Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks. Nat Struct Mol Biol

ArticleinNature Structural & Molecular Biology 18(3):395-400 · February 2011with75 Reads
Impact Factor: 13.31 · DOI: 10.1038/nsmb.1988
Abstract

Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ~1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5' half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.

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Genome-wide mapping of Arabidopsis thaliana origins of
DNA replication and their associated epigenetic marks
Celina Costas
1,7
, Maria de la Paz Sanchez
1,6,7
, Hume Stroud
2,7
, Yanchun Yu
3
, Juan Carlos Oliveros
4
,
Suhua Feng
5
, Alberto Benguria
4
, Irene López-Vidriero
4
, Xiaoyu Zhang
3
, Roberto Solano
4
, Steven E Jacobsen
2,5
&
Crisanto Gutierrez
1
Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication 
initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. 
In this study we profiled origins in Arabidopsis thalianaby high-throughput sequencing of newly synthesized DNA and identified 
~1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) 
experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance 
of nascent DNA strands. The midpoints of most A. thalianaorigin regions are preferentially located within the 5 half of genes, 
enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help 
clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.
Faithful duplication of the genetic material is crucial in maintaining
genomic integrity. DNA replication in eukaryotic cells initiates at mul-
tiple sites, known as replication origins, which are scattered through-
out the genome
1–3
. The number of origins ranges from hundreds to
thousands depending on cell type and/or physiological state
3
. One of
the key steps in understanding the function of replication origins is
determining whether and how they are specified in the genome. In
Saccharomyces cerevisiae, a strict sequence-dependent specification
occurs whereby the origin recognition complex (ORC) recognizes an
11-base-pair (bp) sequence to define the site of each active replication
origin
4,5
. This mechanism seems to be unique because a consensus
sequence has not been found in other organisms. For example, in
Schizosaccharomyces pombe, although origins are associated with
(A+T)-rich stretches, they are not specified by a known consensus
DNA sequence
6,7
.
The identification of the molecular nature of replication origins
in multicellular organisms has been challenging, and only a hand-
ful of origins have been analyzed
2,810
. The large genome size of
multicellular eukaryotes, their different developmental strategies
and the diversity of proliferating cell populations have made it
difficult to determine origin specification, function and spatio-
temporal regulation at a genomic scale
3
. Local epigenetic modifi-
cations can further affect origin selection and usage, for example,
replication timing
3,1113
. Although attempts to obtain genome-
wide maps of replication origins in mammalian cells have been
reported
1417
, the molecular features defining replication origins
in higher eukaryotes and, in particular, their links to epigenetic
modifications still remain largely unknown.
In this study, we identified replication origins, analyzed their
organization and defined their epigenetic signatures at a high-
resolution genome-wide scale in the plant A. thaliana. Its compact
genome (~125 Mb, ~28,000 protein coding genes), which is fully
sequenced and annotated, and its small percentage of repetitive
sequences (~17%), which are largely confined to the pericentro-
meric areas
18
, make A. thaliana a useful system for studying ori-
gins. Furthermore, the comparison of replication origin features
in organisms with very different developmental and growth strate-
gies could clarify the basic principles governing origin specifica-
tion and function in eukaryotes. In addition, genome-wide maps
of epigenetic marks such as DNA methylation and several histone
modifications have already been reported
1921
. Through massive
sequencing of short-pulse 5-bromo-2-deoxyuridine (BrdU)-labeled
DNA, we identified ~1,500 putative replication origins across
the A. thaliana genome. We also identified ORC1- and CDC6-
binding regions using ChIP-chip; notably, these are enriched in
BrdU-labeled regions. Furthermore, we validated origin activity
independently by measuring nascent DNA strand abundance. Our
studies reinforce the idea that some origin features are shared with
animal cells whereas others are unique to plants
22,23
. The A. thaliana
originome’ reported here provides a basis for identifying the key
features of eukaryotic replication origins and delineating their
possible regulatory mechanisms.
1
Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad autónoma de Madrid (UAM), Madrid, Spain.
2
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA.
3
Department of Plant Biology, University of Georgia,
Athens, Georgia, USA.
4
Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
5
Howard Hughes Medical Institute, University of California, Los Angeles, California,
USA.
6
Present address: Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico DF, Mexico.
7
These authors contributed equally to this work.
Correspondence should be addressed to C.G. (cgutierrez@cbm.uam.es) or S.E.J. (jacobsen@ucla.edu).
Received 19 February 2010; accepted 24 November 2010; published online 6 February 2011; doi:10.1038/nsmb.1988
© 2011 Nature America, Inc. All rights reserved.
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396 VOLUME 18 NUMBER 3 MARCH 2011 nature structur al & molecular biology
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RESULTS
Genome-wide mapping of A. thalianaDNA replication origins
Functional origins mark the sites where the synthesis of nascent
DNA strands occurs. Thus, our strategy was to sequence purified
DNA labeled in vivo with a pulse of BrdU and confirm these data
with the mapping of pre-replication complex (pre-RC) binding
(Supplementary Fig. 1). To obtain sufficient amounts of BrdU-
labeled DNA, we used A. thaliana cultures containing a substantial
number of proliferating cells. We synchronized cells in the G0 stage
of the cell cycle using sucrose deprivation and labeled them with
BrdU a few hours after release from the block when cells were just
entering the S-phase
24,25
(Supplementary Figs. 1 and 2). DNA was
extracted and fractionated by CsCl gradient centrifugation, and the
BrdU-labeled material was purified and used to generate genomic
libraries for sequencing using Solexa (Illumina) technology. We
obtained ~4 million high-quality reads that uniquely mapped to the
A. thaliana genome. Likewise, we processed a sample of unlabeled
DNA as a control (see Online Methods). This BrdU-seq method
rendered a comprehensive list of genomic locations with a signifi-
cant enrichment in BrdU-labeled DNA strands (Fig. 1a). To define
origin regions using the BrdU-labeled DNA sequencing data, we
merged BrdU-positive regions separated by <10 kilobases (kb), as
described in Online Methods (see also Supplementary Fig. 3). An
alignment of DNA sequences of ±100 bp around the midpoint of
BrdU-labeled regions did not render any consensus sequence. To
corroborate the analysis of BrdU-labeled regions and deal with pos-
sible experimental variations, we carried out an independent assay of
cell synchronization, BrdU-labeling and CsCl purification followed
by massively parallel sequencing. Significantly, 78.2% (P < 1.0 × 10
−6
)
of the BrdU-labeled regions overlapped with the regions defined in
the previous experiment, supporting the reproducibility of the two
independent experiments.
To identify pre-RC binding sites, in the absence of specific antibod-
ies, we used plants expressing constitutively tagged versions of two
pre-RC components, ORC1 (ref. 26) and CDC6 (ref. 27). We purified
ORC1- and CDC6-bound DNA fragments by ChIP (Supplementary
Fig. 1) and hybridized them to whole-genome A. thaliana tiling arrays
to identify their genome-wide binding sites (Fig. 1a). ORC1 bind-
ing was spread over many sites (Supplementary Fig. 4), whereas
CDC6-binding sites were less abundant (Supplementary Fig. 5).
First, we determined the fraction of the BrdU-labeled regions that
contained bound pre-RC components. We found that ~76.7% and
17.0% of BrdU-labeled regions overlapped with ORC1 and CDC6
regions, respectively (midpoint of BrdU region, ±2.1 kb, P < 0.001;
see colocalization range in Fig. 1b). Notably, the midpoints of these
regions significantly colocalized with both ORC1- and CDC6-binding
sites within ±2 kb regions (Fig. 1b). Therefore, we considered the
1,543 regions rendered by our approach to be bona fide replication
origins (Supplementary Table 1). They seem uniformly distributed
across the genome, although it is possible to identify clusters of more
closely spaced origins in some genomic locations (Supplementary
Fig. 6). The number of origins varies for different chromosomes but
is roughly correlated with chromosome size (Fig. 1c). The distribution
of distances between origin region midpoints has a median of 51.1 kb,
and a mean of 77.2 kb (Fig. 1d).
Assessing origin activity by nascent strand abundance
The BrdU-labeled regions identified in our study and the marked colo-
calization with ORC1- and CDC6-binding sites support the notion
that they represent active DNA replication origins. To assess origin
activity directly, we measured the relative abundance of nascent DNA
strands of various putative origin regions relative to adjacent regions
in a sample of short DNA molecules purified by sucrose-gradient cen-
trifugation and containing a RNA primer at their 5 ends
28,29
. Thus,
we determined origin activity by real-time PCR methods using primer
pairs spanning 5–16 kb around putative origin regions. In all cases we
analyzed, origin sequences were highly enriched in the short nascent
DNA strand sample (Fig. 2ac). Notably, one of the BrdU-labeled
regions included in this analysis showed a relatively low CDC6 sig-
nal in the ChIP-chip experiment (Fig. 2a). Despite this, it showed a
a
b c
d
0.12
ORC1
0.12
0.06
1.0
0.6
Chr. 1 (376)
Chr. 5 (357)
Chr. 2 (252)
Chr. 4 (219)
Chr. 3 (339)
4,940,0004,935,0004,930,000
10,000,000
20,000,000 30,000,000
0
BrdU-
labeled
Control
Chromosome 1
CDC6
ORC1
ori1-0850
0.2
0.2 1.00.6
0.06
–0.06
0
0
0
50
150
250
0
–10
Relative signal
Number Relative
chromosome size
Relative origin number
1060 02–2–6
–10 1060 0 100 200 300 >400
Distance from midpoint of
origin region (kb)
Interorigin distance (kb)
2
CDC6
–2–6
Genes
+
Figure 1 Identification of DNA replication origins in the A. thaliana genome.
(a) Representative genome-browser view of a region in chromosome 1.
Genes (green) transcribed from each strand are along the chromosome
above and below the position scale. Bottom, an enlarged region containing
a replication origin, determined as a region enriched for BrdU-labeled DNA
strands (light blue) relative to the unlabeled control DNA (black), together
with the ORC1 (red) and CDC6 (dark blue) binding patterns (posterior
probabilities for ORC1 and CDC6 data sets). Origins, for example,
ori1-0850, are named based on their chromosomal location
(ori1 through ori5), followed by the four digits indicating the origin
number within each chromosome. They are named consecutively starting
at the left tip of each chromosome; that is, for chromosome 1, in which we
identified 376 origins, the leftmost origin is ori1-0010 and the rightmost
one is ori1-3760. (b) The pattern of ORC1 and CDC6 binding over origin
regions was obtained by plotting their relative binding signal ±10 kb from
the origin region midpoint (0) using 50-bp sliding windows (smoothed).
The P values (two-sided) of the difference in the ChIP-chip signals in origins
(midpoint ±300 bp), using a two-tailed Welch test, were 7.25 × 10
−6
and
1.29 × 10
−10
for ORC1 and CDC6, respectively. (c) Number of origins
relative to chromosomal size. Chromosome size (relative to chromosome
(chr.) 1) versus the number of origins identified in each chromosome
(relative to origin number in chromosome 1). Number of origins identified in
each chromosome is in parentheses. (d) Distribution of interorigin distances,
measured as distance between the midpoints of two contiguous origins
(median, 51.1 kb; average, 77.2 kb; s.d., 83.4 kb).
© 2011 Nature America, Inc. All rights reserved.
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nature structural & molecular biology VOLUME 18 NUMBER 3 MARCH 2011 397
r e s o u r c e
high abundance of nascent DNA strands measured by quantitative
PCR (qPCR), demonstrating the activity of this region as a functional
origin as well as the robustness of our approach. A control region,
lacking BrdU-labeled DNA sequences, did not show any appreciable
enrichment (Fig. 2d). These data together led us to conclude that the
set of origins identified here provides a starting point for defining
their molecular landscape.
Genomic location ofA. thaliana DNA replication origins
To test whether origins are randomly distributed along the genome
or show a preferential location, we estimated origin location rela-
tive to various genomic elements. We found that 77.7% and 10.2%
of origins colocalized with gene units and transposons, respec-
tively. These percentages are significantly different from the pro-
portion of the A. thaliana genome represented by these elements
(Fig. 3a). Next, we analyzed origin density across genes and their 5
and 3 upstream regions. We observed that most origins were iden-
tified within gene bodies (Fig. 3b), but preferentially toward their
5 ends (Supplementary Fig. 7). Origin localization to the bodies
of genes did not correlate with gene expression levels (Fig. 3b),
according to expression data obtained from cell suspensions at the
same synchronization time used for BrdU labeling
30
. However,
highly expressed genes, compared with weakly expressed genes,
tended to have more origins in regions immediately upstream
(Wilcoxon rank-sum test, P < 0.005) or downstream (Wilcoxon
rank-sum test, P < 0.01) of genes (Fig. 3b).
The body of highly expressed genes in A. thaliana is enriched in
CG methylation, whereas the three types of C methylation (CG, CHG
and CHH, where H is A, T or C) are highly enriched in the repeat-rich
pericentromeric regions of the A. thaliana genome
19,31
. Notably, we
found a slight decrease in CG methylation around origin midpoints
as compared with regions flanking them (Fig. 4a). Furthermore, we
observed that regions ±0.1 kb from the origin midpoints showed
higher G+C contents (44.5%), as compared with the whole A. thaliana
genome (Fig. 4b). The histone variant H2A.Z is preferentially depos-
ited near the 5 end of target genes and is inversely correlated with CG
methylation
32
. We found a strong presence of H2A.Z within ±1 kb of
the origin midpoints (Fig. 4c).
Epigenomic landscape ofA. thaliana DNA replication origins
To further determine features defining A. thaliana replication ori-
gins, we next sought to profile the landscape of epigenetic histone
marks that seem to associate with replication origins. A. thaliana
1,200
800
400
0
0
0
0
10
20
20
30
40
40
60
40
80
120
50
19,034,000
13,334,000 8,422,000
12,566,000
Control
2 kb
2 kb 2 kb
2 kb
Ori
Ori
CDC6
CDC6
ORC1
ORC1
Fold enrichmentFold enrichment
a b
c d
ori1-2300 ori2-1340
ori2-1430
Genes
+
Genes
+
Figure 2 DNA replication origin activity determined by nascent DNA
strand abundance. (a–d) Several putative origin-containing regions were
chosen for detailed measurement by real-time PCR of nascent strand
abundance in a sample of short DNA molecules containing an RNA primer
at their 5 end (see Online Methods). Genomic region under study is at
bottom of each panel and shows the location of genes (green), ORC1-
binding (red) and CDC6-binding (dark blue) signals, and putative origin
location (light blue), defined by direct sequencing of the BrdU-labeled
DNA sample (see Online Methods). DNA fragments (~200 bp long)
amplified by primer pairs scanning each region are small black rectangles
on the x axis. Coordinates in each chromosome are at the bottom of
each panel. Results correspond to PCR amplifications using fraction 5
(see Online Methods). Data for origins ori1-2300 (a), ori2-1340 (b) and
ori2-1430 (c). Data for a region used as a negative control around gene
at4g14700 that lacks BrdU-labeled DNA sequences (d).
None
Upstream Downstream
Gene body
35
25
15
5
All genes
Top 25%
Bottom 25%
All genes
Top 25%
Bottom 25%
All genes
Top 25%
Bottom 25
%
Origin density
Both
Transposons
Genes
0.6
(0.8)
11.5
(30.4)
10.2
(20.6)
77.7
(49.8)
b
a
Figure 3 Genomic location of A. thaliana replication origins.
(a) Percentage of origins colocalizing with various genomic elements.
Numbers in parentheses, proportion of A. thaliana genome represented
by each class. (b) Origin densities were computed for regions upstream,
downstream and within genes of different expression levels (all genes,
highest 25%, lowest 25%). Regions 2 kb upstream and downstream of
genes, as well as the bodies of genes, were each divided into ten bins,
and the origin densities (origins per 10
6
bp) were calculated for each
bin and represented as box plots. White lines, median; edges of boxes,
25
th
(bottom) and 75
th
(top) percentiles; error bars, minimum and
maximum points that fell within 1.5×IQR (interquartile range) below
the 25
th
percentile or above the 75
th
percentile.
© 2011 Nature America, Inc. All rights reserved.
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398 VOLUME 18 NUMBER 3 MARCH 2011 nature structur al & molecular biology
r e s o u r c e
epigenomics data are already available for dimethylation of histone
H3 at Lys9 (H3K9me2) and for the three methylated forms of H3 Lys4
(H3K4; refs. 20,21). We found that most origins tend to be depleted
in singly methylated H3K4 (H3K4me1; Fig. 5a) but are highly
enriched in dimethylated and trimethylated H 3K4 (H3K4me2 and
H3K4me3; Fig. 5b,c). We observed that H3K4me3 and/or H3K4me2,
with or without H3K4me1, seems to be a signature of ~80% of ori-
gins associated with genes (Fig. 5). This is consistent with the pref-
erential localization of origins in 5 gene body regions observed here
and the negative correlation of these marks and CG methylation
21
.
Furthermore, H3K9me2 is highly depleted in most of the origins
identified in our study (Fig. 5d).
Histone hyperacetylation and origin activation are correlated in
Xenopus laevis
11
and Drosophila melanogaster cells
33–35
. Consistent with
this, immunofluorescence data obtained in several plant species indicate
that increases in histone acetylation occurs during S-phase
22,23
. Recently,
ChIP experiments have shown that H4 Lys 5 (H4K5) and H4K12 (and
to a lesser extent H4K8), but not H4K16, need to be acetylated by the
HBO1 histone acetylase at origins in human cells to overcome gemi-
nin inhibition and facilitate minichromosome maintenance (MCM)
loading
36
. Thus, we profiled H4K5ac over the genome by ChIP-chip and
found an enrichment of this mark at the origin midpoint (Fig. 5f).
DISCUSSION
Initiation of DNA replication in eukaryotes depends on the assembly
of pre-RCs in G1 of the cell cycle at certain chromosomal locations
and their further activation to initiate DNA replication in S-phase.
Both steps must be tightly coordinated to ensure that the genome is
duplicated once per cell cycle
2
. We have found that ORC1-binding
sites tend to form clusters, similar to the situation in D. melanogaster
cells
37
but very different from that in S. cerevisiae
5
. The presence of
ORC1-binding sites across the genome may not only represent broad
initiation zones with several potential initiation sites but also reflect
the function of ORC1 in other processes, for example, heterochroma-
tin silencing
38
, transcriptional control
26,39
or chromatid cohesion
40
.
In any case, detection of CDC6 in BrdU regions takes into account the
release of CDC6 from the pre-RC once an origin is fired
41
.
The distribution of distances between origin region midpoints
fell within the range estimated for other eukaryotes
42
and roughly
matched estimates of replicon size in A. thaliana
13,43
. A fraction of the
putative origin regions identified here could correspond to elongating
forks rather than to initiation events. However, our direct measure-
ments of origin activity by abundance of RNA primer–containing
nascent strands support the idea that the originome reported here
is a bona fide list of putative A. thaliana DNA replication origins.
Future analysis should address this point. The abundance of origin
Figure 4 Relationship of A. thaliana
replication origins to CG methylation
and histone H2A.Z. (a) Relative levels
of CG, CHG and CHH methylation ±10 kb
relative to the origin midpoint (0) in 50-bp
sliding windows (smoothed). Methylation
data have been reported
19
. (b) G+C content (%)
of replication origins (black) and indicated
genomic regions (white). These values were
calculated from the sequence data files
available at The Arabidopsis Information
Resource (TAIR), http://www.arabidopsis.org/.
(c) Density of the histone variant H2A.Z in a
±10 kb region relative to the origin midpoint (0) in 50-bp sliding windows (smoothed). The genomic distribution of H2A.Z has been reported
32
.
The P value of the difference in the ChIP-chip signals in origins (calculated as in Fig. 1b; see Online Methods), was 9.34 × 10
−34
.
a
0.06
0.30
0.15
0
0
–0.06
0.2
0.4
0.08
0.02
–0.04
–10 –6 –2 0 2 6 10
0.2
0
me1 + + + +
+ + + +
+ + + +
Genes with origins
H4K5ac
H3K9me2
me2
me3
–0.12
–0.18
–0.24
–10 –6 –2 0 2 6 10
0.1
0
–10 –6 –2 0 2 6 10
Relative signalRelative signalRelative signal
Relative signal
Fraction of genes
Combinations of H3K4me
Distance from origin center (kb)
H3K4me1
H3K4me2
Distance from origin center (kb)
H3K4me3
–10 –6 –2 0 2 6 10 –10 –6 –2 0 2 6 10
b
e f
d
c
All genes
Figure 5 Histone modification landscape around replication origins.
(a–d) Relative level of indicated histone mark ±10 kb relative to the center
of origins (0) in 50-bp sliding windows (smoothed). Data for H3K4me and
H3K9me2 have been reported
20,21
. The P values of the difference in the
ChIP-chip signals in origins (calculated as in Fig. 1b; see Online Methods)
were 0.86, 3.52 × 10
−28
, 1.07 × 10
−41
and 7.33 × 10
−14
for H3K4me1,
H3K4me2, H3K4me3 and H3K9me2, respectively. (e) Relationship
between H3K4 methylation status and the presence of origins. We
calculated the fraction of genes containing origins and different
combinations of H3K4 methylation, and compared it with the fraction of
all genes containing the same H3K4me combinations
21
. Different classes
are ordered with decreasing values of the fraction of genes with origins.
(f) Relative level of H4K5ac ±10 kb relative to the center of origins (0)
in 50-bp sliding windows (smoothed). Calculations are based on the
ChIP-chip data set generated in this work. The P value of the difference in
the ChIP-chip signals in origins (calculated as in 1b; see Online Methods)
was 1.23 × 10
−23
.
a
0.20
0.10
0
45
35
25
0.45
H2A.Z
0.30
0.15
–10 –6 –2 0 2 6 10
Genome average
Origin midpoint
Intergenic
Exons
Introns
–10 –6 –2 0 2 6 10
CG
CHG
CHH
Distance from origin (kb)
Relative signal
G+C (%)
Relative signal
Distance from origin (kb)
b c
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nature structural & molecular biology VOLUME 18 NUMBER 3 MARCH 2011 399
r e s o u r c e
sequences and the width of the peak of amplified fragments varied
for different origins we analyzed, suggesting differences in the effi-
ciency of origin usage or in the usage of initiation sequences within
an origin region
10,42
.
Notably, the location of most A. thaliana origins is different from
that in other systems, in which a large proportion of highly effi-
cient origins are associated with gene promoters or transcriptional
start sites
16,17,37
. We have found that the ±0.1-kb region around
A. thaliana DNA replication origins has a higher-than-average G+C
content and a slight decrease in CG methylation. Consistent with this
observation, early and mid replicons in A. thaliana chromosome 4
are also depleted in CG methylation
13
. One possibility is that in
A. thaliana the relatively high G+C content at origins favors a par-
ticular nucleosome organization in these regions. This is reinforced
by the colocalization of origins with histone H2A.Z, which affects
nucleosome stability
44
, and could facilitate pre-RC assembly and/or
origin firing. Together, our data show that whereas CG methylation
within gene bodies is relevant for gene expression in A. thaliana
19
, it
does not seem to be a requirement for origins. Metazoan origins are
highly correlated with unmethylated CpG islands located at the pro-
moters of active genes or in proximity to transcriptional start sites
6,42
.
Although CpG islands are not present in the A. thaliana genome, our
results show a conserved trend of relatively lower CG methylation at
origins, and a high correlation among origin activity, a local high G+C
content and the presence of H2A.Z.
Post-translational histone modifications can also affect origin speci-
fication and function. Most A. thaliana origins tend to be enriched in
H3K4me2 and H3K4me3, as well as in H4K5ac, similarly to human
origins
17,36
. Whether all human origins have the same H4ac pattern, as
a consequence of HBO1 activity to overcome geminin inhibition
36
, and
whether all A. thaliana origins require H4ac for activation, remain open
questions for the future. However, the H4 acetylation pattern is relevant
owing to the presence in A. thaliana of (i) an HBO1-related acetyltrans-
ferase
45
, (ii) increased tetraH4ac residues around ORC1-binding sites
26
and (iii) a CDT1-interacting protein, GEM, structurally unrelated to
metazoan geminin
46,47
. Acetylation of other histone residues may be
also relevant for origin function, as has been suggested by the presence
of H3K56ac in early replicons of chromosome 4 (ref. 13).
How replication origins are specified in large eukaryotic genomes
has been a long-standing question. Early-firing origins are associated
with transcribed genomic regions
48,49
. The origins that have been
studied in mammalian cells, covering only 0.4–1% of their genomes,
show a preferential association with active promoters that contain
CpG islands
15–17
. We have found that origins located in the upstream
regions of genes are preferentially associated with highly expressed
genes. However, the differences in the genomic distribution of CG
methylation pattern in A. thaliana may contribute to the use of dif-
ferent mechanisms to specify origins. In fact, a higher proportion of
origins are located in the 5 half of gene bodies in A. thaliana than in
mammalian cells.
Our work has defined a landscape of epigenetic marks associated with
a genome-wide set of replication origins in A. thaliana. The midpoints of
most origin regions preferentially colocalize with a higher-than-average
G+C content, but lower CG methylation, and are enriched in histone
H2A.Z, H3K4me2, H3K4me3 and acetylated H4K5, and depleted in
H3K4me1 and H3K9me2. Elucidating how epigenetic mechanisms and
gene expression coordinate with DNA replication is important for under-
standing these processes in a genomic and developmental context. The
A. thaliana originome reported here provides a foundation for future
studies of the mechanisms of origin specification as well as the regulation
and function of DNA replication origins in different eukaryotes.
METHODS
Methods and any associated references are available in the online
version of the paper at http://www.nature.com/nsmb/.
Accession codes. NCBI GEO: ORC1 and CDC6 ChIP-chip, GSE21928;
BrdU-seq and H4K5ac ChIP-chip, GSE21828.
Note: Supplementary information is available on the Nature Structural
&
Molecular
Biology website.
ACKNOWLEDGMENTS
We thank E. Martinez-Salas, J.A. Tercero and E. Caro for comments and discussions,
S. Diaz-Triviño and P. Hernandez for initial efforts in origin mapping, and M. Gomez
and J. Sequeira-Mendes for advice with the purification and analysis of nascent DNA
strands. The technical help of V. Mora-Gil is deeply acknowledged. M.P.S. and C.C.
are recipients of JAE-Doc contracts from CSIC. S.F. is a Howard Hughes Medical
Institute Fellow of the Life Sciences Research Foundation. This research has been
supported by grants BFU2006-5662, BFU2009-9783 and CSD2007-00057-B (Spain
Ministry of Science and Education) and P2006/GEN0191 (Comunidad de Madrid)
to C.G., by an institutional grant from Fundación Ramón Areces to C.B.M., by
grant GM60398 (US National Institutes of Health) to S.E.J., by grant 0960425 (US
National Science Foundation) to X.Z. and by grants BIO2004-02502, BIO2007-66935,
GEN2003-20218-C02-02 and CSD2007-00057-B (Spain Ministry of Science and
Innovation) and GR/SAL/0674/2004 (Comunidad de Madrid) to R.S. S.E.J. is an
investigator of the Howard Hughes Medical Institute.
AUTHOR CONTRIBUTIONS
C.C., M.P.S., Y.Y., S.F., A.B. and I.L.-V. carried out experiments. H.S., J.C.O., C.C.,
M.P.S., X.Z. and R.S. analyzed data. C.G. and S.E.J. prepared the manuscript.
COMPETING FINANCIAL INTERESTS
The authors declare no competing financial interests.
Published online at http://www.nature.com/nsmb/.
Reprints and permissions information is available online at http://npg.nature.com/
reprintsandpermissions/.
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Page 6
nature structural & molecular biology
doi:10.1038/nsmb.1988
ONLINE METHODS
Plant material. A. thaliana seedlings (Col-0 ecotype) were grown in Murashige
and Skoog (MS) salts medium supplemented with 1% (w/v) sucrose and
1% (w/v) agar in a 16 h:8 h light/dark regime at 22 °C. Plants constitutively
expressing the Myc-ORC1a–tagged and the hemagglutinin (HA)-tagged
A. thaliana CDC6a protein have been described
26,27
.
Chromatin immunoprecipitation and microarray assays. ChIP assays of plants
expressing His-ORC1 and HA-CDC6 were carried out using 10-day-old plants prein-
cubated with 50 µM MG132 before the fixation step. For immunoprecipitation, 10 µl
of antibody to Myc (SC-40ac; Santa Cruz Biotechnology) or antibody to HA (A2095;
Sigma) were incubated with 1 mg of protein extract, previously sonicated, to obtain
DNA fragments of ~500–1,000 bp. After they were washed, immunocomplexes were
incubated at 65 °C for 6 h, treated with 20 µg of proteinase K and phenol-chloroform
extracted. The DNA obtained (ChIP and input) was purified using Affymetrix cDNA
cleanup columns. Three biological replicates for each condition were independ-
ently hybridized to GeneChip A. thaliana Tiling 1.0R Array (Affymetrix). DNA
was amplified using Affymetrix Chromatin Immunoprecipitation Assay protocol.
Amplification product (7.5 µg) was fragmented and labeled using GeneChip WT
Double-Stranded DNA Terminal Labeling Kit (Affymetrix). Scanning was carried
out at a resolution of 0.7 µm using a GeneChip Scanner 3000 7G (Affymetrix).
One of the CDC6 replicates was discarded owing to low correlation with the other
replicates. The H4K5ac ChIP was carried out using an antibody from Millipore
(06-759), and the H3 ChIP control was carried out using an antibody from Abcam
(ab1791), as described
21,31,50,51
.
Cell culture, BrdU labeling and isolation of nascent strands. A. thaliana
MM2d cells were grown in MS medium supplemented with 3% (w/v)
sucrose (Sigma), 0.5 mg ml
−1
naphthalene acetic acid (NAA; Sigma) and
0.05 mg ml
−1
kinetin (Sigma), pH 5.8, and subcultured every 7 d (ref. 52). For
cell synchronization, a mid-exponential-phase culture was grown in MS medium
lacking sucrose for 24 h, released by changing to medium supplemented with
sucrose and cultured for an additional 3.5 h (ref. 25).
Newly synthesized DNA was labeled by adding 200 µM of BrdU, 20 µM
5-fluoro-2-deoxyuridine and 10 mM hydroxyurea to the medium for the last
60 min of incubation (Supplementary Fig. 1). Cells were collected by filtra-
tion and DNA was purified
53
. Genomic DNA was digested with BamHI
and centrifuged in 5.0 ml of a CsCl solution containing 10 mM Tris-HCl,
pH 7.5, 1 mM EDTA and 150 mM NaCl (refractive index adjusted to 1.4000,
at 25 °C) in a Beckman Vti 65.2 rotor at 227,300g for 21 h at 20 °C. Fractions
(100 µl) collected from the bottom were analyzed by immunoblot with antibody
to BrdU (Becton-Dickinson) to identify the heavy-light (HL) density fractions.
BrdU DNA in the HL fractions and genomic DNA in the unlabeled (LL) fractions,
used as control, were pooled separately, dialyzed on TE buffer and analyzed by
qPCR or massive sequencing.
To isolate short nascent DNA strands, genomic DNA was isolated from
A. thaliana MM2d cells treated as described above, under RNase-free conditions.
Purified DNA was denatured by heating and size-fractionated in a seven-step
sucrose gradient (5–20% (w/v)) by centrifugation at 102,300g in a Beckman
SW-40Ti rotor for 20 h at 20 °C (ref. 29). Fractions (1 ml) were collected and aliquots
were analyzed by electrophoresis in an alkaline agarose gel to monitor size frac-
tionation. Fractions containing replication intermediates (300–2,000 nucleotides
in size) were subjected to polynucleotide kinase treatment and λ-exonuclease
digestion, which degrades contaminating random sheared DNA and leaves
replication intermediates protected by a 5 RNA primer
28
. The relative abundance of
nascent DNA strands around putative origins was monitored by qPCR.
Library preparation for Illumina sequencing of BrdU DNA. DNA libraries
for both BrdU DNA and LL DNA were generated and sequenced on Genome
Analyzer II according to the manufacturer’s instructions (Illumina).
Quantitative real-time PCR. qPCR was carried out with a LightCycler Real-Time
PCR System (Roche) using SYBR Green PCR mix and following the manufac-
turer’s instructions. All qPCR reactions were carried out at least in duplicate and
analyses were carried out using the commercial software. Oligonucleotides used
for fragment amplification are listed in Supplementary Table 2.
Data processing and analysis. Sequenced reads were based-called using the
standard Illumina software. The reads were trimmed down to 50-mer bases
from the 3 end and then mapped to the A. thaliana genome using SeqMap
54
.
Uniquely mapping reads with mismatches up to 3 bp were used for the analysis,
resulting in 3,849,549 BrdU reads and 9,799,171 unlabeled DNA sequences, after
collapsing identical reads. The reads were extended so that the data represent
the actual DNA fragments of the libraries (130 bp, determined from distribution
of DNA fragments in the library). For all the analyses, identical reads were col-
lapsed into single reads, and each data set was normalized to the total number
of uniquely mapping reads. BrdU-positive regions were defined using MACS
55
,
with the unlabeled DNA sample as a control. A Poisson distribution P-value
cutoff of 10
−6
, calculated from the local λ value, was applied. Then, regions
separated by <10 kb were combined, a restrictive criterion supported by other
origin analysis
42,56
.
The CDC6 and ORC1 ChIP data were quantile-normalized to genomic DNA
using Affymetrix Tiling Analysis Software (TAS). Intensity peaks were searched
using the TileMap algorithm
57
with hidden Markov model for combining
neighboring probes (posterior probability cutoffs of 0.5). Histone modification
data were quantile normalized to unmodified H3 ChIP data. Each data set was
then normalized so that the mean signal across all probes in the genome was
zero. The Affymetrix Integrated Genome Browser (IGB) was used by applying
thresholds as described
31
.
Enrichment of ChIP signals at BrdU midpoints was assessed by first calculat-
ing the average scores of probes within ±300 bp of BrdU midpoint of all origin
regions and scores in the same number of randomly generated probes in regions
flanking the midpoints by 5–10 kb. Then, significance of differences was calcu-
lated by Wilcoxon rank-sum test (two-sided P-values). The H4K5ac data were
analyzed as described
21,31,50,51
.
Illustrations were generated using Adobe Illustrator CS2 and Adobe
Photoshop CS3.
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Arabidopsis. PLoS Biol. 5, e129 (2007).
51. Zhang, X. et al. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27
trimethylation. Nat. Struct. Mol. Biol. 14, 869–871 (2007).
52. Menges, M., Hennig, L., Gruissem, W. & Murray, J.A. Cell cycle-regulated gene
expression in Arabidopsis. J. Biol. Chem. 277, 41987–42002 (2002).
53. Soni, R., Carmichael, J.P., Shah, Z.H. & Murray, J.A. A family of cyclin D homologs
from plants differentially controlled by growth regulators and containing the
conserved retinoblastoma protein interaction motif. Plant Cell 7, 85–103 (1995).
54. Jiang, H. & Wong, W.H. SeqMap: mapping massive amount of oligonucleotides to
the genome. Bioinformatics 24, 2395–2396 (2008).
55. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137
(2008).
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Page 7
    • "Duplicated and triplicated blocks could therefore, have different origins. To address this question, we asked whether breakpoint junctions of the two different copy number states display differential association to various genomic and chromatin features such as genes and repeated elements (Lamesch et al., 2012), DNA replication origins (Costas et al., 2011), DNase I hypersensitive sites (DHS) (Zhang et al., 2012) and nine non-overlapping chromatin states that partition the Arabidopsis genome (Sequeira-Mendes et al., 2014) (Supplementary file 5). When analyzing windows of 1000 bp centered around the breakpoints of duplicated blocks, we observed an enrichment in genic DNA (from 53% background level to 70%, p < 0.01,Figure 5D,F). "
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    Full-text · Article · May 2015 · eLife Sciences
    • "We frequently observed QC divisions in plants treated overnight with TSA (Figures 7A to 7C), whereas QC divisions are much rarer in untreated plants. Furthermore, we observed that treatment with TSA induced ectopic expression of H2A.Z in QC cells (Figures 7D and 7E); this histone variant has been shown to be associated with replication activity (Costas et al., 2011) and is absent from QCs (Figure 7D). We also showed that this H2A.Z variant is mainly expressed in meristematic tissue (SupplementalFigure 10). "
    [Show abstract] [Hide abstract] ABSTRACT: The mechanism whereby the same genome can give rise to different cell types with different gene expression profiles is a fundamental problem in biology. Chromatin organization and dynamics have been shown to vary with altered gene expression in different cultured animal cell types, but there is little evidence yet from whole organisms linking chromatin dynamics with development. Here, we used both fluorescence recovery after photobleaching and two-photon photoactivation to show that in stem cells from Arabidopsis thaliana roots the mobility of the core histone H2B, as judged by exchange dynamics, is lower than in the surrounding cells of the meristem. However, as cells progress from meristematic to fully differentiated, core histones again become less mobile and more strongly bound to chromatin. We show that these transitions are largely mediated by changes in histone acetylation. We further show that altering histone acetylation levels, either in a mutant or by drug treatment, alters both the histone mobility and markers of development and differentiation. We propose that plant stem cells have relatively inactive chromatin, but they keep the potential to divide and differentiate into more dynamic states, and that these states are at least in part determined by histone acetylation levels. © 2014 American Society of Plant Biologists. All rights reserved.
    Full-text · Article · Dec 2014 · The Plant Cell
    • "Published ChIP-seq and ChIP-chip data (Zhang et al. 2009; Costas et al. 2011; Roudier et al. 2011; Luo et al. 2012; Park et al. 2012; Stroud et al. 2012) were originally mapped to the TAIR8 version of the A. thaliana reference genome. For ChIP-seq data, 50-bp fragments were retrieved from the TAIR8 genome and mapped to TAIR10. "
    [Show abstract] [Hide abstract] ABSTRACT: The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks, and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.
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