Transcription factors mediate long-range enhancer-promoter interactions

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 48, 2009, Pages 20222-20227

  Nolis, Ilias K ^a   McKay, Daniel J ^b   Mantouvalou, Eva ^a   Lomvardas, Stavros ^b,c   Merika, Menie ^a   Thanos, Dimitris ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA looping; Transcription; Transcription factors

Indexed keywords

BETA INTERFERON; DNA; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CHROMATIN; ENHANCER REGION; GENE INTERACTION; GENE LOCUS; GENE TARGETING; INSULATOR ELEMENT; PRIORITY JOURNAL; PROKARYOTIC CELL; PROMOTER REGION;

CHROMATIN IMMUNOPRECIPITATION; DNA; DNA PRIMERS; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; INTERFERON-BETA; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

PROKARYOTA;

EID: 73949116253     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0902454106     Document Type: Article

References (34)

1. Maston GA, Evans SK, Green MR (2006) Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 7:29-59.
2. Smale ST, Kadonaga JT (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72:449-479.
3. McKnight SL, KingsburyR(1982) Transcriptional control signals of a eukaryotic proteincoding gene. Science 217:316-324.
4. Atchison ML (1988) Enhancers: Mechanisms of action and cell specificity. Annu Rev Cell Biol 4:127-153.
5. Maniatis T, Goodbourn S, Fischer JA (1987) Regulation of inducible and tissue-specific gene expression. Science 236:1237-1245.
6. Merika M, Thanos D (2001) Enhanceosomes. Curr Opin Genet Dev 11:205-208.
7. Cook PR (2003) Nongenic transcription, gene regulation and action at a distance. J Cell Sci 116:4483-4491.
8. Fraser P (2006) Transcriptional control thrown for a loop. Curr Opin Genet Dev 16:490-495.
9. Kadauke S, Blobel GA (2009) Chromatin loops in gene regulation. Biochim Biophys Acta 1789:17-25.
10. Vilar JM, Saiz L (2005) DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise. Curr Opin Genet Devt 15:136-144.
11. Drissen R, et al. (2004) The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes Dev 18:2485-2490.
12. Jing H, et al. (2008) Exchange ofGATAfactors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. Mol Cell 29:232-242.
13. Liu Z, Garrard WT (2005) Long-range interactions between three transcriptional enhancers, active Vκgene promoters, and a 3′ boundary sequence spanning 46 kilobases. Mol Cell Biol 25:3220-3231.
14. Tolhuis B, Palstra RJ, Splinter E, Grosveld F, de Laat W (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 10:1453-1465.
15. Hatzis P, Talianidis I (2002) Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol Cell 10:1467-1477.
16. Wang Q, Carroll JS, Brown M (2005) Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell 19:631-642.
17. Szutorisz H, Dillon N, Tora L (2005) The role of enhancers as centres for general transcription factor recruitment. Trends Biochem Sci 30:593-599.
18. Marenduzzo D, Faro-Trindade I, Cook PR (2007) What are the molecular ties that maintain genomic loops? Trends Genet 23:126-133.
19. Fan CM, Maniatis T (1989) Two different virus-inducible elements are required for human beta-interferon gene regulation. EMBO J 8:101-110.
20. Goodbourn S, Zinn K, Maniatis T (1985) Human beta-interferon gene expression is regulated by an inducible enhancer element. Cell 41:509-520.
21. Agalioti T, et al. (2000) Ordered recruitment of chromatin modifying and general transcription factors to the IFN-β promoter. Cell 103:667-678.
22. Lomvardas S, Thanos D (2001) Nucleosome sliding via TBP DNA binding in vivo. Cell 106:685-696.
23. Parekh BS, Maniatis T (1999) Virus infection leads to localized hyperacetylation of histones H3 and H4 at the IFN-β promoter. Mol C ell 3:125-129.
24. Thanos D, Maniatis T (1995) Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83:1091-1100.
25. Bertolino E, Singh H (2002) POU/TBP cooperativity: A mechanism for enhancer action from a distance. Mol Cell 10:397-407.
26. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306-1311.
27. Kunsch C, Ruben SM, Rosen CA (1992) Selection of optimal κB/Rel DNA-binding motifs: Interaction of both subunits of NF-κB with DNA is required for transcriptional activation. Mol Cell Biol 12:4412-4421.
28. Dodd IB, et al. (2004) Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev 18:344-354.
29. Minezaki Y, Homma K, Nishikawa K (2005) Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea. DNA Research 12:269-280.
30. Bartkuhn M, Renkawitz R (2008) Long range chromatin interactions involved in gene regulation. Biochim Biophys Acta 1783:2161-2166.
31. Calhoun VC, Stathopoulos A, Levine M (2002) Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex. Proc Natl Acad Sci USA 99:9243-9247.
32. Lomvardas S, et al. (2006) Interchromosomal interactions and olfactory receptor choice. Cell 126:403-413.
33. Li Q, Barkess G, Qian H (2006) Chromatin looping and the probability of transcription. Trends Genet 22:197-202.
34. Apostolou E, Thanos D (2008) Virus infection induces NF-κB- dependent interchromosomal associations mediating monoallelic IFN-β gene expression. Cell 134:85-96.