BMB Reports 2025; 58(1): 24-32  https://doi.org/10.5483/BMBRep.2024-0191
Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements
Sihyeong Nho & Hajin Kim*
Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
Correspondence to: Tel: +82-52-217-2557; Fax: +82-52-217-3229; E-mail: hajinkim@unist.ac.kr
Received: November 27, 2024; Revised: January 2, 2025; Accepted: January 2, 2025; Published online: January 24, 2025.
© Korean Society for Biochemistry and Molecular Biology. All rights reserved.

cc This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
ABSTRACT
The nucleosome is the fundamental structural unit of chromosome fibers. DNA wraps around a histone octamer to form a nucleosome while neighboring nucleosomes interact to form higher-order structures and fit gigabase-long DNAs into a small volume of the nucleus. Nucleosomes interrupt the access of transcription factors to a genomic region and provide regulatory controls of gene expression. Biochemical and physical cues stimulate wrapping-unwrapping and condensation-decondensation dynamics of nucleosomes and nucleosome arrays. Nucleosome dynamics and chromatin fiber organization are influenced by changes in the ionic background within the nucleus, post-translational modifications of histone proteins, and DNA sequence characteristics, such as histone-binding motifs and nucleosome spacing. Biochemical and biophysical measurements, along with in silico simulations, have been extensively used to study the regulatory effects on chromatin dynamics. In particular, single-molecule measurements have revealed novel mechanistic details of nucleosome and chromatin dynamics. This minireview elucidates recent findings on chromatin dynamics from these approaches.
Keywords: Chromatin fiber, Molecular dynamics simulation, Nucleosome, Post-translational modification, Single-molecule manipulation
INTRODUCTION

A nucleosome is a nucleoprotein complex comprising a histone octamer wrapped by a double-stranded DNA. The DNA wraps around the histone core particle with 147 base pair (bp) length, making 1.65 turns in a left-handed manner (1). Histone proteins have two distinct domains. The histone core domain forms the core of the nucleosome, which the DNA wraps around. The histone tail domain is an intrinsically disordered domain in the C- and N-terminus of each histone, and makes variable contact with the core domains, the nucleosomal DNA, and even the linker DNA connecting to neighboring nucleosomes (2-4). Located within the core domains of the H2A/H2B dimer, a characteristic motif, termed the ‘acidic patch’, operates as a docking station for transcription factors, histone modification complexes, and remodeling complexes (5-7). This region also interacts with the H4 tail of a neighboring nucleosome, which is crucial for the higher-order chromatin structure (8). A nucleosome dynamically alters its structural conformation in diverse ways. DNA-histone contact reversibly switches between a wrapped state and an unwrapped state (9, 10). By modulating the DNA-histone contact, the DNA double helix can also locally overwind or underwind, relative to the normal winding of 1 turn per 10 bp (11, 12). Due to its relatively weak binding, H2A/H2B dimers can be evicted from the histone octamer (13, 14). The tail domains of the histones stabilize the wrapped DNA and extend to interact with neighboring nucleosomes (8, 15). The structural dynamics of nucleosomes and their arrays modulate the accessibility of genomic regions to proteins to regulate gene expression, DNA repair, replication, and chromosome organization (16-18).

The structure and stability of nucleosomes are modulated by various factors. These include the post-translational modification (PTM) of histones, the ionic environment, and the sequence and spacing of the nucleosome-binding DNA. Acetylation of lysine residues or phosphorylation of serine, threonine, or tyrosine residues in both the histone core and the tail domains weakens the electrostatic attraction between DNA and histones, destabilizing the nucleosome (18-21). Lower nucleosome stability leads to more frequent exposure of nucleosomal DNA and facilitates the binding of transcription factors (18). Acetylation on histone tails reduces their affinity for DNA, disrupting DNA-histone tail interactions and promoting the formation of α-helical structures (22). However, a recent simulation study suggests that the conformational response of histone tails to acetylation is position-dependent showing variations in the change of secondary structures observed across different tail regions (23). Cations around the nucleosomes play crucial roles in forming the nucleosome stacks and chromatin fibers, which can hinder the binding of transcription factors (24). The sequence context of nucleosomal DNA modulates the flexibility of the DNA itself to affect the stability of nucleosomes (9). The spacing between nucleosomes is also crucial in determining the structure of chromatin fibers as solenoid, zigzag, or other variants (25-29).

Advances in single-molecule techniques provided new insights into nucleosome dynamics from biophysical perspectives (Fig. 1). Force spectroscopy techniques such as magnetic tweezers and optical tweezers allow precise application of sub-piconewton (pN) forces to nucleosomes and chromatin (30-32). In magnetic tweezers, a magnetic field exerts forces on magnetic beads tethered to a long DNA oligo. Manipulation of the beads with the magnet allows the control of the force and torque on the DNA, and the resulting extension and rotation can be measured by imaging the beads. Optical tweezers use a focused laser beam to create an optical trap for transparent beads, and the control of the laser beam or the sample stage allows the control of the force and extension of the DNA. Using these techniques, the mechanical response of nucleosomes and chromatin can be measured, which reveals the changes in the stability of individual nucleosomes and nucleosome stacks. Single-molecule Förster resonance energy transfer (smFRET) technique measures the distance between two labeled sites on nucleosomes with sub-nanometer precision, offering insight into the conformational transitions in nucleosomes or nucleosome arrays (24, 28). Atomic force microscopy (AFM) complements these approaches by directly revealing the conformation and ordering of nucleosomes in chromatin fibers (33-35). This minireview introduces and discusses recent findings on the conformational dynamics of nucleosomes and chromatin fibers from single-molecule approaches, as well as from biochemical and in silico approaches.

DYNAMIC MODES OF NUCLEOSOMES

The complicated nature of the multi-nucleoprotein structure results in nucleosomes manifesting various modes of dynamics that intricately relate to their stability and functions. These dynamic modes can be categorized as follows:

Breathing and unwrapping dynamics

The outer part of the nucleosomal DNA can spontaneously unwrap and rewrap by thermal perturbation. Unwrapping can proceed for 15-25 bp on each side of the nucleosome. Such partial unwrapping of DNA is affected by its interaction with both histone core and tail domains. Simulating all-atom molecular dynamics simulations, Armeev et al. found that a region in H3, termed “H3-latch”, holds the nucleosomal DNA ends, reinforced by the H3 N-tail and H2A C-tail (36). H2A-H2B dimers also insert their arginine residues into the DNA minor groove to hold and recover the outer turns (37). Recent studies found that the outer turns at both ends of a nucleosomal DNA unwrap in an anti-cooperative manner. Huynh et al. observed that the unwrapping of one arm results in the stabilization of the opposite arm (38). Konrad et al. also found similar anti-cooperative unwrapping of outer turns, except when H3K36 is tri-methylated (33). Spontaneous unwrapping modulates the accessibility of the DNA to transcription factors. Simon et al. showed that the artificial destabilization of the outer turns by H3K56 acetylation resulted in increased recruitment of transcription factors near the nucleosomal DNA (18). Conversely, nucleosome unwrapping has been found to facilitate chromosome condensation, and might also confer varied chromatin conformation by the formation of nucleosome clutches under external forces (39, 40).

Sliding dynamics

Nucleosomes can translocate along the DNA to its vicinity, which translocation is facilitated by various factors, including chromatin remodelers, histone chaperones, or partial unwrapping by external forces (41-44). Chromatin remodelers actively reposition nucleosomes to form regular spacing between nucleosomes (45). Chromatin remodeler ISWI softens condensed chromatin by actively repositioning itself, as well as sliding nucleosomes (46). Diffusivity of nucleosomes varies for histone variants. The sliding dynamics was found to be facilitated by a histone variant H2A.Z, indicating the importance of histone composition in the arrangement of nucleosomes (43).

Twist defect

DNA wrapped around the histone core undergoes transitions in its helical structure. Local over-twisting builds and releases in nucleosomes, resulting in 1 bp sliding of the outer turn (36). Diaz-Celis et al. reported a vibration in distance caused by the twisting dynamics by smFRET measurements (47). The twist defect was proposed as a key mechanism for nucleosome sliding and plays a critical role in facilitating ATP-dependent remodeling. Brandani et al. proposed a model of nucleosome sliding, where twist defect propagates over the whole nucleosomal DNA in a corkscrew-like manner (12). Winger et al. proposed that to slide the nucleosome, remodeler Chd1 employs twist defect to create a DNA bulge and shift the bulge to the dyad (48).

Absorbing torsional stress

Nucleosomes and chromatin fibers can absorb the torsional stress generated during transcription or replication. Torsional stress was applied by magnetic tweezers to H3-H4 tetramers assembled on DNA by NAP-1, where the torsional stress was absorbed by changing the DNA configuration from left- to right-handed (49, 50). In a similar manner, chromatin fibers containing long nucleosome arrays were found to absorb torsional stress (51).

Nucleosome stacking

Neighboring nucleosomes interact to form higher-order chromatin structures. Histone tails play a crucial role in mediating the inter-nucleosome contact. Roopa et al. observed that after digesting histone tails with trypsin, chromatin fibers become fluidic (52). Cleaving histone tails resulted in slower sedimentation of chromatin in the presence of the linker histone H5 (53). Interestingly, the truncation of H3 N-tail had little effect on chromatin compaction, while the truncation of H4 N-tail hindered chromatin compaction. This is in agreement with a crystal structure revealing the interaction of H4 N-tail with the acidic patch of H2A-H2B dimers from the neighboring nucleosome in the two-start zigzag conformation (8). It is worth noting that the stacked nucleosomes can undergo reversible transitions to a partially unstacked structure without significant deformation. Kilic et al. reported the dynamic transition of nucleosome arrays from a fully stacked conformation to an alternatively stacked one (28). Li et al. also observed a tetra-nucleosome stack reversibly unfolding under external forces (54). Multiple simulation studies have reported the thermally induced dynamics of chromatin stacks (39, 40, 55).

Force spectroscopy at the lower-force regime revealed a force-extension characteristics of nucleosome arrays representing continuous unstacking or unwrapping transitions in the array, which are manifested as a spring-like response of the whole chromatin fiber to the pulling force (34, 56, 57). Whether the elastic response originates from nucleosome unstacking or outer turn unwrapping has been a matter of debate. Meng et al. devised a numerical model to describe the elastic behavior of chromatin fiber for the two different chromatin conformations (58). The model showed tightly stacked two-start zigzag fibers developing cooperative deformation, in which all nucleosomes in the fiber simultaneously unfolded to partially unwrapped nucleosomes, while one-start solenoidal fiber developed non-cooperative deformation (Fig. 2). A computational study found that linking histone H4 tail to the acidic patch of the H2A/H2B core domain in the neighboring nucleosome stabilized nucleosome stacking (59).

MODULATION OF NUCLEOSOME DYNAMICS

Nucleosome dynamics is modulated by various factors (Fig. 2). Ionic environment, DNA sequence, and the PTM of histones affect nucleosome dynamics through charge interaction and steric hindrance. Table 1 summarizes recent findings on how each factor modulates the dynamics of nucleosome monomers, which findings are reviewed below.

Ion concentration

Histone proteins reduce the negative charge of DNA by approximately half and the overall nucleosome remains highly negatively charged (66). This strong negative charge attracts cations, which readily interact with nucleosomal DNA and screen the electrostatic interactions, ultimately destabilizing DNA-histone binding (67). The destabilizing effects of ionic screening have been extensively studied. Single-pair Förster resonance energy transfer (spFRET) experiments showed that increasing concentrations of monovalent ion induce more frequent unwrapping of the outer turn, eventually leading to the disassembly of nucleosomes (13, 68). Similarly, an smFRET study revealed an increasing unwrapping rate of the outer turn with increasing salt concentrations (69). Optical tweezers studies observed that raising the concentration of potassium from 10 mM to 200 mM of lowered the force required to unwrap the nucleosome, from approximately 35 pN at 10 mM KOAc to 24 pN at 200 mM KOAc (47). Transmission electron microscopy of DNA origami demonstrated that increased salt concentrations lead to nucleosome unwrapping and histone dissociation (70).

Multivalent cations, such as Mg2+, exhibit a higher affinity to the nucleosome than monovalent cations, resulting in their larger effects on nucleosome stability even at relatively low concentrations (66). Biogenic polyamines such as spermine and spermidine strongly promoted the disassembly of H2A-H2B dimer highlighting their roles in controlling chromatin stability (71).

DNA sequence

Nucleosome positioning sequences such as Widom 601 or 5S rRNA sequence exhibit higher affinity to histones than other sequences. Accordingly, nucleosomes display sequence-dependent stability. A magnetic tweezers study on nucleosomes with regular histones or CENP-A histones demonstrated strong sequence dependence of their stability (72). Nucleosomes reconstituted on a random DNA sequence required much higher forces to unwrap than those reconstituted on a centromeric sequence. Force-clamping experiments supported this by showing longer lifetimes for the nucleosomes with the random sequence. Interestingly, CENP-A nucleosomes also exhibited sequence-dependent stability, but with an opposite trend. An optical tweezers study also compared the stability of nucleosomes with Widom 601 and 5S rRNA sequences (47). Nucleosomes with Widom 601 sequence required higher forces for both outer-turn and inner-turn unwrapping, compared to those with 5S rRNA sequence.

Such sequence-dependence, however, does not arise from the sequence recognition by histone proteins. Molecular dynamics simulations showed that most DNA-histone contacts are formed at the backbone or sugar of DNA, rather than the bases (36). The sequence dependence presumably stems from the intrinsic flexibility of the DNA itself (73). An optical tweezers study showed that a relatively rigid DNA sequence near the H2A-H2B dimer contact region promoted the unwrapping of the outer turn. Further modifications of the sequence altered the threshold force required to open the nucleosomal arms, highlighting the effects of DNA flexibility on nucleosome stability and dynamics (9).

Post-translational modification

Histones have a large repertoire of PTM on both tail and core domains (74). Among many known PTMs, the acetylation, methylation, and ubiquitination of lysines have been extensively studied by single-molecule methods. Acetylation of a lysine neutralizes the positive charge of the residue, thus lowering the electrostatic affinity to negatively charged DNA backbone; this is considered an important cause of acetylation loosening nucleosomes. Optical tweezers study of hyperacetylated nucleosomes showed gradual destabilization of nucleosomes upon acetylation by p300 (21), while horizontal magnetic tweezers study showed that hyperacetylated histones lower the stability of nucleosomes, as evidenced by an increased portion of partially unwrapped nucleosomes (64). Another magnetic tweezers study showed that after repeated cycles of pulling and releasing nucleosome arrays, acetylation near the dyad (H3K115ac, K122ac) resulted in inefficient recovery, while acetylation near the DNA entry/exit region (H3K56ac) facilitated access to transcription factors, which is attributed to the more active outer turn unwrapping (18). Histone acetylation by SAGA or HAT enhances nucleosome remodeler binding, presumably by facilitating the exposure of SWI/SNF binding site near the nucleosome (75). smFRET measurements revealed that H3K56 acetylation resulted in the DNA entry site opening much faster, without affecting the Pol II elongation rate (38). Pol II transcription assay was performed for nucleosomes with H3K4/9/14 acetylation, H3K18/23/27 acetylation, or both; the level of acetylation was found to correlate with the destabilization of both the outer and inner turns (15).

Acetylation removes the positive charge on the histones, while phosphorylation adds a negative charge. Histone phosphorylation near the dyad destabilizes nucleosomes or alters their structure. H3T118 phosphorylation near the dyad lowers the nucleosome stability and raises the chance of opening the dyad; it also forms non-canonical structures, like nucleosome duplex or altosomes, which is presumed to be due to the negative charge at the histone dyad sterically or electrically disturbing proper DNA-histone interaction (19, 20).

Although ubiquitination does not alter the charge state of histones, it causes steric hindrance to the nucleosome formation. H2BK34 ubiquitination widens the nucleosome gyre by steric hindrance, while H2BK120 ubiquitination has little effect on the nucleosome structure (61). H2BK120 ubiquitination, however, significantly weakens the DNA-histone interaction (62). In contrast, ubiquitination of H2AK119 was shown to increase the force required to unravel both the outer and inner turns of nucleosomal DNA (60, 76). This stabilization results from steric hindrance caused by ubiquitination at the C-terminal tail of H2A, which might block the unraveling of nucleosomal DNA.

Methylation also affects nucleosome dynamics without altering the charge state of histones. High-throughput AFM imaging revealed that H3K36 tri-methylation results in nucleosome dynamics that are distinct from that of the wild-type, H3 tail phosphorylation, or H4 tail acetylation (33). While wild-type and the other PTMs exhibited around 30% fully wrapped and 70% partially unwrapped nucleosomes, H3K36 tri-methylation exhibited approximately 84% partially unwrapped nucleosomes. Furthermore, H3K36 tri-methylation did not show the anti-cooperative opening of the outer turn that other variants showed.

MODULATION OF CHROMATIN FIBER DYNAMICS

As with nucleosome monomers, various factors modulate the structure and dynamics of chromatin fibers (Fig. 2). The higher-order structure of chromatin fibers is also sensitive to the electrostatic or steric interaction between its components. Since DNA is relatively rigid at short range, in addition to the factors listed above, spacing between neighboring nucleosomes is important in determining the overall structure. Compared to nucleosome monomers, structural changes of chromatin fibers are more challenging to quantify from biochemical approaches, while single-molecule approaches provide valuable tools to study the dynamics. Table 1 summarizes recent findings from single-molecule measurements on how the dynamics of chromatin fibers is modulated by these factors, which are reviewed below.

Ion concentration

Ionic interaction plays an important role in nucleosome stacking, as solvent cations are needed to shield the electrostatic repulsion between nucleosomes (67). Increased cation concentration enhances the folding of chromatin fibers. Optical tweezers μeasurements revealed that increased NaCl concentration increased the resistance of chromatin fibers to pulling forces, due to chromatin condensation (57). Divalent cations showed a similar effect of enhancing the formation of chromatin fibers at much lower concentrations, while the depletion of Mg2+ resulted in the destabilization of chromatin fibers (34). Lin et al. showed a stronger affinity of Mg2+ to the phosphate group on nucleosomal DNA than that of Na (67). smFRET measurements showed that upon the addition of Mg2+, a tetra-nucleosome complex reversibly folds (28). Magnetic tweezers measurements showed that in the presence of Mg2+, nucleosome arrays exhibit reversible stacking dynamics (54). Nucleosome stacking by divalent ions also increases the rigidity of nuclei (77). Increasing concentrations of multi-valent biogenic polyamines resulted in strong condensation of nucleosomes, followed by dispersal by charge inversion at high polyamine concentration (78).

Linker length

The length of ordinary DNA linker between nucleosomes is much shorter than the persistence length of approximately 150 bp. Thus, the bending mechanics and helical orientation of the linker DNA profoundly affect chromatin structure. The crystal structure of a nucleosomal array with a 31 bp linker showed a different conformation than that with a 34 bp linker (25). A nucleosome array with a short spacing of 157 bp showed an open zigzag conformation, distinct from the ordinary zigzag conformation (79). Force spectroscopy and simulations revealed 10 bp periodicity in the free energy of chromatin folding and dissociation. Although a 20 bp linker showed a peak in dissociation energy, a mere 1 bp increase in the linker length significantly lowered the dissociation energy (63). While chromatin fibers with a 50 bp linker exhibited gradual unstacking of nucleosomes, chromatin fibers with a 20 bp linker showed Hookian spring behavior, resisting unfolding until they eventually collapsed (58, 65). Such spring-like behavior was not a function of fiber length. Chromatin fibers of 45 nucleosome repeat and a 50 bp linker showed similar behaviors to those of 15-repeat fibers (80). Conversely, shortening the linker length to 30, 25, 19, and 15 bp gradually increased the rigidity of the fibers. Notably, H4 tail showed differentiating effects on chromatin fibers with 20 and 50 bp linkers. While H4 tail truncation reduced the deformation energy of chromatin fibers with a 20 bp linker, it had little effect on those with a 50 bp linker (59).

Post-translational modification

Histone acetylation destabilizes nucleosome stacking, as well as individual nucleosomes. Shimamoto et al. observed lower rigidity of the nucleus with hyperacetylated histones (77). In the presence of H5 linker histone, Robinson et al. showed that H4K16 acetylation revealed more drastic change in its conformation than did the whole H4 tail truncation (53). Meanwhile, a point mutation of H4K16Q did not affect the chromatin fiber conformation, signifying that histone acetylation might imply more than mere charge neutralization. Acetylation of the tail residue shortens and stiffens the overall conformation of the tail domain (23, 81). A computational study showed that PTMs on histone tails change the mode of dynamics (16). Although H2BK34 ubiquitination enhanced di-nucleosome stacking, H2BK120 ubiquitination had little effect (61). H2BK34 ubiquitination was suggested to widen the gap between DNA gyres by steric hindrance and promote di-nucleosome stacking.

CONCLUDING REMARKS

The dynamic transition of nucleosome conformations provides their versatility in performing various functions. The unwrapping dynamics works with nucleosome remodelers to regulate access to transcription factors. Transient twist defects on the DNA facilitate chromosome remodelers or pioneering factors to interact with nucleosomal DNA. The stacking dynamics of chromatin fibers regulates the compactness and accessibility to proteins. Ionic composition, DNA sequence context, and the chemical modification of histones regulate these dynamic features in various ways. Cutting-edge single-molecule tools provide unique opportunities to investigate the dynamics of nucleosomes and chromatin fibers while complementing biochemical and computational approaches. Given the complexity of the in vivo nuclear environment and the hierarchical organization of chromatin, other approaches, such as spatial genomics, super-resolution genome imaging, and live chromatin tracking, are required to determine the systematic regulation of chromatin functions.

CONFLICTS OF INTEREST

The authors have no conflicting interests.

FIGURES
Fig. 1. Single-molecule tools to study nucleosome dynamics. The single-molecule techniques that have been used to study nucleosome dynamics are shown in schematic, which techniques include magnetic tweezers, optical tweezers, smFRET measurements, and AFM imaging. Created in BioRender. Kim, H. (2025) https://BioRender.com/e61y533.
Fig. 2. Regulation of the dynamics of nucleosomes and chromatin fibers. The unwrapping dynamics of nucleosomes, which facilitates the access of transcription factors, and the inter-nucleosome stacking dynamics, along with various factors that regulate the dynamics, which factors include ion concentrations, PTM on histones, and nucleosome spacing, are shown in schematic. Created in BioRender. Kim, H. (2025) https://BioRender.com/p00t645.
TABLE

Factors regulating the dynamics of nucleosomes and chromatin fibers

Nucleosome Method Recon method Buffer conditions DNA template Modifications Outer wrap Inner wrap Stacking Recovery Ref.
Single MT salt-dialysis pH 8.0, no other salt Widom 601 H2AK119ub Stabilized Stabilized - None (60)
Single smFRET salt-dialysis pH 8.0, 50 mM NaCl, 2 mM MgCl2 Widom 601 H2BK34ub - - Stabilized - (61)
Single MT salt-dialysis pH 8.0, no other salt Widom 601 H2BK120ub Destabilized Destabilized - None (62)
Single MT salt-dialysis pH 8.0, 50 mM NaCl, 2 mM MgCl2 Widom 601 H2BK120ub - - None - (61)
Array OT salt-dialysis pH 8.0, 100 mM NaCl, 1.5 mM MgCl2 5S positioning sequence (17 X 208-17) H2A/H2B tail truncated Destabilized Destabilized - - (21)
Single AFM salt-dialysis pH 7.6, 200 mM NaCl Widom 601 H3K36me3 Destabilized - - - (33)
Array MT salt-dialysis - Widom 601 (17 X 178 bp NRL) H3K56ac More frequent - - Destabilized (18)
Single smFRET salt-dialysis pH 7.8, 10 mM NaCl Widom 601 H3K56ac + Yeast Pol II More frequent None - None (38)
Array MT salt-dialysis - Widom 601 (17 X 178 bp NRL) H3K115ac- 122ac None Destabilized - None (18)
Array smFRET salt-dialysis 40 mM KCl Widom 601 (12 X 197 bp NRL) H3K9me3 - - None - (28)
Array MT salt-dialysis - Widom 601 (17 X 178 bp NRL) H4K77ac- 79ac None - - None (18)
Array MT salt-dialysis pH 7.6, 100 mM NaCl, 2 mM MgCl2 Widom 601 (15 X 167 bp NRL) H4 tail-H2A crosslink - Stabilized Stabilized - (59)
Array MT salt-dialysis pH 7.6, 100 mM NaCl,2 mM MgCl2 Widom 601 (15 X 197 bp NRL) H4 tail-H2A crosslink - Stabilized Stabilized - (59)
Array OT salt-dialysis pH 8.0, 100 mM NaCl, 1.5 mM MgCl2 5S positioning sequence (17 X 208-17) H3/H4 tail truncated Destabilized Destabilized - - (21)
Array MT salt-dialysis - Widom 601 (16 X 167 bp NRL) H4 tail truncation - - Diminished - (63)
Array MT salt-dialysis - Widom 601 (16 X 197 bp NRL) H4 tail truncation - - None - (63)
Array MT NAP1 1X TE, 150 mM NaCl Lambda DNA Hyper- acetylated - Destabilized - - (64)
Array OT salt-dialysis pH 8.0, 100 mM NaCl, 1.5 mM MgCl2 5S positioning sequence (17 X 208-17) Hyper- acetylated Destabilized Destabilized - - (21)
Array OT salt-dialysis pH 8.0, 100 mM NaCl, 1.5 mM MgCl2 5S positioning sequence (17 X 208-17) All tail truncated Destabilized Destabilized - - (21)
Array OT sucrose gradient pH 7.5, 5/40/150 mM NaCl Chromatin DNA - - - +/++/++ - (57)
Array MT salt-dialysis pH 7.4, 1.5 mM MgCl2 Widom 601 (24 X 177 bp NRL) - - - Enhanced - (54)
Array smFRET salt-dialysis 40 mM KCl, MgCl2 0/0.5/1/4 mM Widom 601 (12 X 177 bp NRL) - - - +/++/ +++/ ++++ - (28)
Single Fleezers salt-dialysis pH 7.0, 5mM MgCl2, KOAc 10/50/200 mM Widom 601 - +++/++ /+ +++/++ /+ - +/++/+ (47)
Array MT salt-dialysis pH 7.5, 100 mM KCl, 2 mM MgCl2 Widom 601 (25X 197 NRL) - - - Less rigid - (65)
Array MT salt-dialysis pH 7.6, 100 mM Kac, 2 mM MgAc2 Widom 601 (30X 167 NRL) - - - More rigid - (58)
Array MT salt-dialysis pH 7.5, 100 mM KCl, 2 mM MgCl2 Widom 601 (30X 167 NRL) - - - More rigid - (65)
Array MT salt-dialysis - Widom 601 (16X 167-202 NRL) - - - Oscillate by 10n bp - (63)
Array MT salt-dialysis pH 7.6, 100 mM Kac, 2 mM MgAc2 Widom 601 (15X 197 NRL) - - - Less rigid - (58)

Note: Single-molecule studies on chromatin are listed, showing the design of chromatin, buffer conditions, PTM, and their effects on nucleosome unwrapping, stacking, and recovery (MT, magnetic tweezers OT, optical tweezers AFM, atomic force microscopy).


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