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Annual Review of Physical Chemistry

Chromatosome Structure and
Dynamics from Molecular
Simulations
Annu. Rev. Phys. Chem. 2020.71. Downloaded from www.annualreviews.org

Mehmet Ali Öztürk,1 Madhura De,2,3,4

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Vlad Cojocaru,5,6 and Rebecca C. Wade2,4,7,8

1
Centre for Biological Signalling Studies (BIOSS) and Centre for Integrative Biological
Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany;
email: mehmet.oeztuerk@bioss.uni-freiburg.de
2
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS),
69118 Heidelberg, Germany; email: rebecca.wade@h-its.org
3
Department of Biophysics of Macromolecules, German Cancer Research Center (DKFZ),
69120 Heidelberg, Germany; email: m.de@dkfz-heidelberg.de
4
Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
5
In Silico Biomolecular Structure and Dynamics, Hubrecht Institute, 3584 CT Utrecht,
The Netherlands; email: v.cojocaru@hubrecht.eu
6
Computational Structural Biology Group, Max Planck Institute for Molecular Biomedicine,
48149 Muenster, Germany
7
Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University,
69120 Heidelberg, Germany
8
Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany

Annu. Rev. Phys. Chem. 2020. 71:5.1–5.19 Keywords

The Annual Review of Physical Chemistry is online at
physchem.annualreviews.org
https://doi.org/10.1146/annurev-physchem-071119-
040043
Copyright © 2020 by Annual Reviews.
All rights reserved
Brownian dynamics, chromatin, chromatosome, linker histone, multiscale
molecular simulation, nucleosome
Abstract
Chromatosomes are fundamental units of chromatin structure that are
formed when a linker histone protein binds to a nucleosome. The posi-
tioning of the linker histone on the nucleosome influences the packing of
chromatin. Recent simulations and experiments have shown that chromato-
somes adopt an ensemble of structures that differ in the geometry of the
linker histone–nucleosome interaction. In this article we review the ap-
plication of Brownian, Monte Carlo, and molecular dynamics simulations
to predict the structure of linker histone–nucleosome complexes, to study
the binding mechanisms involved, and to predict how this binding affects

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chromatin fiber structure. These simulations have revealed the sensitivity

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of the chromatosome structure to variations in DNA and linker histone sequence, as well as to
posttranslational modifications, thereby explaining the structural variability observed in experi-
ments. We propose that a concerted application of experimental and computational approaches
will reveal the determinants of chromatosome structural variability and how it impacts chromatin
packing.

INTRODUCTION
“…but was histone H1 really there?” wrote Aaron Klug in his Nobel lecture in December 1982
(1, p. 580), as he described his studies in the 1970s to work out where the linker histone (LH) was
bound to the nucleosome and how its binding led to higher-order structure in chromatin. At the
time, it was not possible to directly observe the LH by electron microscopy or any other tech-
nique. The atomic detail structure of the globular domain (gH) of the chicken H5 LH was solved
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by X-ray crystallography in 1993 [Protein Data Bank (PDB) ID: 1HST] (2), but it took another
22 years before a crystal structure of the complex between an LH gH and a nucleosome was de-
termined experimentally (PDB ID: 4QLC) (3). In this period, computational approaches based on
docking and simulation were extensively used to predict the structure of LH–nucleosome com-
plexes. A range of different off- and on-dyad binding modes were proposed. While the first crystal
structure of an LH–nucleosome complex seemed to validate only one predicted binding mode,
structure determinations by NMR, X-ray crystallography, and cryo-electron microscopy have re-
vealed a variety of structures of LH–nucleosome complexes, indicating that the simple view of one
structure for all chromatosomes may not reflect the real situation in chromatin. Instead, an ensem-
ble of structures exists that shifts depending on the sequences of its constituent macromolecules
and the environmental conditions (4). Thus, approaches to understand not only the determinants
of the structural ensemble of chromatosomes but also their dynamics have become important.
Indeed, chromatosome structure and dynamics are key determinants of chromatin packing and
fiber formation and can influence epigenetic regulation (5). Therefore, the structure and dynam-
ics of nucleosomes, chromatosomes, and chromatin have been the subject of several recent reviews
of computational (6–9) and experimental (10–12) research. Molecular simulation, with its ability
to provide a “computational microscope” (13, 14), is an important tool for investigating chro-
matosome formation and how it affects chromatin structure, and is therefore the focus of this
review.
In this article, we begin by outlining the key features of the chromatosome and its importance
for the packing of DNA and the regulation of its expression. We then describe the molecular
Linker histone (LH): simulation techniques that have been applied to study nucleosome and linker histone dynamics,
a histone protein chromatosome formation, and the effect of this process on chromatin fiber formation. We next
important for the discuss the mechanistic insights into LH–nucleosome complexes revealed by molecular simula-
packing of chromatin; tions and compare these results with those from experiments. Finally, we discuss future directions
the binding of an LH
for simulation studies of chromatosomes.
to a nucleosome
results in
chromatosome FROM NUCLEOSOMES TO CHROMATOSOMES TO CHROMATIN:
formation THE DNA PACKING PROBLEM
gH: the globular Interest in the cell nucleus and its composition dates back to the late nineteenth century, with
domain, or head, of a
Friedrich Miescher discovering nucleic acids (15) and Walther Flemming observing mitosis and
linker histone
coining the term chromatin to describe nuclear material (16). About 100 years later, when the

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Olinses first visualized chromatin from ruptured cell nuclei, they described it as “particles on a
string,” (17, p. 331) with the particles, or ν (nucleohistone) bodies, being 6 to 8 nm in diameter
(17). The very next year, Oudet et al. (18) proposed the term nucleosomes to denote these particles
bp: DNA base pair
and showed that they are repeating entities, interconnected by DNA stretches.
However, it was not until 10 years later that the first X-ray crystallographic structure of these Linker DNA
(L-DNA):
particles was obtained (19). At 7-Å resolution, the DNA was shown to wind around the disc-shaped
the DNA that
core histone octamer [already previously shown by Kornberg (20) to contain two copies each of connects nucleosomes
the histone proteins H3, H4, H2A, and H2B] in 1.8 turns. After another decade of progress in at their entry and exit
X-ray crystallography, a high-resolution (2.8-Å) structure of the nucleosome was elucidated by sites
Luger and colleagues in 1997 (PDB ID: 1AOI) (21). This structure gave us a detailed insight into
the nucleosome as we know it: a 146-bp double-stranded DNA wound around the core octamer in
1.65 turns of left-handed superhelix, as shown in Figure 1. This view also showed that the highly
positively charged H4 tail made ionic contacts with the so-called acidic patch, an exposed region
of negatively charged amino acid residues on the H2A-H2B dimer. This observation paved the
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way to a model of higher-order chromatin structure in which the H4 tail makes internucleosomal
contacts with a neighboring nucleosome.
In addition to sequencing the individual histone molecules, the 1970s saw multiple groups (20,
22–25) report that a lysine-rich fifth, or linker histone (also called H1 or H5) is present in half
the amount of the other histones, per 160 to 200 bp of DNA. Simpson coined the term chro-
matosome to describe what he obtained by micrococcal nuclease digestion assays: one LH and
the nucleosome, plus about 20 bp of linker DNA (L-DNA), i.e., 166 bp of DNA and the core his-
tone octamer (22). He noted that the entry and exit L-DNAs diverged on removal of LH, making
it highly likely that the LH was bound to the outside of the nucleosome and interacted with the
incoming and outgoing DNA (22). Cryogenic electron microscopy (cryo-EM) studies in the late
1990s led to the idea of chromatosomes having a stem-like structure (26), with the incoming and
outgoing L-DNA strands brought close together due to charge neutralization by the highly posi-
tively charged LH. Bednar et al. (26) noted that absence of LH does not affect the core nucleosome
structure but leads to the divergence of the two L-DNA arms due to mutual repulsion. X-ray crys-
tallographic studies on the chromatosome proved to be notoriously difficult, because nearly 50%
of the LH is intrinsically disordered and so had to be removed for these studies. Therefore, a
wide range of experiments, as well as molecular modeling and simulation studies, were required
to work out how the LH binds to nucleosomes (Table 1). A key question was whether the LH
binds to the nucleosome at a location equidistant to the entry-exit sites (on-dyad) or close to one
of the entry-exit sites (off-dyad) (Figure 1a). Successful structure determination by crystallogra-
phy and other methods in the last few years has revealed both arrangements, as we describe below
(see the section titled The Structures and Binding Mechanisms of LH–Nucleosome Complexes).
However, the implications of these two positions for higher-order structure formation are unclear:
Zhou et al. (3) suggested from measurements of ultracentrifugation sedimentation coefficients of
nucleosome arrays that on-dyad LH binding would lead to a structurally distinct and possibly
more compacted chromatin than off-dyad binding, whereas Schlick and colleagues (27) found in
a mesoscale modeling study that the highest compaction of chromatin was achieved with off-dyad
binding.
The chromatosome represents the first level of packaging of a 2-m-long DNA strand into
a nucleus that is a million times smaller. How this feat is achieved is a matter of much debate,
hinging on whether the chromatin has a hierarchical folding or whether it is packed into the
nucleus in a disorderly fashion. The first evidence of the former hypothesis came from electron
microscopic studies of chromatin extracted from nuclei (28), showing a nucleofilament, 30 nm

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a Components of a chromatosome

H3 H2A Chromatosome Chromatin

Core histone H4
octamer
H2B
Perišić et al. (27)
Dyad axis Zhou et al. (3) hypothesis mesoscale simulation

Entry/exit Entry/exit On-dyad

site site

More compact Less compact

Linker or
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Linker histone (full length)

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DNA
N [~100 aa] C
Off-dyad

Less compact More compact

b Possible models of the 30-nm hierarchically folded chromatin fiber (based on EM/XRC)

1
2
3
or Nucleosome
5 4
2 6
6 5 4 6 1 2
30 nm

30 nm
4 4
DNA
7 3 6 1
8 1
9 7
3 5 7
2 3 LH globular
10 5
11 domain
12

30 nm 30 nm

c Models of chromatin packaging based on in vivo results

Heat-map representation • Euchromatin
Fractal globule model of the Low
of variable-density • High gene expression
nucleus made up of different
Density

chromosome territories chromatin clumps

(based on Hi-C/particle observed by ChromEMT
tracking)
• Heterochromatin
High
• No gene expression

Figure 1
Illustration of the packing of DNA in chromatin, indicating how the binding of LHs to nucleosomes influences packing.
(a) Chromatosomes are comprised of a core histone octamer wrapped by 1.65 turns of DNA, linker DNA arms, and an LH. On- or
off-dyad positioning of the LH globular domain may influence chromatin condensation. (b) Models of the 30-nm hierarchically folded
chromatin fiber from in vitro studies. Nucleosomes are numbered to describe their arrangement. For instance, the ith and (i+1)th
nucleosomes are oriented at 60o with respect to each other in the one-start solenoid model and are oriented at 180o with respect to each
other in the two-start zigzag model. The ith and (i+2)th nucleosomes are close together in the zigzag model. (c) Models of chromatin
packaging based on in vivo results that consider chromatosome territories and variable-density chromatin clumps. Abbreviations:
aa, amino acid; ChromEMT, ChromEM tomography (38); EM, electron microscopy; LH, linker histone; XRC, X-ray crystallography.

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Table 1 Summary of modeling and simulation studies of the binding of linker histones to nucleosomes
Systema System details
Mononucleosome + gH 166-bp NRL nucleosome without
core histones or nucleosome
either without any L-DNAs or
with different lengths of L-DNA
gH5 (chicken) or gH1d (rat)
100-nucleosome 177–207 bp NRL nucleosomes with
chromatin fiber + gH core histone tails
gH5 (chicken)
2–4 nucleosomes + gH Nucleosomes without core histone
tails
gH1 (chicken)
100-nucleosome Oblate spherocylindrical
February 4, 2020. (Changes may
still occur before final publication.)
chromatin fiber nucleosomes
LH represented by a stem structure
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from the nucleosome to the
L-DNAs and the L-DNA angles
are based on observations of
chicken chromatin fibers
100-nucleosome 202–222 bp NRL nucleosomes
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chromatin fiber Oblate spherocylindrical
•
nucleosomes with six-angle and
three-distance model to describe
geometry of LH binding
100–8,000 nucleosome Nucleosomes represented by
chromatin fibers cylinders
LH defect probabilities modeled by
fixing/unfixing two
L-DNA-nucleosome angles
LH-bound 12–96 Rigid body charged nucleosomes
nucleosome chromatin (173–226 bp) with bead–chain
fiber core histone tails and L-DNAs
LHs (rat H1.4 without NTD)
bound on-dyad and represented
Molecular Simulation of Chromatosomes
by three beads at different
stoichiometries
5.5
PC71CH05_Wade
Method Findings Reference(s)
Molecular modeling and gH1d binds close to dyad axis, off-dyad, interacting with Bharath et al. (64)
docking L-DNA. Fan et al. (65)
LH CTD interacts with L-DNA. Cui et al. (66)
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gH5 has three putative binding patches and has different
docking positions relative to the nucleosome.
Molecular docking using Chromatin fibers containing LH have a polymorphic Wong et al. (67)
single nucleosome results structure.
of Fan & Roberts (65) Different fiber conformations formed on tuning LH
orientation at the nucleosome entry/exit.
Molecular modeling and L-DNA and LH constrain the dynamics of the Ramaswamy et al. (68)
NMA nucleosome dimer in the first NMA mode, but they
January 24, 2020
are dynamic in the second mode.
Dynamics of L-DNA/LH are more pronounced in the
nucleosome dimer with H2A variant.
MC simulation with CG Longer L-DNA NRL nucleosomes require binding of Stehr et al. (69)
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model LHs to form higher-order chromatin.
MC simulation with CG Without LH, the nucleosome array adopts an open fiber Kepper et al. (70)
model incorporating LH conformation.
on the basis of atomic Presence of LH causes fiber compaction into an
detail structures from interdigitated one-start helical conformation.
molecular docking by
Bharath et al. (64)
CG MC Missing LHs may lead to compact fibers. Diesinger et al. (71, 72)
Fibers with random depletion of LHs or nucleosomes
are necessary for random chromatin contacts
important in gene regulation.
CG MC simulation based LH and H3 tails compete for L-DNA binding. Arya et al. (73)
on atomic detail Divalent cations condense around chromatin. Schlick et al. (74)
structures from LH and divalent cations cause chromatin compaction. Grigoryev et al. (75)
molecular docking L-DNA is rigid around LH CTD. Gan et al. (76)
Bharath et al. (64) Chromatin fibers with NRL up to 209 bp and LHs Perišić et al. (77)
condense into zigzag structures, whereas longer NRL Grigoryev et al. (78)
fibers take on a solenoidal form.
LH has a small effect on the condensation of short-NRL
arrays but an important condensation effect on
medium-NRL arrays.
Oligonucleosomes with LH lead to tight two-start
zigzag arrangement of nucleosomes.
Divalent ions further compact fiber by increased
L-DNA bending.
(Continued)
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Table 1 (Continued)
,
Systema System details
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Mononucleosome + gH Nucleosome without core histone
tails
gH5 (chicken)
LH-bound, 173- and 209-bp NRL rigid
24-nucleosome nucleosomes with mobile core,
chromatin fiber histone tails, and L-DNA
5.6
H1.4 (rat) LHs without NTD;
three bead–chain model permits
LH binding and rebinding and
has flexibility to allow beads to
adopt optimized positions near
the dyad axis.
Öztürk et al.
LH-bound 173–226 bp NRL nucleosomes as
mononucleosomes and rigid bodies with flexible
oligonucleosomes of bead–chain models of core
2–427 nucleosomes histone tails and L-DNAs
H1.4 (rat) LH without NTD bound
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on-dyad modeled by 6 beads for
gH and 22 beads for the CTD
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with model derived from atomic
detail structure; 0–1 LHs per
nucleosome
Mononucleosome + gH 167-bp DNA nucleosome without
core histone tails
gH5 (chicken)
Method Findings Reference(s)
NMA LH binds off-dyad dominantly, and its configuration Pachov et al. (42)
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BD depends on angle of L-DNA opening.
CG MC simulation with Stiffer fiber when LH permanently bound than when it Collepardo-Guevara
additional fiber can unbind and rebind. et al. (79)
stretching force Chromatin fiber is softer for longer NRLs, slower LH Collepardo-Guevara
rebinding, and lower LH concentration. et al. (80)
ARjats.cls
Divalent ions produce a fiber- stiffening effect. Ozer et al. (81)
During unfolding in presence of LH and divalent ions,
heteromorphic superbeads-on-a-string structures
occur.
LH effect increases when the nonuniform L-DNA
length increases.
Nonuniform and uniform NRL fibers have different
unfolding mechanisms.
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CG MC simulation LH CTD charge reduction unfolds the domain and Luque et al. (82)
decondenses chromatin. Luque et al. (83)
LH CTD condenses at low salt concentration, and LH Perišić et al. (84)
interacts with one L-DNA, resulting in a semiopen Bascom et al. (85, 86)
nucleosome configuration. At higher salt
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concentration, LH interacts with two L-DNAs and
promotes chromatin compaction.
Stem configuration formed by LH CTD and L-DNA
depends on the strength of electrostatic interactions
between LH and L-DNA.
LH–nucleosome interaction depends on L-DNA length,
and LH orientation is variable and environment
dependent.
LH in oligonucleosomes mostly interacts with one
L-DNA, whereas in mononucleosomes it tends to
interact with both L-DNAs.
LH and L-DNA flexibility increase with NRL and fiber
size.
LH concentration threshold triggers chromatin
compaction into 30-nm fibers, and this threshold
increases linearly with NRL.
LH concentration affects persistence length.
Cooperative effects are observed between LH binding
and histone tail acetylation.
MD, AMD, NMA, and BD gH5 prefers the closed state in solution. Öztürk et al. (39)
The closed state of gH5 in the off-dyad position opens
in chromatosome simulations.
The open gH5 conformation interacts with thymidines
in the L-DNA, remodels L-DNA dynamics, and
induces a more rigid chromatosome structure.
Nucleosome dynamics determine the binding mode of
the gH conformations.
BD simulations reveal experimentally determined
off-dyad and on-dyad gH-nucleosome configurations.
(Continued)
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Table 1 (Continued)
Systema System details Method Findings Reference(s)
LH-bound 187-bp NRL nucleosomes with core All-atom MD with a H3 tail interactions with L-DNA; H3 and H4 tails are Izadi et al. (40)
40-nucleosome model histone tails multiscale mostly in the core of the structure, H2A and H2B tails
of 30-nm chromatin gH5 (chicken) implementation of the are mostly solvent exposed.
fiber Model (1.16 million atoms) based implicit solvent GB
on that of Wong et al. (67) model
January 24, 2020

Mononucleosome + gH
MD-generated 167-bp DNA
nucleosome structures without
core histone tails
gH5 (chicken), gH1 (Drosophila)
BD BD simulations reproduce experimentally determined Öztürk et al. (46)
NMA LH–nucleosome complex configurations.
Single point mutations and PTMs in the LH GD affect
the chromatosome structural ensemble.
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mutants, and gH1 PTMs

still occur before final publication.)

Mononucleosome + gH Nucleosomes with 10-bp L-DNAs Homology modeling and DNA and LH sequences influence whether off-dyad or Gorkovets et al. (87)

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gH variants in on- and off-dyad DNA deformation on-dyad binding mode is adopted, with L-DNA
positions analysis bending energy playing a role.
LH-bound 182–218 bp NRL nucleosomes with CG MC simulation Off-dyad LH binding modes cause increased Perišić et al. (27)
oligonucleosomes of core histone tails nucleosome packing.
24–100 nucleosomes H1.4 (rat) or H1.2 (mouse) LHs Increased LH density bends chromatin.

www.annualreviews.org
without NTD represented by 6 H1.4-bound nucleosomes condense more than

•
beads for the gH and 21–22 beads H1.2-bound nucleosomes.
for the CTD in 3 different on- Structure of higher NRL fibers is more robust to
and off-dyad binding modes, with variations in LH binding mode and density.
the off-dyad geometry based on
the BD docking model of Öztürk
et al. (46).
LH densities of 0.5 –1.6
LH/nucleosome with 0, 1, or 2
LH per nucleosome

In these studies, modeling and/or simulation approaches were used to predict the structure of linker histone–nucleosome complexes, to study chromatosome formation, or to investigate the
effects of linker histone binding on chromatin structure and dynamics and their dependence on sequence and environmental conditions.
Abbreviations: AMD, accelerated molecular dynamics; BD, Brownian dynamics; bp, DNA base pair; CG, coarse graining; CTD, C-terminal domain; GB, Generalized Born; GD; gH, globular
domain; L-DNA, linker DNA; LH, linker histone; MC, Monte Carlo; MD, molecular dynamics; NMA, normal mode analysis; NRL, nucleotide repeat length; NTD, N-terminal domain; PTM,

Molecular Simulation of Chromatosomes

posttranslational modification.
a
+ gH denotes that the gH is added to a nucleosome to study formation of the complex; LH-bound means that the LH is placed on the nucleosome(s) for simulations of the complex, usually in a

5.7
nucleosome array or fiber (and in some cases with LH unbinding and rebinding permitted).
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in diameter. Finch and Klug noted that the LH was essential in stabilizing the 30-nm fiber and
that LH–depleted chromatin did not show such condensed formations but rather an extended
chainlike appearance [also shown by Oudet et al. (18) in LH–depleted chromatin micrographs].
Molecular dynamics
(MD): a method used It was proposed that the 30-nm fiber was comprised of chromatosomes arranged in a one-start,
to simulate molecular solenoidal fashion (Figure 1b, left) with the LH lining the central bore. Further electron micro-
motion with atoms, scopic studies by Klug and coworkers (29) established the requirement for LHs in higher-order
represented as folding of the chromatin. Apart from the one-start, solenoidal model of folding, the chromatin
spherical particles,
is also seen to have a two-start, zigzag fold. The crystal structure of tetranucleosomes arranged
interacting according
to a classical molecular in a zigzag fashion was first solved by Richmond and colleagues (30) (PDB ID: 1ZBB), showing
mechanics force field that either a high concentration of multivalent cations or the LH was necessary for higher-order
and moving according folding of the chromatin. More recently, a cryo-EM structure of an array of 12 chromatosomes
to Newton’s equations (31) suggested that an off-dyad location of the LH both favors a twisted zigzag conformation
of motion
and confers a polarity to the 30-nm fiber. Although the 30-nm fiber has been observed in vitro,
Brownian dynamics whether such higher-order folding exists in vivo has been controversial. Three-dimensional se-
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(BD): a method used

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quencing studies of interphase chromatin hinted at a two-start formation (32). The absence of
to simulate the
direct evidence for the 30-nm fiber in vivo led to another school of thought on chromatin pack-
diffusional motion of
solute molecule(s) in a aging, which stated that the chromatin is found in a fractal globule form in the nucleus (33,
solvent modeled as a 34). Evidence for this came from particle tracking experiments of quantum dots in the nucleus
continuum (35), showing that the chromatin has a fractal form at lengths of less than 100 nm, and from
Hi-C mapping of the chromatin (36, 37) (Figure 1c). Very recently, advanced electron micro-
scopic studies (38) in vivo have shown chromatin packed in a disordered manner in the nucleus
with variable densities: the highly dense, transcriptionally inactive heterochromatin and the less
dense, transcriptionally active euchromatin. These studies show an absence of 30-nm fibers in vivo
(Figure 1c). The contradicting ideas about and evidence for chromatin packaging remain a puzzle
to this day.

MOLECULAR SIMULATION TECHNIQUES FOR STUDYING

CHROMATOSOME STRUCTURE AND DYNAMICS
The most widely used simulation technique for studying biomacromolecules is all-atom molec-
ular dynamics (MD) simulation (14). Each atom in the system simulated is modeled as a van der
Waals sphere, and bonded atoms are connected by harmonic springs. The interactions between
atoms are computed using a classical molecular mechanics force field describing bonded and non-
bonded interactions. Molecules can be simulated with either an implicit or an explicit model of
the solvent. Most MD studies of nucleosome systems have been done with an explicit solvent
model in which the biomolecules are immersed in a periodic box of water molecules and ions.
A periodic box containing an LH gH–nucleosome complex in aqueous solvent contains about
200,000 atoms (39). Thus, significant computational resources are required for doing MD simu-
lations of chromatosome (and chromatin) systems, and it is a challenge to obtain sufficient sam-
pling of the configurational space of the macromolecules, even with state-of-the-art computing
facilities.
One way to overcome this problem is to simplify the description of the system in the simula-
tions, which allows bigger systems to be simulated for longer times with available computational
resources (Figure 2). This is done in implicit solvent MD simulations, such as the simulations
of Izadi et al. (40) in which a 40-nucleosome chromatin fiber model with more than one million
atoms was simulated using a modified Generalized Born model. Another approach is to perform
Brownian dynamics (BD) simulations, in which the diffusion of solutes in a continuum solvent is

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Chromatin fiber

LH globular
domain in explicit
solvent
Chromatosome
H2A Nucleosome
Monte Carlo core
μm

H3
H4
Linker DNA
Brownian
dynamics Linker
histone
Size

Coarse-
grained
molecular
dynamics
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Diffusion of linker
Implicit solvent
histone globular
molecular
All-atom domain to
dynamics
molecular nucleosome
nm

dynamics Molecular mechanics

Quantum mechanics

CC

fs ps ns μs ms
Time
Figure 2
Simulation methods at multiple scales can be used to investigate chromatosome structure and dynamics as well as chromatin fiber
formation. All-atom molecular dynamics is depicted with an illustration of a linker histone globular domain (LH gH) in explicit
aqueous solvent. Implicit solvent molecular dynamics and coarse-grained molecular dynamics are depicted with an illustration of an LH
gH–nucleosome complex. Brownian dynamics is depicted with an illustration of diffusion of an LH gH to a nucleosome, and Monte
Carlo is depicted with an illustration of a mesoscale chromatosome model from Reference 62 and a chromatin-fiber model from
Reference 63.

(41). By removing the solvent degrees of freedom, the number of particles is reduced and compu-
tational efficiency is increased. Moreover, in BD simulations, the macromolecules are often treated Monte Carlo (MC)
as rigid bodies, thus removing the need to consider internal degrees of freedom. Different confor- simulation: a method
mations of a solute molecule can, nevertheless, be considered by running independent simulations used to sample
with different molecular conformations or by switching between precomputed conformations dur- configurations of a
molecular system
ing an MD simulation (41). These treatments have been used in rigid-body BD docking studies
according to a
to generate diffusional encounter complexes between a nucleosome and the globular domain of Boltzmann
an LH (39, 42), as shown in Figure 2. distribution
Monte Carlo (MC) simulations provide a further simplification by using a relatively uncom-
Coarse-graining
plicated and more flexible procedure for generating snapshots. They can be used to sample a (CG): a simulation
Boltzmann distribution of configurations. Explicit time dependence is lost, although effective technique in which
times can sometimes be estimated in the simulations (43). MC simulations have been used to groups of atoms are
study the dynamics of systems containing many nucleosomes described by coarse-grained parti- subsumed into single
particles (sometimes
cles (6). Coarse-graining (CG) can be done at the level of one bead for four water molecules (44)
referred to as
or at a coarser level, e.g., one bead per DNA turn or one cylinder per nucleosome, for mesoscopic

·.•�-
pseudoatoms)
modeling (6, 7) (Figure 2). The need to capture all the relevant contributions in CG models,

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e.g., the effects of divalent cation binding in addition to solvent ionic strength, can lead to quite
elaborate parameterizations of force fields.
Enhanced sampling simulation techniques provide a means to explore lengthy events that can-
Accelerated
molecular dynamics not be sampled adequately in standard simulations. Accelerated molecular dynamics (AMD) im-
(AMD): a method proves the efficiency of conformational sampling of molecules modeled in atomic detail by adding
that improves the additional potentials to the force field to reduce the barriers for conformational transitions (45).
sampling of After correcting for the additional potentials, information on the possible relative different molec-
configurational space
ular conformations and their relative probabilities can be obtained. This approach has been used to
in MD simulations by
reducing the energy sample the dynamics of a loop on the globular domain of an LH in both the absence and presence
barriers between of a nucleosome (39).
conformations The different simulation techniques can be applied together in a multiscale simulation sce-
nario (Figure 2). Reliable structures for starting simulations can be obtained from experiments or
from classical molecular modeling, homology modeling, or docking methods (Table 1). For stud-
ies of chromatosome systems, simulations have been performed with one technique to generate
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structures for simulations with another. For example, rigid-body BD docking of an LH to a nu-
cleosome has been applied to generate diffusional encounter complexes, and these structures have
then provided starting points for MD simulations, using full atomic detail to generate structures
of the LH–nucleosome complexes (39, 46). Information from such atomic detail modeling and
simulation provides the basis for describing the LH–nucleosome interactions in CG simulations
of chromatin structuring with tens of nucleosomes, as shown, for example, by Perišić et al. (27). An
alternative approach to multiscale simulation is to incorporate different scales in one simulation
system. While some mesoscopic models employ different resolutions for the different compo-
nents (27), adaptive resolution simulations with high and low resolution parts have not yet been
applied to simulations of chromatosome systems but may, in the future, provide a means to both
zoom in on the details of the interactions of flexible histone tails and zoom out to the higher-order
structuring of chromatin.

THE STRUCTURES AND BINDING MECHANISMS

OF LH–NUCLEOSOME COMPLEXES
Several on- and off-dyad binding modes of LH–nucleosome complexes have been reported in
the last few years (Figure 3) and are compared in detail by Öztürk et al. (4). By using NMR
constraints, Zhou et al. (47) proposed an off-dyad binding of Drosophila melanogaster gH1 to the
Widom nucleosome assembly 601 sequence DNA. Using cryo-EM, Song et al. (31) identified
off-dyad binding of Homo sapiens H1.4 to an array of nucleosomes with Widom 601 sequences.
The first X-ray crystal structure of the LH–nucleosome complex was reported by Zhou et al. (3)
and showed Gallus gallus gH5 bound on-dyad to a Widom 601 nucleosome (PDB ID: 4QLC).
Zhou et al. (48) later reported that by introducing penta-mutations on G. gallus gH5, its on-dyad
binding configuration could be changed to a D. melanogaster gH1-like off-dyad binding mode,
indicating that the LH sequence determines the binding mode. Most recently, in a combined
cryo-EM (employing a full-length LH) and X-ray crystallographic (employing a globular domain)
study, Bednar et al. (49) revealed an almost complete picture of a chromatosome with a full Xenopus
laevis H1 bound to a nucleosome with a palindromic Widom 601L sequence with the gH bound
at the dyad axis in an on-dyad position, and the long C-terminal domain associated with one of
the L-DNAs.
To gain a mechanistic understanding of how LH–nucleosome complexes form, Öztürk et al.
(39, 46) used a combination of MD and BD simulations. They showed that BD simulations can

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a b LH d
L-DNA1 L-DNA2 L-DNA1 L-DNA2

α1
α2 C
H3

β1 H2A
β2 H4
H2B
α3

90°
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c e

L-DNA1 L-DNA2
α1 L-DNA1 L-DNA2
N α2

β1

α3

Figure 3
Experimentally determined linker histone globular domain (LH gH) and LH gH–nucleosome complex structures. (a) X-ray crystal
structure of the Gallus gallus H5 gH in the closed conformation (2) (PDB ID: 1HST, chain B), shown in two orientations. The α-helices
are shown in cyan, the β-strands in magenta, and the unstructured regions in pale pink. (b) Drosophila melanogaster H1 gH binding
off-dyad to a nucleosome, as reported by Zhou et al. (47) (structure kindly provided by Yawen Bai). (c) Homo sapiens H1.4 gH binding
off-dyad to a nucleosome as reported by Song et al. (31) (structure kindly provided by Ping Zhu). (d) G. gallus H5 gH binding on-dyad
to a nucleosome as reported by Zhou et al. (3) (PDB ID: 4QLC). (e) Xenopus laevis H1 gH binding on-dyad to a nucleosome as reported
by Bednar et al. (49) (PDB ID: 5NL0). The linker DNAs L-DNA1 and L-DNA2 are labeled according to DNA sequence similarity, as
in Öztürk et al. (46). Abbreviations: C, C-terminal end; L-DNA, linker DNA; LH, linker histone; N, N-terminal end.

recapitulate experimentally determined structures of LH–nucleosome complexes (Figure 4).

AMD simulations of the G. gallus gH5 indicated that the LH gH predominantly stays in a closed
form in solution and opens when bound to a nucleosome. The simulations revealed that the
L-DNA flexibility is constrained by off-dyad–bound gH5, which forms a stable chromatosome
when in an open form by interacting with thymidines in one L-DNA arm. Finally, BD simulations

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a b

L-DNA1 L-DNA2

LH in diffusional
encounter complex

L-DNA1 L-DNA2

LH in
crystal structure
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Figure 4
Brownian dynamics (BD) simulations can reproduce experimentally determined linker histone (LH)–nucleosome complex structures.
The docking position of the LH globular domain (gH) in the computed diffusional encounter complex (cyan) is shown with the X-ray
crystal structures of LH (red) and the nucleosome (gray) complexes (a) for Gallus gallus gH5 (PDB ID: 4QLC) and (b) for Xenopus laevis
gH1 (PDB ID: 5NL0). For simulation details, see Öztürk et al. (46); the figure is adapted from this reference.

started with a range of nucleosome conformations that differed in L-DNA opening angle and
LH gH conformation (open or closed) indicated that both on-dyad and off-dyad gH5-bound
nucleosome configurations can occur (Figure 5). These findings suggest that the conforma-
tional dynamics of both the LH and the nucleosome define the chromatosome geometry by a
combination of conformational selection and induced fit mechanisms.

EFFECTS OF SEQUENCE VARIATIONS, POSTTRANSLATIONAL

MODIFICATIONS, AND ENVIRONMENT ON LH–NUCLEOSOME
COMPLEXES
Different LH isoforms may have distinct functions due to different nucleosome interactions, re-
sulting in differences in chromatin compaction (49, 50, 51). Additionally, LH posttranslational
modifications (PTMs) are associated with various cellular events, such as apoptosis (52), cellular
aging (53), and DNA repair (54). Although there have been many studies of the PTMs of the core
histone tails (55–57), the effects of single point mutations and PTMs of LHs are still not under-
stood in detail. In a recent BD study, Öztürk et al. (46) used an ensemble of nucleosome structures
obtained from MD simulations and investigated the effects of single point mutations and PTMs of
D. melanogaster and G. gallus LH gHs on nucleosome binding. They found that chromatosome for-
mation, in addition to being sensitive to L-DNA opening angles, is also sensitive to LH mutations
and PTMs. Such effects should be considered when comparing the results of studies conducted
with different LHs and nucleosomes. Furthermore, environmental factors such as ionic strength
and the presence of divalent cations can influence LH–nucleosome interactions and chromatin
structure, as has been seen in mesoscopic models (6, 7). Further experimental studies are required
to characterize LH mutants and PTMs in terms of their effects on chromatosome structure and
their relation to phenotypic effects.

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H2A
H2B DNA
Unbound LH gH

Closed gH Open gH

H4 H3 Conformational
selection
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Closed gH

Induced fit

Open gH

Figure 5
Conformational selection and induced fit mechanisms of LH–nucleosome complex formation proposed
from Brownian and molecular dynamics simulations of the binding of chicken gH5 to a nucleosome [Öztürk
et al. (39)]. The unbound LH gH (shown in surface representation with a cartoon depiction of the secondary
structure) is in an equilibrium between open (brown) and closed (pink) states, in which the closed form is the
dominant state in solution (as indicated by the solid arrows). Upon binding of the closed-state LH gH to a
nucleosome in an off-dyad binding mode, the L-DNA flexibility is constrained and the LH gH opens,
making transient hydrophobic contacts with thymidines of the L-DNA. Purple double curved lines
schematically indicate the degree of flexibility of the linker DNA arms. Abbreviations: gH, globular domain;
L-DNA, linker DNA; LH, linker histone.

CONCLUSION
The determinants of the formation of chromatosomes, the fundamental repeating units of chro-
matin, are not yet fully understood, but molecular simulation techniques and experiments are
revealing important insights into chromatosome structure and dynamics. LH proteins vary in
sequence and undergo PTMs. Consequently, chromatosome formation due to LH binding to
nucleosomes may provide key epigenetic regulatory control of gene expression. Here, we have
provided an overview of simulation approaches to study chromatosome formation and its role
in chromatin structuring (see the section titled Summary Points). We anticipate that further
biophysical experiments, e.g., by fluorescence techniques such as fluorescence resonance energy
transfer (FRET) (58) and fluorescence correlation spectroscopy (FCS), both at ensemble and

·.•�-
single-molecule levels (59, 60); by force spectroscopy, with optical and magnetic tweezers; and

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by atomic force microscopy (AFM) (61), will provide more data on chromatosome and oligonu-
cleosome structure and dynamics. Along with improved multiscale simulation techniques, this will
enable us to address the current challenges in studying the structure, dynamics, and function of
chromatosomes and chromatin structure, some of which are listed in the section titled Future
Issues.

SUMMARY POINTS
1. Chromatosomes are the fundamental units of chromatin structure and are formed when
a linker histone binds to a nucleosome.
2. The binding and positioning of the linker histone on the nucleosome influence the pack-
ing of chromatin, but chromatosome structure is still the subject of debate.
3. The simulation of chromatosome formation is computationally challenging due to the
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size and flexibility of the chromatosome; therefore, a multiscale simulation approach is

appropriate.
4. Simulations combining Brownian and molecular dynamics techniques have shown that
linker histone–nucleosome binding involves both conformational selection and induced
fit mechanisms.
5. Brownian dynamics simulations have revealed the sensitivity of chromatosome structure
to nucleic acid and linker histone sequence variation and to posttranslational modifica-
tions of linker histones.
6. Simulations and recent experimentally determined structures of linker histone–
nucleosome complexes suggest that chromatosomes can adopt an ensemble of structures,
with the structural population distribution being dependent on sequence, posttransla-
tional modifications, and environmental conditions.
7. Structures of linker histone–nucleosome complexes derived from atomic detail models
can be used to construct mesoscopic models to investigate chromatin fiber formation.
8. Concerted application of recent experimental and computational advances is necessary
to obtain a complete understanding of the determinants of chromatosome formation and
their influence on chromatin packing.

FUTURE ISSUES
1. Comprehensive reporting of the details of the sequences and environmental condi-
tions of linker histone–nucleosome systems studied experimentally is required for gain-
ing a detailed understanding of the relationships between chromatosome structure and
sequence.
2. Full reporting of modeling methods and assumptions is necessary when interpreting
experimental data.
3. In simulations of chromatosome formation, fully accounting for and sampling the flex-
ible N- and C-terminal tails of linker histones and the flexible tails of the core histones
is a major computational challenge.

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4. Simulations of multiple nucleosomes and chromatosomes and how they interact require
multiscale simulation approaches.
5. In terms of binding mechanisms, is the off-dyad configuration of the linker histone just
an intermediate state on the route to a more stable on-dyad configuration?
6. How are linker histone–nucleosome interactions affected by the presence of histone
chaperones and other DNA-binding proteins, such as pioneer factors?
7. What is the linker histone–nucleosome stoichiometry, and how does this affect chro-
matin structure and regulation?
8. What are the determinants of the kinetics of linker histone–nucleosome binding?

DISCLOSURE STATEMENT
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The authors are not aware of any affiliations, memberships, funding, or financial holdings that
might be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS
Our work on the simulation of linker histone–nucleosome complexation has in part been funded
by the German Research Foundation (grant no. WA 1381/1-1), the Klaus Tschira Foundation,
the Heidelberg Biosciences International Graduate School (M.A.Ö.), and the Max Planck Soci-
ety (V.C.). The development of the SDA software for Brownian dynamics simulation in the Wade
group at HITS is in part supported by the EU FET Flagship Program Human Brain Project [grant
numbers 604102 (European Union Seventh Framework Program, FP7/2007–2013) and 720270
(European Union Horizon 2020 Framework Program for Research and Innovation Specific Grant
Agreements 1 and 2)]. M.D. acknowledges the Helmholtz International Graduate School for Can-
cer Research for funding. We thank Katalin Tóth for critical comments and helpful discussions.
We dedicate this review to the memory of Jörg Langowski, a firm believer in the value of
the combined application of simulations and experiments to study chromatin and one of the first
scientists to perform Brownian dynamics simulations of nucleic acids.

LITERATURE CITED
1. Klug A. 1983. From Macromolecules to Biological Assemblies (Nobel Lecture). Angew. Chem. Int. Ed.
22(8):565–82
2. Ramakrishnan V, Finch JT, Graziano V, Lee PL, Sweet RM. 1993. Crystal structure of globular domain
of histone H5 and its implications for nucleosome binding. Nature 362(6417):219–23
3. Zhou B-R, Jiang J, Feng H, Ghirlando R, Xiao TS, Bai Y. 2015. Structural mechanisms of nucleosome
recognition by linker histones. Mol. Cell 59(4):628–38
4. Öztürk MA, Cojocaru V, Wade RC. 2018. Toward an ensemble view of chromatosome structure: a
paradigm shift from one to many. Structure 26(8):1050–57
5. Fyodorov DV, Zhou B-R, Skoultchi AI, Bai Y. 2017. Emerging roles of linker histones in regulating
chromatin structure and function. Nat. Rev. Mol. Cell Biol. 19(3):192–206
6. Perišić O, Schlick T. 2016. Computational strategies to address chromatin structure problems. Phys. Biol.
13:35006

·.•�-
7. Ozer G, Luque A, Schlick T. 2015. The chromatin fiber: multiscale problems and approaches. Curr. Opin.
Struct. Biol. 31:124–39

www.annualreviews.org • Molecular Simulation of Chromatosomes 5.15

, Review in Advance first posted on

February 4, 2020. (Changes may
still occur before final publication.)
 PC71CH05_Wade ARjats.cls January 24, 2020 15:29

8. Korolev N, Fan Y, Lyubartsev AP, Nordenskiöld L. 2012. Modelling chromatin structure and dynamics:
status and prospects. Curr. Opin. Struct. Biol. 22:151–59
9. Biswas M, Langowski J, Bishop TC. 2013. Atomistic simulations of nucleosomes. WIREs Comput. Mol.
Sci. 3:378–92
10. Boulé J-B, Mozziconacci J, Lavelle C. 2015. The polymorphisms of the chromatin fiber. J. Phys. Condens.
Matter. 27(3):033101
11. Armeev GA, Gribkova AK, Pospelova I, Komarova GA, Shaytan AK. 2019. Linking chromatin composi-
tion and structural dynamics at the nucleosome level. Curr. Opin. Struct. Biol. 56:46–55
12. Zhou B-R, Bai Y. 2019. Chromatin structures condensed by linker histones. Essays Biochem. 63(1):75–
87
13. Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. 2012. Biomolecular simulation: a computational
microscope for molecular biology. Annu. Rev. Biophys. 41:429–52
14. Lee EH, Hsin J, Sotomayor M, Comellas G, Schulten K. 2009. Discovery through the computational
microscope. Structure 17(10):1295–306
15. Miescher F. 1871. Über die chemische Zusammensetzung der Eiterzellen. In Medicinisch-chemische Unter-
Annu. Rev. Phys. Chem. 2020.71. Downloaded from www.annualreviews.org

suchungen, Vol. 4, ed. F Hoppe-Seyler, pp. 441–60. Berlin: Hirschwald

Access provided by Goteborg University on 02/05/20. For personal use only.

16. Flemming W. 1882. Zellsubstanz, Kern und Zelltheilung. Leipzig, Ger.: F.C.W. Vogel
17. Olins AL, Olins DE. 1974. Spheroid chromatin units (v bodies). Science 183(4122):330–32
18. Oudet P, Gross-Bellard M, Chambon P. 1975. Electron microscopic and biochemical evidence that chro-
matin structure is a repeating unit. Cell 4(4):281–300
19. Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A. 1984. Structure of the nucleosome core particle
at 7 Å resolution. Nature 311(5986):532–37
20. Kornberg RD. 1974. Chromatin structure: a repeating unit of histones and DNA. Science 184(139):868–71
21. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleo-
some core particle at 2.8 Å resolution. Nature 389(6648):251–60
22. Simpson RT. 1978. Structure of the chromatosome, a chromatin particle containing 160 base pairs of
DNA and all the histones. Biochemistry 17(25):5524–31
23. Olins AL, Senior MB, Olins DE. 1976. Ultrastructural features of chromatin ν bodies. J. Cell Biol.
68(3):787–93
24. Olins DE, Olins AL. 1978. Nucleosomes: the structural quantum in chromosomes. Am. Sci. 66(6):704–11
25. Bates DL, Thomas JO. 1981. Histones H1 and H5: one or two molecules per nucleosome? Nucleic Acids
Res. 9(22):5883–94
26. Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC, et al. 1998. Nucleosomes, linker
DNA, and linker histone form a unique structural motif that directs the higher-order folding and com-
paction of chromatin. PNAS 95(24):14173–78
27. Perišić O, Portillo-Ledesma S, Schlick T. 2019. Sensitive effect of linker histone binding mode and sub-
type on chromatin condensation. Nucleic Acids Res. 47(10):4948–57
28. Finch JT, Klug A. 1976. Solenoidal model for superstructure in chromatin. PNAS 73(6):1897–901
29. Thoma F, Koller T, Klug A. 1979. Involvement of histone H1 in the organization of the nucleosome and
of the salt-dependent superstructures of chromatin. J. Cell Biol. 83(2, Part 1):403–27
30. Schalch T, Duda S, Sargent DF, Richmond TJ. 2005. X-ray structure of a tetranucleosome and its impli-
cations for the chromatin fibre. Nature 436(7047):138–41
31. Song F, Chen P, Sun D, Wang M, Dong L, et al. 2014. Cryo-EM study of the chromatin fiber reveals a
double helix twisted by tetranucleosomal units. Science 344(6182):376–80
32. Risca VI, Denny SK, Straight AF, Greenleaf WJ. 2017. Variable chromatin structure revealed by in situ
spatially correlated DNA cleavage mapping. Nature 541(7636):237–41
33. Grosberg A, Rabin Y, Havlin S, Neer A. 1993. Crumpled globule model of the three-dimensional struc-
ture of DNA. EPL 23(5):373–78
34. Mirny LA. 2011. The fractal globule as a model of chromatin architecture in the cell. Chromosome Res.
19(1):37–51
35. Bancaud A, Huet S, Daigle N, Mozziconacci J, Beaudouin J, Ellenberg J. 2009. Molecular crowding af-

·.•�-
fects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of
chromatin. EMBO J. 28(24):3785–98

5.16 Öztürk et al.

, Review in Advance first posted on

February 4, 2020. (Changes may
still occur before final publication.)
 PC71CH05_Wade ARjats.cls January 24, 2020 15:29

36. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. 2009. Compre-
hensive mapping of long-range interactions reveals folding principles of the human genome. Science
326(5950):289–93
37. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, et al. 2017. The 4D nucleome project. Nature
549(7671):219–26
38. Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O’Shea CC. 2017. ChromEMT: Visualizing 3D
chromatin structure and compaction in interphase and mitotic cells. Science 357(6349):eaag0025
39. Öztürk MA, Pachov GV, Wade RC, Cojocaru V. 2016. Conformational selection and dynamic adaptation
upon linker histone binding to the nucleosome. Nucleic Acids Res. 44(14):6599–613
40. Izadi S, Anandakrishnan R, Onufriev AV. 2016. Implicit solvent model for million-atom atomistic simu-
lations: insights into the organization of 30-nm chromatin fiber. J. Chem. Theory Comput. 12(12):5946–59
41. Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, et al. 2015. SDA 7: a modular and parallel
implementation of the simulation of diffusional association software. J. Comput. Chem. 36(21):1631–45
42. Pachov GV, Gabdoulline RR, Wade RC. 2011. On the structure and dynamics of the complex of the
nucleosome and the linker histone. Nucleic Acids Res. 39(12):5255–63
Annu. Rev. Phys. Chem. 2020.71. Downloaded from www.annualreviews.org

43. Paquet E, Viktor HL. 2015. Molecular dynamics, Monte Carlo simulations, and Langevin dynamics: a
Access provided by Goteborg University on 02/05/20. For personal use only.

computational review. BioMed Res. Int. 2015:183918

44. Yesylevskyy SO, Schäfer LV, Sengupta D, Marrink SJ. 2010. Polarizable water model for the coarse-
grained MARTINI force field. PLOS Comput. Biol. 6(6):1000810
45. Tiwary P, van de Walle A. 2016. A review of enhanced sampling approaches for accelerated molecular
dynamics. In Multiscale Materials Modeling for Nanomechanics, ed. CR Weinberger, GJ Tucker, pp. 195–221.
Cham, Switz.: Springer
46. Öztürk MA, Cojocaru V, Wade RC. 2018. Dependence of chromatosome structure on linker histone
sequence and posttranslational modification. Biophys. J. 114(10):2363–75
47. Zhou B-R, Feng H, Kato H, Dai L, Yang Y, et al. 2013. Structural insights into the histone H1-nucleosome
complex. PNAS 110(48):19390–95. Erratum. 2014. PNAS 111(3):1222
48. Zhou B-R, Feng H, Ghirlando R, Li S, Schwieters CD, Bai Y. 2016. A small number of residues can
determine if linker histones are bound on or off dyad in the chromatosome. J. Mol. Biol. 428(20):3948–59
49. Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai G, et al. 2017. Structure and dynamics of a 197 bp
nucleosome in complex with linker histone H1. Mol. Cell 66(3):384–97.e8
50. Kowalski A, Pałyga J. 2016. Modulation of chromatin function through linker histone H1 variants. Biol.
Cell 108(12):339–56
51. Millán-Ariño L, Izquierdo-Bouldstridge A, Jordan A. 2016. Specificities and genomic distribution of so-
matic mammalian histone H1 subtypes. Biochim. Biophys. Acta Gene Regul. Mech. 1859(3):510–19
52. Kim K, Jeong KW, Kim H, Choi J, Lu W, et al. 2012. Functional interplay between p53 acetylation and
H1.2 phosphorylation in p53-regulated transcription. Oncogene 31(39):4290–301
53. Happel N, Doenecke D, Sekeri-Pataryas KE, Sourlingas TG. 2008. H1 histone subtype constitution and
phosphorylation state of the ageing cell system of human peripheral blood lymphocytes. Exp. Gerontol.
43(3):184–99
54. Chubb JE, Rea S. 2010. Core and linker histone modifications involved in the DNA damage response. In
Genome Stability and Human Diseases, ed. HP Nasheuer, pp. 17–42. Subcell. Biochem. Vol. 50. Dordrecht,
Neth.: Springer
55. Papamokos GV, Tziatzos G, Papageorgiou DG, Georgatos SD, Politou AS, Kaxiras E. 2012. Structural
role of RKS motifs in chromatin interactions: a molecular dynamics study of HP1 bound to a variably
modified histone tail. Biophys. J. 102(8):1926–33
56. Collepardo-Guevara R, Portella G, Vendruscolo M, Frenkel D, Schlick T, Orozco M. 2015. Chromatin
unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions:
a multiscale computational study. J. Am. Chem. Soc. 137(32):10205–15
57. Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. 2018. Modulation of nucleosomal DNA acces-
sibility via charge-altering post-translational modifications in histone core. Epigenet. Chromatin 11:11
58. Lakowicz JR. 2006. Principles of Fluorescence Spectroscopy. New York: Springer. 3rd ed.

·.•�-
59. Ngo TTM, Zhang Q, Zhou R, Yodh JG, Ha T. 2015. Asymmetric unwrapping of nucleosomes under
tension directed by DNA local flexibility. Cell 160(6):1135–44

www.annualreviews.org • Molecular Simulation of Chromatosomes 5.17

, Review in Advance first posted on

February 4, 2020. (Changes may
still occur before final publication.)
 PC71CH05_Wade ARjats.cls January 24, 2020 15:29

60. Gansen A, Hieb AR, Böhm V, Tóth K, Langowski J. 2013. Closing the gap between single molecule and
bulk FRET analysis of nucleosomes. PLOS ONE 8(4):e57018
61. Ordu O, Lusser A, Dekker NH. 2016. Recent insights from in vitro single-molecule studies into nucleo-
some structure and dynamics. Biophys. Rev. 8(Suppl. 1):33–49
62. Collepardo-Guevara R, Schlick T. 2014. Chromatin fiber polymorphism triggered by variations of DNA
linker lengths. PNAS 111(22):8061–66
63. de Jong BE, Brouwer TB, Kaczmarczyk A, Visscher B, van Noort J. 2018. Rigid basepair Monte Carlo
simulations of one-start and two-start chromatin fiber unfolding by force. Biophys. J. 115:1848–59
64. Bharath MMS, Chandra NR, Rao MRS. 2003. Molecular modeling of the chromatosome particle. Nucleic
Acids Res. 31(14):4264–74
65. Fan L, Roberts VA. 2006. Complex of linker histone H5 with the nucleosome and its implications for
chromatin packing. PNAS 103(22):8384–89
66. Cui F, Zhurkin VB. 2009. Distinctive sequence patterns in metazoan and yeast nucleosomes: implications
for linker histone binding to AT-rich and methylated DNA. Nucleic Acids Res. 37(9):2818–29
67. Wong H, Victor J-M, Mozziconacci J. 2007. An all-atom model of the chromatin fiber containing linker
Annu. Rev. Phys. Chem. 2020.71. Downloaded from www.annualreviews.org

histones reveals a versatile structure tuned by the nucleosomal repeat length. PLOS ONE 2(9):e877
Access provided by Goteborg University on 02/05/20. For personal use only.

68. Ramaswamy A, Ioshikhes I. 2007. Global dynamics of newly constructed oligonucleosomes of conven-
tional and variant H2A.Z histone. BMC Struct. Biol. 7(1):76
69. Stehr R, Kepper N, Rippe K, Wedemann G. 2008. The effect of internucleosomal interaction on folding
of the chromatin fiber. Biophys. J. 95(8):3677–91
70. Kepper N, Foethke D, Stehr R, Wedemann G, Rippe K. 2008. Nucleosome geometry and internucleo-
somal interactions control the chromatin fiber conformation. Biophys. J. 95(8):3692–705
71. Diesinger PM, Heermann DW. 2008. The influence of the cylindrical shape of the nucleosomes and H1
defects on properties of chromatin. Biophys. J. 94(11):4165–72
72. Diesinger PM, Kunkel S, Langowski J, Heermann DW. 2010. Histone depletion facilitates chromatin
loops on the kilobasepair scale. Biophys. J. 99(9):2995–3001
73. Arya G, Schlick T. 2009. A tale of tails: how histone tails mediate chromatin compaction in different salt
and linker histone environments. J. Phys. Chem. A 113(16):4045–59
74. Schlick T, Perišić O. 2009. Mesoscale simulations of two nucleosome-repeat length oligonucleosomes.
Phys. Chem. Chem. Phys. 11(45):10729–37
75. Grigoryev S, Arya G, Correll S, Woodcock CL, Schlick T. 2009. Evidence for heteromorphic chromatin
fibers from analysis of nucleosome interactions. PNAS 106(32):13317–22
76. Gan HH, Schlick T. 2010. Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach.
Biophys. J. 99(8):2587–96
77. Perišić O, Collepardo-Guevara R, Schlick T. 2010. Modeling studies of chromatin fiber structure as a
function of DNA linker length. J. Mol. Biol. 403(5):777–802
78. Grigoryev SA, Bascom G, Buckwalter JM, Schubert MB, Woodcock CL, Schlick T. 2016. Hierarchical
looping of zigzag nucleosome chains in metaphase chromosomes. PNAS 113(5):1238–43
79. Collepardo-Guevara R, Schlick T. 2011. The effect of linker histone’s nucleosome binding affinity on
chromatin unfolding mechanisms. Biophys. J. 101(7):1670–80
80. Collepardo-Guevara R, Schlick T. 2012. Crucial role of dynamic linker histone binding and divalent ions
for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes. Nucleic
Acids Res. 40(18):8803–17
81. Ozer G, Collepardo-Guevara R, Schlick T. 2015. Forced unraveling of chromatin fibers with nonuniform
linker DNA lengths. J. Phys. Condens. Matter 27(6):064113
82. Luque A, Collepardo-Guevara R, Grigoryev S, Schlick T. 2014. Dynamic condensation of linker histone
C-terminal domain regulates chromatin structure. Nucleic Acids Res. 42(12):7553–60
83. Luque A, Ozer G, Schlick T. 2016. Correlation among DNA linker length, linker histone concentration,
and histone tails in chromatin. Biophys. J. 110(11):2309–19
84. Perišić O, Schlick T. 2017. Dependence of the linker histone and chromatin condensation on the nucle-
osome environment. J. Phys. Chem. B 121(33):7823–32

·.•�-
5.18 Öztürk et al.

, Review in Advance first posted on

February 4, 2020. (Changes may
still occur before final publication.)
 PC71CH05_Wade ARjats.cls January 24, 2020 15:29

85. Bascom GD, Schlick T. 2018. Chromatin fiber folding directed by cooperative histone tail acetylation
and linker histone binding. Biophys. J. 114(10):2376–85
86. Bascom G, Schlick T. 2017. Linking chromatin fibers to gene folding by hierarchical looping. Biophys.
J. 112(3):434–45
87. Gorkovets TK, Armeev GA, Shaitan KV, Shaytan AK. 2018. Joint effect of histone H1 amino acid se-
quence and DNA nucleotide sequence on the structure of chromatosomes: analysis by molecular model-
ing methods. Mosc. Univ. Biol. Sci. Bull. 73(2):82–87
Annu. Rev. Phys. Chem. 2020.71. Downloaded from www.annualreviews.org
Access provided by Goteborg University on 02/05/20. For personal use only.

·.•�-
www.annualreviews.org • Molecular Simulation of Chromatosomes 5.19

, Review in Advance first posted on

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still occur before final publication.)