A 'one-pot' Assay for the Accessibility of DNA in a Nucleosome Core Particle

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2004 Aug 27

PMID 15329384

Citations 9

Authors

Chenyi Wu

Andrew Travers

Affiliations

Soon will be listed here.

Abstract

The accessibility of nucleosomal DNA to transcription factors and other sequence-specific DNA binding proteins is of importance in the consideration of mechanisms of transcriptional control. Here, we report a simple novel assay which determines this accessibility at eight different rotationally equivalent sites on nucleosomal DNA and shows that linker histones and the chromosomal HMGB proteins, HMG-D and HMG-Z, have opposite effects on the accessibility of nucleosomal DNA. We compare this assay to previously described methods.

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References

Fitzgerald D, Anderson J . DNA distortion as a factor in nucleosome positioning. J Mol Biol. 1999; 293(3):477-91. DOI: 10.1006/jmbi.1999.3171. View

Polach K, Widom J . Restriction enzymes as probes of nucleosome stability and dynamics. Methods Enzymol. 1999; 304:278-98. DOI: 10.1016/s0076-6879(99)04017-3. View

Gottesfeld J, Luger K . Energetics and affinity of the histone octamer for defined DNA sequences. Biochemistry. 2001; 40(37):10927-33. DOI: 10.1021/bi0109966. View

Ner S, Blank T, Perez-Paralle M, Grigliatti T, Becker P, Travers A . HMG-D and histone H1 interplay during chromatin assembly and early embryogenesis. J Biol Chem. 2001; 276(40):37569-76. DOI: 10.1074/jbc.M105635200. View

Widom J . Role of DNA sequence in nucleosome stability and dynamics. Q Rev Biophys. 2002; 34(3):269-324. DOI: 10.1017/s0033583501003699. View

Anderson J, Thastrom A, Widom J . Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Mol Cell Biol. 2002; 22(20):7147-57. PMC: 139820. DOI: 10.1128/MCB.22.20.7147-7157.2002. View

Srinivas Bharath M, Chandra N, Rao M . Molecular modeling of the chromatosome particle. Nucleic Acids Res. 2003; 31(14):4264-74. PMC: 167642. DOI: 10.1093/nar/gkg481. View

Ragab A, Travers A . HMG-D and histone H1 alter the local accessibility of nucleosomal DNA. Nucleic Acids Res. 2003; 31(24):7083-9. PMC: 291865. DOI: 10.1093/nar/gkg923. View

Thastrom A, Gottesfeld J, Luger K, Widom J . Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments. Biochemistry. 2004; 43(3):736-41. DOI: 10.1021/bi0302043. View

10.

Thastrom A, Bingham L, Widom J . Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J Mol Biol. 2004; 338(4):695-709. DOI: 10.1016/j.jmb.2004.03.032. View

11.

Angelov D, Lenouvel F, Hans F, Muller C, Bouvet P, Bednar J . The histone octamer is invisible when NF-kappaB binds to the nucleosome. J Biol Chem. 2004; 279(41):42374-82. DOI: 10.1074/jbc.M407235200. View

12.

Satchwell S, Drew H, Travers A . Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986; 191(4):659-75. DOI: 10.1016/0022-2836(86)90452-3. View

13.

Polach K, Widom J . Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J Mol Biol. 1995; 254(2):130-49. DOI: 10.1006/jmbi.1995.0606. View

14.

Payet D, Travers A . The acidic tail of the high mobility group protein HMG-D modulates the structural selectivity of DNA binding. J Mol Biol. 1997; 266(1):66-75. DOI: 10.1006/jmbi.1996.0782. View

15.

An W, Leuba S, van Holde K, Zlatanova J . Linker histone protects linker DNA on only one side of the core particle and in a sequence-dependent manner. Proc Natl Acad Sci U S A. 1998; 95(7):3396-401. PMC: 19847. DOI: 10.1073/pnas.95.7.3396. View

16.

An W, van Holde K, Zlatanova J . Linker histone protection of chromatosomes reconstituted on 5S rDNA from Xenopus borealis:a reinvestigation. Nucleic Acids Res. 1998; 26(17):4042-6. PMC: 147788. DOI: 10.1093/nar/26.17.4042. View

17.

Zhou Y, Gerchman S, Ramakrishnan V, Travers A, Muyldermans S . Position and orientation of the globular domain of linker histone H5 on the nucleosome. Nature. 1998; 395(6700):402-5. DOI: 10.1038/26521. View

18.

An W, van Holde K, Zlatanova J . The non-histone chromatin protein HMG1 protects linker DNA on the side opposite to that protected by linker histones. J Biol Chem. 1998; 273(41):26289-91. DOI: 10.1074/jbc.273.41.26289. View

19.

Anderson J, Widom J . Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J Mol Biol. 2000; 296(4):979-87. DOI: 10.1006/jmbi.2000.3531. View