0 25 2 10 215

0

25

210

215

Human embryonicstem cells

Whole genome arrays4.6 million features

Scatter plot(ChIP / reference)

ChIP

a-Pol IIa-Suz12

53130000 5314000

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Enric

hmen

t (IP

/WCE

)

SMCX

Chromosomal position (bp)53135000

2

6

0

4

Promoters bound byRNA polymerase II or Suz12

b

a

Figure 1. Genome-wide ChIP-Chip in human embryonic stem cellsFo

ld e

nrich

men

t

123125000 123090000Chromosomal position

1

3

5

7

TOP1(topoisomerase I)

EIF4G2(translation initiation factor 4)

CCNA2(cyclinA2)

9

11

39079000 39114000Chromosomal position

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enr

ichm

ent

1

3

5

7

9

11

10805000 10771000Chromosomal position

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enr

ichm

ent

1

3

5

7

9

11

c

81760000 81710000Chromosomal position

15513000 15468000Chromosomal position

MEOX2(mesenchyme homeo box 2)

BNC1(Basonuclin 1, zinc fingertranscription factor )

Fold

enr

ichm

ent

1

3

5

7

9

11

Fold

enr

ichm

ent

1

3

5

7

88130000 88080000Chromosomal position

GRID1(glutamate receptor,Ionotropic, delta 1)

1

5

9

13

17

Pol II30%

Neither

Both1.9%

Suz12 6.5%

d 35%30%

25%

20%

15%

10%

5%Frac

tion

of b

ound

pro

bes

-10 -8 -6 -4 -2 0 2 4 6 8 10Distance from nearest transcription start site (kb)

e

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enr

ichm

ent