Structure and Function of the Core Nucleosome Particle:

The Molecular Basis of Chromatin Organization

Cassidy Crook

Chromatin and Genome Organization

All cells face the considerable challenge of compacting the genome to a

small fraction of its original volume such that it can exist within the space of a cell.

Prokaryotes as well as eukaryotes accomplish this feat through the combined

effects of protein interactions and DNA supercoiling. However, dissimilar to

eukaryotes, the genetic material of prokaryotes is maintained in an irregular

entanglement known as the bacterial nucleoid. The fluid nature of the nucleoid is

governed principally by enzyme-mediated (as well as spontaneous) topological

modifications, with the association of structural proteins serving largely to stabilize

supercoiled DNA states. In contrast, DNA compaction in eukaryotes is achieved

through an extensively ordered genome architecture for which an organizational

hierarchy is defined. The nucleosome represents the fundamental unit of

eukaryotic genome organization (Bates & Maxwell, 2006). Roughly 200 bp

segments of relaxed eukaryotic DNA are regularly coiled around octameric histone

proteins to form an assembly of nucleosome particles with a DNA packing ratio of

around seven (Lewin, 2004). Nucleosomes arranged along a span of duplex DNA

constitute a 10 nm chromatin fiber and have the canonical appearance of beads-on-

a-string (Olins & Olins, 1974). Subsequently, nucleosomes aggregate to form a 30

nm second-order chromatin fiber with a helical super-structure and a packing ratio

of around forty. The 30 nm fiber is arranged into 20-100 kbp loop domains which

associate with nuclear matrix proteins and scaffold proteins, including

topoisomerases and RNA polymerases, to achieve a packing ratio exceeding 1000.

Surprisingly, little is known about chromatin organization beyond the level of the

30 nm filament. Higher order structures appear to include looped rosette

configurations (or chromomeres), 100-130 nm chomomena, a 200-250 nm fiber,

and, ultimately, the eukaryotic chromosome (Nelson & Cox, 2008). Based on this

model of DNA compaction in eukaryotes, it has been suggested that the

composition of the bacterial nucleoid exemplifies a rudimentary chromosome. Still,

a fundamental difference between chromosome organization and nucleoid

composition is the primary role of DNA-histone interactions in the manifestation of

DNA supercoiling in eukaryotes as opposed to topological regulation achieved

cheifly by the competition of topoisomerase enzymes within the nucleoid.

Specifically, prokaryotes rely on the essential bacterial enzyme DNA gyrase, a type

II topoisomerase (topo), to introduce negative supercoils into DNA through an ATP-

dependent mechanism , while negative supercoiling in eukaryotic DNA is achieved

exclusively through the winding of DNA around nucleosomal histone octamers.

Interestingly, eukaryotic type II topos are not able to induce negative supercoiling

in DNA, yet they carry out ATP hydrolysis through a mechanism reminiscent of

bacterial gyrase. The free energy of ATP hydrolysis in eukaryotic topoII is utilized

in what has been described as a highly inefficient manner, to needlessly drive sub-

equilibrium topological simplification of DNA (Bates & Maxwell, 2006). Thus, one

might speculate that ATP-hydrolysis in eukaryotic topoII is an evolutionary relic of

an ancestral prokaryotic topoII once essential for the maintenance of genome

compaction through negative supercoiling.

A Historical Perspective of Chromatin and the Nucleosome

The term ‘chromatin’ was first introduced by the highly-renowned German

cytogeneticist Walther Flemming in the early 1880’s and was so-named to convey

its refractive properties and its affinity for dyes. In 1884 Albrecht Kossel described

‘histon’, a ‘proteoid’ isolated from the phosphrous-rich acidic ‘nuclein’ extracts of

avian erythrocyte nuclei. Jointly, these preliminary discoveries established the

basis for our current understanding of eukaryotic DNA organization. Yet,

approximately 80 years after histones were first described, the discovery of a basic

subunit of chromatin structure in 1973-1974, coined the ‘nucleosome’ shortly

thereafter, revolutionized the field of chromosome organization and sparked what

has been recognized as the ‘nucleosome era’ (Olins & Olins, 2003).

Prior to the earliest results indicating a discrete sub-structure repeated in

chromatin, the most widely accepted model for chromatin structure was the

Pardon-Wilkins super-helical model. Based on the results of low-angle x-ray

diffraction, the super-helical model of chromatin compaction essentially described

a nucleohistone coiled-coil in which the histone protein structure was that of a long

fibrillous coil around which DNA was wrapped (Olins & Olins, 1972, 1974, 1997;

Pardon & Wilkins, 1972). In the early 1970’s the work of Olins and Olins (1974),

Woodcock (1973), and Kornberg and Thomas (1974) independently utilized

electron scattering to visualize chromatin filaments at low-resolution. Consistently,

chromatin appeared to form irregularly distributed spherical bodies, designated

‘nu-bodies’, which exhibited a tendency to arrange in clusters (Olins & Olins, 1974;

Woodcock, 1973; Kornberg & Thomas, 1974). Micrograph images of nucleosomes

were paralleled by experimental evidence demonstrating a repeating structure in

condensed DNA which facilitated protection of contiguous 200 bp segments in

DNase digest assays (Hewish & Burgoyne, 1973). Furthermore, studies

characterizing the properties of histone proteins made vital contributions to a

unified theory of chromatin structure. Notably, such studies demonstrated the

presence of one of each class of histone per 100 bp of DNA (excluding H1), the in

vitro assembly of an (H3-H4)2 tetramer, and the vital role of histones H2A, H2B,

H3, and H4 in the formation of chromatin ‘beads’ (Kornberg, 1974). Thus, by the

mid-1970’s the sum of experimental data relating to chromatin was sufficient to

formulate a cohesive theory for chromatin structure – and so the nucleosome

model was conceived. In a basic sense, the nucleosome model identifies the

nucleosome unit as the basic repeating sub-structure of chromatin. Specifically,

this model recognized, in considerable detail, the structure and organization of the

nucleosome as comprised of a 200 bp segment of DNA oriented around a tripartite

histone octamer composed of a (H3-H4)2 tetramer and two H2A-H2B dimers (see

figs. 2, 3, & 4) (Kornberg, 1974).

The Core Histone Architecture

Fundamentally, the histone octamer is composed of the four primary histone

monomers, H2A, H2B, H3, and H4, each of which is structurally similar to the rest.

In particular, the core histones are distinguished by a unique secondary structure

known as the histone-fold. The histone-fold is a three-helix motif composed of an N-

terminal 11-residue alpha-helix (αI), a long central 27-residue helix (αII), and a C-

terminal 11-residue helix (αIII) consecutively joined by two short flexible linking

domains each containing a single beta-sheet. The three helices of the histone-fold

are arranged with respect to one another such that they create an overall ‘Z’-like

form.The N and C terminal regions are described as helix-sheet-helix regions

(HSH) and are designated HSH1 and HSH2 respectively (see fig. 1). Additionally,

the amino acid residues of the histone-fold have been categorized into four classes:

surface, self, pair, and interface residues. Of relevance, surface residues are

positioned on the outside of the histones in the context of the nucleosome to

facilitate histone-DNA interactions, pair residues are involved in histone

dimerization, and interface residues contribute to the contacts formed between

two dimers – either between the H2A-H2B dimers or in the formation of the (H3-

H4)2 tetramer. Surface residues demonstrate sequence conservation of the basic

amino acids Arg and Lys, which are critical in the binding of DNA to the histone

octamer through ionic interactions. The high degree of structural similarity

between the core histones is thought to be essential to the nature of DNA binding

and chromatin organization in general. It has been suggested that transitions in

chromatin are achieved through discrete changes in dimer-dimer and dimer-

tetramer interactions. One mode of structural regulation may be an inherent

susceptibility of the histones to subtle environmental changes at the interface

regions between the three histone multimers. This idea is supported by the

observation that interface residues are generally found to be less hydrophobic and

more diversified than pair residues (Arents & Moudrianakis, 1995).

The stability of the core histone octamer is DNA-dependent at physiological

conditions; however, biochemical studies have demonstrated that the octamer is

also stable in vitro under highly ionic conditions, particularly at high NaCl

concentrations. This property of the octamer ultimately enabled the elucidation of

high-resolution structures in the absence of DNA (Ramakrishnan, 1997). The first

accurate crystal structure of the core histone complex was not solved until 1991

(Arents et al, 1991). The 1991 structure, solved at 3.1 Ǻ, demonstrated that a

previous structure, resolved at 3.3 Ǻ, was critically flawed – the unfortunate

consequence of a subtle error in the coordinates for heavy atoms along the

octamer’s two-fold axis of symmetry, resulting in an erroneous phase estimate

(Ramakrishnan, 1997). Nonetheless, the 3.1 Ǻ resolution structure of the

nucleosome core histone complex represents a major leap in our understanding of

the nucleosome and its role in chromatin structure and regulation.

The nucleosomal core histone octamer is arranged in a tripartite left-handed

superhelix made up of two H2A-H2B dimers and a central (H3-H4)2 tetramer. Core

complex assembly is preceded by the binding of individual histone monomers in an

antiparellel head-to-tail arrangement, forming a characteristic “handshake” motif.

This motif describes the unique way in which the long helices of paired histone

monomers intersect such that the HSH domains converge to create a structure

that is distinctly similar to two hands clasped together. In contrast to localized

contacts formed when most proteins associate, histones form extensive

interactions spanning the entire chains (Arents et al. 1991). Following H3-H4

dimerization, formation of the (H3-H4)2 tetramer occurs through the binding of a

pair of H3-H4 heterodimers at the HSH2 domains of the H3 subunits.

Tetramerization represents the initial step of nucleosome assembly. The H3-H3 C-

terminal interaction is arranged in a 4-helical bundle and is facilitated in part by an

essential His113 residue, which forms a hydrogen bond with Asp123 buried within the

two helices of the adjacent chain (Luger et al. 1997). Docking of HSH2 domains to

form the (H3-H4)2 complex results in a twisted crescent structure with a central

hinge at the H3-H3 interface through which a two-fold axis of symmetry lies (see

fig. 3) (Ramakrishnan, 1997). Moreover, each half-crescent of the tetramer is

rotated approximately 15° away from the two-fold axis (Arents et al. 1991).

Assembly of the core histone complex is completed through a final octamerization

step in which H2A-H2B heterodimers bind to the (H3-H4)2 tetramer at its terminal

regions. The H2B histone interacts with the H4 histone at their respective HSH2

domains. Due to the conserved structure of the HSH2 domain among the four

histones the H2B-H4 interaction is remarkably similar to the association of the H3

histones during tetramerization. HSH2 domains at the H2B-H4 interface constitute

the 4-helical bundle in which His74 of H4 inserts between the two adjacent helices

to form a hydrogen bond with Glu90 on the H2B chain (Luger et al. 1997).

Importantly, the H2B-H4 interaction is weaker than the tetrameric H3-H3

interaction, despite a more extensive contact interface between H2B and H4; thus,

the association of H2B and H4 is more susceptible to changes in the surrounding

solvent (Ramakrishnan, 1997). Importantly, the fully assembled histone octamer

assumes the form of a left-handed protein superhelix. The radial axis of symmetry

for the superhelical conformation of the octamer runs perpendicular to its two-fold

axis of symmetry. When the complex is viewed down its radial axis it assumes the

appearance of a disk with a diameter of around 65 Ǻ; this would be akin to viewing

a vertically oriented cylinder from above or below. The outer surface of the protein

complex is characterized by regularly arranged ridges and grooves that constitute

an unambiguous path with a pitch of 28 Ǻ that follows the left-handed superhelical

form of the protein. This path creates an ideal binding site for DNA to wrap around

the surface of the histone octamer like thread on a spool (see fig. 4; Arents et al.

1997).

DNA Binding on the Histone Octamer

Structural studies of the nucleosome have been largely facilitated by

the use of micrococcal nuclease (MNase). Digestion of unraveled chromatin using

MNase is initiated at the nucleosomal DNA linker regions to produces a size

distribution of 10 nm chromatin fragments, described as oligonucleosomes.

However, oligonucleosomes tend to exhibit poor stability in solution. Extended

digests with MNase result in structures of progressively increased stability, such

that particle stability is directly proportional to the length of the free DNA fixed to

the nucleosome core. Of interest, particles consisting of a 165 bp DNA component

can be obtained from digests and are unique in that they are often associated with

the H1 histone. This More extensive nuclease digestion results in the isolation of

the highly stable core nucleosomal particle. This discrete unit is defined by a DNA

element of around 146 bp wound approximately 1.65 turns around the histone

octamer in a left-handed superhelix (Bates & Maxwell, 2006). Due to its stability,

the nucleosome core particle has provided the basis for x-ray diffraction studies

and is, thus, central to our present understanding of nucleosomal DNA-histone

surface interactions.

Similar to the subunit organization of the histone octamer, binding of a

continuous DNA segment on the surface of the histone complex is facilitated

predominantly through the conserved intrinsic properties of the histone-fold motif.

Yet, DNA-protein interactions are coordinated largely on the scale of the

handshake motif – that is, through surface contacts formed with the four histone

pairs and irrespective of the tripartite nature of the octamer. Each dimer is directly

associated with approximately 27-28 bp of DNA, while unbound 4-bp segments of

duplex join the discrete regions of DNA-histone contacts. Furthermore, an

invariable Lys residue occupying the second position of the C-terminal loop II

doman (L2) of each histone monomer (see fig. 1) forms a salt bridge with a distal

phosphate group of the DNA backbone such that Lys residues of adjacent dimers

traverse one another and effectively form a dimer-DNA-dimer cross-linkage (see

fig. 5; Ramakrishnan, 1997; Luger et al. 1997). Extruding L2 Lys residues of the

H2A-H2B dimers at the superhelical ends of the histone octamer facilitate docking

of the remainder of DNA bases in the formation of the 165 bp core particle. The

histone-DNA contacts occur predominantly through basic amino acid residues

bonding with the negatively charged phosphate groups of the DNA duplex to

establish a sequence-independent association. This general mode of ionic

interaction is a recurrent theme in nucleoprotein complexes. However, the helical

structure of DNA in the nucleosome is such that only two adjacent phosphate

groups per DNA strand are within direct hydrogen bonding range of the histone-

fold dimers. Despite this, it is thought that solvation of the individual

macromolecules mediates nucleosome assembly through the formation of water-

bridges which transiently stabilize indirect hydrogen bonding between the two

structures (Davey et al. 2006). The primary DNA binding site for each histone

dimer is positioned parallel to the central junction of the αII helices, such that it is

localized amid the N-termini of the α1 helices, which form arm-like protrusions

converging on the adjacent DNA backbone phosphates. Thus, the positive charges

of the two αI dipoles, as well as main chain amide groups, and variable side chain

interactions act cooperatively to create a stable interaction between the DNA and

histone dimer (Luger et al. 1997).

Nucleosome Phasing and Gene Expression

Histone-DNA interactions within the nucleosome are achieved

predominantly through non-specific histone contacts with the DNA phosphodiester

backbone. Nevertheless, a preferential specificity for histone binding at certain

DNA sequences has been observed. Early descriptions of nucleosome specificity

include work by Simpson and coworkers (1983) in which nucleosome

reconstitution was carried out in vitro using a 260 bp DNA fragment encoding the

5S rRNA from the sea urchin L. variegatus. A strong preference was identified for

nucleosome localization within the rRNA coding sequence such that the

transcription start site was positioned precisely at the center of the nucleosomal

DNA superhelix (i.e. proximal to the H3-H3 junction) (Simpson & Stafford, 1983).

In addition to preferential nucleosome binding in L. variegatus, this intrinsic

property of nucleosomes has been distinguished in various other contexts,

including the 5S rRNA locus of Drosophila and Xenopus, as well as at discrete sites

in the SV40 genome (Ramakrishnan, 1997). The phenomenon of sequence-

dependent nucleosome positioning is broadly referred to as ‘nucleosome phasing’.

In terms of function, it has been suggested that nucleosome phasing is integral to

the formation of higher-order chromatin structures by directly impacting linker

DNA length and, thus, the flexibility of the 10 nm fiber. Moreover, sequence-

dependent phasing suggests a unique role for the nucleosome in the suppression of

transcription by physically obstructing RNA polymerases during initiation and

elongation of RNA synthesis; thus, nucleosomes (and perhaps higher order

chromatin structures as well) possess crucial gene-regulatory significance (Blank

& Becker, 1996). However, prior to considering the myriad cellular consequences

of nucleosome phasing, it is critical to resolve the molecular underpinnings of

nucleosomal sequence specificity.

Nucleosome phasing principally implies that electrostatic interactions

cannot be the sole factor governing the way in which DNA is wrapped around a

histone octamer. Rather, the process of nucleosome formation is inherently

multipartite and, accordingly, far more dynamic than first suggested by structural

studies. Demonstrating remarkable intuition, studies by Drew and Travers (1985)

provided early insights to the molecular basis of sequence specificity in

nucleosome positioning. Such work united two distinct emerging fields,

nucleosome phasing and intrinsic DNA bending, to consider the former in terms of

the latter. Electrophoretic fractionation studies of tightly compacted DNA

minicircles in the trypanosome L. tarentolae led to the discovery of DNA bending

at phased adenine/thymine (AT) tracts due to intrinsic deformation of the DNA

helix, characterized by minor groove compression (Marini et al. 1982; Koo et al.

1986). It was found that intrinsically bent DNA is configured such that the minor

groove at AT tracts is positioned on the inner face of the DNA bend, whereas

intermittent GC clusters appear to be distinguished by a minor groove oriented

outwards. Nucleosome reconstitution experiments using DNA oligonucleotides

with sequence-directed curvature demonstrated that the helical conformation of

intrinsic bending was conserved in the arrangement of DNA in the nucleosome (i.e.

the ‘rotational setting’ of the nucleosome). Consequently, it was suggested that

intrinsically bent DNA may favor histone binding, while inherently rigid DNA

sequences may prohibit nucleosome assembly (Drew & Travers, 1985). Further

studies comparing the structure of DNA in the nucleosome to that of free DNA

have bolstered the idea that the inherent flexibility of a DNA sequence conveys

preference in nucleosome positioning (Hayes et al. 1990). Importantly, histone

octamerization is accomplished in a DNA-dependent manner, wherein the (H3-H4)2

histone tetramer binds to DNA before the two H2A-H2B dimers are incorporated in

the core histone complex. If one considers the general curved architecture of the

histone tetramer (see Fig. x) it is apparent that this structure provides a suitable

scaffold for preferential DNA binding on the basis of intrinsic flexibility (Dong &

Holde, 1991). Although the bent shape of the histone tetramer may underlie

nucleosome phasing, it is critical to conceptualize phasing in terms of the kinetic

and thermodynamic challenges to nucleosome formation. Namely, DNA bending by

the (H3-H4)2 tetramer is a thermodynamically unfavorable process due to the

structural distortions imposed on native B-form DNA. However, AT rich sequences

are relatively more flexible than GC rich sequences due to the fact that A-T base

pairing forms two hydrogen bonds, whereas G-C base pairing involves three. Thus,

the free energy required to induce deformation of an AT rich sequence is

comparatively lesser than that needed to deform GC rich DNA. Likewise, DNA that

possesses intrinsic curvature due to the presence of A/T tracts in phase with the

helical periodicity presents an optimally suited binding site for the (H3-H4)2

tetramer. Such sequences with highly favorable rotational settings minimize the

energetic requirements of nucleosome formation and, consequently, facilitate

preferential nucleosome binding (Ramakrishnan, 1997). Therefore, while

nucleosome positioning is certainly sequence-directed, it is not precisely sequence-

specific; rather, a nucleosome will bind over a contiguous range of sites about a

preferred sequence due to the comparable rotational settings of adjacent DNA

regions. Consistent with this idea, nucleosome positioning has been found to be

characterized by major and minor sites at a given locus (,). This property of

nucleosome phasing reflects a limited role for DNA sequence in nucleosome

binding. Major and minor nucleosome binding sites are thought to reflect local

fluctuations in nucleosome position, wherein the complex transiently dissociates

and reassembles at an adjacent site. This kinetic hallmark of the nucleosome is

referred to as ‘nucleosome mobility’ and is dependent on the degree of stability

that a given complex possesses. Accordingly, nucleosomes are found to occupy

major and minor sites at an equilibrium distribution (,).

Mobility is a fundamental characteristic of nucleosomes because complex

stability directly establishes the ease with which RNA polymerase (RNAP) can

transcribe through nucleosomal DNA. It is thought that many RNAPs, including

phage RNAP, bacterial RNAP and eukaryotic RNA polymerases II and III (Pol II

and PolIII), adopt a paused conformation upstream of a nucleosome, such that the

histone complex may effectively ‘step around’ the transiently immobilized RNAP by

means of a DNA loop (Workman & Kingston, 1998; Hodges et al. 2009; Workman,

2006). Of primary significance, nucleosome displacement and histone transfer

during transcription-elongation are explicitly dependent on the mobile capacity of

a given nucleosome complex. A seeming quandary then arises: while AT rich DNA

sequences favor nucleosome formation, nucleosomes with an AT rich DNA moiety

(including intrinsically bent DNA) are so-favored because they possess optimal

thermodynamic stabilization and, thus, preclude transcription by RNAP. This

problematic relationship between nucleosome positioning and nucleosome mobility

during transcription-elongation appears to be resolved through nucleosome

(de)stabilization factors and epigenetic histone modifications that regulate the

strength with which a histone octamer binds DNA (Henikoff, 2008). Post-

translational [histone] modifications (PTMs) are localized to the C-terminal

domains (CTDs), which are characteristically short ‘tails’, less than 40 amino acids,

extending from the globular body of the histone complex (Campos & Reinberg,

2009). In this way, histone CTD tails are thought to act as platforms for covalent

modifications, including ubiquitination, phosphorylation, methylation, acetylation,

and SUMOylation (i.e. the addition of small ubiquitin-like modifier proteins).

Collectively, histone modifications comprise a highly orchestrated ‘epigenetic’

histone code, which appears to specifically regulate the strength and efficiency of

intra-nucleosomal contacts, as well as extra-nucleosomal interactions (e.g.

nucleosome-nucleosome contacts in the 30 nm fiber) by inducing conformational

changes in the nucleosome complex. In addition to directly altering intra- and

extra-nucleosomal histone contacts, PTMs can be ‘read’ by effector proteins

through particular domains, such as chromodomains, which recognize methylated

sites, and bromodomains, which distinguish acetylated residues (Campos &

Reinberg, 2009). The tremendous complexity of the histone code is established

through the diverse classes of PTMs, the various residues to which PTMs can be

made, and the fact that a single amino acid can acquire several modifications

(Berger, 2007). Ongoing research aims to further decipher the histone code and

improve our current understanding of nucleosome remodeling. Nevertheless, it is

apparent that such phenomena contribute significantly to global chromatin

organization and the large-scale regulation of gene expression.

In the past forty years our understanding of chromatin organization and its

functional implications has expanded exponentially. Since the nucleosome model of

chromatin organization was first described by Roger Kornberg in 1974, our

perception of chromatin and its fundamental structure, the nucleosome, has

undergone an ideological metamorphosis. No longer is the nucleosome simply the

primary unit of chromatin by which genome compaction is achieved in eukaryotes.

Rather, we now recognize the nucleosome, as well as chromatin in general, in

terms of the paradigms of gene expression, and thus cellular diversity, which they

mutually establish. Most remarkable, this monumental function of chromatin

organization is communicated through discrete molecular modifications to the

primary structure of the nucleosomal histone core; thereby, specifying nucleosome

structure as central to the vast epigenetic ‘language’ of our cells.

I

Figure 1. Histone H2A of X. laevis resolved at 2.8 Å resolution – the histone fold. N and C terminal helix-sheet-helix motifs are displayed at helices I and II. Also, note the overall inverted Z-form characteristic of the fold.

Figure 2. The H2A-H2B heterodimer of X. laevis resolved at 2.8 Å resolution.

HSH2

III

N term.

HSH2

HSH1

HSH2

HSH1

Loop I

Figure 3. H3-H4 tetramer of X. laevis resolved at 2.8 Å resolution. The general form of the tetramer is that of a crescent. The tetramer is formed through contacts between the H3 histones of the two dimers via binding at the HSH1 domains to form a four

Figure 4. Complete nucleosome complex (top- side view, bottom-birds-eye.). The DNA follows the left-handed superhelical organization of the histone complex (above). H2A-H2B dimers are displayed in yellow and cyan, while H3-H4 dimers are shown is blue and magenta. The structure was obtained from X. laevis and

References

Arents, G. et al. (1991). The nucleosomal core histone octamer at 3.1 Å resolution:

a tripartite protein assembly and a left-handed superhelix. PNAS. 88: 10148-

52.

Figure 5. Loop II Lys residues at the H3-H3 tetramer interface facilitate cross-linkage between adjacent histone dimers through contact with distal phosphate groups on the DNA backbone.

Arents, G. & Moudrianakis, E.N. (1995). The histone fold: a ubiquitous

architectural motif utilized in DNA compaction and protein dimerization.

PNAS. 92: 11170-74.

Bates A. D. & Maxwell A. (2006) DNA topology. New York, NY: Oxford University

Press, Inc.

Berger (2007). The complex language of chromatin regulation during transcription.

Nature. 447: 407-412.

Blank, T.A. & Becker, P.B. (1996). The effect of nucleosome phasing sequences and

DNA topology on nucleosome spacing. J. Mol. Biol. 260: 1-8.

Campos & Reinberg (2009). Histones: annotating chromatin. Annu. Rev. Genet. 43:

559-599.

Davey, C.A. et al. (2006). Solvent mediated interactions in the structure of the

nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319: 1097-1113.

Dong, F. & Holde, K.E. (1991). Nucleosome positioning is determined by the (H3-

H4)2 tetramer. PNAS. 88: 10596-10600.

Drew & Travers (1985). DNA bending & its relation to nucleosome positioning. J.

Mol. Biol. 186: 773-90.

Hayes, J.J. et al (1990). The structure of DNA in a nucleosome. PNAS. 87: 7405-09.

Hodges et al (2009). Nucleosomal fluctuations govern the transcription dynamics

of RNA polymerase II. Science. 325: 626-628.

Koo, H. et al (1986). DNA bending at adenine·thymine tracts. Nature 320, 501–506.

Lewin, B. (2004) Genes VIII. Upper Saddle River, NJ: Pearson Prentice Hall

Luger, K. et al. (1997). Crystal structure of the nucleosome core particle at 2.8 Å

resolution. Nature. 389: 251-60.

Marini, J.C. et al. (1982). Bent helical structure in kinetoplast DNA. Proc. Natl.

Acad. Sci. USA 79, 7664–7668.

Nelson, D.L. & Cox, M.M (2008) Principles of Biochemistry. New York, NY: W.H.

Freeman and co.

Olins, D.E. & Olins A.L. (1974). Spheroid chromatin units (nu bodies). Science.

183 : 330-32.

Olins, D.E. & Olins A.L. (2003). Chromatin history : our view from the bridge.

Nature. 4 : 809-14.

Olins, D.E. & Olins A.L. (1972). Physical Studies of isolated eukaryotic nuclei. J Cell

Biol. 53 : 715-36.

Pardon, J.F. & Wilkens, M.H. (1972). A super-coil model for nucleohistone. J. Mol.

Biol. 68: 115-24.

Ramakrishnan (1997). Histone structure and the organization of the nucleosome.

Annu. Rev. Biophys. Biomol. & Struct. Biol. 26: 83-112.

Simpson, R.T. & Stafford, D.W. (1983). Structural features of a phased nucleosome

core particle. PNAS. 80: 50-51.

Thomas, J.O. & Kornberg, R.D. (1974). An octamer of histones in chromatin and

free in solution. 72: 2626-30.

Woodcock, C.L.F. (1973). Ultrastructure of inactive chromatin. J. Cell. Biol. 59:

368.

Workman & Kingston (1998). Alteration of nucleosome structure as a mechanism

of transcriptional regulation. Annu. Rev. Biochem. 67: 545-79.

Workman (2006). Nucleosome displacement in transcription. Genes Dev. 20: 2009-

17.

Henikoff, S. (2008). Nucleosome destabilization in the epigenetic regulation of

gene expression. Nature. 9: 15-26.