Wang et al., Figure S8

Figure S8: Enrichment of sequence motifs and DNase I hypersensitivity around bound motif sites. Color indicates log2(enrichment); see Methods for definition of enrichment. The element in the i-th row and and j-th column indicates the log2(enrichment) of motif located in the j-th column in the bound regions vs. unbound regions of the motif located in the i-th row. The rows and columns are in alphabetical order by motif name. We also considered subsets of peaks for the TFs through which EP300 and HDAC2 may tether. For example, the PU.1–EP300 row in the GM12878 heatmap indicates the subset of SPI1 peaks that overlap by at least 1 bp with EP300 peaks in GM12878 cells, likewise the rows labeled with “–EP300” or “–HDAC2”. GM12878 A-Box AP-1 B-Box CREB-ext CREB CTCF EGR1 ELF1 ETS1 GABP MAX NFKB1 NF-Y NRF1 PAX5 POU2F2 PU.1 PU.1 – EP300 REST RFX5 RUNX1 SP1 SRF STAT1 TCF12 UA1 UA2 UA7 USF YY1 ZEB1 ZNF143-ext ZNF143 DNase SP1 YY1 UA1 UA2 UA7 SRF USF MAX AP-1 PU.1 NF-Y ELF1 ZEB1 ETS1 RFX5 PAX5 NRF1 CTCF MEF2 REST A-Box B-Box EGR1 CREB GABP TCF12 DNase STAT1 NFKB1 RUNX1 ZNF143 POU2F2 CREB-ext ZNF143-ext 250 Count 100 0 0 2 4 log2 (enrichment) A-Box AP-1 B-Box CEBPB CREB-ext CTCF EGR1 ELF1 ETS1 GABP GAT1-ext GA TA1 GFI1 MAX NFE2 NF-Y NR2C2 NRF1 PRDM1 PU.1 REST RFX5 K562 SP1 SRF ST AT1 ST AT2 TAL1 TBP UA1 UA11 UA6 UA2 UA3 UA4 UA5 UA7 USF v-JUN v-Maf YY1 ZNF143-ext ZNF143 ZNF263 ZNF281 Count DNase DNase ZNF281 ZNF263 ZNF143 ZNF143-ext YY1 v-Maf v-JUN USF U U U U U U U U TBP T S S SRF SP1 RFX5 REST PU.1 PRDM1 NRF1 NR2C2 NF-Y NFE2 MYC MAX GFI1 GATA1 –HDAC2 GATA1 GATA1-ext –EP300 GATA1-ext GABP ETS1 ELF1 EGR1 E2F4 CTCF CREB-ext CEBPB B-Box AP-1 A-Box AL1 T T A7 A5 A4 A3 A2 A6 A11 A1

0 200 500 A A T2 T1 -4 l o g -2 2 (enrichment)

0 2 4 AP-1 BARHL2 CREB CTCF EGR1 GABP MAX NF-Y NRF1 POU2F2 REST RFX5 RXRA

SOX2-OCT4 H1—hESC SP1 SRF TBP TCF12 TEAD1 UA2 UA7 UA9 USF v-JUN YY1 ZNF143-ext ZNF143 DNase Count DNase ZNF143 ZNF143-ext YY1 v-JUN USF UA9 –HDAC2 U U U TEAD1 –EP300 TEAD1 TCF12 TBP SRF SP1 S SOX2-OCT4 –HDAC2 S RXRA RFX5 REST POU2F2 NRF1 NF-Y MAX GABP EGR1 CTCF CREB BARHL2 AP-1 O O 0 100 250 A9 A7 A2 X2 X2-OCT4 -4 log2 (enrichment) -2 0 2 4 AP-1 BHLHE40 CEBPB CREB-ext CREB CTCF ELF1 ESRRA FOXA GABP HNF4 HSF1 MYC NFE2 NF-Y

NR2C2 HepG2 NRF1 REST RFX5 RXRA SP1 SREBF1 SRF TCF7L2 UA1 UA2 UA7 USF v-JUN v-Maf YY1 ZNF143-ext DNase

Count DNase ZNF143-ext YY1 v-Maf v-JUN USF U U U TCF7L2 SRF SREBF1 SP1 RXRA RFX5 REST NRF1 NR2C2 NF-Y NFE2 MYC HSF1 HNF4 –HDAC2 HNF4 GABP FOXA –EP300 F ESRRA ELF1 CTCF CREB CREB-ext CEBPB BHLHE40 AP-1 O A7 A2 A1

0 150 300 XA -4 lo -2 g 2

(enrich 0 m e 2 n t ) 4 B-Box RFX5 PRDM1 NR2C2 CEBPB v-JUN REST ZNF143-ext STAT1 YY1 MAX

A-Box HeLa—S3 MYC USF CREB UA2 CTCF NF-Y SP1 AP-1 GABP ELK4 UA1 E2F4 NRF1 Dnase

Count Dnase NRF1 E2F4 U ELK4 GABP AP-1 SP1 NF-Y CTCF U CREB USF MYC A-Box MAX YY1 S ZNF143-ext REST v-JUN CEBPB NR2C2 PRDM1 RFX5 B-Box T A1 A2

0 50 150 A T1 lo -2 g 2

(enrich 0 m e n 2 t )