Table S1: qPCR Primer for cDNA - Springer Static Content Server

Table S1: qPCR Primer for cDNA GAPDH f GAPDH r ALKBH3 f ALKBH3 r MX1 f MX1 r MX2 f MX2 r OAS1 f OAS1 r OASL f OASL r IFI6 f IFI6 r IFI27 f IFI27 r RSAD2 f RSAD2 r DCP1A f DCP1A r RPS25 f RPS25 r TATDN3 f TATDN3 r OTUD7B f OTUD7B r BRF2 f BRF2 r DVL2 f DVL2 r TMEM126A f TMEM126A r BLID f BLID r FBXO22 f FBXO22 r STARD9 f STARD9 r ANP32A f ANP32A r CACNA1G f CACNA1G r NCF4 f NCF4 r FECH f FECH r DBIL5P2 f DBIL5P2 r

GGAGCGAGATCCCTCCAAAAT GGCTGTTGTCATACTTCTCATGG CATGGAAGGAGCGACACAAGC CTAGAGTGGTATTCTTTGGGC GTTTCCGAAGTGGACATCGCA CTGCACAGGTTGTTCTCAGC CAGAGGCAGCGGAATCGTAA TGAAGCTCTAGCTCGGTGTTC TGTCCAAGGTGGTAAAGGGTG CCGGCGATTTAACTGATCCTG CTGATGCAGGAACTGTATAGCAC CACAGCGTCTAGCACCTCTT GGTCTGCGATCCTGAATGGG TCACTATCGAGATACTTGTGGGT TGCTCTCACCTCATCAGCAGT CACAACTCCTCCAATCACAACT TGGGTGCTTACACCTGCTG GAAGTGATAGTTGACGCTGGTT GAATGACTGTCACCGCATAGC CTGAGTGCTTGGCTGTAACCC AAGGACGCTGGAAAGTCGG CTTTGCCTTTGGACCACTTCT GTAGGCTTGGTGGACTGTCAC CCACAAGGGCCACAACATTG GTCAGATTTTGTCCGTTCCACA CATGGACTTGACGTAGCTGTT GGTGGAAGACTCGCACTATTC CGACTAACTTGTTCGTTTTCCCC GAGGAAGAGACTCCCTACCTG CGGGCGTTGTCATCTGAAAT TAACACGGAGTGGACTGACTG CTTTGTGTGGTAACAGAGCTGAT TACACAGGATGGATAGAGCGAG CTTTGTTGGAACCCAAGAGCG CGGAGCACCTTCGTGTTGA CACACACTCCCTCCATAAGCG AGGTGGACAATCGACCAGATG CCAGTAGCAGTAATCAAAGCCAA CACCTCAATCGCAAACTTACCA AACACATTTTCTCGGTAGTCGTT TGTCTCCGCACGGTCTGTAA AAGCCGGTTCCAAGTGTCTC CGGGCCGAGAGTGACTTTG TCTTCACCTCGATGACGAAAAC GGAGATGTTCACGACTTCCTTC GAATGGTGCCAGCTTATTCTGA CTGAAGGGTACTGTGTGCGAT CATGCCTCCTACTTGGCCT

Table S2: qPCR Primer for ChIP ALKBH3 upstr f ALKBH3 upstr r ALKBH3 f ALKBH3 r NOSIP f NOSIP r GIN1/PPIP5K2 f GIN1/PPIP5K2 r ANAPC5 f ANAPC5 r ADAT2/PEX3 f ADAT2/PEX3 r GAPDH f GAPDH r

CAAGAGCTGCCTACCAAAGG TACTGTTGGCCTGTGCAGAA TATCCCCTCATCAGCACCTT GACTCCAGCAACTCCCAATC ATCCGGAACTTTCGATTAGC CAGAAGGCACCGGAAGTAGA ACACAGCACACCAGAACGAC CTTTCTGACCGTGGTTCCAA GAGCTCCTCAGTCCCTTCAG TGTCAGAGCACATGGGAGAG AGCGTAGCTGCTTTGCTGTA CGTCCCGTTCTGTGCTCT CAATTCCCCATCTCAGTCGT TAGTAGCCGGGCCCTACTTT

Table S3: Datasets used for bioinformatics analysis Factor ALKBH3 IgG AR BRD2 BRD3 BRD4 CBX1 CBX2 CBX3 CBX5 CBX8 CDK8 CHD1 CHD2 CHD4 CHD7 CTCF DNase I ELF1 ELK4 ERG ETS1 ETV1 ETV4 EZH2 GABPA GTF2B GTF2F1 H2A.Z H2A.Zac H3K4me1 H3K4me2 H3K4me3 H3K9Ac H3K9me1 H3K9me3 H3K27ac H3K27me3 H3K79me2 H3K122Ac H4K5Ac HDAC1 HDAC2 HDAC6 KDM5B KDM1A MED1 MED12 KMT2D Myc NIPBL Nucleosomes PCAF P300 PHF8 RAD21 RBBP5 RNA Polymerase II RNA Polymerase II S5P RNF2 SETDB1 SIRT6 SMC1A SMC3 TAF1 TAF7 TBP XPB XPD YY1 ZNF143

ID GSM1385219 GSM1385220 GSM1328945/GSM1328947 GSM971946 GSM971947 GSM1328959 GSM971950 GSM1003567 GSM1003568 GSM971949 GSM1003569 GSM937561 GSM1003575 GSM935502 GSM1003510 GSM1003478 GSM822311 GSM822387 GSM1424527 GSM1424528 GSM353648 GSM738821 GSM1145322 GSM738817 GSM969570 GSM738822 GSM935394 GSM935501 GSM686941 GSM1059388 GSM353634 GSM353635 GSM353626 GSM733778 GSM733777 GSM353625 GSM686937 GSM969571 GSM733653 GSM1059385 GSM686939 GSM1003448 GSM1003447 GSM1003504 GSM1003586 GSM1003570 GSM894081 GSM686945 GSM1240109 GSM822310 GSM1208661 wgEncodeEH000922 GSM831007 GSM686943 GSM1003450 GSM1208668 GSM1003449 GSM699636 GSM831016 GSM1003563 GSM1003452 GSM1003560 GSM1208678 GSM1208679 GSM803431 GSM803407 GSM935495 GSM1092544 GSM1092545 GSM803354 GSM959047

Cell Type PC3 PC3 VCaP HEK293 HEK293 VCaP HEK293 K562 K562 HEK293 K562 HCT116 K562 K562 K562 K562 K562 LNCaP DU145 DU145 LNCaP RWPE1 LNCaP PC3 LNCaP RWPE1 K562 K562 LNCaP MCF7 LNCaP LNCaP LNCaP K562 K562 LNCaP LNCaP LNCaP K562 MCF7 LNCaP K562 K562 K562 K562 K562 H2171 LNCaP HCT116 K562 LoVo GM12878 K562 LNCaP K562 Lovo K562 LNCaP K562 K562 K562 K562 LoVo LoVo K562 K562 K562 HT1080 HT1080 HCT116 K562

Reference this study this study [1] [2] [2] [1] [2] [3] [3] [2] [3] [4] [3] [3] [3] [3] [3] [5] [6] [6] [7] [8] [9] [8] [10] [8] [3] [3] [11] [12] [7] [7] [7] [3] [3] [7] [11] [10] [3] [12] [11] [3] [3] [3] [3] [3] [13] [11] [14] [3] [15] [16] [3] [11] [3] [15] [3] [17] [3] [3] [3] [3] [15] [15] [3] [3] [3] [18] [18] [3] [3]

1.

2. 3. 4. 5. 6. 7. 8. 9.

10. 11. 12. 13. 14. 15. 16.

17. 18.

Asangani IA, Dommeti VL, Wang X, Malik R, Cieslik M, Yang R, Escara-Wilke J, Wilder-Romans K, Dhanireddy S, Engelke C, et al: Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature 2014, 510:278-282. LeRoy G, Chepelev I, DiMaggio PA, Blanco MA, Zee BM, Zhao K, Garcia BA: Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins. Genome Biol 2012, 13:R68. ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. Galbraith MD, Allen MA, Bensard CL, Wang X, Schwinn MK, Qin B, Long HW, Daniels DL, Hahn WC, Dowell RD, Espinosa JM: HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia. Cell 2013, 153:1327-1339. He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS: Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res 2012, 22:1015-1025. Plotnik JP, Budka JA, Ferris MW, Hollenhorst PC: ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells. Nucleic Acids Res 2014, 42:11928-11940. Yu J, Mani RS, Cao Q, Brenner CJ, Cao X, Wang X, Wu L, Li J, Hu M, Gong Y, et al: An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell 2010, 17:443-454. Hollenhorst PC, Ferris MW, Hull MA, Chae H, Kim S, Graves BJ: Oncogenic ETS proteins mimic activated RAS/MAPK signaling in prostate cells. Genes Dev 2011, 25:2147-2157. Chen Y, Chi P, Rockowitz S, Iaquinta PJ, Shamu T, Shukla S, Gao D, Sirota I, Carver BS, Wongvipat J, et al: ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss. Nat Med 2013, 19:1023-1029. Xu K, Wu ZJ, Groner AC, He HH, Cai C, Lis RT, Wu X, Stack EC, Loda M, Liu T, et al: EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science 2012, 338:1465-1469. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, et al: Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 2011, 474:390-394. Tropberger P, Pott S, Keller C, Kamieniarz-Gdula K, Caron M, Richter F, Li G, Mittler G, Liu ET, Buhler M, et al: Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell 2013, 152:859-872. Lin CY, Loven J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA: Transcriptional amplification in tumor cells with elevated c-Myc. Cell 2012, 151:56-67. Hu D, Gao X, Morgan MA, Herz HM, Smith ER, Shilatifard A: The MLL3/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers. Mol Cell Biol 2013, 33:4745-4754. Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J: Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 2013, 154:801-813. Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A: Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res 2012, 22:1735-1747. Tan PY, Chang CW, Chng KR, Wansa KD, Sung WK, Cheung E: Integration of regulatory networks by NKX3-1 promotes androgen-dependent prostate cancer survival. Mol Cell Biol 2012, 32:399-414. Gray LT, Vallur AC, Eddy J, Maizels N: G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD. Nat Chem Biol 2014.

Table S4: Genes with hyperactive promoters in PC3 cells AAR2 ACOT13 ACP2 ADAT2 ADPRHL1 AHSA1 ALG10B ALG3 ALKBH3 ANAPC5 ANKRD40 AQR ARHGAP1 ASAH2B AURKAIP1 BBS1 BMS1 BMS1P4 BRF2 C8orf33 C11orf31 C11orf49 C11orf57 C11orf74 C12orf73 C12orf76 C17orf75 C18orf21 C19orf52 C19orf82 C21orf59 C21orf67 CCAR2 CDC16 CDK5RAP1 CENPP CGGBP1 COMMD2 COPS2 COPS4 COPS7B COX16 CPSF1 CSTF2T DCAF10 DCDC1 DCP1A DDX55 DHX33 DMAP1 DNAJC2 DNAJC24 DNAJC25 DPAGT1 DPM3 DPY19L4 DRG2 DSCR3 DSTYK DTWD1 ECD EFCAB7 EIF1AD EIF3F EIF4E2 EMC4 EMG1 ERH EXD2 EXOSC4 FAM126B FAM149B1 FAM207A FAM227B FAM98B FBXO28 FBXW11 FEM1B FRA10AC1 GABPA GALK2 GIN1 GOLGA3 GRPEL2 GSTCD GTF2H2 GTF2H2B GTF2H2C GTF2H2D

chr20 chr6 chr11 chr6 chr13 chr14 chr12 chr3 chr11 chr12 chr17 chr15 chr11 chr10 chr1 chr11 chr10 chr10 chr8 chr8 chr11 chr11 chr11 chr11 chr12 chr12 chr17 chr18 chr19 chr19 chr21 chr21 chr8 chr13 chr20 chr9 chr3 chr3 chr15 chr4 chr2 chr14 chr8 chr10 chr9 chr11 chr3 chr12 chr17 chr1 chr7 chr11 chr9 chr11 chr1 chr8 chr17 chr21 chr1 chr15 chr10 chr1 chr11 chr11 chr2 chr15 chr12 chr14 chr14 chr8 chr2 chr10 chr21 chr15 chr15 chr1 chr5 chr15 chr10 chr21 chr15 chr5 chr12 chr5 chr4 chr5 chr5 chr5 chr5

GTF3C3 GTPBP3 HDAC8 HELQ HEMK1 HMGXB3 HNRNPA1L2 HUS1 ICT1 IGHMBP2 INO80B INTS12 INTS5 IPO4 ITGB3BP JMJD4 JPX JRK KBTBD4 KCTD10 KCTD5 KIAA0391 KLHL20 KRR1 LINC00657 LINC00910 LOC100133315 LOC100288974 LOC652276 LSG1 MAN2C1 MED18 MED23 METTL15 MITD1 MKRN2 MNAT1 MPLKIP MRPL1 MRPL13 MRPL16 MRPL21 MRPL3 MRPL30 MRPL39 MRPL44 MRPL48 MRPS18C MRPS31 MRPS31P5 MTBP MTHFD2L MTIF2 MTRF1 NDUFA12 NDUFAF1 NDUFB3 NDUFS3 NDUFS7 NFKBIL1 NIF3L1 NKAP NKAPP1 NME1 NMNAT1 NOL12 NOSIP NR1H2 NR1H3 NSL1 NUF2 NUP107 OPA1 OTUD7B PCYT1A PEX3 PIGL PIH1D2 PLEKHM3 POLR3B PPIP5K2 PSMF1 PTRH2 RARS RBBP5 RBM25 RBM28 RFXANK RGS5

chr2 chr19 chrX chr4 chr3 chr5 chr13 chr7 chr17 chr11 chr2 chr4 chr11 chr14 chr1 chr1 chrX chr8 chr11 chr12 chr16 chr14 chr1 chr12 chr20 chr17 chr11 chr10 chr16 chr3 chr15 chr1 chr6 chr11 chr2 chr3 chr14 chr7 chr4 chr8 chr11 chr11 chr3 chr2 chr21 chr2 chr11 chr4 chr13 chr13 chr8 chr4 chr2 chr13 chr12 chr15 chr2 chr11 chr19 chr6 chr2 chrX chrX chr17 chr1 chr22 chr19 chr19 chr11 chr1 chr1 chr12 chr3 chr1 chr3 chr6 chr17 chr11 chr2 chr12 chr5 chr20 chr17 chr5 chr1 chr14 chr7 chr19 chr1

RP11-608O21.1 RPL29 RPL37 RPS18 RPS25 RPS27 RPS7 RRP15 RTTN SAR1B SBDSP1 SEC13 SEC22B SENP1 SF3A3 SF3B14 SLC33A1 SLC39A9 SMG7-AS1 SMG8 SNHG6 SNRNP27 SNRPB SPAG8 SREK1IP1 SSBP1 STX16 STX18 SUPT7L TACO1 TARS2 TATDN3 TBC1D19 TDP2 TEFM THAP10 THEM4 TIAL1 TIGD1 TIGD6 TIMM9 TMEM101 TMEM128 TMEM222 TMEM242 TMEM41A TMEM69 TOP3B TRAPPC4 TRIP4 TTC26 TTC4 TUBGCP3 TUT1 TVP23B TXNDC9 UBA5 UBE3B USP30 UTP3 VPS25 VPS45 VPS51 VPS52 VWA9 WDR11 WDR24 WDR31 WDR36 YBEY YIPF2 ZBTB11 ZKSCAN4 ZMPSTE24 ZNF205 ZNF248 ZNF35 ZNF408 ZNF461 ZNF490 ZNF579 ZNF581 ZNF646 ZNF668 ZNF770 ZNF791 ZNF846 ZSCAN9

chr4 chr3 chr5 chr6 chr11 chr1 chr2 chr1 chr18 chr5 chr7 chr3 chr1 chr12 chr1 chr2 chr3 chr14 chr1 chr17 chr8 chr2 chr20 chr9 chr5 chr7 chr20 chr4 chr2 chr17 chr1 chr1 chr4 chr6 chr17 chr15 chr1 chr10 chr2 chr5 chr14 chr17 chr4 chr1 chr6 chr3 chr1 chr22 chr11 chr15 chr7 chr1 chr13 chr11 chr17 chr2 chr3 chr12 chr12 chr4 chr17 chr1 chr11 chr6 chr15 chr10 chr16 chr9 chr5 chr21 chr19 chr3 chr6 chr1 chr16 chr10 chr3 chr11 chr19 chr19 chr19 chr19 chr16 chr16 chr15 chr19 chr19 chr6

Figure S1: Additional control experiments in PC3 and NCI-H23 cells. a) Immunofluorescence using ALKBH3 antibody in PC3 cells expressing an ALKBH3 shRNA or a control shRNA. The ALKBH3 immunofluorescence signal was enhanced in the right panel. b) ChIP experiment in PC3 cells measured on 2 additional ALKBH3 targets (see Figure 1F) and the GAPDH promoter as negative control. c) Quantitative expression analysis of inflammatory genes upon knockdown of ALKBH3 in NCI-N23 lung cancer cells. Data were normalized to GAPDH. d) ALKBH3 ChIP in NCI-H23 cells show enrichment of ALKBH3 at some of its targets, found in PC3 cells.

Figure S2: ALKBH3 promoter binding and gene expression correlates with presence of ETS transcription factors. a-c) Promoters were categorized based on the presence (called by MACS with p-value 1e-05) of seven ETS transcription factors (GABPA, ELF1, ELK4, ERG, ETS1, ETV1, ETV4) in prostate cancer cells (from “0” to “>5” n = 15815; 8330; 3942; 1968; 853; 309; 64). a) The level of ALKBH3 at promoters strongly correlates with the number of ETS transcription factors present. b) Gene expression (data from PC3 cells) shows correlation with the presence of ETS transcription factors. Genes with at least one bound ETS transcription factor are significantly more active than genes without ETS factor (p-value = 0), suggesting that upregulation of ETS transcription factors in prostate cancer increases the global gene expression level. c) Group I promoters are typically targeted by more ETS factors than other promoters. d) In prostate cancer cells, the ALKBH3 gene promoter is occupied by at least five ETS transcription factors. The ALKBH3 gene promoter possesses an ETS transcription factor binding motif 90 bp upstream from the TSS.

Figure S3: Detailed analysis of ALKBH3 bound promoter with comparison of group I and group II promoters. a-e;g-i) Same Analysis as in Figure 2, but here the two groups of ALKBH3 bound promoters were investigated separately and ALKBH3-unbound promoters were added as additional group. Group I promoters are generally in a more active state compared to group II promoters. f) Five genes were randomly selected from each promoter group and expression levels in PC3 cells were quantitatively measured by qPCR. The results show a similar trend as the microarray data.

Figure S4: ALKBH3 is genome wide enriched at gene bodies, enhancers and location of G4 DNA. a) All genes were grouped in quintiles based on the gene expression. ALKBH3 is enriched within gene bodies of highly expressed genes. b-d) ALKBH3 is enriched at enhancer sites and sites with putative quadruplex DNA. The heatmaps in (d) were sorted after mean intensity.

Figure S5: Whisker blots for analyzed features. For each investigated feature presented in Figure 5a the ChIP-Seq tags were counted for each individual promoter (-1000/+1000). The whisker blots represents the distribution of those tags in each promoter group (from left: all promoters, Group II promoters, Group I promoters) with the lower quartile, median and upper quartile of the data and with 5% and 95% whiskers. The red line connects the mean tag number. The number in the plots indicates the p-value for a student’s t-test between group I and group II.

ALKBH3 250

p-value: 5.17235E-55

AR 3.58972E-07

250

200

200

150

150

BRD2

BRD3

5.1106E-07

300 250

100

50

50

0 All

Group II Group I

5.20458E-08

8

All

300 250 200 150

20

100

10

50

All

0 All

Group II Group I

CBX3

0.880080773

90

Group I

All

CBX5

0.000415446

80

Group II

9

0.009446275

8

70

7

70

60

6

60

50

5

50

4

30

40

4

40

30

3

30

20

2

20

10

1

10

0

0

20 10

1 0

0 All

Group II

Group I

All

CDK8 0.000705549

500 450 400 350 300 250 200 150 100 50

0.34648829

600

800

80

300

600

60

200

400

40

100

200

20

0

0

0

All

ELF1 50

350

40

60

0.02359875

50

5

0 Group II Group I

4.99663E-10

160

Group II

Group I

120

2.72341E-09

30

80 60

20

40

10

20 0

0 All

Group II Group I

30 20 10 0 All

25

All

Group II Group I

Group II

Group I

ETS1

1.3349E-10

70

2.62073E-07

60

40

All

Group II

30 20

5

10

0 All

Group II

0 All

Group I

EZH2

40

100

40

10

ETV4 60 50

140

50

50

0 All

ETV1 180

7.14001E-09

90

60

15

10

0 All

CHD7

70

20

20

15 10

7.77955E-06

Group I

30

20

100

Group II

ERG

40

25

150

Group II Group I

50

30

All

80

ELK4

35

200

All

Group II Group I

Group I

0.603816004

120

400

45

250

5.46296E-09

1200

Group II

CHD4

CHD2 100

400

300

0 All

Group I

1000

Group II Group I

0.714353545

Group II

500

CTCF 450

All

Group I

CHD1

0 All

Group II

0.453000743

80

40

2

Group II Group I

CBX8 90

5

3

Tags per promoter

350

0

CBX2 70

50

6

400

30

Group II Group I

60

7

70

0

CBX1 9

450

40

50

0.000523108

500

80

50

100

0

6.09859E-11

90

60

200 150

100

BRD4

Group I

40

1.13151E-06

35

30

30

25

25

20

20

15

15

10

10

5

5

0

0 Group II

Group I

All

GABPA 40

35

All

Group II

Group I

5.21672E-25

Group II

Group I

GTF2B 140

0.147943133

120 100 80 60 40 20 0 All

Group II

Group I

All

Group II Group I

GTF2F1 300

0.002272808

H2A.Z 50

H2A.Zac

0.170221205

45

250

35 25

10

50

0 All

All

1.03857E-05

250

0.170155829

30

150

0

150 100

10

50

5

0.000256713

Tags per promoter

2.89348E-08

1400

Group II

Group I

0.113753345

70

600

40

25

30

20

200

10

0

0 All

All

HDAC2 0.008742215

300 250 200 150 100 50

Group II

0.000668864

200

10

0

0 All

Group II

120

100

100

80

80

60

60

40

40

20

20

MED12 25

1.71501E-18

15

500

0.000437497

Group II Group I

0 All

Group II

Group I

All

Group I

KDM5B 0.854498367

1200 1000

100

800

80

600

60

400

40

200

20 0 All

Group II Group I

All

NIPBL 450

2.42112E-19

Group II Group I

p300 20

400

350

16

1.87623E-06

14

300

12

250

10

200

8

150

6

100

100

4

50

50

2

0

0 Group II Group I

1.27205E-18

120

18

All

Group II Group I

KMT2D

400

200

5

Group II

450

150

All

0 All

MYC

300

10

0

100

Group II Group I

250

50

200

0 All

350

100

300

0 Group II Group I

20

150

400

Group I

0.518323861

180

120

All

0.29778545

700

500

KDM1A

140

MED1 250

5

140

Group II Group I

HDAC1 600

20

160

0 All

0.024388483

80

30

160

0

H4K5ac

Group II Group I

40

Group I

0.518018504

All

Group II Group I

50

HDAC6 180

0 All

60

10

Group II Group I

200

70

15

20

400

1.30149E-09

30

800

400

0 Group II Group I

35

50

1000

800

200

40

60

1200

1000

400

H3K9me3 45

1.96161E-05

1200

600

All

H3K9me1

H3K79me2

600

0 All

Group II Group I

800

20

H3K9ac 1600

7.47125E-12

1400

1000

60

Group II Group I

All

H3K4me3

80

0 All

Group II Group I

1200

40

0

All

H3K4me2

100

15

0

Group II Group I

140

20

50

50

120 200

100

100

160

25

150

200

All

Group I

H3K4me1

H3K27me3 300

Group II

200

250

0

Group II Group I

0.106380754

250

300

100

5

0

350 300

350

200

15

2.68129E-08

400

300

20

100

H3K27ac

H3K122ac 500 450

400

30

150

4.68504E-09

500

40

200

600

0 All

Group II Group I

All

Group II

Group I

PCAF 120

0.669862891

PHF8 4000

8.37934E-07

3500

100

6.48247E-16

0

0

0

1000 800

All

SETDB1 0.000877193

140

0.01476584

120

100

100

80

80

60

60

40

40

5 0 All

Group II Group I

SIRT6 140

120

15 10

200

RBBP5 1200

20

400

200

Group II Group I

4.34214E-06

25

300

All

40

30

100

Group II Group I

RAD21 35

800

500

0

0.577753273

600

1000

All

1200

400

1500

20

RNA Polymerase II Serine 5 phosphorylated 1000

2000

40

Tags per promoter

0.618081012

500

2500

60

700 600

3000 80

RNA Polymerase II

Group II Group I

All

2.14039E-08

Group I

SMC3

SMC1A 250

Group II

3.12267E-07

350 300

200

250 150

200

600 400 200

20

20

0

0

0

All

Group II Group I

All

6.65347E-15

1400

0.048630474

400 200 0 All

All

YY1

Group II Group I

ZNF143 1800

0.304598542

1600

2500

1400 1200

2000

1000

1500

800 600

1000

400

500

200

0

0 All

Group II Group I

1000

200

800

150

150

100

100

50

50

0

Group II Group I

0.00114102

3000

250

200

200

0

All

Group II Group I

4.56851E-21

0 All

Group II Group I

Group II Group I

XPD/ERCC2 350

250

400

50

350

300

600

100

All

300

1200

150

600

0.387366401

Group II Group I

XPB/ERCC3

TBP 1800

0 All

Group II Group I

1400

200

800

All

1600

1200

50

0

TAF7 300 250

1000

100 50

Group II Group I

TAF1 1600

150

100

3.13297E-12

0 All

Group II Group I

All

Group II Group I