Bead-on-a-string

If chromatin is swelled suddenly in water and prepared for viewing in the electron microscope, the nucleosomes are evident as beads on a string, dsDNA being the string (Figure 12.28). The structure of the histone octamer core has been determined by X-ray crystallography without DNA by E. N. Moudrianakis s laboratory (Figure 12.29) and wrapped with DNA by T. J. 

FIGURE 12.28 Electron micrograph of Drosophila melanogaster chromatin after swelling reveals the presence of nncleosomes as beads on a string. (Electron micrograph courtesy of Oscar L. Miller, Jr, of the University of Virginia)... 

Protein-protein interactions between the histone subunits are undoubtedly important in promoting formation of a nucleosome in which 146 base pairs of DNA are coiled around the outside of the histone core. One molecule of histone HI binds to an exterior region of each nucleosome, but histone HI is not needed to determine nucleo-some structure. The distance between nucleosomes is approximately 200 base pairs consequently, in electron micrographs, nucleosomes resemble evenly spaced beads on a string of DNA. Neutron and x-ray diffraction data are also consistent with this structure. 

Figure 9. Top Two tetraurea calixarene monomers connected by a rigid spacer at their bottom rim display diverging hydrogen-bonding sites ideally suited for polymerization. The polymer (53) bears capsules of ca. 1.6 nm x 2.2 nm dimensions like beads on a string. Bottom Photomicrographs of typical Schlieren textures of 53 in chloroform (top row, left) and p-difluorobenzene (top row, middle) as viewed...

Figure 4.4. Structure of actin filaments (a) shows the beads on a string appearance of an actin filament. This filament comprises actin monomers, which themselves have a polarity, so that they can only assemble head to tail , as shown in (b) thus, the actin filament is polarised, having a barbed and a pointed end.

At low ionic strength, chromatin has the appearance of beads-on-a-string as observed in the EM (Olins and Olins, 1974 Woodcock, 1973). However, it is more compact in its native environment in the nucleus (for references, see Chambon, 1978). Several levels of compaction beyond the nucleosome are required to account both for the... 

Biochemical reconstitution of the 30 nm fiber has recently been succeeded by using a salt-dialysis procedure with a long DNA template (>100 kb) (Hizume et al, 2005). AFM imaging of the reconstituted chromatin has shown that the beads-on-a-string structure of the nucleosomes ( 400 nucleosomes on 100 kb DNA) are converted to a thicker fiber in the presence of histone HI. The thickness of the fiber changes reversibly between 20 nm and 30 nm, depending on the salt environment (in 50 mM and 100 mM NaCl, respectively) (Fig. 4) namely, the linker histone directly promotes a thicker fiber formation in a salt-dependent manner. 

The genome of the eukaryotic cell is packaged in a topologically complex, fibrous superstructure known as chromatin. The nucleosome core particle is the fundamental building block of chromatin and contains 146 bp of DNA wrapped in roughly two super helical turns around an octamer of four core histones (H3, H2B, H2A and H4) resulting in a beads on a string structure. This 10 nm structure further folds and... 

DNA is wound around the outside of this octamer to form a nucleosome (a series of nucleosomes is sometimes called beads on a string ). 

We are now in a position to ask a more sophisticated question related to protein structure what is the three-dimensional structure of the protein This question assumes something that is by no means obvious that a protein has a unique three-dimensional structure. Think of the protein ribonuclease A as 124 beads on a string. You can imagine that it could fold up in a great many ways, just like you can fold up a string of beads in a great many ways. 

Beads-on-a-string morphology center-to-center distances of 36... 

Beads-on-a-string fibers seen only in Hl/H5-depleted fibers ... 

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 ... 

As already noted above, AFM imaging and quantitations on LH-stripped chromatin fibers revealed extended beads-on-a-string structures, in agreement with early EM results [17]. Nucleosomal arrays reconstituted from naked DNA fragments and histone octamers had similar appearance [36 2]. 

Several reports have used AFM imaging, in conjunction with traditional biochemical methods, to address this question (it must be noted that an in-depth AFM study of this issue is still to be performed). The AFM data suggest thus far that hyperacetylated histones isolated from cells treated with histone deacetylase inhibitors produce beads-on-a string structures somewhat more extended than those obtained using histones purified from control cells [37,38], in agreement with EM imaging results obtained on circular chromatin templates [49]. In addition, acetylation seems to enhance the non-random nucleosome-loading behavior seen in subsaturated nucleosomal arrays (see above, and Table 1). 

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