Lehmann K , Felekyan S , Kühnemuth R , Dimura M , Tóth K , Seidel CAM , Langowski J .

	Figure 1. Schematic representation of the used labeled constructs and ensemble analysis of salt-induced proximity changes between H3NtT and the nucleosomal DNA. (A) In the cartoon representations H2A–H2B dimer on α-side is shown in orange, H2A–H2B dimer on β-side is shown in yellow, (H3–H4)2 tetramer in turquoise, DNA in gray. The black triangle on the H2A–H2B dimers indicates mutated nucleosomes bearing two point mutations in the α3 domain of H2A, namely H2A R81E/R88E. The donor on H3K9C is shown as a green circle. The acceptor is shown as a red circle and labeling positions on the DNA are given as relative base shifts to the dyad axis. Dyα: acceptor close to dyad axis at position −9, Dyβ: acceptor close to dyad axis at position +21, Eα: acceptor at the end of a 170 bp long DNA at position −77, Lα(170): acceptor at position −77 on a 210 bp long DNA, mut: nucleosomes bearing the H2A R81E/R88E mutation. (B) Ensemble FRET analysis of distance changes between wild type H3NtT and various positions on the DNA. For visualization, data were normalized to the maximal and minimal amplitude of the sigmoidal fit (Equation 2). Labeled nucleosomes were measured at 300 pM total concentration after 1 h incubation in buffers with different NaCl content. (C) Ensemble FRET analysis of distance changes between H3NtT and the DNA in mutated nucleosomes. Inflection points of the proximity curves are significantly lower in mutDα and mutDyβ nucleosomes; curve progression is changed to two-step behavior in Eα and Lα(170), indicating allosteric effects induced by the mutation. (D) Results of global fit of Equation (2) to the data in B, C (for full set of fit parameters and individual fits see Supplementary Table S1 and Figure S4, respectively). Empty fields: parameter not needed in the fit, joint fields: global parameter.
	Figure 2. MFD-PIE analysis of H3NtT:DNA interactions and sub-ensemble donor decay analysis in presence of FRET based on donor–acceptor distance distribution. Data for all plots are obtained at 100 mM NaCl from 40 pM Dyβ nucleosomes in the presence of 1960 pM or 260 pM unlabeled nucleosomes. (A) MFD-plot for stoichiometry, SPIE (Equation 6) versus FRET efficiency EFRET (Equation 5). Subspecies (D1A, D2A and D1D2A) are identified according to their position in the 2D distribution and indicated with circles. (B) Sub-ensemble histogram of the donor fluorescence intensity decay (lower left panel) from the selected FRET bursts (wine box in Figure 2A) and best fit model curve (green line). The decay histogram was analyzed by two models composed of two and three species (lower right panel): (M1) one Gaussian distributed distance (blue dashed line) and a donor-acceptor NoFRET-species (purple dashed line, corresponding to the distances larger than 95 Å), and (M2) two Gaussian distributed distances (cyan and blue lines) and a donor-acceptor NoFRET-species (magenta vertical line, corresponding to the distances larger than 95 Å) (see Material and Methods: Sub-ensemble TCSPC). The weighted residuals shown on top with the reduced sum of the weighted squared deviation between the model and the data of the decay histogram, χ2r ⁠, demonstrate that higher fit quality was achieved by model M2. (C) Visualization of the dye accessible volume mean positions (spheres) for donors on both H3NtTs estimated from two distinct MD simulations: nucleosome without linker DNA (147 bp) (34): green—H3NtTα, orange—H3NtTβ, and nucleosome with linker DNA (187 bp) (25): blue—H3NtTα, purple—H3NtTβ (lighter shades indicate later simulation time). The accessible volume of the acceptor position +21 bp is shown as transparent red surface, the corresponding mean position is shown as a sphere. The preferential interaction areas of the linker DNA with the histone tails that were identified by crosslinking studies (31) are highlighted in magenta. (D) 〈RDA〉E distance distributions from two distinct MD traces in (C) computed by FPS (45) for the four cases. Two separate populations are clearly visible for H3NtTα (38–68 Å) and H3NtTβ (95–120 Å). These distance ranges agree well with the two distance ranges of experimental observations (gray regions) obtained by sub-ensemble time correlated single photon counting (seTCSPC) decay histogram analysis, Table 1.
	Figure 3. MFD analysis of H3NtT:DNA interactions in presence of FRET. (A) Dyβ: FRET efficiency (EFRET) plotted versus fluorescence weighted average donor lifetime (〈τD(A)〉F). (B) FRET efficiency (EFRET) versus fluorescence weighted average donor lifetime (〈τD(A)〉F) for mutDyβ nucleosomes. (C) Total static fractions of wt Dyβ (red bar) and mutDyβ (green bar) nucleosome samples obtained by dynPDA. (D) Eα: FRET efficiency (EFRET) plotted versus fluorescence weighted donor lifetime (〈τD(A)〉F). (E) FRET efficiency (EFRET) versus fluorescence weighted average donor lifetime (〈τD(A)〉F) for mutEα nucleosomes. (F) Total static fractions of wt Eα (red bar) and mutEα (green bar) nucleosome samples obtained by dynPDA. The orange line represents the EFRET–〈τD(A)〉F relation for static FRET species (all parameters for the FRET lines are described in Supplementary Note 1). The magenta line represents the EFRET–〈τD〉F relation for dynamic FRET species. The comparison of the total static fractions in Dyβ and Eα nucleosome samples demonstrates the fast dynamics of the DNA arm.
	Figure 4. Structural model for H3NtT conformations and observed transitions in nucleosomes. (A) Proposed four conformational states for each H3NtT. The dynPDA model reveals three possible transitions between them: (i) compact ↔ compact*, (ii) compact* ↔ extended and (iii) compact* ↔ protein associated/dim state. (B) Assignment of all possible combinations of the assumed H3NtT conformations (⁠NH3NtTa x NH3NtTb= 4 × 2 = 8 NH3NtTa x NH3NtTb=4×2=8⁠) to the five static FRET states. The dynPDA model with five static states was defined based on sub-ensemble donor decay analysis results. The states are named with respect to their corresponding FRET efficiency level. The RDA distances were extracted from the MFD measurements by dynPDA analysis. The average FRET efficiencies, 〈E〉, for species with two bright donors were calculated as arithmetical mean of two FRET efficiencies corresponding to the shown RDαA and RDβA distances (67). Bright donor and acceptor fluorophores are shown as green or red stars, respectively. Dim donor fluorophores are shown as dark green circles. (C) dynPDA model containing five static states and seven dynamics species. Green and orange arrows correspond to possible transitions in wt nucleosomes and mutated nucleosomes, respectively. Filled arrows indicate that transitions are significantly populated (>7%), whereas open arrows refer to transitions, which are allowed in the dynPDA model, but are not significantly populated according to the PDA global fit. Three transitions are generally excluded based on direct structural transition defined in (A): HF↔NoFRET, HF↔VLF and VLF↔NoFRET.
	Figure 5. Dynamic Photon Distribution Analysis (dynPDA) of Dyβ and mutDyβ nucleosomes reveals frequency of conversion between H3NtT conformations and allosteric effects. Bursts were divided into 1, 2 and 3 ms (presented here) time windows and the resulting three apparent donor-acceptor distance histograms were used for global fitting. Their distribution function was approximated by seven interconverting, dynamic species (dyn(HF↔MF), dyn(MF↔LF), dyn(HF↔LF), dyn(MF↔VLF), dyn(LF↔VLF), dyn(MF↔NoFRET) and dyn(LF↔NoFRET), lower panels B and D) and five static states (HF, MF, LF, VLF and NoFRET, top panels B and D). Donor-acceptor distances (x-axis) were calculated from integer photon counts and are affected by photon shot noise, leading to not entirely smooth distributions. Normalized contribution: the area of each distribution on these model plots is proportional to the fraction of the corresponding species. The total area of all species multiplied by the total number of time windows in the histogram represents the area under the experimental data histogram. (A) (dyn)PDA of 40 pM Dyβ plus 1960 pM unlabeled nucleosomes at 100 mM NaCl (corresponding MFD–PIE plot shown in Figure 2A). Best fit quality is shown as weighted residuals (w. res.) in the upper panel (black line). In order to demonstrate contribution of dynamic species, weighted residuals are presented (gray line) with only three major (dyn(MF↔LF), dyn(MF↔VLF) and dyn(MF↔NoFRET)) and without all (light gray line) dynamic species in the top two panels. (B) Model distribution of 〈RDA〉E distances for Dyβ nucleosomes. For the limit of large photon counts (i.e. no shot noise), the distance distribution is calculated by a sum of five Gaussian-distributed probabilities of donor-acceptor distances (top panel) and seven allowed dynamic transitions between pairs of those static species (lower panel) (56). (C) dynPDA of 40 pM mutDyβ plus 1960 pM unlabeled nucleosomes at 100 mM NaCl (corresponding MFD–PIE plot is shown in Supplementary Figure S2B). Best fit quality is shown by weighted residuals (w. res.) in the upper panel (black line). In order to demonstrate contribution of dynamic species, weighted residuals are presented (gray line) with only four major (dyn(MF↔LF), dyn(MF↔VLF), dyn(MF↔NoFRET) and dyn(LF↔NoFRET)) and without any dynamic species (light gray line) in top two panels. (D) Model distribution of 〈RDA〉E distances for mutDyβ nucleosomes. The shot noise free distance distribution is calculated by a sum of five Gaussian-distributed probabilities of donor-acceptor distances (top panel) and seven allowed dynamic transitions between pairs of those static species (lower panel, pathways see Figure 4B) (56).
	Figure 6. The interconversion between possible H3NtT conformations depends on the NaCl concentrations and can be altered by allosteric effects. Considering different NaCl concentrations, rate constants from dynPDA fits are displayed only for dynamic species with an average fraction larger than 7% in (A) Dyβ and (B) mutDyβ nucleosomes. The fractions of dynamic species in (C) Dyβ and (D) mutDyβ nucleosomes at different NaCl concentrations are shown (the 7% limit is indicated by dashed line) together with the static species fractions in (E) Dyβ and (F) mutDyβ nucleosomes. The resulting total fractions of static states in (G) Dyβ and (H) mutDyβ nucleosomes are also presented. The dynamic fractions Xdyn(A↔B) Xdyn(A↔B) are redistributed to the limiting A and B states proportional to the residence time in each state via rate constants (kAB, kBA) as X(B)dyn(A↔B)=kABkAB+kBA Xdyn(A↔B) Xdyn(A↔B)(B)=kABkAB+kBA Xdyn(A↔B) and X(A)dyn(A↔B)=kBAkAB+kBA Xdyn(A↔B) Xdyn(A↔B)(A)=kBAkAB+kBA Xdyn(A↔B) The total fractions of the static states are calculated as a sum of static fraction and contributions from all considered dynamic fractions.
	Figure 7. Comprehensive nucleosome disassembly scheme including the multiple interaction modes of the H3NtT. Considering similarly reconstituted nucleosomes with different dye labeling positions, this scheme is based on disassembly steps that were observed under similar conditions. This comprehensive scheme summarizes consistent results from: [a] this paper in Fig. 1B and D, [b] Ref. (13), [c] Ref. (12), and [d] so far unpublished data (K. Tóth). The nomenclature of the labeled constructs refers to the position of the donor and the acceptor. H2B: labeled at T112C, H3: labeled at H3 K9C, H4: labeled at H4 E63C, E: labeled at the end of the DNA, Dy: labeled close to the dyad axis (either −9 bp or +21 bp away from the dyad axis), I: labeled internally (either at +41 bp and −53 bp away from the dyad axis). α- and β-side refer to the two halves of the nucleosome (see Material and Methods). c1/2-values correspond to NaCl concentrations where the averaged proximity ratio P reaches 50% of the corresponding step height. The transition width b was calculated from the sigmoidal fit that is related to the slope at the respective inflection point (see Equation (2)). Trackable disassembly steps are visualized in the last column. The transparent green clouds indicate the accessible space of the H3NtTα and the black crosses point to the four proposed conformational state positions of the donor dye on it. The opening of the linker DNA can be detected in the dynamic octasome (Eβ–Eα), but the DNA is not yet significantly unwrapped. The first prominent event is the α-dimer release (H2Bα–Dyα) that results in the formation of dynamic hexasomes. Further NaCl increase leads to a stepwise asymmetric unwrapping of the DNA ends: starting from the α-side (Dyβ–Eα). Under the same conditions, we observe the weakening of the H3 tail linker DNA interaction (H3–Eα) followed by loosening of the β side (Dyα-Eβ). Next, DNA opening within the hexasome (Iβ-Iα) together with the weakening of the H3 tail inner DNA interaction (H3-Dyα, H3-Dyβ) and formation of the tetrasome with extended DNA through release of the second dimer (H2Bβ–Dyα) occurs. The final step is the release of the tetramer (H4–Dyα).
	Supplementary Figure 1. MFD‐PIE analysis of Donor only (nucleosomes with unlabeled DNA) and double labeled mutDyβ nucleosomes. Stoichiometry, SPIE, versus FRET efficiency, EFRET, of data obtained from (A) 40 pM E nucleosomes plus 260 pM unlabeled nucleosomes at 5 mM NaCl and (B) 40 pM mutDyβ nucleosomes plus 1960 pM unlabeled nucleosomes at 100 mM NaCl. (C) Histogram of the donor fluorescence intensity decay from selected D1A bursts (red line) and best fit model curve (black line, lower left panel). (D) Histogram of the donor fluorescence intensity decay from selected D2A bursts (green line) and best fitmodel curve (black line, lower left panel). (E) Histogram of the donor fluorescence intensity decay from selected D1 D2A bursts (blue line) and best fit model curve (black line, lower left panel). The decay histograms are analyzed by the M2 model. The weighted residuals shown on top (gray line) with the reduced sum of the weighted squared deviation between the model and the data of the decay histogram, 𝜒 . Model distance distributions are shown on right panels. Subspecies (D1A, D2A and D1D2A) positions indicated with circles are kept as in Fig. 2A. FRET bursts selection is indicated by wine colored rectangle.
	Supplementary Figure 2. All potential quenchers in the nucleosome crystal structure (PDB ID: 1KX5) with full histone H3NtT tails. Fluorescence of Alexa dyes can be quenched by interactions with Trp, Tyr, Met, and His residues through a combination of static and dynamic quenching mechanisms (1). Donor dyes attachment amino acids C/9 (A) and G/9 (B) on the H3NtT are shown with magenta and blue color, respectively. Acceptor dye attachment nucleotide B/21 on DNA is shown in red color.
	Supplementary Figure 3. seTCSPC decay histograms generated from selected bursts /molecules between D‐only (gray region) and FRET (wine rectangle) selections on Fig. 2A (dashed blue rectangle, 0.8 < SPIE < 0.9). Decay histograms for photons detected in the donor detection channels are shown as dark and bright green lines and for photons detected in the acceptor channels are shown as red and orange lines (parallel and perpendicular channels, respectively). The existence of a second delayed decay in the acceptor detection channels proves that the selected molecules carry both donor and acceptor bright dyes (on the acceptor decay histograms acceptor emission after direct excitation by the delayed red laser pulse around 17 ns is visible).
	Supplementary Figure 4. Ensemble analysis of salt‐induced proximity changes between H3NtT and DNA. Independent fits of all samples. (A) Ensemble FRET analysis of distance changes between wild type H3NtT and various positions on the DNA. For visualization data were normalized to the maximal and minimal amplitude of the sigmoidal fit. (B) Ensemble FRET analysis of distance changes between H3NtT and the DNA in nucleosomes bearing two point mutations in the 𝛼3 domain of H2A, H2A R81E/R88E. Inflection points of the proximity curves are significantly left‐shifted in mutD𝛼 and mutDyβ nucleosomes; curve progression is changed to a two‐step behavior in mutE𝛼 and mutL(170), indicating allosteric effects induced by the mutation.
	Supplementary Figure 5. Dynamic Photon Distribution Analysis (dynPDA) of Dyβ and mutDyβ nucleosomes revealsfrequencyof conversionbetweenH3NtTconformationsandallostericeffects.Burstsweredivided into 1, 2 and 3 ms (presented here) time windows. Donor‐acceptor distances (x‐axis) were calculated from integer photon counts and are affected by photon shot noise, leading to not entirely smooth distributions. The resulting three RDAE distance distribution histograms for each salt concentration were used for global fitting. Their distribution function (left panel, black line) was approximated by seven interconverting dynamic species (dynHF‐MF, dynMF‐LF, dynHF‐LF, dynMF‐VLF, dynLF‐VLF, dynMF‐NoFRET and dynLF‐ NoFRET) and five static states (HF, MF, LF, VLF and NoFRET). Partial histograms for each contribution are also presented on the left panel (colors are defined in the plot legend). The shot noise free distance distributions calculated as a sum of five Gaussian‐distributed probabilities of donor‐acceptor distances and seven allowed dynamic transitions between pairs of those static species (2) are shown on the right panel. Best fit quality is shown as weighted residuals (w. res.) in the upper panel (black line). (A‐C) dynPDA of 40 pM Dyβ plus 1960 pM unlabeled nucleosomes at 100 (A, the corresponding MFD‐PIE plot is shown in Fig. 2A), 400 (B) and 600 (C) mM NaCl. (D‐F) dynPDA of 40 pM mutDyβ plus 1960 pM unlabeled nucleosomes at 100 (D, the corresponding MFD‐PIE plot is shown in Supplementary Fig. 2B), 400 (E) and 600 (F) mM NaCl.

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