Undifferentiated Differentiated (4 d)

Supplemental Figure S1

0

20

40

60

80

100

120

0 6 12

T3 (h)

Relative expression level of

Nrip1

w t/TR MEF

Nrip/TR MEF

Supplemental Figure S2

0

20

40

60

80

100

0 4 8

Diff. (d)

Relative abundance

Tra

PCAF

GRIP1

0

20

40

60

80

100

0 4 8

Diff. (d)

Relative abundance

Tra

PCAF

GRIP1

TRE

GC box

Supplemental Figure S3

Supplemental Figure 4

Pst1

Sma1

Xho1

Spe1

ApaL1

a/b

f/g

a/c

a/d

a/e

f/h

f/i

Moc

k 0 2 4 6 8 0 2 4 6 8

Moc

k

Diff. (d) Diff. (d)

B

N5

N4

N3

N2

N1

XhoI PstI SmaIApaI

PstI SpeI ApaLI

a b c d e

f g h i

PstI

ApaI

A

N5 N4 N3 N2 N1

8 d

0 d

d

e

f

g

h

i

j

k

a

b

cl

m

n

o

p

q

B

N5

N4

N3

N2

N1

N-1

H2O 0 2 4 6 8 H2O 0 2 4 6 8 Diff. (d)

Diff. (days)

b

d

ef

gh

i

j

klm

on

p

a

c

-1.0 kb + 1-0.5 kb

TRE GC boxes

XhoI PstI SmaI SpeI ApaLI

A

q

86420

N1N2N3N4N5 N-1

Supplemental Figure S5

Gene Sense sequence (5'-3') Antisense sequence (5'-3')

Crabp1 CTT CAA GGT CGG AGA GG GGA ACA AGC TGG CCA CC

Nrip1 AAC ACG AGC TAT AAG AATCA CAA CTG AAG AAG AGT GAC

TRa GAA CAG AAG CCA AGC AAG GTG GAC ACA GCA GCT GTC ATA C

Table S1. Primer pairs for RT-PCR

Primer Sequence (5'-3') Region Length (bp)

a CGA GGA AAG TAA TCT GCT TAG G (S)

TRE 107b GCT CGA GGT CCC CAA AGG TCA CTT TTC (AS)

c TAC CCT AGC GAC TCA AGG CGC TTG (S)

GC boxes 136d TGG CAG TGG TGT TGG CTG TAG CG (AS)

Table S2. PCR primers for ChIP analysis

S and AS represent for sense and antisense sequence, respectively.

Primer Sequence (5'-3') Primer pair Length (bp) Target RE site

a GGG CAG AAG ACC AAT TGC AG (S)

b CCA AAG GTC ACT TTT CC (AS) a/b 383 Positive control

c ATC AAC GCC AGA GCC CAG AG (AS) a/c 586 XhoI

d CAG GTT CAA ACG GGT GCT GG (AS) a/d 816 PstI

e TTA GAG TGG CGG GAA AGG CCC (AS) a/e 887 SmaI

f TTG CTT GTT CCG TCC CTT AGG C (S)

g CAC TAG CCG GTC GAA TTT G (AS) f/g 241 Positive control

h ACG AGG GGT GAG CCC GAC TC (AS) f/h 563 SpeI

i CTT GAG TCG CTA GGG TAG (AS) f/i 655 ApaLI

Table S3. PCR primers for restriction enzyme (RE) accessibility test in Supplemental Figure S2

S and AS represent for sense and antisense sequence, respectively.

Fragment Sense (5'-3') Antisense (5'-3')Length

(bp)

a GGC CTA TTT TCA CAG GGA AGA CTG G CCA AAG GTC ACT TTT CC 157

b CGA GGA AAG TAA TCT GCT TAG G GCT CGA GGT CCC CAA AGG TCA CTT TTC 107

c TGT CAT GAG GAG TGG GCA AGC CTC CAT ATC AGC CGT TGA CC 92

dGAA AAG TGA CCT TTG GGG ACC TCG AGC ACA CAG GTC CCT GTG CCT TAC CAG C 180

e AGA GGC TGC AAG GAA ATG TTG AG ATC AAC GCC AGA GCC CAG AG 95

f AGA GGC TGC AAG GAA ATG TTG AG CAA GAA AGC CTA GCT CC 137

g TTG CTT GTT CCG TCC CTT AGG C CAG GTT CAA ACG GGT GCT GG 115

h GCA TGA GAG GCT TGG TTT CC TTA GAG TGG CGG GAA AGG CCC 108

i GGA TAA GCA AGG GTA GGG GC CAC TAG CCG GTC GAA TTT G 98

j GGA TAA GCA AGG GTA GGG GC TAG TAG TAA GGC CAT AGG C 158

k TGG AAA GAA AGT GGC TTC CAT GC GGT AGG AGA GGG TTT AAT GAA GC 164

l TGA ATC CCC ACT ACC TAG CAC CAC GCC GCC CAC ATT CTG 107

m TGA ATC CCC ACT ACC TAG GCC ACT AGT GAT GCA ACT TGG 154

n GCT GAG AAG ATG AGG AAT GG CTT GAG TCG CTA GGG TAG 153

o AGT CGG GCT CAC CCC TCG TG GCG TTG CAG AGA GAC TGG CGT TCT GCG CCC 148

p TAC CCT AGC GAC TCA AGG CGC TTG TGG CAG TGG TGT TGG CTG TAG CG 136

q TCT CTC TGC AAC GCA GCG TG CGT CGA AAT TCT CGC TGC TG 145

Table S4. PCR primers for mononucleosome survey in Supplemental Figure S3