Circle ligation of in vitro assembled chromatin indicates a highly flexible structure

Nucleic Acids Research

Volumn 30, Issue 23, 2002, Pages 5103-5109

  Stein, A ^a   Dalal, Y ^a   Fleury, T J ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA FRAGMENT; EXODEOXYRIBONUCLEASE III; HISTONE; MAGNESIUM; NAKED DNA; PLASMID DNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; POLYGLUTAMIC ACID; SODIUM CHLORIDE;

CHICKEN; CHROMATIN STRUCTURE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DNA CONTENT; DNA STRUCTURE; GENE CONTROL; IN VITRO STUDY; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN ASSEMBLY; REVIEW;

ANIMALS; CHROMATIN; DNA; DNA LIGASES; DNA, CIRCULAR; HISTONES; NUCLEOSOMES; ULTRACENTRIFUGATION;

GALLUS GALLUS;

EID: 0036920409     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf671     Document Type: Review

References (33)

1. Schleif,R. (1992) DNA looping. Annu. Rev. Biochem, 61, 199-223.
2. Wijgerde,M., Grosveld,F. and Fraser,P. (1995) Transcription complex stability and chromatin dynamics in vivo. Nature, 377, 209-213.
3. Ptashne,M. and Gann,A. (1997) Transcriptional activation by recruitment. Nature, 386, 569-577.
4. Finch,J.T. and Klug,A. (1976) Solenoidal model for superstructure in chromatin. Proc. Natl Acad. Sci. USA, 73, 1897-1901.
5. Thoma,F., Koller,T.H. and Klug,A. (1979) Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J. Cell Biol., 83, 403-427.
6. Woodcock,C.L., Grigoryev,S.A., Horowitz,R.A. and Whitaker,N. (1993) A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc. Natl Acad. Sci. USA, 90, 9021-9025.
7. Zlatanova,J., Leuba,S.H., Yang,G., Bustamante,C. and van Holde,K. (1994) Linker DNA accessibility in chromatin fibers of different conformations: a reevaluation. Proc. Natl Acad. Sci. USA, 91, 5277-5280.
8. Woodcock,C.L. and Horowitz,R.A. (1995) Chromatin organization re-evaluated. Trends Cell Biol., 5, 272-277.
9. van Holde,K.E. and Zlatanova,J. (1995) Chromatin higher order structure: chasing a mirage? J. Biol. Chem., 270, 8373-8376.
10. Garcia-Ramirez,M., Rocchini,C. and Ausio,J. (1995) Modulation of chromatin folding by histone acetylation. J. Biol. Chem., 270, 17923-17928.
11. Ringrose,L., Chabanis,S., Angrand,P., Woodroofe,C. and Stewart,A.F. (1999) Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances. EMBO J., 18, 6630-6641.
12. Jeong,S., Lauderdale,J.D. and Stein,A. (1991) Chromatin assembly on plasmid DNA in vitro: apparent spreading of nucleosome alignment from one region of pBR327 by histone H5. J. Mol. Biol., 222, 1131-1147.
13. Lauderdale,J.D. and Stein,A. (1992) Introns of the chicken ovalbumin gene promote nucleosome alignment in vitro. Nucleic Acids Res., 20, 6589-6596.
14. Liu,K. and Stein,A. (1997) DNA sequence encodes information for nucleosome array formation. J. Mol. Biol., 270, 559-573.
15. Stein,A. and Bina,M. (1999) A signal encoded in vertebrate DNA that influences nucleosome positioning and alignment. Nucleic Acids Res., 27, 848-853.
16. Schwarz,P.M. and Hansen,J.C. (1994) Formation and stability of higher order chromatin structures. J. Biol. Chem., 269, 16284-16289.
17. Stein,A. and Bina,M. (1984) A model chromatin assembly system: factors affecting nucleosome spacing. J. Mol. Biol., 178, 341-363.
18. Germond,J.E., Hirt,B., Oudet,P., Gross-Bellard,M. and Chambon,P. (1975) Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc. Natl Acad. Sci. USA, 72, 1843-1847.
19. Simpson,R.T., Thoma,F. and Brubaker,J.M. (1985) Chromatin reconstituted from tandemly repeated cloned fragments and core histones: A model system for study of higher order structure. Cell, 42, 799-808.
20. Peck,L.J. and Wang,J.C. (1983) Energetics of B to Z transition in DNA. Proc. Natl Acad. Sci. USA, 80, 6206-6210.
21. Strauss,F. and Prunell,A. (1982) Nucleosome spacing in rat liver chromatin. A study with exonuclease III. Nucleic Acids Res., 10, 2275-2293.
22. van Holde,K.E. and Weischet,W.O. (1978) Boundary analysis of sedimentation-velocity experiments with monodisperse and paucidisperse solutes. Biopolymers, 17, 1387-1403.
23. Butler,P.J.G. and Thomas,J.O. (1980) Changes in chromatin folding in solution. J. Mol. Biol., 140, 505-529.
24. Cantor,C.R. and Schimmel,P.R. (1980) Biophysical Chemistry, part II. W.H.Freeman and Co., San Francisco, pp. 560-561.
25. Widom,J. (1986) Physicochemical studies of the folding of the 100Å nucleosome filament into the 300Å filament. Cation dependence. J. Mol. Biol., 190, 411-424.
26. Jacobson,H. and Stockmayer,W.H. (1950) Intramolecular reaction in polycondensations, I: the theory of linear systems. J. Chem. Phys., 18, 1600-1606.
27. Yamakawa,H. and Stockmayer,W.H. (1972) Statistical mechanics of wormlike chains. II. Excluded volume effects. J. Chem. Phys., 57, 2843-2854.
28. Shimada,J. and Yamakawa,H. (1984) Ring closure probabilities for twisted wormlike chains: application to DNA. Macromolecules, 17, 689-698.
29. Shore,D., Langowski,J. and Baldwin,R.L. (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl Acad. Sci. USA, 78, 4833-4837.
30. Carruthers,L.M., Bednar,J., Woodcock,C.L. and Hansen,J.C. (1998) Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: Mechanistic ramifications for higher-order chromatin folding. Biochemistry, 37, 14776-14787.
31. Lorch,Y., La Pointe,J.W. and Kornberg,R.D. (1987) Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell, 49, 203-210.
32. Stein,A. (1979) DNA folding by histones: the kinetics of chromatin core particle assembly and the interaction of nucleosomes with histones. J. Mol. Biol., 130, 103-134.
33. Bednar,J. Horowitz,R.A., Grigoryev,S.A., Carruthers,L.M., Hansen,J.C., Koster,A.J. and Woodcock,C.L. (1998) Nucleosomes, linker DNA and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc. Natl Acad. Sci. USA, 95, 14173-14178.