Figure 2
From: Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters
Single-molecule force spectroscopy reveals not only unstacking and unwrapping of nucleosomes in chromatin fibers but also large rupture events indicative of trans-interactions between remote parts of the chromatin fiber. (A). Example of an experimental stretching curve. Points are recorded data; the red line shows the model fitting. Different stages of the fiber stretching are indicated with numbers referring to the respective transition shown in (B). “0” indicates the extension of the bare DNA. (B). Statistical mechanics model for the single-molecule nucleosome array stretching. Free energy—extension scheme illustrating different stages of the nucleosome array extension under the influence of the stretching force. Deformation of the fiber includes (1) extension of the folded array; (2) transition of the array from a fiber to a bead-on-a-string chain accompanied by nucleosome unstacking and partial DNA unwinding; (3) deformation of the nucleosomes with further DNA unpeeling and possible dissociation of the histone dimer(s); (4) largely irreversible one-step rupture of the last turn of the DNA wrapped on the histone core. A detailed description of the model is given in the Material and Methods section. (C–E) λ-arrays form heterogeneous nucleosome clusters. Sample curves of the λ-array stretching recorded for the HO:DNA ratios 1.0 (C), 0.8 (D), and 0.5 (E). (F,G) native DNA array at HO:DNA ratio 0.9 (F) and ratio 0.5 (G). (H,I) Stretching curves of the arrays reconstituted on the ‘601’ positioning DNA template: (H) 197-75 array; (I) 197-45 array. Inserts show low-force regions corresponding to the stretching of the compacted arrays. Arrows indicate cluster–cluster ruptures. In each panel, the horizontal bar corresponds to 0.5 μm. Points connected by the lines are experimential data, smooth curves are statistical mechanics model fitting, and arrows indicate cluster–cluster ruptures. Dashed lines show the extension of the bare DNA calculated using the DNA contour length and the WLC model. OriginPro software75 (http://www.originlab.com) was used to create the graphs in (A) and (C–I). Microsoft PowerPoint 2016 (http://www.microsoft.com) was used to draw the image in (B).
