Genome-Scale Analysis of Metazoan Replication Origins ... · Title: Genome-Scale Analysis of...
Transcript of Genome-Scale Analysis of Metazoan Replication Origins ... · Title: Genome-Scale Analysis of...
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Submitted on 27 Oct 2011
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Genome-Scale Analysis of Metazoan Replication OriginsReveals their Organization in Specific but Flexible Sites
Defined by Conserved FeaturesChristelle Cayrou, Philippe Coulombe, Alice Vigneron, Slavica Stanojcic,
Olivier Ganier, Isabelle Peiffer, Eric Rivals, Aurore Puy, SabineLaurent-Chabalier, Romain Desprat, et al.
To cite this version:Christelle Cayrou, Philippe Coulombe, Alice Vigneron, Slavica Stanojcic, Olivier Ganier, et al..Genome-Scale Analysis of Metazoan Replication Origins Reveals their Organization in Specific butFlexible Sites Defined by Conserved Features. Genome Research, Cold Spring Harbor LaboratoryPress, 2011, 21 (9), pp.1438-1449. �10.1101/gr.121830.111�. �lirmm-00631491�
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Supplementary Figure1
Genes
D
replicate 1
replicate 2
replicate 3
replicate 4
200 kb
Asynchronous cells - total DNA
Mitotic cells - total DNA
R2=0.79
data microarray replicate 1
data
mic
roar
r ay
repl
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P19 cells
Kc cells200 kb
Geneseplicate 1
eplicate 2
itotic cells - ‘’Nascent Strands’’
data microarray replicate 1
data
mic
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ray
repl
icat
e 2
combination of four replicatesCGI
F
chr11position
Nascent strands(ES cells)
96.080.000 96.100.000 96.120.000 96.140.000 96.160.000 96.180.0000
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Enr ic
hmen
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qPCR of Nascent Strands G
Myc gene
Enric
hme n
t
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chr15position 61.808.000 61.812.000 61.816.000 61.820.000 61.824.000
qPCR of Nascent Strands
GeneTss Intron Exon
R2=0.78
A
Genome chr 11
Rep
licat
ion
tim
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(lo
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Genome chr 11
Tran
scri
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on
(a.u
.)
C
E
P19 cells
Kc cells
Log2
-rat
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chr11
M
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r
Log2
-rat
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Genes
chr3R
Log2
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Author manuscript, published in "Genome Research 21, 9 (2011) 1438-1449" DOI : 10.1101/gr.121830.111
ES cells
P19 cells
ES cells
P19 cells P19 cells P19 cells
ES cells
B
chr2R
chr3L
chr3R chrX
C
GeneMicroarray
(Log2-ratio)
qPCR(fold enrichment)
Supplementary Figure 2
A
0
4
8
12
16
20
Asynchronous Drosophila cells
chr2L position
Enric
hmen
t qPCR of Nascent Strand
21.400.000 21.404.000 21.408.000
Histone genes
locus 1 locus 2
Microarray(Log2-ratio)
qPCR(fold enrichment)
Gene
Microarray(Log2-ratio)
NoGene
GeneMicroarray
(Log2-ratio)
qPCR(fold enrichment)
GeneMicroarray
(Log2-ratio)
qPCR(fold enrichment)
Mouse cells
Drosophila cellschr2L
lirm
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A
B
Supplementary Figure 3
0.002
0.022
0.042
0.062
0.082
0.102
0.122
0.142
0.162
0.182 ChIP ORC2Nascent strand
0
20
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Nas
cent
Stra
ndEn
rich
men
t(a
.u.)
ChIP
ORC
2(%
i npu
t)
Myc gene
P19 cells - Nascent strands
P19 cells - ORC2 sites
Log2
-rat
io
Genes
CGI
Myc
lirm
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B
Supplementary Figure 4
com
mon
orig
ins
(% o
f tot
al o
rigin
s)
40%
45%
50%
55%
60%
65%
70%
P19 MEF ES MEF P19 ES
p-value= 1.187e-11
*p-value = 7.213e-05
*
p-value = 0.1634ns.
vs ES vs P19 vs MEF
ES P19
MEF
23 32
29
22 18
15
1313
12
42 37
44
lirm
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A
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intergenic37%intragenic
63%
Mouse
intragenic randomized origins57%
*intergenic
33%intragenic67%
Drosophila
intragenic randomized origins62%
0
10
20
30
40
50
60 Datarandomized origins
0
10
20
30
40
50
60 Datarandomized origins
*
*
*
*
Mouse P19 cells Mouse MEF cells
Orig
in d
istr
ibut
ion
(%)
Ori g
in d
ist r
ibut
ion
(%)
promoter exon intron promoter exon intron
Supplementary Figure 5
*
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Supplementary Figure 6
TSS TSSTSS TSSA B C D
E F
0200400600800
10001200140016001800
-5000 -3000 -1000 1000 3000 5000
P19 cells - total TSS
0
500
1000
1500
2000
2500
-5000 -3000 -1000 1000 3000 5000
MEF cells - total TSS
0
500
1000
1500
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2500
-5000 -3000 -1000 1000 3000 5000
MEF cells - with CGIMEF cells - without CGI
0200400600800
10001200140016001800
-5000 -3000 -1000 1000 3000 5000
P19 cells - TSS with CGIP19 cells - TSS without CGI
CGI
0500
1000150020002500300035004000
-5000 -3000 -1000 1000 3000 5000
Distance from CGI center (bp)
MEF cells total CGI
origins CGI
31%
73%
CGI
0
500
1000
1500
2000
2500
3000
-5000 -3000 -1000 1000 3000 5000
Distance from CGI center (bp)
P19 cells total CGI
origins CGI
22%
58%
NS
Sign
al s
tren
gth
NS
Sign
al s
tren
gth
NS
Sign
al s
tren
gth
NS
Sign
al s
tren
gth
NS
Sign
al s
tren
gth
NS
Sign
al s
tren
gth
Distance from TSS (bp) Distance from TSS (bp) Distance from TSS (bp) Distance from TSS (bp)
TSSTSS
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P19
MEF
Supplementary Figure 7
76.8%
76.9%
Bimodal TSS
9.1%
10.5%
5’ Unimodal TSS
9.9%
8.3%
3’ Unimodal TSS
4.2%
4.2%
Centered TSSNo signal
-
-
Nascent strandslog2-ratio
Genes
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Supplementary Figure 8lir
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-006
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1, v
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Supplementary Figure 9
Mouse ES cells Drosophila Kc cells
Random Ori firing Random Ori firing
Increasing Ori efficiency
Flexible replicon
A B
Increasing Ori efficiency
0
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0 150 300 450 >600
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0 150 300 450 >600
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0 150 300 450 >600
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0 75 150 225 >375
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0 75 150 225 >375
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0 75 150 225 >375
DNA Combing dataDNA Combing dataOris from model Oris from model
Flexible replicon
Inter-origin distances (kb) Inter-origin distances (kb)
% to
tal e
vent
s
% to
tal e
vent
s
% to
tal e
vent
s
% to
tal e
vent
s
% to
tal e
vent
s
% to
tal e
vent
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lirm
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