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. 2009 Aug 11;106(32):13317-22.
doi: 10.1073/pnas.0903280106. Epub 2009 Jul 27.

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Sergei A Grigoryev  1 , Gaurav Arya, Sarah Correll, Christopher L Woodcock, Tamar Schlick
Affiliations

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Sergei A Grigoryev et al. Proc Natl Acad Sci U S A. .

Abstract

The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Carlo simulations of nucleosome chain folding with EM-assisted nucleosome interaction capture (EMANIC). We show that at physiological concentrations of monovalent ions, linker histones lead to a tight 2-start zigzag dominated by interactions between alternate nucleosomes (i +/- 2) and sealed by histone N-tails. Divalent ions further compact the fiber by promoting bending in some linker DNAs and hence raising sequential nucleosome interactions (i +/- 1). Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chromatin fiber as inferred from both EMANIC and modeling. This conformational variability is energetically favorable as it helps accommodate DNA crossings within the fiber axis. Our results thus show that the 2-start zigzag topology and the type of linker DNA bending that defines solenoid models may be simultaneously present in a structurally heteromorphic chromatin fiber with uniform 30 nm diameter. Our data also suggest that dynamic linker DNA bending by linker histones and divalent cations in vivo may mediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Electron microscopy and modeling of unfolded and compact 12-nucleosome arrays. (A–F) Electron micrographs (platinum shadowing) of regular 207 × 12 core arrays in 5 mM NaCl (A and B), regular LH-arrays condensed in 150 mM NaCl (C) and 1 mM MgCl2 (D), and variable LH-arrays condensed in 150 mM NaCl (E) or 1 mM MgCl2 (F). (G) Average diameter of uniform and variable LH-arrays condensed in 150 mM NaCl (white columns) and 1 mM MgCl2 (black columns). Error bars represent standard errors of mean. (H–J) Models of representative 12 × 207 oligonucleosomes at 0.01 M monovalent salt without LH (H), and 0.15 M monovalent salt with LH (I), and with LH and Mg2+ (J) highlight compaction effects of linker histones and Mg2+.
Fig. 2.
Fig. 2.
Internucleosomal interaction pattern predicted for distinct chromatin 30-nm fiber models. (A–C) Interaction-intensity matrices at 0.15 M monovalent salt without LH and Mg2+ (A), with LH and without Mg2+ (B), and with both LH and Mg2+ (C) show the intensity of the tail-mediated interactions between nucleosome core i and j matrix [I′(i; j)]. (D–F) the associated plots decompose the dominant neighboring interactions, I(k), where k is the nucleosome separator. Interactions at k = 1, 2, and 3 nucleosomes are indicated as ±1, ±2, and ±3, correspondingly. (G–J) reference internucleosomal interaction patterns corresponding to the 3 existing models of nucleosome arrangement: (G) solenoid model (14), (H) 2-start zigzag model (10), and (I) interdigitated nucleosome model (17) compared with that obtained from our Monte Carlo simulations for +LH+Mg chromatin (J).
Fig. 3.
Fig. 3.
EMANIC analysis of internucleosomal interactions. (A) Scheme of the EMANIC procedure. The 2 models for the structure of the chromatin 30-nm fiber, namely solenoid (Top) and zigzag (Bottom), lead to dominant i ± 1 and i ± 2 internucleosome interactions, respectively. (B–S) Capturing internucleosomal interactions after limited formaldehyde cross-linking. EM of nucleosome reconstitutes showing uniform core arrays (B and D), variable core array (C), uniform LH-containing arrays (E, F, I–O, Q–S), and variable LH-containing arrays (G, H, P). Cross-linking was performed in 5 mM NaCl (B, C, E–G), 150 mM NaCl (D, H, I), 1 mM MgCl2 (J–M), and 4 mM MgCl2 (panels N–S). Arrows show nucleosome interactions, and asterisks indicate interacting nearest-neighbor nucleosomes connected by a short DNA loop. D′, I′, M′, and S′ diagram the nucleosome arrays corresponding to the respective EM images.
Fig. 4.
Fig. 4.
Internucleosome interactions in regular and variable nucleosomal arrays. (A–D) Internucleosomal interactions within reconstituted core nucleosome arrays (A and B) and LH-arrays (C and D) scored either without cross-linking (control) or after formaldehyde-cross-linking in the presence of 150 mM NaCl, 1 mM MgCl2, and 4 mM MgCl2. Histograms A and C show % total nucleosomes involved in no interactions (free beads), nearest neighbor (i ± 1), and loops (i ± 2 and more). Histograms B and D show % total nucleosomes involved in particular type of interaction. Student's t test P values for significant differences between the data sets are shown over the brackets. (E–H) % total nucleosomes from uniform (207 × 12) and variable (205 - 207 - 209) × 4 core (E) and LH-arrays (F–H) involved in nearest neighbor interactions (i ± 1) and 2 most prominent types of loops (i ± 2 and i ± 3). The reconstituted arrays were cross-linked by formaldehyde at 150 mM NaCl, 1 mM MgCl2, or 4 mM MgCl2 as indicated. (I) Internucleosomal interactions detected after formaldehyde-cross-linking in the presence of 4 mM MgCl2 and 5 min or 20 min digestion with 1 μg/mL trypsin as indicated.
Fig. 5.
Fig. 5.
Effect of linker histone and divalent cation on chromatin fiber compaction and associated linker DNA configurations. (A–C) Coarse-grained chromatin models of representative 48-unit oligonucleosomes at 0.15 M monovalent salt without LH (A), with LH (B), and with LH and Mg2+ (C) highlight compaction and fiber stiffening effects of linker histones as shown by the fiber axes geometry (dashed black lines). Nucleosome cores are shown by gray disks, linker DNA by large red spheres, linker histone by turquoise spheres, and individual core-histone tails are colored by yellow (H2A), red (H2B), blue (H3), and green (H4). (D and E) Space-filling models based on MC simulation of 48-unit oligonucleosome chains compacted at 0.15 M monovalent salt with LH (D), and with LH and Mg2+ (E). (D) Compaction at 150 mM NaCl leads to a 2-start zigzag chromatin fiber with predominantly i ± 2 interactions between the most proximal nucleosomes (33 and 35, 34 and 36, 36 and 38) shown by green arrows. (E) In the presence of 1 mM MgCl2, several nucleosomes have bent linkers resulting in i ± 1 interactions (nucleosomes 1 and 2, 4 and 5), interspersed with i ± 2 (1 and 3) and i ± 3 (6 and 3) interactions. Odd-numbered nucleosomes are indicated by burgundy for the DNA and blue for the cores. Even-numbered nucleosomes are indicated by red for the DNA and white for the cores.
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References

    1. Felsenfeld G, Groudine M. Controlling the double helix. Nature. 2003;421:448–453. - PubMed
    1. Richmond TJ, Davey CA. The structure of DNA in the nucleosome core. Nature. 2003;423:145–150. - PubMed
    1. Woodcock CL, Dimitrov S. Higher order structure of chromatin and chromosomes. Curr Opin Genet Dev. 2001;11:130–135. - PubMed
    1. Luger K, Hansen JC. Nucleosome and chromatin fiber dynamics. Curr Opin Struct Biol. 2005;15:188–196. - PubMed
    1. Tremethick DJ. Higher-order structures of chromatin: The elusive 30 nm fiber. Cell. 2007;128:651–654. - PubMed

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