Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Molecular Systems Biology

Volumn 4, Issue , 2008, Pages

  Sneppen, Kim ^a   Micheelsen, Mille A ^a   Dodd, Ian B ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Epigenetics; Histone modification; Signal integration; Threshold; Transcription factor

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

ARTICLE; GENE CONTROL; GENE EXPRESSION; NUCLEOSOME; POSITIVE FEEDBACK; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN MODIFICATION; BIOLOGICAL MODEL; CHROMOSOME; DNA RESPONSIVE ELEMENT; FEEDBACK SYSTEM; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; PROTEIN PROCESSING; SIGNAL TRANSDUCTION;

EUKARYOTA;

CHROMOSOMES; EPIGENESIS, GENETIC; FEEDBACK, BIOCHEMICAL; GENE EXPRESSION REGULATION; HISTONES; MODELS, BIOLOGICAL; NUCLEOSOMES; PROMOTER REGIONS (GENETICS); PROTEIN PROCESSING, POST-TRANSLATIONAL; RESPONSE ELEMENTS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 42149184620     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2008.21     Document Type: Article

References (24)

1. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA (2007) Rational design of memory in eukaryotic cells. Genes Dev 21: 2271-2276
2. Anderson JD, Lowary PT, Widom J (2001) Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites. J Mol Biol 307: 977-985
3. Burz DS, Rivera-Pomar R, Jackle H, Hanes SD (1998) Cooperative DNA-binding by Bicoid provides a mechanism for threshold-dependent gene activation in the Drosophila embryo. EMBO J 17: 5998-6009
4. Carey M (1998) The enhanceosome and transcriptional synergy. Cell 92: 5-8
5. Carey M, Lin YS, Green MR, Ptashne M (1990) A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives. Nature 345: 361-364
6. Demers C, Chaturvedi CP, Ranish JA, Juban G, Lai P, Morle F, Aebersold R, Dilworth FJ, Groudine M, Brand M (2007) Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Mol Cell 27: 573-584
7. Dodd IB, Micheelsen MA, Sneppen K, Thon G (2007) Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129: 813-822
8. Eberharter A, Becker PB (2002) Histone acetylation: a switch between repressive and permissive chromatin. EMBO Rep 31: 224-229
9. Ferrell Jr JE (1996) Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci 21: 460-466
10. Fiering S, Whitelaw E, Martin DI (2000) To be or not to be active: the stochastic nature of enhancer action. BioEssays 22: 381-387
11. Grunstein M (1998) Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell 93: 325-328
12. Koshland Jr DE, Goldbeter A, Stock JB (1982) Amplification and adaptation in regulatory and sensory systems. Science 217: 220-225
13. Miller JA, Widom J (2003) Collaborative competition mechanism for gene activation in vivo. Mol Cell Biol 23: 1623-1632
14. Naar AM, Lemon BD, Tjian R (2001) Transcriptional coactivator complexes. Annu Rev Biochem 70: 475-501
15. Newlands S, Levitt LK, Robinson CS, Karpf AB, Hodgson VR, Wade RP, Hardeman EC (1998) Transcription occurs in pulses in muscle fibers. Genes Dev 12: 2748-2758
16. Riviere I, Sunshine MJ, Littman DR (1998) Regulation of IL-4 expression by activation of individual alleles. Immunity 9: 217-228
17. Rossi FM, Kringstein AM, Spicher A, Guicherit OM, Blau HM (2000) Transcriptional control: rheostat converted to on/off switch. Mol Cell 6: 723-728
18. Schreiber SL, Bernstein BE (2002) Signaling network model of chromatin. Cell 111: 771-778
19. Struhl K (1998) Histone acetylation and transcriptional regulatory mechanisms. Genes Dev 12: 599-606
20. Swigut T, Wysocka J (2007) H3K27 demethylases, at long last. Cell 131: 29-32
21. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14: 1025-1040
22. Turner BM (1998) Histone acetylation as an epigenetic determinant of long-term transcriptional competence. Cell Mol Life Sci 54: 21-31
23. Vermeulen M, Mulder KW, Denissov S, Pijnappel WW, van Schaik FM, Varier RA, Baltissen MP, Stunnenberg HG, Mann M, Timmers HT (2007) Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131: 58-69
24. Vignali M, Steeger DJ, Neely KE, Workman JL (2000) Distribution of acetylated histones resulting form Gal4-VP16 recruitment of SAGA and NuA4 complexes. EMBO J 19: 2629-2640