Supplementary material
350 300 265 250 200 158 139 150
100 50 4 0 Biased Forward- Reverse- any orientation reverse (FR) forward (RF) orientation (FR+RF) Supplemental Figure S1. Biased-orientation of DNA motif sequences of transcription factors in
T cells. Total 265 of biased orientation of DNA binding motif sequences of transcription factors have been found to affect the expression level of putative transcriptional target genes in T cells of four people in common, whereas only one any orientation (i.e. without considering orientation) of DNA binding motif sequences have been found to affect the expression level.
1 Supplemental Figure S2. Pairs of biased orientation of DNA binding motif sequences of transcription factors enriched in upstream and downstream of genes. The number of genes having a pair of forward-reverse orientation of DNA motif sequences was counted using all pairs of the DNA motif sequences, and statistical tests (chi-square test) were conducted in monocytes and T cells.
Forward-reverse orientation in monocytes
ZNF93_2 ZNF93_1 ZNF92 ZNF90 ZNF836 ZNF716 ZNF709 ZNF695 ZNF676_2 ZNF676_1 ZNF675 ZNF670 ZNF660 ZNF648 ZNF646 ZNF623 ZNF573 ZNF521 ZNF460 ZNF366 ZNF33B ZNF317 ZNF316 ZNF28 ZNF274 ZNF263_2 ZNF263_1 ZNF219 ZNF214 ZNF148 ZNF143_2 ZNF143_1 ZIC3 ZIC1 ZFP30 ZBTB6 ZBTB33 ZBTB24 YY1 YBX1 XRCC4_2 XRCC4_1 XBP1 WT1 USF TP63 TP53 TFE3 TFAP2A TCF3_2 TCF3_1 TCF12 TBX5 TBP SULT1A2 STAT5B STAT5A_3 STAT5A_2 STAT5A_1 STAT4 STAT3_2 STAT3_1 STAT1_6 STAT1_5 STAT1_4 STAT1_3 STAT1_2 STAT1_1 SRF_2 SRF_1 SPI1_2 SPI1_1 SPEF1 SP1_2 SP1_1 SNTB1 SMC3_2 SMC3_1 SMARCC2_2 SMARCC2_1 SMAD2_SMAD3_SMAD4 SMAD2_2 SMAD2_1 SLC25A20 SIX5 SIRT6 SIN3A SETDB1 RXRA_VDR RUNX2 RREB1_3 RREB1_2 RREB1_1 RFTN1 REST_2 Score REST_1 RELA RAD21_3 RAD21_2 RAD21_1 PTF1A PROX1 40 PRDM9 PRDM15 PPARGC1A POU6F1 30 POU3F2 PLAGL1_2 PLAGL1_1 PITX3 20 Reverse PITX1 PHOX2B PAX8 PAX5 PARG_2 10 PARG_1 NR3C1 NR2F6 NR2F2 NR2C2 0 NR1I2 NKX2−5 NFYB NFKB2 NFKB1 NFIB NFE2 MYB_2 MYB_1 MLXIPL MINI20 MEF2A MAZ_3 MAZ_2 MAZ_1 MAX MAFA LBX2 KLF6 KLF5 KLF3 KLF14_2 KLF14_1 IRF7 IKZF1 HSF2 HOXC9 HOXC11 HOXB1 HOXA7 HOMEZ HNF4A_2 HNF4A_1 HMBOX1_2 HMBOX1_1 HIC1_2 HIC1_1 HES1 HENMT1 GTF3C2 GLIS2 GLI2 GLI1 GCM1_3 GCM1_2 GCM1_1 GATA6 GATA2 FUBP1 FOXO4 FOXN2_2 FOXN2_1 FOXA1 FOSB_2 FOSB_1 FOS_2 FOS_1 ETV4 ETS ESX1 ESR2 EN1 EIF5A2 EHF EGR2_4 EGR2_3 EGR2_2 EGR2_1 EBF E2F8 E2F5 E2F3 E2F_2 E2F_1 DNAAF2 DEC DBP CTCF_8 CTCF_7 CTCF_6 CTCF_5 CTCF_4 CTCF_3 CTCF_2 CTCF_1 CEBPZ_2 CEBPZ_1 CEBPG_2 CEBPG_1 BRF1_2 BRF1_1 BBX 5 − YY1 EBF EN1 ETS TBP BBX EHF USF DBP DEC WT1 GLI1 GLI2 IRF7 MAX SIX5 ZIC1 ZIC3 NFIB E2F3 E2F5 E2F8 KLF3 KLF5 KLF6 TP53 TP63 PAX5 PAX8 LBX2 TFE3 ETV4 TBX5 ESX1 HSF2 NFE2 XBP1 YBX1 ESR2 HES1 RELA NFYB MAFA IKZF1 PITX1 PITX3 SIRT6 NR1I2 GLIS2 STAT4 SIN3A E2F_1 E2F_2 ZFP30 SP1_1 SP1_2 GATA2 GATA6 TCF12 ZNF28 ZNF90 ZNF92 PTF1A SRF_1 SRF_2 ZBTB6 FOS_1 FOS_2 NR2F2 NR2F6 SPEF1 FOXA1 FUBP1 MAZ_1 MAZ_2 MAZ_3 MINI20 NFKB1 NFKB2 RFTN1 SNTB1 NR2C2 NR3C1 MYB_1 MYB_2 SPI1_1 SPI1_2 PROX1 FOXO4 HOXA7 HOXB1 MEF2A EIF5A2 RUNX2 HOXC9 HIC1_1 HIC1_2 PRDM9 STAT5B MLXIPL HOMEZ TCF3_1 TCF3_2 ZNF148 ZNF214 ZNF219 ZNF274 ZNF316 ZNF317 ZNF366 ZNF460 ZNF521 ZNF573 ZNF623 ZNF646 ZNF648 ZNF660 ZNF670 ZNF675 ZNF695 ZNF709 ZNF716 ZNF836 BRF1_1 BRF1_2 ZBTB24 ZBTB33 TFAP2A ZNF33B NKX2 CTCF_1 CTCF_2 CTCF_3 CTCF_4 CTCF_5 CTCF_6 CTCF_7 CTCF_8 REST_1 REST_2 PARG_1 PARG_2 GTF3C2 EGR2_1 EGR2_2 EGR2_3 EGR2_4 FOSB_1 FOSB_2 POU3F2 POU6F1 SETDB1 SMC3_1 SMC3_2 HOXC11 DNAAF2 STAT1_1 STAT1_2 STAT1_3 STAT1_4 STAT1_5 STAT1_6 STAT3_1 STAT3_2 PHOX2B GCM1_1 GCM1_2 GCM1_3 KLF14_1 KLF14_2 PRDM15 HENMT1 ZNF93_1 ZNF93_2 SULT1A2 RAD21_1 RAD21_2 RAD21_3 FOXN2_1 FOXN2_2 HNF4A_1 HNF4A_2 CEBPZ_1 CEBPZ_2 RREB1_1 RREB1_2 RREB1_3 XRCC4_1 XRCC4_2 SMAD2_1 SMAD2_2 CEBPG_1 CEBPG_2 STAT5A_1 STAT5A_2 STAT5A_3 ZNF143_1 ZNF143_2 ZNF263_1 ZNF263_2 ZNF676_1 ZNF676_2 SLC25A20 PLAGL1_1 PLAGL1_2 HMBOX1_1 HMBOX1_2 PPARGC1A RXRA_VDR SMARCC2_1 SMARCC2_2 SMAD2_SMAD3_SMAD4 Forward
2 Reverse-forward orientation in monocytes
ZSCAN5B ZSCAN2_2 ZSCAN2_1 ZNF770 ZNF721 ZNF711 ZNF687 ZNF682 ZNF672 ZNF671 ZNF670 ZNF652 ZNF641 ZNF584 ZNF579 ZNF547 ZNF449 ZNF350 ZNF343 ZNF337 ZNF331 ZNF316 ZNF30_2 ZNF30_1 ZNF286B ZNF28 ZNF233 ZNF225 ZNF202 ZNF195 ZNF181 ZNF148 ZNF121 ZNF112 ZIC2 ZIC1 ZBTB7B ZBTB7A ZBTB2 ZBTB18_2 ZBTB18_1 WT1 USF1 TRIM28 TP53 THRB TFAP2E TFAP2B TFAP2A TEAD1 TCF7 TBP_3 TBP_2 TBP_1 STAT5B STAT5A STAT1 SRF_5 SRF_4 SRF_3 SRF_2 SRF_1 SPIC SPI1 SP8 SP4_2 SP4_1 SP3 SP2 SP1 SOX9_3 SOX9_2 SOX9_1 SOX2 SOX11 Score SMAD9 SMAD4_2 SMAD4_1 SMAD3_2 SMAD3_1 RXRB RXRA_2 RXRA_1 20 RFX5 RFX3 REST RBAK RAD21 PSMD9 15 PPARG POU5F1 POU3F2 POU2F2 POLR3A PLAG1
Forward 10 PBX3 PBX1 PAX6 PAX5_2 PAX5_1 PAX3 5 PAX1 PARP1 OBOX2 NR5A2 NR2F1 NKX3−1 0 NFY NFKB2 NFE2L3 NFE2L2 NFATC1 NANOG MZF1 MYOG MYF6 MYEF2 MYC_MAX MSX2 MAFK LHX4 KLF16 ISL1 IRX2 IRF9 IRF8 IRF4_3 IRF4_2 IRF4_1 IRF3_2 IRF3_1 HSF2 HSF1_2 HSF1_1 HOXD1 HNF1B HAND1_TCF3 GTF2I GABPB1_GABPB2 GABPA FOXR1 FOXP2 FOX FLI1 ETV7 ETV6 ETV5 ETV3 ETV2 ETS2_2 ETS2_1 EP300 ELF5 ELF2 EBF1 E2F3 E2F2 DOBOX5 DNAAF2 CTCF_3 CTCF_2 CTCF_1 CREM CEBPZ CEBPB CDX2 CD59 BDP1 BCL6 BCL3 BCL11A_2 BCL11A_1 ATF3_2 ATF3_1 ATF2_ATF4 ASCL2 ALX1 AHR 1 − SP1 SP2 SP3 SP8 FOX FLI1 NFY ISL1 AHR WT1 IRF8 IRF9 ZIC1 ZIC2 SPI1 IRX2 SPIC E2F2 E2F3 ELF2 ELF5 TP53 PAX1 PAX3 PAX6 ALX1 BCL3 BCL6 EBF1 ETV2 ETV3 ETV5 ETV6 ETV7 LHX4 TCF7 CD59 HSF2 PBX1 PBX3 RFX3 RFX5 USF1 MZF1 SOX2 BDP1 CDX2 MYF6 REST MSX2 RBAK THRB MAFK RXRB GTF2I STAT1 CREM KLF16 MYOG EP300 SP4_1 SP4_2 TBP_1 TBP_2 TBP_3 ZNF28 SRF_1 SRF_2 SRF_3 SRF_4 SRF_5 ZBTB2 PARP1 SOX11 NR2F1 ASCL2 PLAG1 FOXP2 NFKB2 NR5A2 RAD21 TEAD1 FOXR1 HNF1B IRF3_1 IRF3_2 IRF4_1 IRF4_2 IRF4_3 GABPA CEBPZ MYEF2 PPARG HOXD1 OBOX2 CEBPB ATF3_1 ATF3_2 PSMD9 SMAD9 STAT5A STAT5B PAX5_1 PAX5_2 TRIM28 ETS2_1 ETS2_2 ZNF112 ZNF121 ZNF148 ZNF181 ZNF195 ZNF202 ZNF225 ZNF233 ZNF316 ZNF331 ZNF337 ZNF343 ZNF350 ZNF449 ZNF547 ZNF579 ZNF584 ZNF641 ZNF652 ZNF670 ZNF671 ZNF672 ZNF682 ZNF687 ZNF711 ZNF721 ZNF770 NANOG HSF1_1 HSF1_2 NFE2L2 NFE2L3 NFATC1 TFAP2A TFAP2B TFAP2E SOX9_1 SOX9_2 SOX9_3 NKX3 CTCF_1 CTCF_2 CTCF_3 ZBTB7A ZBTB7B POU2F2 POU3F2 POU5F1 RXRA_1 RXRA_2 DNAAF2 POLR3A DOBOX5 ZNF30_1 ZNF30_2 ZNF286B SMAD3_1 SMAD3_2 SMAD4_1 SMAD4_2 ZSCAN5B ZBTB18_1 ZBTB18_2 BCL11A_1 BCL11A_2 MYC_MAX ZSCAN2_1 ZSCAN2_2 ATF2_ATF4 HAND1_TCF3 GABPB1_GABPB2 Reverse
3 Forward-reverse orientation in T cells
ZSCAN2 ZSCAN18 ZNF880 ZNF84_2 ZNF84_1 ZNF790 ZNF75A ZNF73 ZNF717 ZNF714 ZNF701 ZNF676 ZNF658B ZNF639 ZNF595 ZNF586 ZNF582 ZNF575 ZNF548 ZNF486 ZNF436 ZNF394 ZNF366 ZNF287 ZNF263_2 ZNF263_1 ZNF250 ZNF219 ZIC3 ZIC1 ZACN VAMP3 UF1H3BETA TRIM28 TP53_2 TP53_1 THRA TFCP2 TBX5 SRP9 SREBF1 SPZ1 SPI1_2 SPI1_1 SPDEF_2 SPDEF_1 SP1_4 SP1_3 SP1_2 SP1_1 SOX18_2 SOX18_1 SOAT1 SMC3_2 SMC3_1 SMARCC2 SMAD3 RREB1_2 RREB1_1 REST Score RARB RAD21_4 RAD21_3 RAD21_2 RAD21_1 60 POLR3A P50_P50 OTX2_3 OTX2_2 OTX2_1 NR3C1 NFYA 40 NFKB1_2 NFKB1_1 NFIA NEUROD1
Reverse MYOD1 MYF6 MYCN 20 MNX1 MAZ_2 MAZ_1 MAF LHX8 LHX6 KLF5 0 JUN JDP2_2 JDP2_1 IRF9 IRF HNF1B HMGA2_2 HMGA2_1 HEY1_2 HEY1_1 GLI1 GFI1B GCM1 GC GATA2_2 GATA2_1 FUBP1 FOXO3 FOXF2 FGF9 ETV3 EP300_3 EP300_2 EP300_1 ELF4 ELF3 ELF1 EHF EGR1 E2F6_4 E2F6_3 E2F6_2 E2F6_1 E2F4 E2F1_3 E2F1_2 E2F1_1 DUX1 DLX3 DEAF1 DDIT3_CEBPA CUX1 CTCF_6 CTCF_5 CTCF_4 CTCF_3 CTCF_2 CTCF_1 CEBPE BCL3_2 BCL3_1 BATF_2 BATF_1 BARX2 BACH1 ARID3A AHR_ARNT GC IRF JUN EHF MAF GLI1 IRF9 ZIC1 ZIC3 NFIA E2F4 ELF1 ELF3 ELF4 KLF5 DLX3 ETV3 LHX6 LHX8 SPZ1 TBX5 FGF9 NFYA SRP9 CUX1 DUX1 MYF6 REST ZACN THRA EGR1 MNX1 RARB GCM1 GFI1B MYCN SP1_1 SP1_2 SP1_3 SP1_4 ZNF73 SOAT1 FOXF2 TFCP2 DEAF1 FUBP1 MAZ_1 MAZ_2 BARX2 HNF1B NR3C1 SPI1_1 SPI1_2 BACH1 VAMP3 FOXO3 CEBPE SMAD3 MYOD1 E2F1_1 E2F1_2 E2F1_3 E2F6_1 E2F6_2 E2F6_3 E2F6_4 TP53_1 TP53_2 BATF_1 BATF_2 TRIM28 JDP2_1 JDP2_2 ARID3A ZNF219 ZNF250 ZNF287 ZNF366 ZNF394 ZNF436 ZNF486 ZNF548 ZNF575 ZNF582 ZNF586 ZNF595 ZNF639 ZNF676 ZNF701 ZNF714 ZNF717 ZNF790 ZNF880 BCL3_1 BCL3_2 OTX2_1 OTX2_2 OTX2_3 HEY1_1 HEY1_2 ZNF75A CTCF_1 CTCF_2 CTCF_3 CTCF_4 CTCF_5 CTCF_6 SMC3_1 SMC3_2 SREBF1 POLR3A ZSCAN2 EP300_1 EP300_2 EP300_3 P50_P50 GATA2_1 GATA2_2 ZNF84_1 ZNF84_2 SOX18_1 SOX18_2 ZNF658B NFKB1_1 NFKB1_2 RAD21_1 RAD21_2 RAD21_3 RAD21_4 RREB1_1 RREB1_2 SPDEF_1 SPDEF_2 ZSCAN18 HMGA2_1 HMGA2_2 ZNF263_1 ZNF263_2 NEUROD1 SMARCC2 AHR_ARNT UF1H3BETA DDIT3_CEBPA Forward
4 Reverse-forward orientation in T cells
ZNF880 ZNF777 ZNF773 ZNF770 ZNF721 ZNF718 ZNF714 ZNF658 ZNF625 ZNF592 ZNF580 ZNF549 ZNF526 ZNF484 ZNF468 ZNF44 ZNF410 ZNF41 ZNF341 ZNF300 ZNF282 ZNF28 ZNF267 ZNF257 ZNF256 ZNF239 ZNF219 ZNF214 ZNF189 ZNF180 ZNF174 ZNF17 ZNF143 ZNF134 ZIC1 ZFP69B ZFP2 ZBTB7A ZBTB41 ZBTB4 ZBTB33 ZBTB18 YY2 YY1 THRB TEAD1 TCF12_2 TCF12_1 TAL1 SRF_2 SRF_1 SPIC SPI1 SP2_2 SP2_1 SOX2 SMARC SIX6 RUNX2_2 RUNX2_1 RREB1 RORA RFX1_2 RFX1_1 REST RELB RELA REL Score RARA RAD21 PSMD9 PPARGC1A 20 PPARD POU2F2 PITX3 PBX3_2 PBX3_1 PARP1 NRG2 15 NR4A1 NR3C1 NKX2−5_2 NKX2−5_1 NKX2−4 NKX2−1 10 NFYA Forward NFY NFKB1_3 NFKB1_2 NFKB1_1 NFE2L2 5 MYOG MYCN MXI1 MTF1_2 MTF1_1 MLX 0 MEIS1 LHX6 LHX4 LBX1 KLF8 KLF6 KLF16 KLF13 IRF8 IRF5 IRF HSF1 HOXB6 HOXA10 HLTF_2 HLTF_1 HAND1 GTF2I GFI1 GATA4 GATA1_2 GATA1_1 GABPA FOXP3 FOXO3 FOXN4 FOXJ3_2 FOXJ3_1 FOXG1 FOXA2 FOXA1 FOXA FOS_2 FOS_1 ETV6 ETV3 ETV1 ETS2 ETS1_2 ETS1_1 ESR1 EP300 ELF3_3 ELF3_2 ELF3_1 EHF_2 EHF_1 EGR1 E2F1 DMRTA2 DBP_2 DBP_1 CTCF_4 CTCF_3 CTCF_2 CTCF_1 CREB3 CEBPA CAP1 BTD BCLAF1 BCL11B BCL ALX1 1 4 − − IRF 5_1 5_2 YY1 YY2 BCL REL BTD NFY MLX IRF5 IRF8 ZIC1 SIX6 SPI1 GFI1 − − TAL1 MXI1 SPIC E2F1 KLF6 KLF8 ALX1 LBX1 ZFP2 ETS2 ETV1 ETV3 ETV6 LHX4 LHX6 HSF1 NFYA SOX2 CAP1 ESR1 RELA RELB FOXA REST EGR1 THRB NRG2 PITX3 RARA GTF2I RORA KLF13 KLF16 MYCN MYOG EP300 MEIS1 SP2_1 SP2_2 GATA4 ZNF17 ZNF28 ZNF41 ZNF44 EHF_1 EHF_2 SRF_1 SRF_2 ZBTB4 PARP1 DBP_1 DBP_2 FOS_1 FOS_2 FOXA1 FOXA2 FOXP3 NR4A1 RAD21 TEAD1 CEBPA FOXN4 NR3C1 GABPA PPARD FOXG1 FOXO3 HOXB6 CREB3 RREB1 HAND1 PSMD9 ELF3_1 ELF3_2 ELF3_3 HLTF_1 HLTF_2 ETS1_1 ETS1_2 SMARC ZNF134 ZNF143 ZNF174 ZNF180 ZNF189 ZNF214 ZNF219 ZNF239 ZNF256 ZNF257 ZNF267 ZNF282 ZNF300 ZNF341 ZNF410 ZNF468 ZNF484 ZNF526 ZNF549 ZNF580 ZNF592 ZNF625 ZNF658 ZNF714 ZNF718 ZNF721 ZNF770 ZNF773 ZNF777 ZNF880 NFE2L2 PBX3_1 PBX3_2 RFX1_1 RFX1_2 ZBTB18 ZBTB33 ZBTB41 ZFP69B MTF1_1 MTF1_2 BCL11B NKX2 NKX2 BCLAF1 CTCF_1 CTCF_2 CTCF_3 CTCF_4 ZBTB7A HOXA10 POU2F2 DMRTA2 GATA1_1 GATA1_2 FOXJ3_1 FOXJ3_2 TCF12_1 TCF12_2 NFKB1_1 NFKB1_2 NFKB1_3 RUNX2_1 RUNX2_2 NKX2 NKX2 PPARGC1A Reverse
5 Forward-reverse orientation in monocytes using H3K27ac histone modification marks
ZNF99 ZNF91 ZNF836 ZNF808 ZNF775 ZNF76 ZNF716 ZNF709 ZNF676_2 ZNF676_1 ZNF675 ZNF671 ZNF660 ZNF658B ZNF658 ZNF648_2 ZNF648_1 ZNF623 ZNF579 ZNF560 ZNF555 ZNF521 ZNF460 ZNF426 ZNF391 ZNF316 ZNF304 ZNF274 ZNF236 ZNF224 ZNF219 ZNF177 ZNF148 ZNF143_2 ZNF143_1 ZNF131 ZIC1 ZFP92 ZBTB6 ZBTB33 YY1 YBX1 WT1 USF TP63 TP53 THRA_2 THRA_1 THAP1 TFCP2 TFAP2C TFAP2A TEF TCF3 TBXT TBX5 TBX20 TBP SULT1A2 STAT5A_3 STAT5A_2 STAT5A_1 STAT4 STAT3_2 STAT3_1 STAT1_3 STAT1_2 STAT1_1 SRF_2 SRF_1 SREBF2 SPI1 Score SP2 SP1 SNAI3 SNAI1 SMC3_2 SMC3_1 40 SMAD2 SMAD SIX5 SIN3A_2 SIN3A_1 SIGMAR1 30 RXRB RREB1 REST_2 REST_1 RAD21 PTF1A 20 PPARGC1A Reverse POU1F1 PLAGL1 PKNOX1 PITX3 PITX1 10 PBX2 NR5A2_2 NR5A2_1 NR2F2 NR2C2 NFE2 MINI20 0 MECP2 MAZ LHX2 KLF7 KLF5 KLF14 KLF1 JUND ITGAL IRF IKZF1_3 IKZF1_2 IKZF1_1 HNF4A_2 HNF4A_1 HNF1B HINFP HIF1A HIC1_2 HIC1_1 HEY2 HES1 HAND1 GLI2 GLI1 GCM1_3 GCM1_2 GCM1_1 FUBP1 FOXA1 FOSB FOS_2 FOS_1 ETV4_2 ETV4_1 ETV3 ETS1 ETS ESR2 ESR1 EPAS1 ENO1 ELK4 ELF3 ELF1_2 ELF1_1 EIF5A2 EHF EGR4 EGR2_2 EGR2_1 EGR1 EBF E2F6 E2F DEC CTCF_6 CTCF_5 CTCF_4 CTCF_3 CTCF_2 CTCF_1 CHD2 CEBPB_2 CEBPB_1 CDC42EP3 BBX APEX1 IRF E2F SP1 SP2 TEF YY1 EBF ETS TBP EHF USF BBX DEC MAZ WT1 ZIC1 GLI1 GLI2 SIX5 SPI1 E2F6 ELF3 KLF1 KLF5 KLF7 TP53 TP63 ELK4 TCF3 ETS1 ETV3 LHX2 TBX5 NFE2 PBX2 TBXT YBX1 ESR1 ESR2 HES1 HEY2 JUND CHD2 EGR1 EGR4 ENO1 FOSB PITX1 PITX3 RXRB HIF1A STAT4 ITGAL SMAD SNAI1 SNAI3 KLF14 HINFP ZFP92 TBX20 ZNF76 ZNF91 ZNF99 EPAS1 PTF1A SRF_1 SRF_2 ZBTB6 NR2F2 TFCP2 FOS_1 FOS_2 FOXA1 FUBP1 MINI20 RAD21 THAP1 APEX1 HNF1B NR2C2 EIF5A2 RREB1 HAND1 HIC1_1 HIC1_2 MECP2 SMAD2 ELF1_1 ELF1_2 ETV4_1 ETV4_2 ZNF131 ZNF148 ZNF177 ZNF219 ZNF224 ZNF236 ZNF274 ZNF304 ZNF316 ZNF391 ZNF426 ZNF460 ZNF521 ZNF555 ZNF560 ZNF579 ZNF623 ZNF658 ZNF660 ZNF671 ZNF675 ZNF709 ZNF716 ZNF775 ZNF808 ZNF836 ZBTB33 TFAP2A PLAGL1 TFAP2C CTCF_1 CTCF_2 CTCF_3 CTCF_4 CTCF_5 CTCF_6 REST_1 REST_2 EGR2_1 EGR2_2 IKZF1_1 IKZF1_2 IKZF1_3 THRA_1 THRA_2 POU1F1 SMC3_1 SMC3_2 SREBF2 STAT1_1 STAT1_2 STAT1_3 STAT3_1 STAT3_2 PKNOX1 GCM1_1 GCM1_2 GCM1_3 SIN3A_1 SIN3A_2 SULT1A2 ZNF658B NR5A2_1 NR5A2_2 HNF4A_1 HNF4A_2 CEBPB_1 CEBPB_2 SIGMAR1 STAT5A_1 STAT5A_2 STAT5A_3 ZNF143_1 ZNF143_2 ZNF648_1 ZNF648_2 ZNF676_1 ZNF676_2 CDC42EP3 PPARGC1A Forward
6 Reverse-forward orientation in monocytes using H3K27ac histone modification marks
ZSCAN4 ZSCAN2_2 ZSCAN2_1 ZNF879 ZNF799 ZNF770 ZNF721 ZNF701 ZNF684 ZNF672 ZNF668 ZNF547 ZNF449 ZNF37A ZNF33B ZNF304 ZNF239 ZEB1 ZBTB33 ZBTB2 ZBTB18_2 ZBTB18_1 ZBED6 YY2 TRIM28 THRB_2 THRB_1 TFE3 TFAP2C TCF7L2 TBP STAT5B SRF_5 SRF_4 SRF_3 SRF_2 SRF_1 SREBF1 SP8 SP5 SP4_2 SP4_1 SP3 SP1_2 SP1_1 SOX9 SOX5 SOX2 SOX13 SOX12 SOX11 SMARCC2 SMAD4 SMAD3 RXRA_2 RXRA_1 RFX5 RFX3 RELA REL PPARG POU5F1 POU3F2 POU1F1 Score POLR3A PAX5 OBOX2 15 NR2F1 NR2C2 NKX3−1 NFY NFE2L3 NFE2L2 NANOG_2 NANOG_1 10 MYF6 MYEF2 MYC_MAX MSX2 MSC
Forward MGA MECOM MAML1_NOTCH4 5 MAML1_NOTCH3 MAML1_NOTCH2_2 MAML1_NOTCH2_1 MAFB KLF8 KLF7 KLF16 JDP2_2 0 JDP2_1 IRF3 HSF2 HSF1 HNF4A HDAC1 GTF2IRD1 GLI3 GLI2 GABPA_4 GABPA_3 GABPA_2 GABPA_1 GABP FOXP2 FOXO1 FLI1_2 FLI1_1 ETV7 ETV6 ETV5_2 ETV5_1 ETV4 ETV3_2 ETV3_1 ETV2_2 ETV2_1 ETV1_4 ETV1_3 ETV1_2 ETV1_1 ETS2_2 ETS2_1 ETS1_2 ETS1_1 ETS ESRRA ERG_3 ERG_2 ERG_1 ELK4_2 ELK4_1 ELK3 ELF3 CTCFL CTCF_3 CTCF_2 CTCF_1 CREM CNOT3 CEBPB CCNT2 BPTF BCL11A ATF5_2 ATF5_1 ATF3 ASH1L ARNTL APEX1 1 − SP3 SP5 SP8 YY2 ETS REL TBP NFY GLI2 GLI3 IRF3 MSC MGA ATF3 ELF3 KLF7 KLF8 PAX5 TFE3 ELK3 ETV4 ETV6 ETV7 ZEB1 BPTF HSF1 HSF2 RFX3 RFX5 SOX2 SOX5 SOX9 RELA MYF6 MSX2 MAFB GABP CREM KLF16 SP1_1 SP1_2 SP4_1 SP4_2 FLI1_1 FLI1_2 SRF_1 SRF_2 SRF_3 SRF_4 SRF_5 ZBTB2 SOX11 SOX12 SOX13 ASH1L NR2F1 FOXP2 APEX1 CTCFL ZBED6 ARNTL HNF4A NR2C2 ERG_1 ERG_2 ERG_3 HDAC1 FOXO1 CCNT2 MYEF2 CNOT3 PPARG OBOX2 CEBPB ATF5_1 ATF5_2 ESRRA SMAD3 SMAD4 STAT5B ELK4_1 ELK4_2 JDP2_1 JDP2_2 TRIM28 ETS1_1 ETS1_2 ETS2_1 ETS2_2 ETV1_1 ETV1_2 ETV1_3 ETV1_4 ETV2_1 ETV2_2 ETV3_1 ETV3_2 ETV5_1 ETV5_2 TCF7L2 ZNF239 ZNF304 ZNF449 ZNF547 ZNF668 ZNF672 ZNF684 ZNF701 ZNF721 ZNF770 ZNF799 ZNF879 NFE2L2 NFE2L3 ZBTB33 BCL11A ZNF33B ZNF37A NKX3 TFAP2C CTCF_1 CTCF_2 CTCF_3 MECOM THRB_1 THRB_2 POU1F1 POU3F2 POU5F1 RXRA_1 RXRA_2 SREBF1 ZSCAN4 POLR3A GABPA_1 GABPA_2 GABPA_3 GABPA_4 NANOG_1 NANOG_2 ZBTB18_1 ZBTB18_2 GTF2IRD1 SMARCC2 MYC_MAX ZSCAN2_1 ZSCAN2_2 MAML1_NOTCH3 MAML1_NOTCH4 MAML1_NOTCH2_1 MAML1_NOTCH2_2 Reverse
7 Forward-reverse orientation in T cells using H3K27ac histone modification marks
ZSCAN2 ZSCAN18 ZNF880 ZNF84_2 ZNF84_1 ZNF790 ZNF75A ZNF73 ZNF717 ZNF714 ZNF701 ZNF676 ZNF658B ZNF639 ZNF595 ZNF586 ZNF582 ZNF575 ZNF548 ZNF486 ZNF436 ZNF394 ZNF366 ZNF287 ZNF263_2 ZNF263_1 ZNF250 ZNF219 ZIC3 ZIC1 ZACN VAMP3 UF1H3BETA TRIM28 TP53_2 TP53_1 THRA TFCP2 TBX5 SRP9 SREBF1 SPZ1 SPI1_2 SPI1_1 SPDEF_2 SPDEF_1 SP1_4 SP1_3 SP1_2 SP1_1 SOX18_2 SOX18_1 SOAT1 SMC3_2 SMC3_1 SMARCC2 SMAD3 RREB1_2 RREB1_1 REST Score RARB RAD21_4 RAD21_3 RAD21_2 RAD21_1 60 POLR3A P50_P50 OTX2_3 OTX2_2 OTX2_1 NR3C1 NFYA 40 NFKB1_2 NFKB1_1 NFIA NEUROD1
Reverse MYOD1 MYF6 MYCN 20 MNX1 MAZ_2 MAZ_1 MAF LHX8 LHX6 KLF5 0 JUN JDP2_2 JDP2_1 IRF9 IRF HNF1B HMGA2_2 HMGA2_1 HEY1_2 HEY1_1 GLI1 GFI1B GCM1 GC GATA2_2 GATA2_1 FUBP1 FOXO3 FOXF2 FGF9 ETV3 EP300_3 EP300_2 EP300_1 ELF4 ELF3 ELF1 EHF EGR1 E2F6_4 E2F6_3 E2F6_2 E2F6_1 E2F4 E2F1_3 E2F1_2 E2F1_1 DUX1 DLX3 DEAF1 DDIT3_CEBPA CUX1 CTCF_6 CTCF_5 CTCF_4 CTCF_3 CTCF_2 CTCF_1 CEBPE BCL3_2 BCL3_1 BATF_2 BATF_1 BARX2 BACH1 ARID3A AHR_ARNT GC IRF JUN EHF MAF GLI1 IRF9 ZIC1 ZIC3 NFIA E2F4 ELF1 ELF3 ELF4 KLF5 DLX3 ETV3 LHX6 LHX8 SPZ1 TBX5 FGF9 NFYA SRP9 CUX1 DUX1 MYF6 REST ZACN THRA EGR1 MNX1 RARB GCM1 GFI1B MYCN SP1_1 SP1_2 SP1_3 SP1_4 ZNF73 SOAT1 FOXF2 TFCP2 DEAF1 FUBP1 MAZ_1 MAZ_2 BARX2 HNF1B NR3C1 SPI1_1 SPI1_2 BACH1 VAMP3 FOXO3 CEBPE SMAD3 MYOD1 E2F1_1 E2F1_2 E2F1_3 E2F6_1 E2F6_2 E2F6_3 E2F6_4 TP53_1 TP53_2 BATF_1 BATF_2 TRIM28 JDP2_1 JDP2_2 ARID3A ZNF219 ZNF250 ZNF287 ZNF366 ZNF394 ZNF436 ZNF486 ZNF548 ZNF575 ZNF582 ZNF586 ZNF595 ZNF639 ZNF676 ZNF701 ZNF714 ZNF717 ZNF790 ZNF880 BCL3_1 BCL3_2 OTX2_1 OTX2_2 OTX2_3 HEY1_1 HEY1_2 ZNF75A CTCF_1 CTCF_2 CTCF_3 CTCF_4 CTCF_5 CTCF_6 SMC3_1 SMC3_2 SREBF1 POLR3A ZSCAN2 EP300_1 EP300_2 EP300_3 P50_P50 GATA2_1 GATA2_2 ZNF84_1 ZNF84_2 SOX18_1 SOX18_2 ZNF658B NFKB1_1 NFKB1_2 RAD21_1 RAD21_2 RAD21_3 RAD21_4 RREB1_1 RREB1_2 SPDEF_1 SPDEF_2 ZSCAN18 HMGA2_1 HMGA2_2 ZNF263_1 ZNF263_2 NEUROD1 SMARCC2 AHR_ARNT UF1H3BETA DDIT3_CEBPA Forward
8 Reverse-forward orientation in T cells using H3K27ac histone modification marks
ZNF880 ZNF8 ZNF777 ZNF718 ZNF681 ZNF678 ZNF579 ZNF551 ZNF549 ZNF491 ZNF468 ZNF440 ZNF366 ZNF335 ZNF281 ZNF256 ZNF239 ZNF235 ZNF174 ZNF155 ZNF132 ZIC3 ZIC1 ZFP69B_2 ZFP69B_1 ZBTB7A ZBTB11 ZBTB1 YY1 YBX1 TP73 TGIF1 TFAP2C_2 TFAP2C_1 TEAD1 TBX5 TBX2 STAT1 SRY SRF_2 SRF_1 SPDEF SP4 SP2_4 SP2_3 SP2_2 SP2_1 SP1 SOX17 SOX1 RXRA_3 RXRA_2 RXRA_1 RUNX2 RREB1 Score RFX4 RFX1 REST RELA RARA 40 PSMD9 PROX1 PPARD PBX3 PBX2 30 PAX4 PARP1 ONECUT2 NRL_2 20 NRL_1 Forward NR2C1 NR0B1 NKX2−4 NKX2−1 10 NFKB2 NFKB1_2 NFKB1_1 NFE2L2_2 NFE2L2_1 0 MYOD1 MEIS1 MEF2A MAZ MAFA LHX6 LHX4 LEF1 LBX1 KLF6 KLF3 JDP2 IRF HAND1 GFI1B GFI1 GATA GABPA_2 GABPA_1 FOXN3 FOXK1 FOXJ3 FOXA3_2 FOXA3_1 FOS_3 FOS_2 FOS_1 ETV6 ETS1 ESR1_2 ESR1_1 EP300 ELF3_2 ELF3_1 ELF2 EHF EGR1 EDF1 E2F4 E2F DBP CTCFL_2 CTCFL_1 CTCF_4 CTCF_3 CTCF_2 CTCF_1 CEBPA BHLHE41 BHLHE40 BCLAF1 AR 1 4 − − AR IRF E2F SP1 SP4 YY1 EHF SRY DBP MAZ ZIC1 ZIC3 GFI1 E2F4 ELF2 KLF3 KLF6 LEF1 TP73 PAX4 JDP2 LBX1 GATA ZNF8 ETS1 ETV6 LHX4 LHX6 TBX2 TBX5 EDF1 PBX2 PBX3 RFX1 RFX4 YBX1 SOX1 RELA REST MAFA EGR1 RARA TGIF1 STAT1 GFI1B EP300 MEIS1 SP2_1 SP2_2 SP2_3 SP2_4 FOXJ3 NRL_1 NRL_2 SRF_1 SRF_2 ZBTB1 PARP1 SOX17 FOS_1 FOS_2 FOS_3 FOXK1 NFKB2 NR0B1 TEAD1 CEBPA FOXN3 NR2C1 PROX1 PPARD MEF2A RREB1 SPDEF RUNX2 HAND1 PSMD9 MYOD1 ELF3_1 ELF3_2 ZNF132 ZNF155 ZNF174 ZNF235 ZNF239 ZNF256 ZNF281 ZNF335 ZNF366 ZNF440 ZNF468 ZNF491 ZNF549 ZNF551 ZNF579 ZNF678 ZNF681 ZNF718 ZNF777 ZNF880 ZBTB11 ESR1_1 ESR1_2 NKX2 NKX2 BCLAF1 CTCF_1 CTCF_2 CTCF_3 CTCF_4 ZBTB7A RXRA_1 RXRA_2 RXRA_3 FOXA3_1 FOXA3_2 CTCFL_1 CTCFL_2 NFKB1_1 NFKB1_2 GABPA_1 GABPA_2 BHLHE40 BHLHE41 NFE2L2_1 NFE2L2_2 ONECUT2 ZFP69B_1 ZFP69B_2 TFAP2C_1 TFAP2C_2 Reverse
9