Toward a detailed description of the thermally induced dynamics of the core promoter

PLoS Computational Biology

Volumn 5, Issue 3, 2009, Pages

  Alexandrov, Boian S ^a   Gelev, Vladimir ^b   Yoo, Sang Wook ^b   Bishop, Alan R ^a   Rasmussen, Kim Ø ^a   Usheva, Anny ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DNA SEQUENCES; MAMMALS; MOLECULAR DYNAMICS; SEPARATION; TRANSCRIPTION;

CORE PROMOTERS; DYNAMIC FEATURES; GENE TRANSCRIPTIONS; LANGEVIN MOLECULAR DYNAMICS SIMULATION; MECHANISTICS; PEYRARD BISHOPS; SEQUENCE-DEPENDENT; STRAND SEPARATION; THERMALLY INDUCED; TRANSCRIPTION INITIATION;

DNA;

DNA; RNA POLYMERASE; TRANSCRIPTION FACTOR; DNA DIRECTED RNA POLYMERASE;

ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA HELIX; DNA SEQUENCE; DNA STRAND; DNA TEMPLATE; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; REGULATORY MECHANISM; SIMULATION; TEMPERATURE SENSITIVITY; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HEAT; METHODOLOGY; MOLECULAR GENETICS; ULTRASTRUCTURE;

MAMMALIA;

BASE SEQUENCE; COMPUTER SIMULATION; DNA; DNA-DIRECTED RNA POLYMERASES; HOT TEMPERATURE; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 63549108096     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000313     Document Type: Article

References (28)

1. Cheetham GM, Zeruzalmi D, Steitz TA (1999) Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399: 80-83.
2. Fiedler U, Marc Timmers HT (2000) Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II. Bioessays 22: 316-326.
3. Timmers HT (1994) Transcription initiation by RNA polymerase II does not require hydrolysis of the beta-gamma phosphoanhydride bond of ATP. EMBO J 13: 391-399.
4. Parvin JD, Sharp PA (1993) DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 73: 533-540.
5. Leblanc Bp Fau - Benham CJ, Benham Cj Fau - Clark DJ, Clark DJ (2000) An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled. Proc Natl Acad Sci U S A 97: 10745-10750.
6. Usheva A, Shenk T (1996) YY1 transcriptional initiator: protein interactions and association with a DNA site containing unpaired strands. Proc Natl Acad Sci U S A 93: 13571-13576.
7. Pan G, Greenblatt J (1994) Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site. J Biol Chem 269: 30101-30104.
8. Choi CH, Kalosakas G, Rasmussen KO, Hiromura M, Bishop AR, et al. (2004) DNA dynamically directs its own transcription initiation. Nucleic Acids Res 32: 1584-1590.
9. Peyrard M, Bishop AR (1989) Statistical mechanics of a nonlinear model for DNA denaturation. Phys Rev Lett 62: 2755-2758.
10. Campa A, Giansanti A (1998) Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains. Phys Rev E 58: 3585.
11. Das T, Chakraborty S (2006) Helicase mediated active DNA unwinding in a stochastic field. Appl Phys Lett 89: 153901-153903.
12. Voulgarakis NK, Redondo A, Bishop AR, Rasmussen KO (2006) Probing the mechanical unzipping of DNA. Phys Rev Lett 96: 248101.
13. Ares S, Voulgarakis NK, Rasmussen KO, Bishop AR (2005) Bubble nucleation and cooperativity in DNA melting. Phys Rev Lett 94: 035504.
14. Choi CH, Rapti Z, Gelev V, Hacker MR, Alexandrov B, et al. (2008) Profiling the thermodynamic softness of adenoviral promoters. Biophys J 95: 597-608.
15. Alexandrov BS, Wille LT, Rasmussen KO, Bishop AR, Blagoev KB (2006) Bubble statistics and dynamics in double-stranded DNA. Phys Rev E 74: 050901.
16. Dauxois T, Peyrard M, Bishop AR (1993) Entropy-driven DNA denaturation. Phys Rev E 47: R44.
17. Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT (2008) The RNA polymerase II core promoter-the gateway to transcription. Curr Opin Cell Biol 20: 253-259.
18. Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, et al. (2007) Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 8: 424-436.
19. Gueron M, Kochoyan M, Leroy J-L (1987) A single mode of DNA base-pair opening drives imino proton exchange. Nature 328: 89-92.
20. van Erp TS, Cuesta-Lopez S, Hagmann JG, Peyrard M (2005) Can one predict DNA transcription start sites by studying bubbles? Phys Rev Lett 95: 218104.
21. Choi CH, Usheva A, Kalosakas G, Rasmussen KO, Bishop AR (2006) Comment on "Can one predict DNA transcription start sites by studying bubbles?" Phys Rev Lett 96: 239801.
22. Wu Z, Ono A, Kainosho M, Bax A (2001) H. . .N hydrogen bond lengths in double stranded DNA from internucleotide dipolar couplings. J Biomol NMR 19: 361-365.
23. Mitchell B, Mugiya M, Youngblom J, Funes-Duran M, Miller R, et al. (2000) The genomic structure and promoter analysis of the human ABF-1 gene. Biochim Biophys Acta 1492: 320-329.
24. Chen H, Ray-Gallet D, Zhang P, Hetherington CJ, Gonzalez DA, et al. (1995) PU.1 (Spi-1) autoregulates its expression in myeloid cells. Oncogene 11: 1549-1560.
25. Ebralidze AK, Guibal FC, Steidl U, Zhang P, Lee S, et al. (2008) PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. Genes Dev 22: 2085-2092.
26. Dornberger U, Leijon M, Fritzsche H (1999) High base pair opening rates in tracts of GC base pairs. J Biol Chem 274: 6957-6962.
27. Wells RD, Larson JE, Grant RC, Shortle BE, Cantor CR (1970) Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. J Mol Biol 54: 465-497.
28. Sponer J, Riley KE, Hobza P (2008) Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 10: 2595-2610.