1. Undifferentiated Differentiated (4 d) Supplemental Figure S1

2. Supplemental Figure S2

3. TRE GC box Supplemental Figure S3

4. Supplemental Figure 4 Pst1 Sma1 Xho1 Spe1 ApaL1 a/b f/g a/c a/d a/e f/h f/i Mock 0 2 4 6 8 Mock Diff. (d) B N5 N4 N3 N2 N1 XhoIPstISmaIApaI PstI SpeI ApaLI abcde fghi PstI ApaI A N5N4N3N2N1 8 d 0 d

5. d e f g h i j k a b c l m n o p q B N5 N4 N3 N2 N1 N-1 H 2 O 0 2 4 6 8 Diff. (d) Supplemental Figure S5

6. GeneSense sequence (5'-3')Antisense sequence (5'-3') Crabp1CTT CAA GGT CGG AGA GGGGA ACA AGC TGG CCA CC Nrip1AAC ACG AGC TAT AAG AATCACAA CTG AAG AAG AGT GAC TRaGAA CAG AAG CCA AGC AAG GTGGAC ACA GCA GCT GTC ATA C Table S1. Primer pairs for RT-PCR PrimerSequence (5'-3')RegionLength (bp) aCGA GGA AAG TAA TCT GCT TAG G (S) TRE107 bGCT CGA GGT CCC CAA AGG TCA CTT TTC (AS) cTAC CCT AGC GAC TCA AGG CGC TTG (S) GC boxes136 dTGG 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.

7. PrimerSequence (5'-3')Primer pairLength (bp)Target RE site aGGG CAG AAG ACC AAT TGC AG (S) bCCA AAG GTC ACT TTT CC (AS)a/b383Positive control cATC AAC GCC AGA GCC CAG AG (AS)a/c586XhoI dCAG GTT CAA ACG GGT GCT GG (AS)a/d816PstI eTTA GAG TGG CGG GAA AGG CCC (AS)a/e887SmaI fTTG CTT GTT CCG TCC CTT AGG C (S) gCAC TAG CCG GTC GAA TTT G (AS)f/g241Positive control hACG AGG GGT GAG CCC GAC TC (AS)f/h563SpeI iCTT GAG TCG CTA GGG TAG (AS)f/i655ApaLI Table S3. PCR primers for restriction enzyme (RE) accessibility test in Supplemental Figure S2 S and AS represent for sense and antisense sequence, respectively.

8. FragmentSense (5'-3')Antisense (5'-3') Length (bp) aGGC CTA TTT TCA CAG GGA AGA CTG GCCA AAG GTC ACT TTT CC157 bCGA GGA AAG TAA TCT GCT TAG GGCT CGA GGT CCC CAA AGG TCA CTT TTC107 cTGT CAT GAG GAG TGG GCA AGCCTC CAT ATC AGC CGT TGA CC92 d GAA AAG TGA CCT TTG GGG ACC TCG AGCACA CAG GTC CCT GTG CCT TAC CAG C180 eAGA GGC TGC AAG GAA ATG TTG AGATC AAC GCC AGA GCC CAG AG95 fAGA GGC TGC AAG GAA ATG TTG AGCAA GAA AGC CTA GCT CC137 gTTG CTT GTT CCG TCC CTT AGG CCAG GTT CAA ACG GGT GCT GG115 hGCA TGA GAG GCT TGG TTT CCTTA GAG TGG CGG GAA AGG CCC108 iGGA TAA GCA AGG GTA GGG GCCAC TAG CCG GTC GAA TTT G98 jGGA TAA GCA AGG GTA GGG GCTAG TAG TAA GGC CAT AGG C158 kTGG AAA GAA AGT GGC TTC CAT GCGGT AGG AGA GGG TTT AAT GAA GC164 lTGA ATC CCC ACT ACC TAGCAC CAC GCC GCC CAC ATT CTG107 mTGA ATC CCC ACT ACC TAGGCC ACT AGT GAT GCA ACT TGG154 nGCT GAG AAG ATG AGG AAT GGCTT GAG TCG CTA GGG TAG153 oAGT CGG GCT CAC CCC TCG TGGCG TTG CAG AGA GAC TGG CGT TCT GCG CCC148 pTAC CCT AGC GAC TCA AGG CGC TTGTGG CAG TGG TGT TGG CTG TAG CG136 qTCT CTC TGC AAC GCA GCG TGCGT CGA AAT TCT CGC TGC TG145 Table S4. PCR primers for mononucleosome survey in Supplemental Figure S3