and NFAT elements that direct different tissue-specific patterns of nucleosome positioning and inducible chromatin remodeling. Mol Cell Biol 2007; 27: 2870-2885.
15. Goriely S, Demonté D, Nizet S, De Wit D, Willems F, Goldman M et al. Human IL-12(p35) gene activation involves selective remodeling of a single nucleosome within a region of the promoter containing critical Sp1-binding sites. Blood 2003; 101: 4894-4902.
16. Agalioti T, Lomvardas S, Parekh B, Yie J, Maniatis T, Thanos D. Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell 2000; 103: 667-678.
17. Rando OJ, Ahmad K. Rules and regulation in the primary structure of chromatin. Curr Opin Cell Biol 2007; 19: 250-256.
18. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z et al High-resolution mapping and characterization of open chromatin across the genome. Cell 2008; 132: 311-322.
19. Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 2007; 25 244-248.
20. Ganapathi M, Singh GP, Sandhu KS, Brahmachari SK, Brahmachari V. A whole genome analysis of 5′ regulatory regions of human genes for putative cis-acting modulators of nucleosome positioning. Gene 2007; 391 242-251.
21. Isogai Y, Keles S, Prestel M, Hochheimer A, Tjian R. Transcription of histone gene cluster by differential core-promoter factors. Genes Dev 2007; 21: 2936-2949.
22. Liang G, Lin JC, Wei V, Yoo C, Cheng JC, Nguyen CT et al. Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc Natl Acad Sci USA 2004; 101: 7357-7362.
23. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW et al A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 1992; 89: 1827-1831.
24. Fatemi M, Pao MM, Jeong S, Gal-Yam EN, Egger G, Weisenberger DJ et al Footprinting of mammalian promoters: Use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res 2005; 33: E176.
25. Davies N, Freebody J, Murray V. Chromatin structure at the flanking regions of the human beta-globin locus control region DNase I hypersensitive site-2: Proposed nucleosome positioning by DNA-binding proteins including GATA-1. Biochim Biophys Acta 2004; 1679: 201-213.
26. Agarwal S, Viola JP, Rao A. Chromatin-based regulatory mechanisms governing cytokine gene transcription [Review] [56 refs]. J Allergy Clin Immunol 1999; 103: 990.
27. Ehrlich M. Expression of various genes is controlled by DNA methylation during mammalian development. J Cell Biochem 2003; 88: 899-910.
28. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A. Widespread monoallelic expression on human autosomes. Science 2007; 318 1136-1140.
29. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 2005; 120: 169-181.