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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�

B

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

ica t

e 2

P19 cells

Kc cells200 kb

Geneseplicate 1

eplicate 2

itotic cells - ‘’Nascent Strands’’

data microarray replicate 1

data

mic

roar

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

50

100

150

200

250

Enr ic

hmen

t

qPCR of Nascent Strands G

Myc gene

Enric

hme n

t

0

20

40

60

80

100

120

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

ing

(lo

g2-

rati

o)

Genome chr 11

Tran

scri

pti

on

(a.u

.)

C

E

P19 cells

Kc cells

Log2

-rat

io

chr11

M

r

r

Log2

-rat

io

Genes

chr3R

Log2

-rat

io

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m-0

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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

40

60

80

100

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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A

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

m-0

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A

B

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

2000

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

lirm

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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

mm

-006

3149

1, v

ersi

on 1

- 12

Oct

201

1

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

5

10

15

20

0 150 300 450 >600

0

5

10

15

20

0 150 300 450 >600

0

5

10

15

20

0 150 300 450 >600

0

5

10

15

20

25

30

0 75 150 225 >375

0

5

10

15

20

25

30

0 75 150 225 >375

0

5

10

15

20

25

30

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

slirm

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