© 2002 European Molecular Biology OrganizationEMBO reports vol. 3 | no. 4 | pp 319–322 | 2002 319
Chromatin remodeling enzymes: taming the machines
Third in review series on chromatin dynamics
Craig L. Peterson+
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Received January 9, 2002; revised February 15, 2002; accepted February 18, 2002
Members of the ATP-dependent family of chromatin remodeling
enzymes play key roles in the regulation of transcription,
development, DNA repair and cell cycle. Each of these
enzymes are multi-subunit assemblies that hydrolyze thousands
of molecules of ATP in order to change nucleosome positions,
disrupt DNA–histone interactions and perhaps destabilize
chromatin folding. Here I review recent studies that suggest
these potent machines can be ‘tamed’ by one of several
mechanisms: targeting their activity to localized regions,
blocking their chromatin binding activity or inhibiting their
During interphase of the eukaryotic cell cycle, the bulk of DNA
is assembled into highly folded, 100–400 nm nucleoprotein
filaments. DNA-mediated processes can function in this environment
due to the actions of highly conserved chromatin ‘remodeling’
enzymes. One class of chromatin remodeling factor comprises a
family of related ATP-dependent complexes that use the energy
of ATP hydrolysis to enhance the accessibility of nucleosomal
DNA (Vignali et al., 2000). This family can be further subdivided
into three groups based on their biochemical properties and the
overall sequence similarity of their ATPase subunits: (i) the SWI–SNF
group; (ii) the ISWI group; and (iii) the Mi-2/CHD group (Figure 1;
Boyer et al., 2000a). Whereas many members of the ISWI-like
and Mi-2-like subgroups appear dedicated to transcriptional
repression pathways (Kehle et al., 1998; Deuring et al., 2000),
most SWI–SNF-like enzymes play roles in the activation of
transcription. In contrast to these transcriptional roles, some
ISWI-based enzymes, such as ACF, may play key roles in nucleo-
some assembly (Ito et al., 1997), and other family members may
facilitate other diverse chromatin-based processes, such as
homologous recombination and DNA repair (Peterson, 1996).
Operating the machine
In the case of ATP-dependent remodeling enzymes, ‘chromatin
remodeling’ refers to numerous in vitro ATP-dependent changes
in a chromatin substrate, including disruption of histone–DNA
contacts within nucleosomes, movement of histone octamers
in cis and in trans, loss of negative supercoils from circular mini-
chromosomes, and increased accessibility of nucleosomal DNA
to transcription factors and restriction endonucleases (Peterson
and Workman, 2000). In vivo, SWI–SNF-like enzymes can help
DNA-bending proteins facilitate nucleosome sliding, as well as
drive formation of Z-DNA structures (Liu et al., 2001; Lomvardas
and Thanos, 2001). Recent genetic and biochemical studies
have also led to the suggestion that SWI–SNF may disrupt
higher-order chromatin folding (Krebs et al., 2000; Horn et al.,
How do these enzymes catalyze such diverse events? Early
models for ATP-dependent remodeling focused on changes in the
histone component of the nucleosome. For instance, SWI–SNF-like
enzymes were proposed to use the energy of ATP hydrolysis to
drive removal of one or both of the histone H2A–H2B dimers
(Peterson and Tamkun, 1995). Later, Hayes and Kingston
proposed an alternative model in which dimers might not be
lost, but dramatically rearranged, generating a novel ‘remodeled’
nucleosome conformation (Lee et al., 1999). However, these
types of models seem less likely in light of recent work showing
that histone–histone cross-linking does not block or even slow
the rate of remodeling (Cote et al., 1998; Boyer et al., 2000b). In
contrast, there is now increasing evidence that ATP-dependent
remodeling may involve (perhaps exclusively) changes in the
topology of nucleosomal DNA. For instance, Owen-Hughes and
colleagues demonstrated that members of all three subclasses of
the ATP-dependent remodeling family use ATP hydrolysis to
introduce superhelical torsion into chromatin (Havas et al.,
2000). Furthermore, SWI–SNF action is blocked by the
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320 EMBO reports vol. 3 | no. 4 | 2002
constrained topology of small, circular chromatin, suggesting
that such changes in DNA topology are required for remodeling
(Gavin et al., 2001). Consequently, mechanistic studies are now
focused on determining how DNA topology is altered. Current
models propose that ATP-dependent remodeling may involve
DNA tracking activity (Havas et al., 2000), rotation of DNA along
its long axis (Boyer et al., 2000b), or formation of DNA bulges or
small loops (Langst and Becker, 2001; Narlikar et al., 2001).
Delivering the machine
Given their capacity to disrupt chromatin structure and to hydro-
lyze thousands of molecules of ATP, it should not be surprising
that ATP-dependent remodeling enzymes are kept under tight
rein in vivo. In the past few years, most studies have focused on
the active recruitment of remodeling enzymes by DNA site-specific
transcriptional activators or repressors (Peterson and Workman,
2000). For example, yeast SWI–SNF interacts with the acidic
activation domains of several activators, and these contacts can
target remodeling activity in vitro and in vivo. Likewise, human
SWI–SNF can be targeted by a host of activators, including
erythroid kruppel-like factor (EKLF), C/EBP-β, MyoD, heat shock
factors and several steroid receptors. Similarly, transcriptional
repressors, such as Drosophila hunchback, can recruit members
of the Mi-2 subclass of remodeling enzymes. In general, the
recruitment of remodeling activity by sequence-specific DNA-
binding proteins seems an effective way to direct localized
changes in chromatin structure.
While the direct targeting of remodeling complexes clearly
plays a central role in re-programming the chromatin structure of
specific loci, it may prove equally important for a cell to ‘shield’
chromosomal domains from renegade remodeling enzymes. For
instance, inappropriate chromatin remodeling could cause
enhanced rates of DNA recombination, disruption of chromosome
condensation, or promiscuous transcriptional activation of
silenced genes. One way of shielding the genome is to globally
inactivate the enzyme. For example, subunits of the human
SWI–SNF complex are phosphorylated during mitosis, which
correlates with removal of the complex from condensing
chromosomes (Sif et al., 1998). Recent studies (Shao et al., 1999;
Francis et al., 2001; Horn et al., 2002b) also suggest that
chromatin ‘shielding’ factors exist, which block the ATP-dependent
remodeling of chromatin fibers.
Braking the machine: a global
role for linker histone
Linker histones are ubiquitous components of cellular chromatin
that constrain the entry/exit DNA of the nucleosome and
incorporate another ∼20 bp of DNA into a particle called a
chromatosome. In addition to this effect on the basic structure of
the nucleosome, linker histones also stabilize the higher-order
folding of nucleosomal arrays (Carruthers et al., 1998). One
possibility is that the binding of linker histone to nucleosomes
might inhibit the ATP-dependent changes in DNA topology that
are key to remodeling activity and might serve as a means to
control enzyme function. Consistent with this idea, the activity
of a human SWI–SNF complex is markedly decreased on a
chromatosome compared with a mononucleosome substrate
(Hill and Imbalzano, 2000). To test whether linker histones
might exert a general inhibitory effect on remodeling enzymes,
nucleosomal arrays were reconstituted with or without linker
histone, and the remodeling activities of yeast SWI–SNF, human
SWI–SNF, ACF and Mi-2 complexes were determined using a
quantitative restriction enzyme accessibility assay (Horn et al.,
2002a). Strikingly, linker histone incorporation virtually
eliminated the activity of all of these enzymes.
How do linker histones block ATP-dependent remodeling?
Although linker histones constrain nucleosomal DNA, they also
stabilize the higher-order folding of arrays, and thus inhibition
could result from an inability of the enzyme to bind folded
arrays. Indeed, at least part of the linker histone inhibition has
been shown to be caused by a decreased affinity of the enzyme for
the chromatin array (Horn et al., 2002b). To determine whether
linker histone might also inhibit remodeling through the topo-
logical constraint of individual chromatosomes within the array,
Fig. 1. Three subclasses of ATP-dependent chromatin remodeling complexes. Shown here are representative members of the SWI–SNF, ISWI and Mi-2/CHD subclasses
of chromatin remodeling enzymes that are found in human cells. Depicted subunit organization is for illustrative purposes only (for a review see Vignali et al., 2000).
EMBO reports vol. 3 | no. 4 | 2002 321
Chromatin remodeling enzymes
a second set of arrays was produced using trypsinized core histones.
Limited trypsinization of the core histones removes the histone tails,
which are essential for nucleosomal and chromatin array folding
(Fletcher and Hansen, 1996; Carruthers and Hansen, 2000), but
do not affect chromatosome formation (Carruthers and Hansen,
2000). Surprisingly, even on these unfolded substrates, linker histone
inhibited remodeling by SWI–SNF, albeit to a lesser degree (Horn
et al., 2002b). Interestingly, incorporation of linker histone onto a
trypsinized array did not inhibit the binding of SWI–SNF. Based
on these results and studies with individual chromatosomes (Hill
and Imbalzano, 2000), linker histone appears to act at two levels
to block chromatin remodeling: (i) the condensed state of linker
histone-containing chromatin inhibits the binding of remodeling
complexes to the fiber; and (ii) the binding of linker histone to
each nucleosome is able to inhibit the catalytic function of a
chromatin-bound remodeling activity. These results suggest a model
in which linker histones produce a generally repressive chromatin
environment that is inhibitory to ATP-dependent chromatin
remodeling enzymes. Such repression could provide a means to
maintain large chromosomal domains in a neutral chromatin config-
uration, as well as to shield chromatin that lies immediately adjacent
to a domain of targeted chromatin remodeling activity (Figure 2).
Braking the machine:
Some interesting parallels can be drawn between the actions of
linker histone and members of the polycomb group (PcG) of
proteins. PcG proteins are conserved from flies to mammals, and
they are required for maintaining patterns of transcriptional
repression through cell divisions (Pirrotta, 1998). In Drosophila,
PcG products play essential roles during development, maintaining
the transcriptional silencing of homeotic genes. In mammalian cells,
products of the PcG genes are essential for control of cell
proliferation. In contrast to the global localization of linker histone,
PcG proteins are targeted to specific chromosomal regions by DNA
sequences called polycomb response elements (PREs). How PcG
proteins maintain repression of transcription is not clear, but most
models propose that they exert their effects through chromatin
structure. Consistent with such models, genetic studies in Drosophila
have suggested that PcG proteins function by antagonizing the
activity of the trithorax group of proteins, which includes subunits
of the Drosophila SWI–SNF (brm) remodeling complex.
Recently, Kingston and colleagues have purified a PcG-containing
complex, PRC1, from Drosophila embryos (Shao et al., 1999).
PRC1 is enormous (2–6 MDa) and contains a host of polypeptide
subunits, including four known PcG proteins (Pc, Psc, Ph and
dRING1), the DNA-binding protein Zeste and several TBP-associated
factors (Saurin et al., 2001). PRC1 does not appear to have
catalytic activities (e.g. ATPase activity), although several subunits
of PRC1 bind DNA (Francis et al., 2001). Strikingly, pre-incubation
of PRC1 with a nucleosomal array eliminates the remodeling
activity of human SWI–SNF (Shao et al., 1999). Inhibition was
not observed when SWI–SNF bound the array first, nor did PRC1
inhibit SWI–SNF when the two complexes were pre-incubated
in solution prior to addition to the array. These results suggest
that PcG products, once recruited to a locus by a PRE, might
maintain patterns of transcriptional repression by shielding
chromatin domains from remodeling enzymes.
Do linker histones and PRC1 use a similar mechanism to
block chromatin remodeling? Linker histones block the binding
of a SWI–SNF-like enzyme to chromatin, as well as the activity
of a chromatin-bound enzyme. It is not yet clear whether PRC1
can block the catalytic activity of SWI–SNF, although several
subunits of PRC1 can interact with DNA, and could conceivably
constrain nucleosomal DNA topology enough to have such an
effect. In contrast, PRC1 prevention of chromatin binding by
SWI–SNF has been clearly demonstrated by chromatin immuno-
precipitation assays (Francis et al., 2001). In the case of linker
histones, inhibition of SWI–SNF binding correlates best with the
ability of linker histones to drive the oligomerization of nucleo-
somal arrays (Horn et al., 2002b). This type of chromatin higher-
order structure is believed to mimic fiber–fiber interactions that
are important for formation of chromonema fibers in vivo (Fletcher
and Hansen, 1996; Carruthers et al., 1998). It is unknown whether
PcG proteins also create folded structures like oligomerized arrays,
although PRC1 does inhibit SWI–SNF at substoichiometric levels
with respect to nucleosomes (Shao et al., 1999), consistent with a
condensation mechanism. Furthermore, PRC1-containing chromatin
is similar to oligomerized chromatin in that it can exclude SWI–SNF,
but not restriction enzymes (Carruthers et al., 1998; Francis et al.,
2001). These observations raise the interesting possibility that
stabilization of fiber–fiber interactions may be a common feature
of chromatin shielding proteins (Figure 2C).
Over the past few years, attention has begun to shift towards
studies that center on the regulation of ATP-dependent remodeling
machines. The targeting of remodeling enzymes by gene-specific
transcriptional repressors or activators is now a well-documented
Fig. 2. Regulation of ATP-dependent chromatin remodeling. (A) Recruitment
of remodeling activity by a sequence-specific DNA binding protein (red
ovals). (B) Inhibition of remodeling activity by a chromatin binding protein
(blue ovals) that constrains nucleosomal DNA topology. (C) Blocking the
binding of a chromatin remodeling enzyme by a chromatin shielding factor
(blue ovals) that stabilizes nucleosomal array oligomerization.
322 EMBO reports vol. 3 | no. 4 | 2002 Download full-text
method for controlling the local concentration of ATP-dependent
remodeling complexes. In contrast, there are only two examples
of what I have coined here as ‘chromatin shielding’ activities
that appear to protect chromatin domains from remodeling. One
interesting candidate for a new member of this group is yeast
Sir3p, which plays a key role in establishing heterochromatic
structures at yeast telomeres and at the silent mating type loci
(Gasser and Cockell, 2001). Recent in vitro studies indicate that
Sir3p can drive formation of chromatin structures that share
several hallmarks of oligomerized nucleosomal arrays (Georgel
et al., 2001). Perhaps one function of the heterochromatic state
of Sir-containing chromatin is to shield domains from the potent
activity of ATP-dependent remodeling machines. Clearly, as we
learn more about how ATP-dependent remodeling enzymes
recognize their chromatin substrate and alter DNA–histone
contacts, we are likely to uncover a multitude of ways in which
these activities can be controlled.
I thank Peter Horn and Tony Imbalzano for critical comments on
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Craig L. Peterson