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. 1998 Nov 24;95(24):14173-8.
doi: 10.1073/pnas.95.24.14173.

Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin

J Bednar  1 , R A Horowitz, S A Grigoryev, L M Carruthers, J C Hansen, A J Koster, C L Woodcock
Affiliations

Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin

J Bednar et al. Proc Natl Acad Sci U S A. .

Abstract

The compaction level of arrays of nucleosomes may be understood in terms of the balance between the self-repulsion of DNA (principally linker DNA) and countering factors including the ionic strength and composition of the medium, the highly basic N termini of the core histones, and linker histones. However, the structural principles that come into play during the transition from a loose chain of nucleosomes to a compact 30-nm chromatin fiber have been difficult to establish, and the arrangement of nucleosomes and linker DNA in condensed chromatin fibers has never been fully resolved. Based on images of the solution conformation of native chromatin and fully defined chromatin arrays obtained by electron cryomicroscopy, we report a linker histone-dependent architectural motif beyond the level of the nucleosome core particle that takes the form of a stem-like organization of the entering and exiting linker DNA segments. DNA completes approximately 1.7 turns on the histone octamer in the presence and absence of linker histone. When linker histone is present, the two linker DNA segments become juxtaposed approximately 8 nm from the nucleosome center and remain apposed for 3-5 nm before diverging. We propose that this stem motif directs the arrangement of nucleosomes and linker DNA within the chromatin fiber, establishing a unique three-dimensional zigzag folding pattern that is conserved during compaction. Such an arrangement with peripherally arranged nucleosomes and internal linker DNA segments is fully consistent with observations in intact nuclei and also allows dramatic changes in compaction level to occur without a concomitant change in topology.

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Figures

Figure 1
Figure 1
(a, b, and k) Soluble chromatin from chicken erythrocyte nuclei vitrified in ≈5 mM M+ and imaged unfixed and unstained in the frozen hydrated state. Nucleosomes and linker DNA are seen in many different orientations in these projections of the 3D structure. Arrows in b and k denote nucleosomes with the linker histone-dependent “stem” conformation described in the text. (c, d, and f–i) EC-M of unstained, unfixed chromatin reconstituted onto tandem DNA sequences containing the nucleosome-positioning sequence of 5S rDNA (30) and vitrified in 10 mM M+. All samples except c contain linker histone H5. En face views of nucleosomes (f, g, and i) show the linker DNA entering and exiting the nucleosome tangentially, then “intersecting” and remaining apposed for 3–5 nm before diverging (arrows). Edge-on views (h) show the two gyres of DNA (arrowheads) and the apposition of linker DNA (arrow). (c) Reconstituted hexanucleosomes without histone H5. In most nucleosomes, the linker DNA segments diverge after leaving the histone core (arrows), but in some cases they appear to “cross over” (arrowhead). (d) Reconstituted hexanucleosomes as in c, but with added linker histone H5. The chromatin particles are more compact and adopt a star-like conformation in which “stem” structures are common (arrows). (e) EC-M images of small oligonucleosomes released from chicken erythrocyte nuclei after micrococcal nuclease digestion. A zigzag, star-like conformation is seen, and, like the reconstituted hexanucleosomes in d, linker DNA segments show the “stem” architecture (arrows). (j) Chromatin released from COS-7 cells and vitrified in 20 mM M+ again shows a 3D zigzag conformation. While most nucleosomes show the stem motif (arrows), a few (arrowhead) have a linker DNA conformation typical of H1-free chromatin. [Bars = 10 nm (f–i); 30 nm for others.]
Figure 2
Figure 2
EC-M of chromatin from COS-7 cells (a–c) vitrified in ≈40 mM ions and chicken erythrocyte nuclei (d and e) imaged in ≈15 mM ions. The fiber structure is consistent with an accordion-like compaction of the loose zigzags seen in Fig. 1. (Bar = 30 nm.)
Figure 3
Figure 3
(a) Stereo pair of a 3D model of a 9-nucleosome segment of a chicken erythrocyte chromatin fiber imaged in ≈5 mM M+. Nucleosomes and their associated “stems” are represented by pear-shaped solids, all of which point toward the fiber interior. (b) Stereo pair of a chicken erythrocyte oligonucleosome vitrified in 80 mM M+ and reconstructed from a tomographic tilt series. The quality of the reconstruction allowed nucleosome locations and linker paths to be identified, but details of nucleosome orientation and linker entry–exit sites were not resolved [Horowitz et al. (34)]. A movie of the reconstructed volume on which the model is based is available at http://www.ummed.edu/pub/r/rhorowit. (c) Models of uniform chromatin fibers based on principles discussed in Woodcock et al. (52), using the mean linker entry–exit angles measured from micrographs and reconstructions. Angles were 85° (I), 45° (II), and 34° (III). (d) Space-filling models of nucleosomes in the presence (+LH) and absence (−LH) of linker histones shown en face and in side views. With the stem conformation, differing linker paths, which appear to be energetically similar, result in differing linking numbers, ΔLk.
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References

    1. van Holde K E. Chromatin. New York: Springer; 1988.
    1. Wolffe A P. Chromatin Structure and Function. 2nd Ed. London: Academic; 1995.
    1. Thoma F, Koller T, Klug A. J Cell Biol. 1979;83:403–427. - PMC - PubMed
    1. Widom J. Annu Rev Biophys Biophys Chem. 1989;18:365–395. - PubMed
    1. van Holde K E, Zlatanova J. J Biol Chem. 1995;270:8373–8376. - PubMed

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