Nucleosome distribution

The assembly of nucleosomes is mediated by one of several chromatin assembly factors facilitated by histone chaperones, proteins such as the anionic nuclear protein nucleoplasmin. As the nucleosome is assembled, histones are released from the histone chaperones. Nucleosomes appear to exhibit preference for certain regions on specific DNA molecules, but the basis for this nonrandom distribution, termed phasing, is not completely... 

Results of the 11 DNA minicircles of the series [28] are shown in Fig. 5(a) and (b) in the form of plots of the relative amounts of the two, sometimes three, adjacent topoisomers in the relaxation equilibrium distributions as functions of their ALk [29]. The pBR control nucleosome plot (Fig. 5(a)) shows shoulders or peaks centered at ALk values around —1.7, —1, and —0.5, which correspond to the closed... 

Fig. 5, Nucleosome relaxation data on the two DNA minicircle series, (a)-(c) Nucleosomes were reconstituted with control (Control) or acetylated histones (Acetylated) on ALk = —2.4 to —3.3 topoisomers of pBR 351-366 bp eleven DNA minicircles series or 5S 349-363 bp ten DNA minicircles series, and relaxed in Tris (Tris) or phosphate buffer (phosphate), as described in legend to Fig. 4(a). Topoisomer relative amounts in the equilibrium distributions (see examples in Fig. 4(c)) were plotted as functions of their ALk, calculated from Eq. (4) using h = QA94 ( 0.003) and 10.47s ( 0.003) bp/turn for pBR DNA in Tris and phosphate buffers [28], respectively, and 0 = 10.538 ( 0.006) bp/turn for 5S DNA in Tris buffer [29]. Smooth curves were calculated as described in the text. [Drawn from data in Ref [28] (Acetylated/phosphate) and adapted from Fig. 3 in Ref [29] (Control/Tris).]...

Beads-on-a-string Frequency distributions of number of nucleo somes/template vary with average nucleosome loading between 4 and 8 nucleosomes/template the distributions are broader than random and contain peaks/shoulders, indicating a tendency for correlated nucleosome loading along templates ... 

AFM imaging can visualize alternative nucleosome positioning on adjacent 2Q8-bp repeats (the distribution of center-to-center distances on 208-12 is bimodal)... 

Fig. 1. The two competing classes of models for the 30-nm fiber can be distributed into (a) solenoid models and (b) crossed-linker models. For both fiber types the side and the top view are shown. Two nucleosomes that are directly connected via DNA linker are shaded in grey. In the solenoid these nucleosomes are located on the same side of the fiber requiring the linker to be bent. In the crossed-linker case they sit on opposite sides of the fiber and are connected via a straight linker.

A more detailed view of the dynamies of a ehromatin chain was achieved in a recent Brownian dynamics simulation by Beard and Schlick [65]. Like in previous work, the DNA is treated as a segmented elastic chain however, the nueleosomes are modeled as flat cylinders with the DNA attached to the cylinder surface at the positions known from the crystallographic structure of the nucleosome. Moreover, the electrostatic interactions are treated in a very detailed manner the charge distribution on the nucleosome core particle is obtained from a solution to the non-linear Poisson-Boltzmann equation in the surrounding solvent, and the total electrostatic energy is computed through the Debye-Hiickel approximation over all charges on the nucleosome and the linker DNA. 

Fig. 2. NAPI facilitates H2A, H2B release from nucleosomes that are on positively coiled DNA (A) but not negatively coiled DNA (B). The positively coiled DNA (6.0 kb) with a superhelical density of + 0.05 and negatively coiled DNA (6.0 kb) with a superhelical density of -0.05 were reconstituted with lysine, arginine-labeled histones H3, H4, H2A, H2B by NaCl dialysis from 2.0 M to 1.2 M to 0.6 M to 0.1 M NaCl over a 14 h period. The samples were incubated with NAPI at 35 °C for 5 min and applied to a 5-20% sucrose/100 mM NaCl/40 mM Tris, pH 7.8 gradient. After sedimentation at 200,000 X g for 5 h, fractions were collected and the distribution of DNA (bottom panel) was determined on agarose gel and the distribution of protein (top panel) on SDS-PAGE followed by fluorography. These data are unpublished observations (V. Levchenko and V. Jackson). The deg-H2A is degraded H2A in which a 15 amino acid peptide of the C terminal has been proteolytically removed. When H2A, H2B is no longer present in a nucleosome, the C terminal region is sensitive to proteolysis [126] from a protease which is a minor contaminate in the NAPI preparation.

The amount of information is still insufficient to predict how packaging of DNA in chromatin modifies the final product distribution in DNA. If the stable end products reflect a doubling in reductive damage while oxidative damage remains the same, then one would expect an increase in frequency and complexity of clustered lesions. If that proves true, the histone proteins and attending nucleosomes structure would act as radiation sensitizers. 

If the DNA is only slightly bent, as observed for the nucleosome-boimd DNA, then the required deformation energy is distributed over many base pairs. Tlie energy requirement per base pair is small and can easily be provided by the interaction energy with the protein. Furthermore, such bending displays little sequence specificty. 

Although nucleosomes are distributed rather evenly along the DNA of a cell, there are some DNA sequences that favor nucleosome formation. The resulting positioned nucleosomes are often found in the vicinity of gene promoters, enhancers, and other... 

A nucleosome core particle is formed by a 146 base pairs DNA fragment wrapped 1.65 times around the histone octamer (formed by two copies of H2A, H2B, H3 and H4 histones). NCP are connected by regions of naked DNA called linkers. The nucleotide sequences of the 146 bp DNA fragments involved in nucleosomes are polymorphic. The regions of contact between DNA and the core of histones are distributed along DNA with a periodicity of around 10.4 bp, which is the number of base pairs per helical turn of DNA in the nucleosome. 

Since the maximum dimensions of the core particle are 11 11 5.7 nm features in the region s < 0.09 nm" ((11 nm) ) are mainly associated with the distribution of the nucleosomes in the fibre. The region of featureless decay (s < 0.025 nm ) in the scattering patterns can be used to determine the radius of gyration of the cross section (R ) and the extrapolated forward scattering intensity (1(0) ) which is proportional to the mass per unit length (M/L). 

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