Báo cáo Y học: Nucleotide excision repair and chromatin remodeling pptx

MINIREVIEW
Nucleotide excision repair and chromatin remodeling
Kiyoe Ura
1
and Jeffrey J. Hayes
2
1
Division of Gene Therapy Science, Osaka University School of Medicine, Suita, Osaka, Japan;
2
Department of Biochemistry and
Biophysics, University of Rochester Medical Center, Rochester, NY, USA
The organization of DNA within eukaryotic cell nuclei
poses special problems and opportunities for the cell. For
example, assembly of DNA into chromatin is thought to
be a principle mechanism by which adventitious general
transcription is repressed. However, access to genomic
DNA for events such as DNA repair must be facilitated by
energy-intensive processes that either directly alter chro-
matin structure or impart post-translational modifications,
leading to increased DNA accessibility. The assembly of
DNA into chromatin affects both the incidence of damage
to DNA and repair of that damage. Correction of most
damage to DNA caused by UV irradiation occurs via the
nucleotide excision repair (NER) process. NER requires
extensive involvement of large multiprotein complexes with
relatively large stretches of DNA. Here, we review recent
evidence suggesting that at least some steps of NER require
ATP-dependent chromatin remodeling activities while
perhaps others do not.
INTRODUCTION
In vivo, eukaryotic DNA is packaged with histones and

other accessory proteins into chromatin. The assembly of
nucleosomes, the basic unit of chromatin, changes the
structure of DNA and restricts access of DNA binding
factors to their recognition sites [1]. In particular DNA
within the nucleosome is highly bent, with  150 bp of
DNA wrapped in  1
3
4
loops around a central ÔspoolÕ
consisting of the core histone proteins [2,3]. Although
nucleosomal DNA is quite accessible to small molecules, the
DNA binding activity of larger molecules and complexes
that require interaction with multiple base pairs is typically
severely restricted within the nucleosome [4]. However,
nucleosomes are dynamic structures and undergo transi-
tions to states in which portions of nucleosomal DNA are as
accessible as naked DNA [5]. Details of these transitions
have been described and indicate that the core histones
behave merely as competitors for binding to DNA,
effectively reducing the association constants for DNA-
binding proteins by factors of 10
3
)10
6
, dependent on
sequence and location within the nucleosome [5,6]. In
addition, it is important to note that strings of nucleosomes
exist in vivo compacted into Ôchromatin fibersÕ  30 nm in
diameter, which are in turn assembled into higher-order
structures [2]. These structures contribute additional, severe

limitations to the accessibility of DNA, beyond that
provided by nucleosomes [1,2].
Clearly, the effects of packaging DNA into nucleosomes
must be considered in investigations of all processes that use
nuclear DNA as a substrate, including transcription,
replication, recombination and DNA repair. Several strat-
egies are employed by eukaryotic cell nuclei to modulate
the accessibility of DNA within chromatin, including
post-translational modification of the histones and ATP-
dependent chromatin remodeling machines [7–10]. These
play important roles in regulation of transcription and other
DNA-dependent nuclear processes and typically involve
targeted modifications of distinct regions in chromatin. In
contrast, although the assembly of DNA into chromatin
does affect the incidence of formation of some DNA lesions,
DNA damage is widespread throughout the genome. Thus,
NER reaction is required everywhere in the genome,
irrespective of chromatin structure or the gene expression
profile of a particular cell.
NUCLEOTIDE EXCISION REPAIR
DNA is frequently damaged by a variety of environmental
and endogenous agents produced as products or byproducts
of physiological reactions. Damage to DNA causes struc-
tural defects that can impede or block transcription or
replication and potentially result in mutations [11]. For
example, all living organisms have suffered the genotoxic
effects of solar UV radiation since the beginning of the
evolution of life. It has been estimated that under the strong
sunlight typically encountered on a beach, an exposed cell in
the human epidermis develops about 40 000 damaged sites

in one hour, primarily from absorption of UV radiation by
DNA ( 200–320 nm). UV light induces two major classes
of mutagenic DNA lesions: cyclobutane pyrimidine dimers
(CPDs) and pyrimidine (6–4) pyrimidone photoproducts
(6–4PPs), which induce a DNA bend or kink of 7–9° and
44°, respectively [11,12].
Correspondence to J. J. Hayes, Department of Biochemistry and
Biophysics, University of Rochester Medical Center, Rochester, NY,
USA. Fax: + 1 716 271 2683, Tel.: + 1 716 273 4887,
E-mail:
Abbreviations: NER, nucleotide excision repair; XP, xeroderma
pigmentosum; RPA, replication protein A; RFC, replication factor C;
CPDs, cyclobutane pyrimidine dimers; 6-4PPs, pyrimidine (6-4)
pyrimidone photoproducts; CHD, chromain ATPase; ACF, ATP-
utilizing chromatin assembly and remodeling factor; GG-NER, global
genome repair; TC-NER, transcription-coupled repair.
Dedication: This Minireview Series is dedicated to Dr Alan Wolffe,
deceased 26 May 2001.
(Received 8 October 2001, revised 21 February 2002,
accepted 28 February 2002)
Eur. J. Biochem. 269, 2288–2293 (2002) Ó FEBS 2002 doi:10.1046/j.1432-1033.2002.02888.x
To insure survival in this background, cells have
developed multiple strategies for dealing with DNA
damage including the direct correction or ÔrepairÕ of
DNA changes. Both bacterial and eukaryotic cells have
several dedicated repair systems that maintain the
integrity of their genomic information. Among these,
nucleotide excision repair (NER) is one of the best-
studied pathways of DNA repair. NER is capable of
eliminating a broad range of structurally unrelated bulky

lesions from DNA, including those from UV-induced
damage and some chemical damage [11]. Indeed, defects
in components of the NER are responsible for genetic
diseases exemplified by sensitivity to UV radiation and
predisposition to skin cancer such as xeroderma
pigmentosum (XP) and Cockayne syndrome (CS) [13].
Thus, the names of many human NER components
often reflect genetic complementation groups from these
phenotypes.
The process of NER is highly conserved in eukaryotes
and consists of the following four steps: (a) recognition of
the damaged DNA; (b) excision of an oligonucleotide of
24–32 residues containing the damage from DNA by
dual incision of the damaged strand on each side of the
lesion; (c) filling in of the resulting gap by DNA
polymerase; and (d) ligation of the nick [13–15]. In
human cells, NER reaction requires at least six core
protein complexes for damage recognition and dual
incision (XPA, XPC-hHR23B, RPA, TFIIH, XPG and
XPF–ERCC1) and other factors for repair DNA synthe-
sis and ligation (PCNA, RFC, DNA polymerase a or d
and DNA ligase I) [16–18]. The molecular mechanisms of
NER have been thoroughly analyzed using highly
purified human proteins or recombinant polypeptides
on damaged naked DNA or UV-irradiated SV40 mini-
chromosomes [18–21].
NER consists of two subpathways termed global
genome repair (GG-NER) that is transcription-independ-
ent and removes lesions from the entire genome, and
transcription-coupled repair (TC-NER) [11,13]. 6-4PPs,

which distort the DNA more than CPDs, are removed
rapidly, predominantly by GG-NER. In contrast, CPDs
arerepairedveryslowlybyGG-NERandareremoved
more efficiently from the transcribed strand of expressed
genes by TC-NER [22]. The elongating transcriptional
machinery is thought to facilitate the recognition of DNA
lesions on the transcribed strand in TC-NER. However,
detailed mechanisms of TC-NER remain undefined, due to
the lack of an in vitro system for analysis. Recent
biochemical and immunocytological studies demonstrate
that the XPC–hHR23B complex appears to be the initiator
of GG-NER [23,24], although several other models have
been proposed [25,26].
It has been a curious problem how the huge multi-
subunit protein complexes of NER recognize and remove
DNA lesions that are formed in chromatin [27,28] (see
below). In addition, organization of DNA in chromatin
affects how UV light and chemical agents impart damage
to DNA. In order to understand the relationship between
chromatin dynamics and NER, it is crucial to elucidate
effects of chromatin structure on DNA damage forma-
tion and to investigate NER processes at the chromatin
level.
EFFECTS OF CHROMATIN STRUCTURE
ON UV-INDUCED DNA DAMAGE
FORMATION
As mentioned above, UV light induces the formation of
both cyclobutane pyrimidine dimers (CPDs) and pyrimidine
(6–4) pyrimidone photoproducts (6–4PPs) [11,28]. Their
yield and distribution depend on DNA sequence, the local

DNA structure and the association of DNA with chromo-
somal proteins [11,27,28]. Specifically, the chromatin envi-
ronment has been shown to affect UV-induced damage
formation distributions in nucleosomes isolated from
UV-irradiated cells [29,30]. In these mixed sequence nucleo-
somes, the CPD distribution shows a striking 10.3-bp
periodicity with a strong preference for sites where the
minor groove is oriented away from the histone surface
[29,30]. Interestingly, this distinctive periodicity coupled
with the ability of UV radiation to penetrate whole nuclei
provided the first evidence that the DNA structure of
isolated nucleosome cores is identical to that found in
nucleosomes within native chromatin [31]. On the other
hand, 6-4PPs are distributed relatively uniformly within
nucleosome cores and preferentially formed in linker DNA
of bulk chromatin from UV-irradiated cells [32].
In order to investigate the effects of nucleosome structure
on the formation of UV-induced DNA lesions, several
groups have used reconstituted model nucleosomes con-
taining a defined DNA sequence [33–36]. A major advant-
age of such systems is that the relationship between
rotational and translational position of the DNA with
respect to the histone octamer is well defined for a majority
of the sample, making correlation of damage incidence to
structure feasible. The distribution of CPDs in reconstituted
nucleosomes containing defined sequences does not show
the obvious 10.3-bp periodicity observed with mixed-
sequence chromatin, although CPD formation is reduced
at sites where the minor groove faces the histone octamer
and around the pseudo-dyad (center) of the nucleosome

compared to naked DNA [33–35]. This is likely due to
sequence-dependent DNA structural effects on the probab-
ility of lesion formation and indicates that the chemical
reactivity of DNA varies significantly about the mean
behavior observed in bulk chromatin. Also, as observed
with bulk chromatin structures, no effect of nucleosome
assembly was observed on 6-4PP distribution in physiolog-
ically spaced reconstituted dinucleosomes composed of two
tandem repeats of 5S RNA genes [36,37]. Interestingly,
regardless of the large effects of histone H1 on chromatin
structure, the formation of either CPDs or 6-4PPs in the
reconstituted dinucleosomes was not significantly affected
by the binding of linker histones [36,38]. Therefore, despite
local variations in lesion formation these defined chromatin
systems demonstrate that chromatin structure of DNA does
not greatly restrict acquisition of UV-induced lesions, even
in the presence of linker histone H1 [26,33–38].
Interestingly, after the acquisition of DNA damage by
UV irradiation, neither DNase I footprinting, hydroxyl
radical footprinting nor micrococcal nuclease mapping
shows any significant changes in the rotational or transla-
tional setting between UV-irradiated and nonirradiated
reconstituted chromatin templates. These results indicate
that local DNA-distortions induced by UV-induced lesions
do not propagate throughout the nucleosome or lead to its
Ó FEBS 2002 Nucleotide excision repair and chromatin remodeling (Eur. J. Biochem. 269) 2289
dissolution [28,33–36]. Thus, the UV-induced DNA lesions
formed throughout chromatin probably do not cause
drastic alternations of nucleosomal structure in vivo.How-
ever, it is interesting to note that assembly of nucleosomes

on DNA containing UV-induced lesions can lead to
changes in the association of histones. The introduction of
UV damage within a 5S rDNA fragment reduced the
relative affinity for binding histones and thus the efficiency
of nucleosome reconstitution in vitro [34,39]. Moreover, UV
irradiation of both mixed-sequence and unique sequence
DNA fragments was found to affect the rotational
positioning of the DNA upon reconstitution into nucleo-
somes [33,35,40].
NER IN CHROMATIN
Several lines of evidence clearly indicate that the presence of
nucleosomes on damaged DNA severely inhibits the activity
of NER machinery. Damage within UV irradiated plasmids
reconstituted into nucleosomes or within SV40 minichro-
mosomes is repaired much less efficiently compared to
naked DNA [20,21]. NER repair studies that used UV-
irradiated reconstituted nucleosomes as templates with
bacterial repair enzymes or Xenopus oocytes repair extracts
demonstrated that nucleosome assembly reduces efficiencies
of DNA repair at many but not all CPD sites in nucleosome
cores [40,41]. Removal of histone tails has little effect on
the repair efficiency of UV-irradiated nucleosomes [40,41].
Interestingly, the variation of efficiency of NER for
nucleosomal DNA does not reveal any periodicity related
to the helical twist of the DNA [41]. Therefore, it is likely
that NER components require full access to DNA com-
pletely released from histone proteins, as is provided by the
spontaneous uncoiling of DNA from the histone surface
discussed above [5,6].
Recently, in order to unravel the molecular mechanisms

of NER in chromatin, defined nucleosomal templates
containing synthetic 6-4PPs at unique sites were used for
NER reactions reconstituted with purified human NER
core factors RPA, XPA, XPC–hHR23B, XPG, ERCC1–
XPF and TFIIH [26,36]. These studies demonstrated that
excision activity at the center of nucleosome cores was
reduced drastically to  15% of that of naked DNA. The
use of synthetic oligonucleotides containing DNA lesions
makes it possible to introduce a specific type of DNA
damage at a specific position within reconstituted chroma-
tin. Surprisingly, strong repression of NER in physiologi-
cally spaced dinucleosome templates was observed even
when the 6-4PP lesion was located in the linker DNA [36].
In yeast cells, NER rates for CPDs and 6-4PPs on the
nontranscribed strand are influenced by the chromatin
environment and are removed more efficiently in linker
DNA than in nucleosomal DNA [42,43]. These results
demonstrate that extra factors other than the six human
NER factors are required to overcome the structural
barriers that chromatin poses to the removal of DNA
damage in vivo.
Although histone acetylation is generally related to
chromatin accessibility, the primary effect of this modifica-
tion may be to destabilize higher order structures [44].
Indeed, increasing the global levels of acetylation by general
inhibition of histone deacetylases causes an approximately
twofold increase in the extent of repair in hyperacetylated
nucleosomes [45]. However, removal of the histone tails
does not enhance repair rates on nucleosomes in a purified
system [41], and histone acetylation has only modest effects

on nucleosome structure and accessibility [1,6,44]. Thus
ATP-dependent chromatin remodeling complexes are likely
candidates for assisting NER in nucleosomes in vivo.Over
10 large protein complexes that locally disrupt or alter the
association of histones with DNA depending on ATP have
been purified to date. All of these chromatin remodeling
complexes contain the ATPase subunit of the SNF2
superfamily that is classified into one of three distinct
groups: SWI/SNF2-like (e.g. SWI/SNF, RSC and BRM),
ISWI-like(e.g.NURF,CHRAC,ACF,yISWIcomplexes
and RSF), and CHD-like (e.g. Mi-2/NURD) [7]. The recent
purification of a complex containing an SNF2-related
ATPase that may be related to DNA repair underscores a
connection between repair and remodeling activities [46; see
below]. It has been recently demonstrated that recombinant
ACF facilitates the excision of 6-4PP lesions by the NER
core factors, in particular those situated in the linker DNA
[36]. ACF, ATP-utilizing chromatin assembly and remode-
ling factor, consists of ISWI and Acf1 in addition to a few
other polypeptides and is well conserved from Drosophila to
human [47–49]. Although the exact function of ACF in cells
remains unknown, this is the first biological evidence to
indicate a direct connection between ATP-dependent chro-
matin remodeling and NER. Interestingly, NER in Xenopus
oocyte nuclear extracts can effectively repair a single CPD
located near the dyad center of a positioned nucleosome
[50]. NER in these extracts presumably relies on the activity
of one or more ATP-dependent chromatin remodeling
complexes [50]. Such activities may facilitate repair at
different sites of chromatin by nucleosome movement,

octamer transfer, or local twist of nucleosomal DNA in
eukaryotic cells [51,52].
XPC–hHR23B can preferentially bind to UV-damaged
DNA, even when DNA is wrapped around the histone
octamer (K. Ura, unpublished data). Once the XPC–
hHR23B complex binds to a DNA lesion of chromatin,
some ATP-dependent chromatin remodeling factors may
induce targeted chromatin reconfiguration around the
lesion to assemble the initiation complex of NER [28] (see
Fig. 1). It is likely that the extensive interactions with DNA
required by the pre- and post-incision complexes and the
synthesis of nascent DNA require disruption of nucleosome
structure, even if damage is located within the linker region
between nucleosomes [28,36] (Fig. 1, steps 4–6). Thus
nucleosomes must be reformed after repair-dependent
DNA synthesis. Importantly, nucleosomes are assembled
selectively on damaged DNA by cell or nuclear extracts
containing both chromatin assembly and NER activities
[50,53]. Thus, rapid chromatin assembly coupled to DNA
synthesis may suggest that the later steps of NER actually
occur in nucleosomes or subnucleosomal intermediates. In
this regard, it should be noted that human DNA ligase I can
efficiently seal DNA nicks in nucleosomes, even in the
presence of linker histone H1 [54] (Fig. 1, step 7).
Recent studies further highlight the possibility of a direct
functional link between chromatin remodeling activities and
DNA repair. Interestingly, the TC-NER component CSB
(Cockayne Syndrome B, see above) has homology to the
SWI2/SNF2 family and indeed has been shown to be a
DNA-dependent ATPase [55]. Moreover, this protein in

2290 K. Ura and J. J. Hayes (Eur. J. Biochem. 269) Ó FEBS 2002
isolation can affect ATP-dependent nucleosome remodeling
in vitro by several criteria [55]. Although the role of CSB
remodeling activity in NER remains to be established, these
results provide a potentially important link between the two
activities. A study in Saccharomyces cerevisiae indicates that
there exists a genetic connection between ATP-dependent
chromatin remodeling and DNA repair [46]. Two ÔRuvB-
likeÕ proteins, Rvb1p and Rvb2p copurified as part of a
complex containing the SNF2/ISWI-related protein Ino80p
[46]. Consistent with the activity of bacterial RuvB, the
INO80 complex contains DNA helicase activity and,
moreover, ino80 null mutants display sensitivity to
hydroxyurea, the alkylating agent methylmethane sulfonate,
and ionizing and UV radiation [46]. In addition, recent
results have shown that a large complex containing the
human TIP60 histone acetylase plays a role in DNA repair
and apoptosis [56]. TIP60 possesses several activities that
influence the activity of repair enzymes in chromatin
including ATPase, DNA helicase, and structural DNA
binding activities.
We expect that in the future, purified reconstituted
systems using purified factors and defined nucleosomal
templates will allow further systematic analyses of NER
in chromatin. Results to date indicate that at least some,
if not all, steps involved in NER requires active disruption
of nucleosome structure by ATP-dependent chromatin
remodeling complexes. Elucidation of the targeting of these
complexes to sites of DNA damage, perhaps via interactions
with damage-recognition complexes will greatly clarify the

relationship between NER and chromatin remodeling. We
also note that some damage within nucleosomes and at least
the final step in the repair process, DNA ligation, appear to
be at least partially compatible with nucleosome structure.
Thus, some individual steps of DNA repair processes may
not require expenditure of ATP by the cell to disrupt
nucleosomes.
ACKNOWLEDGEMENTS
This work was supported by NIH grant RO1G
M
52426 (J. J. H.) and
by a grant from the Ministry of Education, Culture, Sports, Science and
Technology of Japan (K. U.). We would like to dedicate this article to
the memory of our mentor, colleague, and friend Alan P. Wolffe, who
constantly effused a contagious passion for science and life.
REFERENCES
1. Wolffe, A.P. (2000) Chromatin Structure and Function.Academic
Press, San Diego, CA.
2. van Holde, K.E. (1989) Chromatin. Springer Verlag, New York.
3. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. &
Richmond, T.J. (1997) Crystal structure of the nucleosome core
particle at 2.8 A
˚
resolution. Nature 389, 251–260.
4. Hayes, J.J. & Wolffe, A.P. (1992) Transcription factor interaction
with nucleosomal DNA. Bioessays 14, 597–603.
5. Polach, K.J. & Widom, J. (1995) Mechanism of protein access to
specific DNA sequences in chromatin: a dynamic equilibrium
model for gene regulation. J. Mol. Biol. 254, 130–149.
6. Anderson, J.D., Lowary, P.T. & Widom, J. (2001) Effects of his-

tone acetylation on the equilibrium accessibility of nucleosomal
DNA target sites. J. Mol. Biol. 307, 977–985.
7. Vignali, M., Hassan, A.H., Neely, K.E. & Workman, J.L. (2000)
ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol.
20, 1899–1910.
8. Robertson, K.D. & Wolffe, A.P. (2000) DNA methylation in
health and disease. Nat. Rev. Genet. 1, 11–19.
9. Jenuwein, T. & Allis, C.D. (2001) Translating the histone code.
Science 293, 1074–1080.
10. Wolffe, A.P. & Hayes, J.J. (1999) Chromatin disruption and
modification. Nuceic Acids Res. 27, 711–720.
11. Friedberg, E.C., Walker, G.C. & Siede, W. (1995) DNA Repair
and Mutagenesis.ASMPress,Washington,DC.
12. Kim,J.K.&Choi,B.S.(1995)ThesolutionstructureofDNA
duplex-decamer containing the (6–4) photoproduct of thymidylyl
(3¢fi5¢) thymidine by NMR and relaxation matrix refinement.
Eur. J. Biochem. 228, 849–854.
Fig. 1. NER factors are indicated for human but each step appears to be
conserved in yeast. (1) Two major types of UV-induced DNA lesions
CPDs and 6–4PPs (red asterisks), are formed throughout chromatin
with a slight modulation reflecting chromatin structure. (2) XPC–
hHR23B complex first recognizes a DNA damage site perhaps because
of DNA helix distortion in chromatin. (3) The chromatin remodeling
complexes are directed to the damage site by their interactions with
XPC–hHR23B or other NER factors and then change chromatin
structure to create enough space for subsequent binding of other NER
factors in an ATP-dependent manner. (4) Open preincision complex is
formed upon ATP hydrolysis after recruitment of TFIIH, XPG, and
XPA-RPA. (5) NER endonucleases, XPG and ERCC1-XPF make
dual incisions at the 3¢ and 5¢ sites, respectively. (6) DNA polymerase d

and/or e, PCNA, RFC and RPA fill in the gap by repair synthesis. (7)
Redistribution of nucleosomes or reassembly of nucleosomes, which
might be mediated by chromatin assembly factor 1 (CAF-1) and/or
chromatin remodeling complexes, incorporates the repair patch into
chromatin. DNA ligase I efficiently ligates the nicks, perhaps in nas-
cent DNA already assembled into nucleosomes.
Ó FEBS 2002 Nucleotide excision repair and chromatin remodeling (Eur. J. Biochem. 269) 2291
13. de Laat, W.L., Jaspers, N.G.J. & Hoeijmakers, J.H.J. (1995)
Molecular mechanism of nucleotide excision repair. Genes Dev. 13,
768–785.
14. Sancar, A. (1996) DNA excision repair. Annu. Rev. Biochem. 65,
43–81.
15. Batty, D.P. & Wood, R.D. (2000) Damage recognition in
nucleotide excision repair of DNA. Gene 241, 193–204.
16. Mu, D., Park, C.H., Matsunaga, T., Hsu, D.S., Reardon, J.T. &
Sancar, A. (1995) Reconstitution of human DNA repair excision
nuclease in a highly defined system. J. Biol. Chem. 270, 2415–2418.
17. Aboussekhra, A., Biggerstaff, M., Shivji, M.K., Vilpo, J.A.,
Moncollin, V., Podust, V.N., Protic, M., Hubscher, U., Egly, J.M.
& Wood, R.D. (1995) Mammalian DNA nucleotide excision
repair reconstituted with purified protein components. Cell 80,
859–868.
18. Araujo, S.J., Tirode, F., Coin, F., Pospiech, H., Syvaoja, J.E.,
Stucki, M., Hubscher, U., Egly, J.M. & Wood, R.D. (2000)
Nucleotide excision repair of DNA with recombinant human
proteins: definition of the minimal set of factors, active forms of
TFIIH, and modulation by CAK. Genes Dev. 14, 349–359.
19. Araki, M., Masutani, C., Takemura, M., Uchida, A., Sugasawa,
K., Kondoh, J., Ohkuma, Y. & Hanaoka, F. (2001) Centrosome
protein centrin 2/caltractin 1 is part of the xeroderma pigmento-

sum group C complex that initiates global genome nucleotide
excision repair. J. Biol. Chem. 276, 18665–18672.
20. Wang, Z.G., Wu, X.H. & Friedberg, E.C. (1991) Nucleotide
excision repair of DNA by human cell extracts is suppressed in
reconstituted nucleosomes. J. Biol. Chem. 266, 22472–22478.
21. Sugasawa, K., Masutani, C. & Hanaoka, F. (1993) Cell-free repair
of UV-damaged simian virus 40 chromosomes in human cell
extracts. J. Biol. Chem. 268, 9098–9104.
22. van Hoffen, A., Venema, J., Meschini, R., van Zeeland, A.A. &
Mullenders, L.H. (1995) Transcription-coupled repair removes
both cyclobutane pyrimidine dimers and 6–4 photoproducts with
equal efficiency and in a sequential way from transcribed DNA
in xeroderma pigmentosum group C fibroblasts. EMBO J. 14,
360–367.
23. Sugasawa, K., Ng, J.M., Masutani, C., Iwai, S., van der Spek,
P.J., Eker, A.P., Hanaoka, F., Bootsma, D. & Hoeijmakers, J.H.
(1998) Xeroderma pigmentosum group C protein complex is the
initiator of global genome nucleotide excision repair. Mol. Cell 2,
223–232.
24. Volker, M., Mone, M.J., Karmakar, P., van Hoffen, A., Schul, W.,
Vermeulen, W., Hoeijmakers, J.H., van Driel, R., van Zeeland,
A.A. & Mullenders, L.H. (2001) Sequential assembly of the
nucleotide excision repair factors in vivo. Mol. Cell 8, 213–224.
25. Wakasugi, M. & Sancar, A. (1999) Order of assembly of human
DNA repair excision nuclease. J. Biol. Chem. 274, 18759–18768.
26.Hara,R.,Mo,J.&Sancar,A.(2000)DNAdamageinthe
nucleosome core is refractory to repair by human excision
nuclease. Mol. Cell Biol. 20, 9173–9181.
27. Pfeifer, G.P. (1997) Formation and processing of UV photo-
products: effects of DNA sequence and chromatin environment.

Photochem. Photobiol. 65, 270–283.
28. Thoma, F. (1999) Light and dark in chromatin repair: repair of
UV-induced DNA lesions by photolyase and nucleotide excision
repair. EMBO J. 18, 6585–6598.
29. Gale, J.M., Nissen, K.A. & Smerdon, M.J. (1987) UV-induced
formation of pyrimidine dimers in nucleosome core DNA is
strongly modulated with a period of 10.3 bases. Proc. Natl Acad.
Sci. USA 84, 6644–6648.
30. Pehrson, J.R. (1995) Probing the conformation of nucleosome
linker DNA in situ with pyrimidine dimer formation. J. Biol.
Chem. 270, 22440–22444.
31. Gale, J.M. & Smerdon, M.J. (1988) Photofootprint of nucleosome
core dna in intact chromatin having different structural states.
J. Mol. Biol. 204, 949–958.
32. Mitchell, D.L., Nguyen, T.D. & Cleaver, J.E. (1990) Nonrandom
induction of pyrimidine-pyrimidone (6–4) photoproducts in
ultraviolet-irradiated human chromatin. J. Biol. Chem. 265, 5353–
5356.
33. Schieferstein, U. & Thoma, F. (1996) Modulation of cyclobutane
pyrimidine dimer formation in a positioned nucleosome contain-
ing poly (dA.dT) tracts. Biochemistry 35, 7705–7714.
34. Liu, X., Mann, D.B., Suquet, C., Springer, D.L. & Smerdon, M.J.
(2000) Ultraviolet damage and nucleosome folding of the 5S
ribosomal RNA gene. Biochemistry 39, 557–566.
35. Suquet, C. & Smerdon, M.J. (1993) UV damage to DNA strongly
influences its rotational setting on the histone surface of recon-
stituted nucleosomes. J. Biol. Chem. 268, 23755–23757.
36. Ura, K., Araki, M., Saeki, H., Masutani, C., Ito, T., Iwai, S.,
Mizukoshi, T., Kaneda, Y. & Hanaoka, F. (2001) ATP-dependent
chromatin remodeling facilitates nucleotide excision repair of

UV-induced DNA lesions in synthetic dinucleosomes. EMBO J.
20, 2004–2014.
37. Ura, K., Hayes, J.J. & Wolffe, A.P. (1995) A positive role for
nucleosome mobility in the transcriptional activity of chromatin
templates: restriction by linker histones. EMBO J. 14, 3752–3765.
38. Sato, M.H., Ura, K., Hohmura, K.I., Tokumasu, F., Yoshimura,
S.H., Hanaoka, F. & Takeyasu, K. (1999) Atomic force micro-
scopy sees nucleosome positioning and histone H1-induced com-
paction in reconstituted chromatin. FEBS Lett. 452, 267–271.
39. Mann, D.B., Springer, D.L. & Smerdon, M.J. (1997) DNA
damage can alter the stability of nucleosomes: effects are depen-
dent on damage type. Proc. Natl Acad. Sci. USA 94, 2215–2220.
40. Schieferstein, U. & Thoma, F. (1998) Site-specific repair of
cyclobutane pyrimidine dimers in a positioned nucleosome by
photolyase and T4 endonuclease V in vitro. EMBO J. 17, 306–316.
41. Liu, X. & Smerdon, M.J. (2000) Nucleotide excision repair of the
5S ribosomal RNA gene assembled into a nucleosome. J. Biol.
Chem. 275, 23729–23735.
42. Wellinger, R.E. & Thoma, F. (1997) Nucleosome structure and
positioning modulate nucleotide excision repair in the non-tran-
scribed strand of an active gene. EMBO J. 16, 5046–5056.
43. Tijsterman, M., de Pril, R., Tasseron-de Jong, J.G. & Brouwer, J.
(1999) RNA polymerase II transcription suppresses nucleosomal
modulation of UV-induced (6–4) photoproduct and cyclobutane
pyrimidine dimer repair in yeast. Mol. Cell. Biol. 19, 934–940.
44. Wolffe, A.P. & Hansen, J.C. (2001) Nuclear visions: functional
flexibility from structural instability. Cell 104, 631–634.
45. Ramanathan, B. & Smerdon, M.J. (1989) Enhanced DNA repair
synthesis in hyperacetylated nucleosomes. J. Biol. Chem. 264,
11026–11034.

46. Shen, X., Mizuguchi, G., Hamiche, A. & Wu, C. (2000) A chro-
matin remodelling complex involved in transcription and DNA
processing. Nature 406, 541–544.
47. Ito, T., Levenstein, M.E., Fyodorov, D.V., Kutach, A.K.,
Kobayashi, R. & Kadonaga, J.T. (1999) ACF consists of two
subunits, Acf1 and ISWI, that function cooperatively in the
ATP-dependent catalysis of chromatin assembly. Genes Dev. 13,
1529–1539.
48. LeRoy, G., Loyola, A., Lane, W.S. & Reinberg, D. (2000) Pur-
ification and characterization of a human factor that assembles
and remodels chromatin. J. Biol. Chem. 275, 14787–14790.
49. Guschin, D., Geiman, T.M., Kikyo, N., Tremethick, D.J., Wolffe,
A.P. & Wade, P.A. (2000) Multiple ISWI ATPase complexes from
Xenopus laevis: functional conservation of an ACF/CHRAC
homolog. J. Biol. Chem. 275, 35248–35255.
50. Kosmoski, J.V., Ackerman, E.J. & Smerdon, M.J. (2001) DNA
repair of a single UV photoproduct in a designed nucleosome.
Proc. Natl Acad. Sci. USA 98, 10113–10118.
51. Flaus, A. & Owen-Hughes, T. (2001) Mechanisms for ATP-
dependent chromatin remodelling. Curr.Opin.Genet.Dev.11,
148–154.
2292 K. Ura and J. J. Hayes (Eur. J. Biochem. 269) Ó FEBS 2002
52. Gavin, I., Horn, P.J. & Peterson, C.L. (2001) SWI/SNF chromatin
remodeling requires changes in DNA topology. Mol. Cell 7,
97–104.
53. Gaillard, P.H., Martini, E.M., Kaufman, P.D., Stillman, B.,
Moustacchi, E. & Almouzni, G. (1996) Chromatin assembly
coupled to DNA repair: a new role for chromatin assembly factor
I. Cell 86, 887–896.
54. Chafin, D.R., Vitolo, J.M., Henricksen, L.A., Bambara, R.A. &

Hayes, J.J. (2000) Human DNA ligase I efficiently seals nicks in
nucleosomes. EMBO J. 19, 5492–5501.
55.Citterio,E.,VanDenBoom,V.,Schnitzler,G.,Kanaar,R.,
Bonte, E., Kingston, R.E., Hoeijmakers, J.H. & Vermeulen, W.
(2000) ATP-dependent chromatin remodeling by the Cockayne
syndrome B DNA repair-transcription-coupling factor. Mol. Cell.
Biol. 20, 7643–7653.
56. Ikura,T.,Ogryzko,V.V.,Grigoriev,M.,Groisman,R.,Wang,J.,
Horikoshi, M., Scully, R., Qin, J. & Nakatani, Y. (2000)
Involvement of the TIP60 histone acetylase complex in DNA
repair and apoptosis. Cell 102, 463–473.
Ó FEBS 2002 Nucleotide excision repair and chromatin remodeling (Eur. J. Biochem. 269) 2293