In this study, we tested complex formation by the DNA-binding domain of CENP-B with methylated and unmethylated CENP-B box DNAs, and found that CENP-B preferentially binds to the unmethy
Trang 1CENP-B binding
Yoshinori Tanaka1,2,*, Hitoshi Kurumizaka1,3and Shigeyuki Yokoyama1,2,4
1 Protein Research Group, RIKEN Genomic Sciences Center, Suehiro-cho, Tsurumi, Yokohama, Japan
2 Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
3 Waseda University School of Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo, Japan
4 RIKEN Harima Institute at Spring-8, 1-1-1 Kohto, Mikazuki-cho, Sayo, Hyogo, Japan
The centromere of eukaryotic chromosomes plays an
essential role in the proper segregation of
chromo-somes at mitosis and meiosis, and has a special
hetero-chromatin structure, which is composed of a-satellite
DNA repeats and their associated proteins The
human centromere proteins A, B and C (CENP-A,
CENP-B and CENP-C, respectively) are such
centro-mere-specific DNA-binding proteins [1–7] Neither
CENP-A nor CENP-C shows any sequence specificity
in DNA binding In contrast, CENP-B is known to
specifically bind a 17 base-pair sequence (the CENP-B box), which appears in every other a-satellite repeat (171 base-pairs) in human centromeres [8–10]
CENP-B is an 80 kDa protein that contains DNA-binding and dimerization domains at the N-terminus and C-terminus, respectively [11–13] Biochemical ana-lyses with nucleosomes reconstituted in vitro suggested that the CENP-B box sequence functions as a cis element for centromere-specific nucleosome assembly [14] In vivo analyses with cultured human cells
Keywords
CENP-B; centromere; DNA methylation;
chromatin; heterochromatin
Correspondence
2
H Kurumizaka, Waseda University School of
Science and Engineering, 3-4-1 Okubo,
Shinjuku-ku, Tokyo 169-8555, Japan
Fax: +81 3 5292 9211
Tel: +81 3 5286 8189
E-mail: kurumizaka@waseda.jp
S Yokoyama, Protein Research Group,
RIKEN Genomic Sciences Center, 1-7-22
Suehiro-cho, Tsurumi, Yokohama 230-0045,
Japan
Fax: +81 45 503 9195
Tel: +81 45 503 9196
E-mail: yokoyama@biochem.s.u-tokyo.ac.jp
*Present address
Toray Industries, Inc New Frontiers
Research Laboratories, 1111 Tebiro,
Kamak-ura, Kanagawa 248–0036, Japan
(Received 15 September 2004, accepted
1 October 2004)
doi:10.1111/j.1432-1033.2004.04406.x
In eukaryotes, CpG methylation is an epigenetic DNA modification that is important for heterochromatin formation Centromere protein B (CENP-B) specifically binds to the centromeric 17 base-pair CENP-B box DNA, which contains two CpG dinucleotides In this study, we tested complex formation by the DNA-binding domain of CENP-B with methylated and unmethylated CENP-B box DNAs, and found that CENP-B preferentially binds to the unmethylated CENP-B box DNA Competition analyses revealed that the affinity of CENP-B for the CENP-B box DNA is reduced nearly to the level of nonspecific DNA binding by CpG methylation
Abbreviations
CENP-B, centromere protein B; RNAi, RNA interference; siRNA, small interfering RNA.
Trang 2revealed that the presence of the CENP-B box is
essen-tial for the formation of functional minichromosomes
[15,16] Therefore, the CENP-B box is required for the
formation of a functional centromere However,
CENP-B null mice appeared to be normal [17–19]
This discrepancy about the CENP-B dispensibility for
mouse development and the CENP-B box requirement
for minichromosome maintenance in human cells may
be explained by presuming the existence of functional
homologues of CENP-B In fact, CENP-B-like pro-teins have been identified in humans, and the func-tional redundancy of CENP-B homologues has also been found in the fission yeast Schizosaccharomyces pombe [20–22]
In eukaryotic cells, methylation of the cytosine within the CpG dinucleotide is an epigenetic DNA modification that is important for heterochromatin formation The human a-satellite consensus sequence
Fig 1 Human a-satellite DNA and the CENP-B(1–129)–DNA complex structure (A) Schematic diagram showing the organization of human a-satellite DNA and the CENP-B box Arrows and circles in the middle row indicate a-satellite DNA repeats and CENP-B boxes, respectively The a-satellite consensus sequence [23], containing a 17 bp CENP-B box, is shown in the bottom row The three boxes, marked as sites 1,
2 and 3, indicate the essential bases for CENP-B binding to the CENP-B box DNA The three CpG sequences in the a-satellite sequence are shown in red (B) The CENP-B(1–129)–DNA complex structure [25] The essential bases for CENP-B binding are coloured red in the model structure The CpG sites that are sharply kinked by the CENP-B binding are encircled in red The nucleotide sequences of sites 1 and 3 are indicated in the left column (C) Model for the interaction between CENP-B and the CpG-methylated CENP-B box (Left) Interaction between CENP-B and the methylated CENP-B box DNA at sites 1 and 3 The methyl groups, which are modelled on the C5 atoms of cytosines in the CpG dinucleotides, are coloured red The van der Waals radii of the methyl groups (2.0 A ˚ ) are shown in orange circles The van der Waals radii of the Thr44 and Arg125 side chains are shown in grey circles Distances between the cytosine methyl groups and the nearest Thr44 and Arg125 side chain atoms are indicated by arrows (Right) Interaction between CENP-B and the unmethylated CENP-B box DNA at sites
1 and 3 The pink dotted line in the right panel indicates the hydrogen bond between the side chain NH2group of Arg125 and the N7 atom
of guanine.
Trang 3contains only three CpG sequences within its 171
base-pair sequence [23] Interestingly, two of the three CpG
sequences in the a-satellite consensus sequence
are located within site 1 (5¢-pTpTpCpG-3¢) and site 3
(5¢-pCpGpGpG-3¢) of the CENP-B box (Fig 1A; [9])
Demethylation of satellite DNA sequences,
accom-plished by growing cells in the presence of the DNA
methyltransferase inhibitor, 5-aza-2¢-deoxycytidine,
resulted in the redistribution of CENP-B [24],
indica-ting that the CpG methylation affects the
CENP-B–DNA interaction Our structural analysis of the
CENP-B DNA-binding domain [CENP-B(1–129)]
complexed with the CENP-B box DNA revealed that
CENP-B induced sharp kinks at the CpG sequences of
sites 1 and 3 upon DNA binding (Fig 1B; [25])
There-fore, CpG methylation may regulate CENP-B binding
to the CENP-B box DNA within centromeric
a-satel-lite repeats
In this study, we tested the complex formation of
CENP-B(1-129) with methylated and unmethylated
CENP-B box DNAs by a complex-reconstitution
assay, and found that the affinity of CENP-B for CpG
methylated CENP-B box DNA is significantly reduced
Results
Model for the interaction between CENP-B and
the CpG-methylated CENP-B box
In eukaryotes, DNA methylation occurs at the C5
atom of cytosine by the action of methyltransferases
To evaluate the effect of CpG methylation on the
CENP-B–DNA interaction, we modeled additional
methyl groups at the C5 atoms of site 1 (cytosine 6 and
cytosine 7¢) and site 3 (cytosine 15 and cytosine 16¢) in
the CENP-B(1–129)–DNA complex structure (Fig 1C)
In the crystal structure of the CENP-B(1–129)–DNA
complex [25], the CpG sequences in sites 1 and 3 of the
B box DNA were sharply kinked by
CENP-B(1–129) binding (16 for site 1 and 43 for site 3;
Fig 1B) As shown in Fig 1C, additional methyl
groups on cytosine 7¢ and cytosine 15 caused steric
cla-shes with the side chains of Thr44 and Arg125,
respect-ively Therefore, the CENP-B(1–129)–methylated DNA
complex model suggested that the methylations of
cyto-sine 7¢ and cytocyto-sine 15 may sterically interfere with
CENP-B binding to the CENP-B box DNA
The complex-reconstitution assay
We tested whether the CpG methylations of the
CENP-B box DNA actually affect CENP-B binding
to the DNA, as suggested by the CENP-B(1–129)–
methylated DNA complex model To do so, we employed a complex-reconstitution assay with recom-binant CENP-B(1–129) and the methylated and un-methylated CENP-B box DNAs (21 bp; Fig 2A) As the recombinant CENP-B(1–129) was only detected in the insoluble fraction when it was expressed in Escherichia coli cells, CENP-B(1–129) was purified under denaturing conditions in the presence of 6 m urea (Fig 2B) In the complex-reconstitution assay, B(1–129) formed the complex with the
CENP-B box DNA during the refolding process by dialysis against buffer without urea The complex-formation efficiency was monitored by a gel-shift assay (Fig 2C)
A
Fig 2 The complex-reconstitution assay with CENP-B(1–129) and the CENP-B box DNA (A) Schematic presentation of the complex-reconstitution assay CENP-B(1–129) and the CENP-B box DNA strands are shown in blue and red, respectively CENP-B(1–129) and the CENP-B box DNA were mixed under denaturing conditions
in the presence of 6 M urea The CENP-B(1–129)–DNA complex was reconstituted during the refolding process by dialysis against buffer without urea (B) The purified recombinant CENP-B(1–129) protein was analyzed by 15–25% SDS/PAGE Lane 1 indicates molecular mass markers (M), and lane 2 indicates CENP-B(1–129) purified under denaturing conditions in the presence of 6 M urea (C) CENP-B(1–129)–DNA complex formation The CENP-B(1–129)– DNA complex, reconstituted by the method shown in panel A, was analyzed by 20% nondenaturing PAGE Bands were visualized by ethidium bromide staining.
Trang 4CENP-B(1–129) preferentially binds to the
unmethylated CENP-B box DNA rather than the
methylated form
Using the complex-reconstitution assay, we tested the
binding of CENP-B(1–129) to the unmethylated and
methylated CENP-B box DNAs (Fig 3A) As shown
in Fig 3B, CENP-B(1–129) efficiently formed the
com-plex with the unmethylated CENP-B box DNA in a concentration-dependent manner (lanes 1–5) CENP-B(1–129) also formed the complex with the methylated CENP-B box DNA (Fig 3B, lanes 6–10), but with slightly reduced efficiency, as compared with the unmethylated CENP-B box DNA (Fig 3C) Therefore, CENP-B has the potential to bind to the methylated CENP-B box DNA
A
B
D
Fig 3 CENP-B(1–129) preferentially binds to unmethylated CENP-B box DNA (A) The 21-mer CENP-B box DNA and the 21-mer nonspecific DNA (DnaA box DNA [30]), used in this study The methylated cytosine residues in the methylated CENP-B box DNA are labeled by CH3in the middle row (B) Gel-shift analysis of complex formation between CENP-B(1–129) and the CENP-B box DNA, complexed with increasing amounts of CENP-B(1–129), by 20% PAGE The unmethylated CENP-B box DNA (lanes 1–5; 1 l M ) and the methylated CENP-B box DNA (lanes 6–10; 1 l M ) were used in this study The CENP-B(1–129) concentrations were 0 l M (lanes 1 and 6), 0.5 l M (lanes 2 and 7), 1 l M (lanes 3 and 8), 3 l M (lanes 4 and 9), and 5 l M (lanes 5 and 10) (C) Graphic representation of the complex formation rates shown in panel
B Unmethylated (d) and methylated (s) CENP-B box DNAs, respectively (D) Competition analysis for CENP-B binding between the un-methylated and un-methylated CENP-B box DNAs The 32 P-labeled unmethylated CENP-B box DNA (1 l M ) or the 32 P-labeled methylated
CENP-B box DNA (1 l M ) was mixed with the indicated amounts of the unlabeled competitor methylated or unmethylated CENP-B box DNAs, respectively, in the presence of CENP-B(1–129) (3 l M ) The complexes were analyzed by 20% PAGE (E) Graphic representation of the com-plex formation rates shown in panel D Closed and open circles indicate experiments with the 32 P-labeled unmethylated (d) and methylated (s) CENP-B box DNAs Complex formation rates (%) are plotted against the concentrations of the competitor DNAs.
Trang 5Next, we tested the binding affinity of CENP-B(1–
129) to the methylated CENP-B box DNA To do so,
we performed a competition assay In this assay,
complex formation between CENP-B(1–129) and the
32P-labeled unmethylated or methylated CENP-B box
DNAs was tested in the presence of unlabeled
compet-itor DNA As shown in Fig 3D, complex formation
between CENP-B(1–129) and the 32P-labeled
methyla-ted CENP-B box DNA was significantly inhibimethyla-ted in
the presence of only one-third of the amount of
unlabe-led unmethylated CENP-B box DNA (0.33 lm),
relat-ive to the 32P-labeled methylated form (1 lm) (lanes
7–12, and E) In contrast, complex formation between
CENP-B(1–129) and the 32P-labeled unmethylated
CENP-B box DNA was not affected, even in the
pres-ence of a threefold excess of unlabeled methylated
CENP-B box DNA (3 lm) (Fig 3D, lanes 1–6, and E)
These results indicate that CENP-B preferentially
forms a complex with the unmethylated CENP-B box
DNA, rather than the methylated CENP-B box DNA
The CENP-B binding affinity to the methylated CENP-B box DNA is similar to the level of nonspecific DNA binding
In order to compare the CENP-B binding to the CENP-B box DNA and a nonspecific DNA, we per-formed a competition assay with the methylated or unmethylated CENP-B box DNAs and a nonspecific DNA The DnaA box sequence, which is not specific-ally bound by CENP-B, was used as nonspecific DNA (Fig 3A, bottom row) The complex formation between CENP-B(1–129) and the32P-labeled unmethy-lated CENP-B box DNA was not affected when it was titrated with unlabeled nonspecific DNA (Fig 3A and 4A, lanes 1–6, and B) On the other hand, the complex between CENP-B(1–129) and the 32P-labeled methyla-ted CENP-B box DNA was significantly dissociamethyla-ted in the presence of an equal amount of unlabeled nonspe-cific competitor DNA (1 lm) (Fig 4A, lanes 7–12, and B) Therefore, the CpG methylation at sites 1 and 3 of the CENP-B box DNA reduces the CENP-B binding affinity almost to the level of nonspecific DNA binding
Discussion
In this study, we found that CpG methylation of the CENP-B box sequence reduces the binding affinity between CENP-B and the CENP-B box DNA nearly
to the level of nonspecific binding In the CENP-B(1– 129)–methylated DNA complex model, the additional methyl groups on cytosine 7¢ and cytosine 15 caused steric clashes with the side chains of Thr44 and Arg125, respectively (Fig 1C) In site 3, the CENP-B a-helix 8 (120–129 amino acid residues), containing four Arg residues (Arg125, 127, 128 and 129), penet-rates perpendicularly into the major groove around the CpG sequence Interestingly, the Arg125 side chain directly formed a hydrogen bond with the N7 atom of guanine 16, and specifically recognized the site 3 sequence (Fig 1C, right) In contrast, the Arg127, 128 and 129 residues bound to the backbone phosphates, and did not directly interact with the DNA bases Steric hindrance of the specific interaction between Arg125 and the N7 atom of guanine 16 by the CpG methylation may be a reason for the reduced specificity
of CENP-B to the CENP-B box sequence
What is the functional meaning of the CpG methyla-tion of the CENP-B box DNA? Recently, a link between centromeric heterochromatin formation and the RNA interference (RNAi) machinery was discov-ered In fission yeast, the RNAi machinery is required for chromosome segregation, gene silencing and nor-mal centromere function [
A
B
Fig 4 CpG methylation reduces the affinity between CENP-B and
the CENP-B box DNA to nearly the level of nonspecific DNA
bind-ing (A) The32P-labeled CENP-B box DNA (1 l M ) was mixed with
the indicated amounts of the unlabeled nonspecific DNA competitor
in the presence of CENP-B(1–129) (3 l M ) The complexes were
analyzed by 20% PAGE (B) Graphic representation of the complex
formation rates shown in panel A 32 P-labeled unmethylated (d)
and methylated (s) CENP-B box DNAs Formation rates (%) are
plotted against the concentrations of the competitor DNAs.
Trang 6hybrid DT40 cells, the loss of Dicer, which cleaves
double-stranded RNAs into 21- to 23-nucleotide small
interfering RNAs (siRNAs), resulted in cell death with
the accumulation of abnormal mitotic cells, and caused
the accumulation of transcripts from the human
a-sat-ellite [29] In Dicer-proficient cells, the a-sata-sat-ellite RNA
transcripts are quickly processed to siRNAs, which
may induce heterochromatin formation in the
chromo-somal regions with the same sequences as the siRNAs
These findings suggest that the a-satellite RNA
tran-scripts may be involved in functional centromere
for-mation CENP-B has the potential to induce
nucleosome assembly in the vicinity of the CENP-B
box sequence [14] This CENP-B-induced nucleosome
assembly may inhibit the production of RNA
tran-scripts from the a-satellite DNA (Fig 5) Therefore,
the CpG methylations of the CENP-B box sequence
may function in RNAi-dependent heterochromatin
for-mation by regulating CENP-B-binding to the CENP-B
box sequence in the a-satellite repeats The relationship between the DNA binding of CENP-B and the pro-duction of the a-satellite RNA transcripts is an intrigu-ing subject for future studies
In eukaryotes, the CpG methylation patterns are epigenetically conserved In this study, we found that CENP-B preferentially binds to the unmethylated CENP-B box DNA, rather than the methylated form Stable binding of CENP-B to the unmethylated CENP-B box sequence may limit the access of methyl-transferases, and maintain the unmethylated region within the centromere It has been reported that deme-thylation of satellite DNA sequences by the DNA methyltransferase inhibitor, 5-aza-2¢-deoxycytidine, resulted in the redistribution of CENP-B [24] There-fore, the CENP-B localization, which depends on the CpG methylation, may function as an epigenetic marker to form a functional centromeric chromatin structure during cell division
Experimental procedures
The complex-reconstitution assay The recombinant CENP-B(1–129) protein was purified under denaturing conditions in the presence of 6 m urea, as des-cribed previously [25] The synthesized 21-mer oligonucleo-tides were purchased from Espec-Oligo (Ibaraki, Japan)
indicated amounts of the purified CENP-B(1–129) protein and the CENP-B box DNA strands (1 lm for each strand) were mixed in the presence of 6 m urea, 500 mm NaCl, 5 mm dithiothreitol and 0.1 mgÆmL)1BSA, and the volume of the reaction was adjusted to 80 lL The reaction mixtures were first dialyzed against 10 mm Tris⁄ HCl buffer (pH 7.5), con-taining 500 mm NaCl, 5 mm dithiothreitol and 6 m urea, for
4 h at room temperature, and then for 4 h at 4C Then, the samples were dialyzed against 10 mm Tris⁄ HCl buffer (pH 7.5), containing 100 mm NaCl and 1 mm 2-mercapto-ethanol, for 16 h at 4C without urea A 10 lL aliquot of the reaction mixture was mixed with 4 lL of 20% (v⁄ v) gly-cerol, and was analyzed on a 20% (w⁄ v) polyacrylamide gel
in 0.5· TBE buffer (45 mm Tris base, 45 mm boric acid and 1.25 mm EDTA) The gel (20 cm· 20 cm · 0.1 cm) was run
at 10 mA for 5 h Bands were visualized by ethidium bro-mide staining or by autoradiography, if the32P-labeled DNA was used as a substrate, and were quantitated with a BAS2500 image analyzer (Fuji, Tokyo, Japan)
Competition analysis The purified CENP-B(1-129) protein (3 lm) and the32 P-labe-led CENP-B box DNA strands (1 lm for each strand) were mixed in the presence of 6 m urea, 500 mm NaCl, 5 mm di-thiothreitol and 0.1 mgÆmL)1 BSA Then, various amounts
Fig 5 Model for a link between CENP-B box CpG methylation and
RNAi-dependent heterochromatin formation Arrows and purple
cir-cles indicate a-satellite DNA repeats and CENP-B boxes,
respect-ively The methylated CENP-B boxes are labelled ‘Me’ Red and
yellow circles indicate CENP-B and CENP-C, respectively, and
green circles indicate nucleosomes Blue bars indicate RNA
tran-scripts, which are produced from the a-satellite DNA for the
RNA-i-dependent heterochromatin formation In this model, the CpG
methylation pattern of the CENP-B boxes in the a-satellite repeats
are epigenetically maintained, and CENP-B preferentially binds to
the unmethylated CENP-B boxes CENP-B may induce
centromere-specific nucleosome assembly with CENP-A, CENP-C and histones,
and the nucleosomes may inhibit the production of RNA transcripts
from the a-satellite DNA The a-satellite RNA transcripts are quickly
processed by Dicer to siRNAs, which may be involved in
centro-meric heterochromatin formation [29].
Trang 7of unlabeled competitor DNA (21-mer) were added to the
reaction mixture, and the volume was adjusted to 80 lL The
reaction mixtures were first dialyzed against 10 mm Tris⁄ HCl
buffer (pH 7.5), containing 500 mm NaCl, 5 mm
dithiothrei-tol and 6 m urea, for 4 h at room temperature, and then for
4 h at 4C Then, the samples were dialyzed against 10 mm
Tris⁄ HCl buffer (pH 7.5), containing 100 mm NaCl and
1 mm 2-mercaptoethanol, for 16 h at 4C without urea A
10 lL aliquot of the reaction mixture was mixed with 4 lL
of 20% (v⁄ v) glycerol, and was analyzed on a 20% (w ⁄ v)
polyacrylamide gel in 0.5· TBE buffer (45 mm Tris base,
45 mm boric acid and 1.25 mm EDTA) The gel
(20 cm· 20 cm · 0.1 cm) was run at 10 mA for 5 h Bands
were visualized by autoradiography, and were quantitated
with a BAS2500 image analyzer (Fuji)
Acknowledgements
This work was supported by the Bioarchitect Research
Program (RIKEN), the RIKEN Structural
Geno-mics⁄ Proteomics Initiative (RSGI), the National Project
on Protein Structural and Functional Analyses, and
Grants-in-Aid from the Japanese Society for the
Promo-tion of Science (JSPS) and the Ministry of EducaPromo-tion,
Sports, Culture, Science and Technology, Japan
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