Nucleosome array

The structure of the nucleosome is affected by ionic environment. The low ion concentration makes a nucleosomal array well spread whereas 100 mM NaCl induces nucleosome-nucleosome interaction (Hizume et al, 2005 Nakai et al, 2005 Olins and Olins, 1972 Thoma et al, 1979). In vitro transcription system has been applied to understand the relationship between the nucleosome assembly and transcription activity. The results demonstrated that a positive super-coiling introduced during the progress of RNA polymerase makes the nucleosomes ahead of the polymerase unstable (Pfaffle et al, 1990). 

In contrast, according to Fan and colleagues (Fan et al, 2002), the intramolecular folding ability of nucleosome arrays appeared to be facilitated by H2A.Z. 

Angelov D, Verdel A, An W, Bondarenko V, Hans F, Doyen CM, Studitsky VM, Hamiche A, Roeder RG, Bouvet P, Dimitrov S (2004) SWI/SNF remodeling and p300-dependent transcription of histone variant H2ABbd nucleosomal arrays. Embo J 23 3815-3824... 

Tse C, Sera T, Wolffe AP, Hansen JC (1998) Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol 18 4629 4 638... 

Steger DJ, Eberharter A, John S, Grant PA, Workman JL (1998) Purified histone acetyltransferase complexes stimulate HIV-1 transcription from preassembled nucleosomal arrays. Proc Natl Acad Sci... 

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. 

Interaction of HMGN proteins with nucleosome arrays... 

The nucleosome core particle is a relatively stable and homogenous structure that is easily prepared, and as such has formed the basis for numerous studies into chromatin structure and function. However, several recent studies have suggested that what is true for the nucleosome core may not always be true for nucleosome arrays, nor even for nucleosomes containing linker DNA. For example, the core histone tails preferentially interact with linker DNA when is it present, whereas they are constrained to bind intranucleosomal DNA in core particles [46 8]. Consequently, the activities of proteins that require access to the tails or the DNA may be affected, and it has been shown that both DNA ligase and P/CAF are less active on nucleosome core particles than other chromatin substrates [49,50]. Similar concerns apply to the interaction of HMGN proteins with nucleosome core particles, and results from studies of these complexes must be considered in the wider context of how these proteins may interact with nucleosome arrays. 

One unresolved question is whether CENP-A effects the stability of centromeric chromatin. One interesting possibility is that CENP-A promotes an unusually stable chromatin structure that is adapted to withstanding the forces exerted on the centromere during chromosome segregation [23]. Reconstitution of nucleosome arrays with CENP-A may provide insights into this question. 

In contrast, the results of Fan et al. [375] using 208-12 nucleosome arrays that had been reconstituted with a full set of recombinant histones showed that rH2A.Z enhanced the intramolecular folding of these complexes while simultaneously inhibiting the formation of higher folding structures that result from intermolecular... 

Fig. 10. A. Acetic acid-urea-triton-X-100 polyacrylamide gel electrophoresis [15] of the histones used to reconstitute 208-12 nucleosome arrays consisting of recombinant H2A.Z (lane 2) or recombinant H2A.1 (lane 3). Lanes 1 and 4 respectively are chicken erythrocyte and calf thymus histones used as markers [42]. B. Ionic strength (NaCl concentration) dependence of the average sedimentation coelRcient (s2o,w) of reconstituted 208-12 nucleosome arrays containing either H2A.1 (O) or H2A.Z ( ) [42]. The dotted line represents the behavior of a 208-12 complex reconstituted with chicken erythrocyte histones [406]. [Reproduced from Abbott D.W. et al. (2001) I. Biol. Chem. 276, 41945-41949, with permission from The American Society for Biochemistry and Molecular Biology.]...

Fig. 12. Effect of histone acetylation on the folding of nucleosome arrays lacking linker histones.

B. Effect of the ionic strength on hyperacetylated 208-12 nucleosome arrays as visualized by electron microscopy. The numbers to the left indicate the milimolar NaCl concentration [369]. [Reproduced from Garcia-Ramirez M. et al. (1995) J. Biol. Chem. 270, 17923-17928, with permission from The American Society for Biochemistry and Molecular Biology.]... 

In an attempt to study the role of this histone post-translational modification on the folding of the chromatin fiber, Jason et al. [221] performed a series of experiments using nucleosome arrays reconstituted onto the 208-12 DNA template. 

Fig. 14. Effects of histone H2A ubiquitination on the folding and solubility of chromatin [221]. A. Magnesium chloride dependence of the sedimentation coefficient (S2o,w) of 208-12 nucleosome arrays. Sedimentation coefficients at a given magnesium chloride concentration are plotted relative...

The Still limited struetural information on this intriguing post-translational modilieation seems to suggest that at least in the case of uH2A its most important role may be merely informational. Indeed, it has been suggested that histone ubiquitination could label specific chromatin domains [409 11] and as such could be a component of the histone code [121,123,165]. The structural results obtained so far with uH2A nucleosomes and nucleosome arrays clearly support this notion. 

Nucleosomal arrays reconstituted from histone octamers and 208-18 DNA... 

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