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Unformatted text preview: REVIEWS CHROMATIN ASSEMBLY BY
Karl A. Haushalter and James T. Kadonaga
Chromatin assembly is required for the duplication of eukaryotic chromosomes and functions at
the interface between cell-cycle progression and gene expression. The central machinery that
mediates chromatin assembly consists of histone chaperones, which deliver histones to the
DNA, and ATP-utilizing motor proteins, which are DNA-translocating factors that act in
conjunction with the histone chaperones to mediate the deposition of histones into periodic
nucleosome arrays. Here, we describe these factors and propose possible mechanisms by
which DNA-translocating motors might catalyse chromatin assembly. HIGH MOBILITY GROUP
PROTEINS (HMG proteins). Abundant,
proteins. There are three families
of HMG proteins: HMGB
(HMG14/17) and HMGA
(HMG-I/-Y). Section of Molecular Biology,
University of California,
9500 Gilman Drive, La Jolla,
San Diego, California
Correspondence to J.T.K.
doi:10.1038/nrm1177 In the eukaryotic nucleus, DNA is packaged into a periodic nucleoprotein complex, known as chromatin (BOX 1).
The assembly of the genome into chromatin enables the
DNA — which amounts to approximately two metres
of DNA per cell in humans — to be compacted within
the nucleus, which has an average diameter of 10 µm in
a human cell. Importantly, the DNA is packaged in a way
that is compatible with essential DNA processes, such as
transcription, replication, repair and recombination. So,
the organization and utilization of the eukaryotic
genome is dependent on the assembly of DNA into chromatin (for recent reviews, see REFS 1–5).
Chromatin assembly functions at the interface of
cell-cycle progression and gene expression. The replication of the genome requires not only the duplication of
the DNA, but also the assembly of the newly synthesized DNA into chromatin. In addition, the control of
gene activity is strongly influenced by chromatin structure, and the establishment of the correct nucleoprotein
structures of genes requires chromatin assembly.
Therefore, it is important to consider the potential
effects of chromatin assembly factors on processes that
are related to cell growth and gene expression.
Chromatin assembly does not generate a uniform
and static product, but rather it forms a structure with
a diverse and dynamic chemical composition. The
properties of chromatin can be modulated by covalent
modification of histones6, the incorporation of histone variants such as H2A.Z (REF. 7) and H3.3 (REF. 8), the NATURE REVIEWS | MOLECUL AR CELL BIOLOGY association of non-histone chromosomal proteins such
as heterochromatin protein 1 (HP1) and HIGH MOBILITY
GROUP (HMG) PROTEINS , and DNA methylation . These specific and dynamic variations in chromatin structure are
important for many nuclear processes. For example,
acetylation of histones generally correlates with gene activation; phosphorylation of serine 10 of histone H3
occurs during mitosis; methylation of lysine (Lys) 9 of
histone H3 creates a binding site for HP1; and methylation at position 5 of cytosine in CpG dinucleotides correlates with transcriptional repression.
The simplest definition of chromatin assembly is
the process by which DNA is packaged into nucleosomes. In this sense, chromatin assembly is equivalent to nucleosome assembly. The basic chromatin
assembly process is mediated by histone chaperones
and ATP-utilizing factors that catalyse the deposition
of the histones onto DNA to yield periodic arrays of
nucleosomes (FIG. 1). As well as the basic process,
there are factors that are involved in the coupling of
chromatin assembly to processes such as DNA replication and repair. In addition, as noted above, it is
important to consider that native chromatin comprises not only nucleosomes, but also linker histones,
such as histone H1, and non-histone chromosomal
proteins, such as HP1 and the HMG proteins. So,
from a broader perspective, the term ‘chromatin
assembly’ includes the assembly of higher-order
forms of chromatin. VOLUME 4 | AUGUST 2003 | 6 1 3
© 2003 Nature Publishing Group REVIEWS Box 1 | Composition and structure of chromatin
The basic repeating unit of chromatin is the nucleosome. Each nucleosome core consists
of 146 base pairs of DNA wrapped with ~1.7 superhelical turns around a molecular
spool that consists of an octamer of core histone proteins. The histone octamer consists
of two copies each of the histones H2A, H2B, H3 and H4. In the absence of DNA at
physiological ionic strength, the prevalent forms of the histones are (H3–H4)2 tetramers
and H2A–H2B dimers. To form a complete octamer, two H2A–H2B dimers assemble
onto each side of an (H3–H4)2 tetramer. Nucleosome cores are separated by linker DNA
to give an overall nucleosome repeat length that is approximately 180–200 bp. At
physiological ionic strength, nucleosome arrays fold into a more highly compacted
form, such as the 30-nm chromatin filament, in a process that is facilitated by linker
histones, for example histone H1 (REF. 107). High-resolution structural information is
available for the nucleosome core particle108, whereas little is known about the threedimensional structures of the higher-order states of chromatin109,110. In this review, we will provide an overview of the factors that mediate nucleosome assembly. Recent studies
have led to the purification and cloning of the histone
chaperones and molecular motors that mediate the basic
assembly process. In addition, we will discuss possible
models by which the energy of ATP hydrolysis might be
used to assemble periodic arrays of nucleosomes.
Chromatin assembly in vivo HETEROCHROMATIN Chromatin that remains in a
condensed state throughout the
cell cycle; for example,
centromeres and telomeres are
heterochromatic regions. Few
protein-coding genes are located
in heterochromatin and most
protein-coding genes are located
in euchromatin, which
decondenses during interphase. 614 In cycling cells, chromatin assembly occurs immediately
after DNA replication. At the replication fork, histones
from the parental chromosome are randomly distributed
to the two daughter DNA strands, and the remaining
complement of nucleosomes is assembled from newly
synthesized histones (for a review, see REF. 4). The newly
synthesized histones are acetylated at conserved positions
on H3 and H4 before their incorporation into nucleosomes, and the acetyl groups are removed shortly after
assembly1,11. The specific function of the conserved acetylation of newly synthesized histones is still unclear. For
example, the acetylation of the amino termini of histones
H3 and H4 does not seem to be required for chromatin
assembly in vitro12,13.
Chromatin assembly occurs independently of DNA
replication — for example, during DNA repair,
exchange/turnover14. Replication-independent chromatin assembly involves histone variants, such as
H2A.Z and H3.3, which can be referred to as ‘replacement histones’. These replication-independent histones
differ from the S-phase-specific histones in certain
ways. Most notably, the replication-independent histones are synthesized throughout the cell cycle rather
than specifically in S phase. For example, the histone
variant H3.3, which differs from the S-phase-specific
H3 by only four amino-acid residues, is deposited into
chromatin throughout the cell cycle15. It is also notable
that transcripts that encode S-phase-specific histones
lack a polyadenylate (polyA) tail, whereas the transcripts for replication-independent histones are
polyadenylated. So, their genes are transcribed by fundamentally different mechanisms. Although histones
are relatively stable proteins, they are still slowly
degraded. So, in long-lived cells, such as neurons, the
replication-independent histones are needed to replace | AUGUST 2003 | VOLUME 4 histones in chromatin as they are turned over (hence
the name ‘replacement’ histones).
The factors that are involved in the assembly of replication-independent histones might be distinct from those
used in the assembly of S-phase-specific histones15,16. For
example, S-phase-specific H3 that is ectopically expressed
throughout the cell cycle does not exhibit replicationindependent deposition15. This observation indicates that
there might be chromatin assembly factors that function
with the replication-independent histones, but not with
the S-phase-specific histones.
Finally, it is important to consider that the cell-cycleindependent exchange of nucleosomal histones is a
potential mechanism for switching epigenetic states. For
example, methylation of histone H3 on Lys9 is associated
with gene silencing and HETEROCHROMATIN formation, and
one way that methylated histones could be converted to
the unmethylated state is through histone exchange17.
Chromatin assembly factors Chromatin assembly is an active process that involves
histone chaperones and ATP-dependent motor proteins
(FIG. 1). When mixed together at physiological ionic
strength, purified core histones and DNA aggregate to
form an insoluble precipitate. This aggregation is driven
by the ionic interactions between the negatively charged
DNA backbone and the positively charged basic residues
in the histones. This non-specific precipitation can be
prevented by the addition of histone-transfer vehicles —
negatively charged polymers that shield the positive
charge of the histones1–3.A variety of molecules, including
RNA, polyglutamic acid and several histone-binding proteins, have been found to function as histone-transfer
vehicles in vitro.
Here, we will focus on the chaperones that have been
found to associate with histones in vivo1–3,18. These histone
chaperones not only prevent aggregation between histones and DNA, but also function as shuttle proteins that
deliver histones to the appropriate sites of chromatin ATP-dependent
motor protein a b Histone–chaperone
complex Figure 1 | A simple view of chromatin assembly. a | Core
histones are delivered to the site of chromatin assembly by
histone chaperones, such as chromatin assembly factor 1
(CAF1), nucleosome assembly protein 1 (NAP1) or the antisilencing function 1 (Asf1) subunit of replication-couplingassembly factor (RCAF). b | The histones are then deposited
onto the DNA in conjunction with an ATP-dependent motor
protein, such as ATP-utilizing chromatin assembly and
remodelling factor (ACF) or remodelling and spacing factor
(RSF). The product of this reaction is a periodic array of
© 2003 Nature Publishing Group REVIEWS Table 1 | Chromatin assembly factors
Assembly factor Functional roles Binding interactions References CAF1 Histone chaperone
Cell-cycle progression H3–H4
Asf1 24–39,48,49 Asf1 Histone chaperone
Cell-cycle progression H3–H4*
‡ 40–55 NAP1 Histone chaperone
Nuclear import of histones H2A–H2B
p300 60–68 HIR Histone gene regulation
69 Nucleoplasmin Maternal storage of histones H2A–H2B‡
Histone chaperone during
rapid rounds of replication
in early embryo 18 N1/N2 Maternal storage of histones H3–H4
Histone chaperone during
rapid rounds of replication
in early embryo 18 Spt6 Histone-transfer vehicle
factor DF31 Histone-transfer vehicle
Chromatin structural protein 71,72 Nucleophosmin/
B23 Histone transfer vehicle
Replication stimulatory factor 73,74 ACF DNA-translocating motor
Chromatin assembly factor
Chromatin remodelling factor 19,21–23,
98,99 RSF Stimulates transcription
Chromatin assembly factor
(does not require chaperone)
Chromatin remodelling factor 81,100 H3–H4§
H2A–H2B§ 70 *Replication-coupling assembly factor (RCAF) is the complex of anti-silencing factor 1 (Asf1) and
specifically acetylated histones H3 and H4. The H3 and H4 in the RCAF complex are acetylated with
the same pattern as newly synthesized H3 and H4. ‡Nucleosome assembly protein 1 (NAP1) and
nucleoplasmin bind with higher affinity to histones H2A–H2B than to histones H3–H4. §Spt6 protein
binds with higher affinity to histones H3–H4 than to histones H2A–H2B. ACF, ATP-utilizing chromatin assembly and remodelling factor; CAF1, chromatin assembly factor 1; PCNA,
proliferating cell nuclear antigen; RSF, remodelling and spacing factor. PCNA (Proliferating cell nuclear
antigen). PCNA is a slidingclamp protein that forms a
around the DNA, and functions
to increase the processivity of
DNA polymerases. assembly in the cell. In vitro, histone-transfer vehicles can
mediate the deposition of histones onto negatively supercoiled DNA. Negative supercoiling facilitates histone
deposition because the negative superhelical tension is
relieved when the DNA is wrapped around the histones19,20. However, this process does not yield regularly
spaced nucleosome arrays19, as seen in bulk native chromatin.
The ATP-dependent assembly of periodic nucleosome arrays requires an ATP-driven motor protein as NATURE REVIEWS | MOLECUL AR CELL BIOLOGY well as the histone chaperones. With relaxed DNA templates, ATP-dependent motor proteins catalyse the
deposition of histones onto DNA, as well as the generation of periodic arrays of nucleosomes19,21–23. The bulk
of the eukaryotic genome seems to possess little superhelical tension. Therefore, the use of relaxed DNA templates for chromatin assembly is preferable to the use of
negatively supercoiled DNA. In the following section,
we will discuss the histone chaperones and ATP-driven
motors that are thought to be involved in chromatin
assembly. These factors are also summarized in TABLE 1.
Histone chaperones. A variety of proteins interact with
core histones and function as histone-transfer vehicles.
Most of these factors have a preference for either
H3–H4 or H2A–H2B. Although these proteins all bind
to histones, they do not seem to be related at the level of
their primary amino-acid sequences. So, these chaperones, which escort histones to the sites of chromatin
assembly, might have evolved independently into histone-binding proteins, several of which are described
Chromatin assembly factor 1 (CAF1) is a heterotrimeric protein that comprises the p150, p60 and
p48 subunits1,24–28. It can also be isolated in a complex,
known as CAC, that contains histones H3 and H4,
where the H4 has an acetylation pattern that is similar
to that of newly synthesized H4 (REF. 25). CAF1 was discovered through a DNA-replication-coupled chromatin-assembly assay28. In this assay, CAF1 is required
for the preferential assembly of nucleosomes onto
newly synthesized DNA, relative to bulk unreplicated
DNA27. CAF1 is recruited to replication foci29,30 by a
mechanism that involves an interaction with the DNA
polymerase through the PCNA sliding-clamp protein31–33.
In yeast, cells that lack Caf1 are viable but defective in
transcriptional silencing34–39. Many lines of evidence
also indicate a role for CAF1 in DNA repair24.
Replication-coupling-assembly factor (RCAF) is a
complex of anti-silencing function 1 (Asf1) protein and
specifically acetylated histones H3 and H4 (REF. 40). Like
CAF1, RCAF participates in DNA-replication-coupled
chromatin assembly. Notably, the histones H3 and H4
in the RCAF complex show the same pattern of acetylation as newly acetylated histones. In addition to its function in replication-coupled chromatin assembly as a
subunit of RCAF, Asf1 protein has been shown to have
histone chaperone activity in the absence of DNA replication and might also be involved in DNA-replicationindependent chromatin assembly41,42. asf1 was originally
identified in yeast as a gene that derepresses transcriptional silencing when overexpressed43,44. In yeast, deletion of the asf1 gene causes silencing defects, slow
growth and sensitivity to DNA-damaging agents40,43,44.
Like CAF1, Asf1 seems to be important for DNA
repair40,42,45,46. Furthermore, Asf1 (RCAF) has been
found to function synergistically with CAF1 for chromatin assembly in vitro and to interact directly with
CAF1 (REFS 40,47–50) In addition, Asf1 interacts with the
chromatin remodelling protein Brahma51, the
TAFII250/CCG1 subunit of basal transcription factor
VOLUME 4 | AUGUST 2003 | 6 1 5 © 2003 Nature Publishing Group REVIEWS
particularly in conjunction with Asf1 (RCAF)16,38,49,50,59,69.
In Xenopus, nucleoplasmin and N1/N2 are abundant
histone-binding proteins in the early embryo (for a
review and additional references therein, see REF. 18).
Nucleoplasmin binds preferentially to H2A–H2B, whereas
N1/N2 binds to histones H3–H4. These factors, which are
present at high concentrations in the egg cytoplasm, seem
to be important for the storage and deposition of histones during the rapid cycles of DNA replication that
occur before the midblastula transition18. There are no
apparent homologues of nucleoplasmin in yeast or
humans. Other histone-binding factors that have been
shown to have histone-transfer-vehicle activity include
Spt6 (REF. 70), DF31 (REFS 71,72) and nucleophosmin/B23
(REFS 73,74). These proteins are likely to have important
roles in chromosome assembly and maintenance. a b KARYOPHERIN Nuclear import receptor, also
known as importin.
CHRAC (Chromatin accessibility
complex). CHRAC was
originally identified as a factor
that increases the accessibility of
restriction enzymes to DNA that
is packaged into chromatin.
factor). NURF was isolated on
the basis of its ability to modify
the chromatin structure at the
hsp70 promoter in cooperation
with transcription factors.
TRF2 (TATA-box-binding protein
(TBP)-related factor 2). TRF2containing complexes are
involved in transcriptional
TOPOISOMERASE II An abundant, ATP-dependent
topoisomerase that functions by
creating a double-stranded
break in the DNA, passing
another DNA molecule through
this break, and then resealing the
double-stranded break. The
strand passage reaction relaxes
supercoiled substrates and
requires ATP. 616 Disruption and
interactions Figure 2 | Iterative-annealing model of chromatin
assembly. In this model, a | non-nucleosomal histone–DNA
complexes are initially formed upon deposition of the histones
onto the DNA by chaperones, such as chromatin assembly
factor 1 (CAF1) or nucleosome assembly protein 1 (NAP1).
b | Next, a DNA-translocating motor, such as ATP-utilizing
chromatin assembly and remodelling factor (ACF) or
remodelling and spacing factor (RSF), disrupts the histone–DNA
contacts to allow reannealing of the histones and DNA into
nucleosomes. Note, however, that this process yields randomly
distributed nucleosomes. The generation of periodic arrays of
nucleosomes, as seen in vivo, would require the subsequent
rearrangement of the nucleosomes. Dashed arrows indicate the
direction of translocation by the motor protein. TFIID52, the RAD53 checkpoint protein kinase42, the
SAS-I histone acetyltransferase complex53,54, and Hir1
and Hir2 proteins50,55. The HIR proteins were originally
found to be involved in the regulation of histone gene
expression56–58, and they have since been shown to interact with histones in vitro16,59. The collective biochemical
and genetic data support a model in which Asf1 (RCAF)
and HIR proteins function in a chromatin assembly
pathway that partially overlaps with an assembly pathway that involves CAF1 and PCNA. Furthermore, the
interactions of Asf1 with Brahma, RAD53,
TAFII250/CCG1 and SAS-I indicate that Asf1 (RCAF)
functions in a complex network of biological processes
that regulate gene expression and cell growth.
Nucleosome assembly protein 1 (NAP1) was identified as a histone-binding protein that facilitates the random deposition of histones into nucleosomes60,61. NAP1
is a homomultimer of a single polypeptide with an acidic
carboxyl terminus62,63, and it binds preferentially to
H2A–H2B relative to H3–H4 (REFS 62,64,65). Drosophila
NAP1 and the related human NAP2 have been shown to
move from the cytoplasm into the nucleus specifically
during S phase62,66. NAP1 has been found to interact
directly with the Kap114 KARYOPHERIN and participate in
the nuclear import of histones H2A and H2B67,68.
Several other histone-binding proteins have been
identified. As noted above, the HIR proteins bind to histones and participate in the chromatin assembly process, | AUGUST 2003 | VOLUME 4 ATP-dependent chromatin-assembly factors. The assembly of periodic arrays of nucleosomes, which is characteristic of native chromatin, is an ATP-dependent
process75. The fractionation and purification of an ATPdependent chromatin-assembly activity led to the identification of ATP-utilizing chromatin assembly and
remodelling factor (ACF)22. ACF consists of two subunits, ACF1 and the ISWI (imitation switch) ATPase,
which function cooperatively in the assembly of chromatin21. In addition to its role in chromatin assembly,
ACF can function as a chromatin remodelling factor22,76.
Periodic nucleosome arrays can be assembled by
using purified ACF, purified core histones, DNA, ATP
and a purified histone chaperone such as NAP1 (REFS
21,22). With relaxed DNA, ACF is required not only for
the periodic spacing of nucleosomes, but also for the
efficient deposition of histones onto DNA19,21–23. With
negatively supercoiled DNA, NAP1 alone can deposit
histones onto DNA because the wrapping of DNA
around the histones relieves negative superhelical tension, but the resulting nucleoprotein complexes do not
resemble canonical nucleosomes, as assessed by atomicforce microscopy19.
ACF functions as a processive, ATP-driven DNAtranslocating enzyme23. The molecular engine of ACF is
ISWI, an ATPase that is a common subunit of the ACF,
CHRAC, NURF and TRF2 complexes in Drosophila. ISWI-containing complexes have also been found in yeast77,
Xenopus78 and humans79–83. ISWI, which is an essential
protein in Drosophila84, belongs to the SNF2-like family
of ATPases85,86. Other members of the SNF2-like ATPase
family have also been shown to function as catalytic
subunits in complexes that have chromatin remodelling
activity (for reviews, see REFS 87–91).
When discussing ACF, it is important to note its similarity to CHRAC. CHRAC was identified by its ability
to increase the accessibility of nucleosomal DNA to
digestion by restriction enzymes92. Although CHRAC
was originally thought to contain TOPOISOMERASE II, it is
now thought to consist of ACF1, ISWI and two small
subunits, CHRAC14 and CHRAC16 (REFS 79,93,94).
CHRAC14 and CHRAC16 are expressed specifically in
the early Drosophila embryo94 and are not required for
chromatin remodelling activity93. So, CHRAC is closely www.nature.com/reviews/molcellbio
© 2003 Nature Publishing Group REVIEWS a b c Figure 3 | Nucleosome mobilization by a DNA-translocating enzyme. A model for the
movement of nucleosomal histones relative to DNA as a consequence of the passage of an ATPdriven DNA translocating enzyme, such as ATP-utilizing chromatin assembly and remodelling
factor (ACF) or remodel the structure of chromatin (RSC). In this postulated mechanism, a | the
DNA-translocating protein tracks along DNA and b | dissociates a segment of DNA from one end
of the nucleosome. c | As the motor continues to track along the DNA, the DNA ‘in front’ of the
motor dissociates from the nucleosomal histones, whereas the DNA ‘behind’ the motor
reassociates with the histones. In this manner, a bulge or loop of DNA is propagated across the
surface of the nucleosome. After the motor has traversed the nucleosome, the nucleosome has
‘moved’ because there is a net change in the position of the nucleosomal histones relative to the
DNA. Dashed arrows indicate the direction of translocation by the motor protein. NUCLEOSOME SLIDING The translational movement of
nucleosomal histones relative to
the DNA. Because of the
asymmetry of the histone–DNA
contacts in the nucleosome, it is
unlikely that the histones
actually ‘slide’ along the DNA.
WAC MOTIF A protein sequence motif that
was initially found in WSTF
transcription factor), ACF1 and
cbp147. The WAC motif in
ACF1 was found to be required
for binding of ACF to DNA.
WAKZ MOTIF A protein sequence motif that
was initially found in WSTF
transcription factor), ACF1,
KIAA0314 and ZK783.4.
DDT DOMAIN A protein sequence motif found
in transcription and chromatinmodifying factors. The subregion of ACF1 that interacts with
ISWI contains a DDT domain.
PHD FINGER A protein sequence motif that
was termed plant homeodomain
finger. The PHD finger is found
in many proteins that function
BROMODOMAIN A protein sequence motif that is
present in many chromatinmodifying proteins.
Bromodomains have been found
to bind to acetylated lysine
residues. related to ACF. By contrast, the NURF95,96 and TRF2
(REF. 97) complexes are not related to ACF or CHRAC,
except for the presence of its ISWI subunit.
ACF1, the largest subunit of ACF and CHRAC,
enhances the function of the ISWI motor protein. ACF
(ACF1 and ISWI) is ~30 times more active in chromatin
assembly than ISWI alone21. So, ISWI is the motor of
ACF, and ACF1 ‘programmes’ the motor to function in
chromatin assembly. In addition, ACF1 significantly
changes the ability of the ISWI motor to function in
chromatin remodelling. In a NUCLEOSOME SLIDING assay,
ISWI catalyses the movement of nucleosomes from the
centres to the ends of short (< 300 base pairs) DNA
fragments, whereas ACF catalyses the opposite movement of nucleosomes from the ends to the centres of
DNA fragments93. This effect might be due to the
binding of ACF1 to the ends of the DNA fragments.
ACF1 contains a WAC MOTIF, a WAKZ MOTIF, a DDT DOMAIN,
two PHD FINGERS and a BROMODOMAIN21,98. The WAC motif
is involved in the interaction of ACF1 with DNA, and
the DDT domain is in the region of ACF1 that interacts
with ISWI98. Depletion of ACF1 from HeLa cells by
RNA interference caused an alteration in the temporal pattern of bromodeoxyuridine (BrdU) incorporation relative to wild-type cells 99. These results are
consistent with the possibility that ACF1 is involved
in the late stages of DNA replication — for example,
the replication of heterochromatic DNA. An alternative interpretation is that, on depletion of ACF1, DNA
replication progresses faster and the time required to
complete S phase is thereby shortened.
In addition to ACF and related complexes, the RSF
(remodelling and spacing factor) chromatin-remodelling complex has been shown to mediate the ATPdependent assembly of nucleosome arrays100. RSF was
originally identified as a factor that facilitates transcription from chromatin templates81. It was purified from
cultured human cells and was found to consist of a 325kDa polypeptide and hSNF2H, which is related to the
Drosophila ISWI protein81. The mechanism of chromatin assembly by RSF might be distinct from that by
ACF. For example, chromatin assembly by purified RSF NATURE REVIEWS | MOLECUL AR CELL BIOLOGY occurs in the absence of a core-histone chaperone such
as NAP1 (REF. 100), whereas ACF requires the presence of
a histone chaperone for chromatin assembly. Also, the
number of nucleosomes assembled per molecule of
ACF is several-fold higher than the number of nucleosomes assembled per molecule of RSF. These findings
indicate that RSF might possess histone chaperone
activity as well as ATP-dependent assembly activity.
Models of ATP-dependent chromatin assembly ACF seems to function processively as a DNA-translocating enzyme during chromatin assembly23. After initiation of the assembly reaction in vitro, ACF becomes
engaged to the DNA template, as assessed by template
commitment analysis23. In addition, the initial products
of ACF-mediated assembly were found to be periodic
nucleosome arrays, rather than randomly distributed
nucleosomes. These data are consistent with a model in
which ACF binds to the DNA template and assembles
periodic arrays of nucleosomes as it translocates along
Studies of the functions of other chromatin remodelling proteins provide evidence in support of a DNAtranslocation model. For example, the RSC (remodel
the structure of chromatin) complex, whose catalytic
subunit Sth1 is a member of the SWI2/SNF2-like subfamily of ATPases, has triplex DNA displacement activity, as shown in a TRIPLEX DNA DISPLACEMENT ASSAY101. In
addition, the ISWI polypeptide, which is the ATPase
subunit of ACF, CHRAC and NURF, also displaces
triplex DNA102. It should be noted, however, that RSC
complex does not seem to be involved in chromatin
assembly and ISWI polypeptide is a subunit of several
protein complexes, at least one of which (NURF) does
not seem to catalyse chromatin assembly. Moreover, the
ISWI experiments were performed in the absence of
NAP1–histone complexes, which are required to
observe template commitment by ACF. So, the results of
the experiments with the RSC complex and ISWI
polypeptide are useful in relation to DNA translocation
by ACF, but might not be directly applicable to the
assembly of chromatin by ACF.
How can a DNA-translocating motor, such as ACF,
assemble chromatin? We describe below two possible
models by which a DNA-translocating protein could
mediate chromatin assembly. In the first mechanism
(‘iterative annealing’), the DNA-translocating motor
disrupts undesired histone–DNA interactions to allow
the proper annealing of histones and DNA into periodic
arrays of nucleosomes. In the second mechanism
(‘directed deposition’), the DNA-translocating motor
directly deposits histones onto DNA in periodic nucleosome arrays.
It is also important to note that the deposition of
histones H3–H4 in vivo does not seem to occur concurrently with the deposition of H2A–H2B (for example, see REFS 103,104). For simplicity, however, we depict
the deposition of the four core histones in a single step.
Higher-resolution versions of these models could be
envisioned, in which H3–H4 tetramers are deposited
before the incorporation of H2A–H2B dimers. VOLUME 4 | AUGUST 2003 | 6 1 7
© 2003 Nature Publishing Group REVIEWS a b c Figure 4 | Directed-deposition model of chromatin assembly. In this model, a DNAtranslocating motor, such as ATP-utilizing chromatin assembly and remodelling factor (ACF), uses
the energy of ATP hydrolysis to mediate histone deposition in a processive fashion. One possible
version of a directed-deposition mechanism is depicted in this diagram. a | First, the motor
translocates along the DNA and associates with a histone–chaperone complex (such as
nucleosome assembly protein 1; NAP1). b | Then, in a processive fashion, the motor protein
dissociates histone–chaperone interactions while it establishes histone–DNA contacts. c | The
motor continues to translocate along the DNA until the histones are completely dissociated from
the chaperone and a nucleosome is formed. Dashed arrows indicate the direction of assembly
(direction of translocation). TRIPLEX DNA DISPLACEMENT
ASSAY A test for DNA translocation in
which a short oligonucleotide that
binds in the major groove of a
pyrimidine-rich target sequence is
displaced by motor proteins that
translocate through the sequence.
CHAPERONIN ATP-dependent protein complex
that mediates protein folding.
NUCLEOSOME MOBILITY The ability of nucleosomal
histones to move along the
DNA. Under physiological
conditions, nucleosomes are
essentially immobile, but some
are able to catalyse the
movement of nucleosomes.
NUCLEOSOME REMODELLING Also known as chromatin
remodelling. Any detectable
change in histone–DNA
interactions in a nucleosome.
alter the structure of
nucleosomes in an ATPdependent manner. 618 Iterative-annealing model. The iterative-annealing
model for chromatin assembly is similar to the mechanism of protein folding that is used by the bacterial
CHAPERONIN GroEL. Proteins that fold with difficulty
in vivo are thought to become trapped in undesired
conformations, known as kinetic traps. These kinetic
traps represent aggregates or misfolded states that are
occupied during the process of protein folding. GroEL is
a large barrel-shaped machine that uses the energy of
ATP hydrolysis to disrupt improperly folded proteins in
a manner that allows repartitioning of the protein into
folded and misfolded states105. Through several iterations of unfolding and folding by GroEL, the protein is
ultimately able to achieve its native conformation.
In an analogous fashion, it is possible that a DNAtranslocating motor, such as ACF, could mediate chromatin assembly through an iterative mechanism. First,
the chaperones deliver histones to the DNA to form
non-nucleosomal histone–DNA complexes. The
chaperones could then remain associated with the
histone–DNA complexes at this point. Then, these nonnucleosomal complexes are resolved into nucleosomes
by the iterative disruption and re-establishment of
histone–DNA contacts by an ATP-driven DNAtranslocating enzyme (FIG. 2). The chaperones could also
facilitate the disruption and reformation of
histone–DNA contacts by binding to the histones.
In addition, by a related mechanism, a DNA-translocating motor could mediate NUCLEOSOME MOBILIZATION or
REMODELLING. ATP-dependent chromatin remodelling
factors, such as ACF, can catalyse the movement of
nucleosomes, which are intrinsically immobile under
physiological conditions106. A DNA-translocating motor
could catalyse nucleosome movement by disruption of
histone–DNA contacts, followed by reassociation of the
histones with an adjacent stretch of DNA86,106 (FIG. 3).
The iterative-annealing model provides a mechanism for the formation of randomly distributed nucleosomes, but it is important to remember that the
product of ATP-dependent chromatin assembly is a
periodic array of nucleosomes. In this regard, it is possible that the folding or packing of nucleosomes into a
higher-order structure, such as the 30-nm chromatin | AUGUST 2003 | VOLUME 4 fibre, is the basis of the nucleosome periodicity. The
packing of nucleosomes (which are mobile due to the
action of chromatin remodelling factors such as ACF)
into a higher-order structure is one possible mechanism by which a periodic nucleosomal array could be
So, in this two-step process, a periodic nucleosome
array could be formed with an ATP-driven DNAtranslocating enzyme through the iterative-annealing
mechanism. First, non-specific histone–DNA contacts
are reorganized into nucleosomes (FIG. 2). Then, by catalysis of nucleosome mobilization (FIG. 3), a periodic array
of nucleosomes is generated by packing the chromatin
into a higher-order structure to give an evenly packed,
regular array of nucleosomes.
Directed-deposition model. In the directed-deposition
model, which is more straightforward than the iterativeannealing mechanism, the DNA-translocating motor
functions in conjunction with the histone–chaperone
complex to mediate the processive formation of nucleosome arrays. Variations of the directed-deposition
mechanisms are possible. For example, the translocating
motor could simultaneously dissociate histone–chaperone interactions and form histone–DNA contacts, as
shown in FIG. 4. Alternatively, DNA translocation by the
assembly factor could generate a specialized DNA structure to which histones are rapidly transferred.
The nucleosomes that are assembled by a direct
deposition mechanism could be evenly spaced.
Alternatively, if the initial reaction product is irregularly
distributed nucleosomes, then the chromatin could be
rearranged into periodic arrays through a nucleosomemobilization and chromatin-folding process, similar to
that described above in the iterative-annealing section.
Finally, it is important to note that ACF, RSF and related
complexes could potentially function in either or both
of the iterative-annealing and directed-deposition reactions. For example, ACF might assemble chromatin
through a directed-deposition mechanism (see FIG. 4)
and mobilize nucleosomes by an iterative-annealing
process (see FIG. 3).
Summary and perspectives Chromatin assembly is crucially important for the replication, maintenance and activity of chromosomes. At
present, many of the factors that are involved in chromatin assembly have been identified, but it is likely that
there are additional chromatin assembly factors that
remain to be discovered. Moreover, as indicated by
many recent studies, chromatin assembly factors might
function in a specialized, rather than general, fashion.
So, it will be important to elucidate the specific biological activities of these factors. Such endeavours would
include the analysis of the linkage of chromatin assembly to other processes, such as DNA replication, DNA
repair and progression through the cell cycle. In a separate line of experiments, it will be interesting to investigate the mechanisms that are involved in the assembly
of nucleosomes. From a biochemical perspective, the
in vitro assembly of periodic arrays of nucleosomes www.nature.com/reviews/molcellbio
© 2003 Nature Publishing Group REVIEWS
from individual purified components is a remarkable
process. It will be fascinating to learn how ATP-driven
molecular motors, such as ACF and RSF, mediate this
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We thank D. Fyodorov, D. Smith and G. Gemmen for insightful
discussions. We further thank D. Fyodorov, B. Santoso, J.-Y.
Hsu, T. Juven-Gershon, T. Boulay and V. Alexiadis for critical
reading of the manuscript. We apologize to our colleagues
whose work could not be cited due to space limitations. K.A.H.
is a Robert Black Fellow of the Damon Runyon Cancer
Research Foundation. This work was supported by grants from
the National Institutes of Health and the VolkswagenStiftung (to
J.T.K.) Online links
The following terms in this article are linked online to:
Brahma | CHRAC14 | CHRAC16 | DF31 | NAP1 | ISWI
Saccharomyces Genome Database: http://genomewww.stanford.edu/saccharomyces/
Asf1 | Hir1 | Hir2 | Kap114 | Spt6
ACF1 | CAF1 | HP1 | N1/N2 | NAP2 | nucleophosmin/B23 |
nucleoplasmin | RAD53 | hSNF2H | TFIID
Access to this interactive links box is free online. www.nature.com/reviews/molcellbio
© 2003 Nature Publishing Group ...
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This note was uploaded on 12/20/2011 for the course BIOLOGICAL 3310 taught by Professor Goldburg during the Spring '10 term at Cornell University (Engineering School).
- Spring '10