gene silencing in cancer by histone h3 lysine 27 tri ......gene silencing in cancer by histone h3...

Gene silencing in cancer by histone H3 lysine 27 tri-methylation independent of promoter DNA methylation

Supplementary Information

Yutaka Kondo, Lanlan Shen, Alfred S Cheng, Saira Ahmed, Yanis Boumber, Chantale Charo, Tadanori Yamochi, Takeshi Urano, Koichi Furukawa, Bernard Kwabi-Addo,

David L Gold, Yoshitaka Sekido, Tim Hui-Ming Huang and Jean-Pierre J Issa

DNASE1L3ABHD6

RPP14PXK

PDHBKCTD6

ACOX2FAM107A

TU3AFAM3D

FLJ42117

FHIT

PTPRGC3orf14

II

ZNF659UBE2E2

UBE2E1NKIRAS1

PRL15

NR1D2THRB

RARTOP2B

NGLY1NGLY1-OX

OXSM

II II

Chromosome 3p

Chromosome 7q

I II

FLJ13576FLJ31818

GPR85

PPP1R3A

FOXP2

MDFICTFEC

TESCAV2

CAV1

METCAPZA2ST7

WNT2

II

ATXN7L4FLJ23834

SYPL1PBEF1

FLJ36031

PIK3CGPRKAR2B

HBP1GPR22

DUS4L

COG5BCAP29

SLC26A4CBLL1

I

6050403020100

6050403020100

6050403020100

6050403020100

6050403020100

6050403020100

PrECPC3

PrECPC3

Sig

nal r

atio

(IP

/INP

UT)

Sig

nal r

atio

(IP

/INP

UT)

Sig

nal r

atio

(IP

/INP

UT)

Sig

nal r

atio

(IP

/INP

UT)

A

B

Supplementary Fig. 1. ChIP-chip analysis for H3K27triM in prostate cancer cell line PC3 and normal prostate epithelial cell line PrEC. Y axis and X axis indicate signal ratio of IP/input and relative probe location on chromosome 3p (A) and chromosome 7q (B), respectively. Each dot represents value of each probe (red, PrEC; blue, PC3). Regions with bold bar (I and II) are enlarged in bottom column. On the bottom column, each promoter region corresponding to the dots are indicated as a line. Cancer specific H3K27triM enrichment is observed in several loci including RARB, PTPRG and PIK3CG promoters.

-400 -380 -360 -340 -320 -300 60 80 100 120 140 160

25 45 65 85 105 125 145 165 185 205

OTOP3

85 105 125 145 165 185

WNT1

140 160 180 200 220 240 260

5 25 45 65 85 105 125 145 165 185

PGRA

-Up -Down

Supplementary Fig.2 Bisulfite sequencing shows that no specific CpG site is methylated within the H3K27triM target promoters. Each row represents a single sequence analyzed and each circle is a single CpG site. White and black circles represent unmethylated and methylated CpGs, respectively. Numbers indicate the location relative to the transcription start site.

ChIP601bp

(-171~+430)SEAP

SV40 promoterSEAP

RAR 2promoter

SEAP 1151bp(-721~+430)

A

C

B

D

601bp 1151bpPC3 SW480

1151bp

Base601bp1151bpSV40

2

4

6

8

10

0

20

40

60

80

100

0

PC3 SW480

2

4

6

8

10

0

40

80

120

160

200

0

SV40601bp 1151bp3

2

1

0 K4-2M

K9-A

c

K9-2M

K27-1M

K27-3M

3

2

1

0 K4-2M

K9-A

c

K9-2M

K27-1M

K27-3M

3

2

1

0 K4-2M

K9-A

c

K9-2M

K27-1M

K27-3M

PC3 SW480SV40

3

2

1

0 K4-2M

K9-A

c

K9-2M

K27-3M

Base601bp1151bpSV40

601bp

3

2

1

0 K4-2M

K9-A

c

K9-2M

K27-3M

601bp 1151bp3

2

1

0 K4-2M

K9-A

c

K9-2M

K27-3M

Supplementary Fig.3 RAR 2 down regulation in-vitro is dependent on H3K27 trimethylation related silencing but independent of DNA methylation. A, PC3 and SW480 cell lines were transfected with SEAP reporter plasmids containing RAR 2 promoters (601bp or 1151bp, -171 to +430 or -721 to +430 corresponding to the transcription starting site, respectively) or SV40. The bold line indicates the location of ChIP primers. Arrow heads indicate the region of bisulfite sequence (+161 to +337). B, Stable clones for SEAP reporter plasmids in PC3 or SW480 were treated with either PBS (white bar) or TSA (black bar, 300nM) for 20 hours. Supernatants were assayed for SEAP activity. Y axis indicates relative activity to base line control (no promoter activity). Left Y axis and right Y axis are scaled for the activity of RAR 2 promoters and of SV40 promoter, respectively. Error bars indicate standard deviation. C, bisulfite sequencing shows that no specific CpG site is frequently methylated within the RAR 2 promoter. Each row represents a single sequence analyzed and each circle is a single CpG site. White and black circle represent unmethylated and methylated CpGs, respectively. D, ChIP-PCR shows that the both RAR 2 promoters in pSEAP plasmids are enriched for H3K27 trimethylation. By contrast, SV40 promoter shows high level of H3K4 diM and H3K9Ac, which are the marker for active genes. Error bars represent SEM of the averaged values.

Supplement Table 1. Clones with high H3-K27 mono-methylation and/or high H3-K27 tri-methylation in PC3 by CpG microarray Clones with high H3-K27 mono-methylation in PC3 by CpG microarray Clone ID* K27

mono- Me

K27

Tri- Me

Loci CpG¶ Gene name Accession no.†

50_A_3 7.6 1.0 4p15.2 No MER11C (LTR)

48_E_3 5.6 0.0 10q13 No L1MB1 (LINE)

18_G_10 4.8 1.0 Xq21.1 No MER61A-int (LTR)

50_C_7 4.2 1.0 3q12.1 No THE1C (LTR)

94_G_1 4.0 1.0 2p25.3 No MLT1L (LTR)

93_G_1 3.4 0.9 8q21.11 No Tigger3b (DNA)

121_C_12 3.3 1.0 3q22.3 No MLT1A0 (LTR)

22_A_9 3.3 0.0 10q23.33 No AluSx (SINE)

115_G_11 3.0 1.0 1p13.2 No L2 (LINE)

48_E_7 2.9 1.0 2q32.3 No MER5A (DNA)

39_F_5 2.9 0.0 7p14.3 No MER53B (DNA), MIRb (SINE)

83_F_8 2.8 0.0 14q22.1 No Ninein exon5 NM_182944

83_E_3 2.7 0.4 11q14.1 No L1PA3 (LINE)

44_E_8 2.7 0.0 1q42.11 No L1MA4A (LINE)

55_A_3 2.7 0.0 8q24.3 Yes GLI-4, AluSx (SINE), L1ME

(LINE),

NM_138465

90_F_6 2.6 0.0 7p22.2 No AluSx (SINE)

89_G_5 2.6 0.5 2q21 No MIRm (SINE)

48_C_11 2.6 0.2 12q13.2 No CDKN1B (P27) intron2. NM_204256

50_G_12 2.5 0.0 1q32.1 No Hypothetical protein (CHIT1) NM_003465

22_G_5 2.5 1.0 21p11.2 No MLT1E2 (LTR), BAGE intron2 NM_001187

50_F_11 2.5 0.0 8q24.21 No L2 (LINE), DDEF1 intron2 NM_018482

97_E_5 2.4 1.0 7q21.11 No L1PA5 (LINE)

73_B_6 2.4 0.0 1p36.11 Yes FUCA1, AluJb (SINE) NM_000147

16_A_6 2.4 0.0 9q22.31 Yes NFIL3 NM_005384

13_A_12 2.3 0.4 11q24.2 No CDON intron NM_016952

57_G_6 2.3 0.0 6p21.31 Yes ABCF1 NM_001090

47_A_6 2.3 0.0 5q31.3 No MIR (SINE)

100_H_10 2.3 0.4 9q21.12 No MER58A (DNA)

68_H_12 2.3 0.0 2q37.1 No SPP2 exon2 NM_006944

3_H_5 2.3 0.9 20p11.1 No L1MA9 (LINE)

15_F_6 2.2 0.4 12p12.1 Yes CGI-141 AF151899

77_B_12 2.2 0.7 22q13.2 No MER34D (LTR)

69_G_4 2.1 0.8 6p22.2 No Charlie9 (DNA)

75_A_4 2.1 0.8 1q31.3 No No gene

65_G_4 2.1 0.9 11q14.1 No MER20B (DNA)

90_E_12 2.1 1.5 8p22 Yes hypothetical protein LOC286032 NM_020844.2

15_A_1 2.1 0.9 12q13.12 Yes Hypothetical protein

LOC144233, MIR, MIR3 and

MIRb (SINE)

NM_181708

120_C_12 2.1 0.6 12q21.2 No L2 (LINE)

122_D_11 2.1 0.5 8q23.2 No MER63A (DNA)

47_A_9 2.1 0.0 Not

available§

106_C_12 2.1 0.7 5q21.1 No L1MA8 (LINE)

87_E_6 2.1 0.0 7q21.11 No MIR (SINE)

94_F_6 2.1 0.2 Not

available

50_A_6 2.1 1.4 4p15.2 No MER11C (LTR)

85_A_10 2.1 0.3 14q32.12 Yes SLC24A2 NM_020344

92_E_9 2.1 0.3 12q24.23 No MADE1 (DNA), AluY (SINE)

85_F_3 2.1 1.1 Not

available

122_C_12 2.1 0.7 3q22.3 No MLT1A0 (LTR)

84_H_11 2.1 0.5 Not

available

58_C_12 2.1 0.6 18q22.1 No L1PA7 (LINE), AluSx (SINE)

19_G_5 2.1 1.5 7q36.1 No MLT1E2 (LTR)

98_A_6 2.1 1.4 Not

available

88_D_3 2.1 1.3 10q22.1 No Tigger1 (DNA)

22_A_4 2.1 0.7 16p13.12 Yes MKL2, MER20B (DNA), AluJo

(SINE)

NM_014048

67_A_1 2.1 1.3 3p14.2 No L1PB1 (LINE)

6_A_2 2.1 0.9 11p15.5 No L1ME4A (LINE)

14_A_7 2.1 0.9 1q42.2 No L1ME4A and L3b (LINE)

91_H_12 2.1 1.2 8p12 No L1MB2 (LINE)

10_A_3 2.1 1.0 Not

available

92_G_12 2.1 1.0 Not

available

90_H_3 2.1 1.2 8q24.13 Yes L2 (LINE), AluSx (SINE),

WDR67

NM_145647

90_G_11 2.1 1.2 Not

available

47_A_5 2.1 1.1 6p22.1 No MIR (SINE)

8_D_3 2.1 1.5 Not

available

90_H_12 2.1 0.9 4q21.21 No No gene

29_G_1 2.1 1.1 5q23.1 No MER51a (SINE), L1PA16

(LINE)

16_G_7 2.1 1.4 16q12.1 No MIRb (SINE)

22_B_11 2.1 0.7 15q25.1 No Zaphod (DNA), L2 (LINE)

65_G_12 2.1 1.3 3q29 No MLT1A0 (LTR), L2 (LINE)

61_A_4 2.1 0.5 17q21.31 No AluSc (SINE)

14_H_10 2.1 0.5 5p13.2 Yes Hypothetical protein FLJ25439,

AluSx (SINE)

NM_144725

122_C_10 2.1 0.4 2q24.2 No No gene

81_A_11 2.1 0.5 1q32.1 Yes BTG2 NM_006763

17_G_10 2.1 0.0 Not

available

47_A_1 2.1 1.1 1p13.1 No L1ME2 (LINE)

85_G_11 2.1 0.9 6p21.33 No AluJo (SINE)

43_E_8 2.1 1.1 11p11.2 No AluSx (SINE)

41_D_11 2.1 1.4 1q13.1 No L1PB4 (LINE)

49_G_5 2.1 1.0 4p31.3 No No gene

123_G_1 2.1 0.0 Not

available

81_F_1 2.1 1.3 4q13.3 No L1MD4 (LINE)

98_B_11 2.1 0.2 Not

available

119_A_8 2.1 0.1 14q12 No AluJo and MIRm (SINE)

49_A_5 2.1 0.2 7q21.13 No No gene

62_E_1 2.1 0.9 21q22.3 Yes Hypothetical protein C21orf58 NM_058180

122_E_3 2.1 1.3 7q31.1 No No gene

86_G_10 2.1 0.0 10q21.3 No L1ME (LINE)

18_D_4 2.1 1.5 Not

available

42_E_6 2.1 1.2 11p12 No L2 (LINE)

42_A_5 2.1 1.5 3q27.3 Yes No gene

17_H_12 2.1 1.2 Not

available

86_H_1 2.1 0.0 18q23 No TGG simple repeat

74_A_5 2.1 1.0 Not

available

91_G_6 2.1 1.1 6p22.1 No HERVS71(LTR)

121_D_3 2.1 0.8 10p14 Yes No gene

120_A_4 2.1 1.1 16q23.3 No L1MA4 (LINE), FLAM_A

(SINE), MSTB1 (LTR)

14_A_6 2.1 1.0 7q31.33 No L1P (LINE), MLT1J1 (LTR)

46_D_9 2.1 1.1 11q24.2 No PUS3 NM_031307

43_B_2 2.1 0.5 17q21.32 No AluSx (SINE)

80_G_9 2.1 0.9 4p15.1 No L1PA13 (LINE)

80_F_3 2.1 0.7 Not

available

14_H_3 2.1 0.8 Not

available

94_E_7 2.1 1.2 16q21 No L1MC3 (LINE)

25_E_4 2.1 0.4 Not

available

49_A_7 2.1 1.3 17q21.32 Yes ZNF652 NM_014897

50_D_2 2.1 1.1 1p34.3 No AluSx (SINE)

100_H_4 2.1 0.7 15q11.2 No L1P4 (LINE)

9_B_2 2.1 1.3 16p13.3 No AluSq (SINE), L1MC4 (LINE)

93_A_10 2.1 0.2 7q31.33 No L1ME4a (LINE)

81_A_9 2.1 1.2 17p11.2 No L2 (LINE)

48_D_5 2.1 0.1 4q35.2 No L1MA4 (LINE)

124_A_9 2.1 1.5 3q26.31 No MER85 (DNA), L1ME1 (LINE)

119_D_12 2.1 1.3 1q43 No MER33 (DNA), L1ME (LINE)

62_D_6 2.1 0.4 11q23.2 No AluSq (SINE)

57_C_4 2.1 1.0 6p22.2 No HIST1H2BD, MER101(LTR) NM_138720

7_F_10 2.1 1.1 Not

available

19_E_2 2.0 1.1 6p12.3 Yes MIR (SINE), PLA2G7 NM_005084

73_G_10 2.0 0.7 3p14.3 No L2 (LINE)

107_H_11 2.0 0.6 8q12.1 No L1MC3 (LINE)

82_A_11 2.0 0.5 15q11.2 No L1MC3 (LINE)

64_A_5 2.0 0.4 17q21.33 Yes AluJ (SINE)

88_G_9 2.0 1.3 19q13.42 No MLT1E2 (LTR), L1MC4 (LINE)

122_H_12 2.0 0.7 5p13.2 No MIR3 (SINE), L1PB2 (LINE)

23_G_5 2.0 1.0 21p11.1 No MLT1E2 (LTR)

8_C_1 2.0 0.4 17q25.3 Yes L2 (LINE)

92_E_2 2.0 1.0 5p12 No MER51B-int (LTR), AluY

(SINE)

14_A_12 2.0 0.4 Not

available

29_G_12 2.0 0.8 9q34.2 Yes REXO4, LTR2 (LTR) NM_020385

98_D_5 2.0 0.6 3p25.1 No MIRm and MIRb (SINE)

57_E_11 2.0 0.7 8q23.1 No AluSx and MIRb (SINE)

67_B_7 2.0 1.3 3q26.33 Yes ATP11b and AluY (SINE) NM_014616

94_E_6 2.0 1.2 16q21 No L1MC3 (LINE), FRAM (SINE)

34_F_10 2.0 1.0 4q33 No NEK1 intron NM_012224

49_E_5 2.0 0.1 14q24.3 No AHSA intron NM_012111

24_C_11 2.0 1.0 14q21.3 No HAL1 (LINE), LTR22C (LTR)

11_E_12 2.0 1.0 11p15.2 Yes BTBD10, L2 (LINE) NM_032320

121_D_12 2.0 1.3 9q34.3 No Hypothetical protein

LOC389813

NM_001080482

44_F_5 2.0 0.9 3q25.32 No L1ME2 (LINE)

29_B_2 2.0 1.4 8q12.1 Yes No gene

45_A_9 2.0 0.4 2q22.1 No No gene

65_E_10 2.0 1.4 11p15.2 No SOX6 NM_033326

89_C_4 2.0 0.4 18q21.33 No MER107 (DNA)

125_A_9 2.0 1.5 3q26.31 No MER85 (DNA), L1ME1 (LINE)

18_G_5 2.0 1.0 2p11.1 No MLT1E2 (LTR)

8_C_2 2.0 0.2 20p11.23 Yes MIR (SINE)

46_C_2

120_D_5

54_C_8

2.0

2.0

2.0

1.5

1.3

0.7

3p25.1

13q12.13

5q11.2

No

No

No

L1M4 (LINE)

L1MB4 (LINE)

LTR49-int (LTR)

Clones with both high H3-K27 mono-methylation and high H3-K27 tri-methylation in PC3 by CpG microarray Clone ID* K27

mono- Me

K27

Tri- Me


50_A_3 7.6 3.1 13q12.12 No Harlequin (LTR)

2_G_11 5.8 4.2 3q27.1 No L1MC1 (LINE)

88_D_12 5.4 7.6 9p21.1 No MER44B (DNA)

54_A_4 5.1 4.6 Not available§

87_E_11 5.1 6.3 No data

51_C_8 4.6 2.3 5q33.2 No L1M3f (LINE)

89_G_7 4.4 2.2 10p15.2 No MER57A (LTR), L1MA8

(LINE)

89_D_6 4.3 6.2 7q22.2 AluJo (SINE)

94_G_1 4.0 2.0 2p25.3 No MLT1L (LTR)

49_C_9 4.0 4.0 15q14 No L1 (LINE)

121_A_7 4.0 14.5 2q21.2 No AluSx (SINE)

118_C_5 4.0 3.0 2q11.2 Yes MIRb (SINE), MER96 (DNA)

43_E_6 3.9 6.8 Not available

62_D_10 3.8 5.4 3p14.3 No MLT1E3 (LTR)

98_F_2 3.6 4.5 Not available

28_G_1 3.5 2.6 5q23.1 No MER51A (LTR), L1PA16

(LINE)

118_E_6 3.5 4.3 3q13.11 No AluJo (SINE), L1MC3 (LINE)

88_D_1 3.4 2.5 11q13.3 No MER113 (DNA), MIR (SINE)

124_C_6 3.4 4.5 4 random L2 (LINE)

15_A_6 3.4 3.8 Not available

90_G_7 3.3 3.8 2q31.1 No No gene

120_E_12 3.3 5.6 17q24.3 No No gene

6_D_10 3.2 2.6 3p13 No L1MC1 (LINE), AluSx (SINE)

46_B_8 3.1 4.0 2q35 No L1MA2 (LINE)

45_A_5 3.0 3.8 4q32.3 No MLT1L (LTR)

116_C_5 3.0 2.2 2q14.1 No L1M1 (LINE)

5_D_10 3.0 2.3 3p13 No L1MC1 (LINE), AluSx (SINE)

17_A_10 2.9 2.0 3q26.1 No LTR8A (LTR)

14_D_3 2.9 2.9 9p13.2 Yes MER5A (DNA)

90_C_3 2.8 3.8 14q24.2 Yes SFRS5 NM_006925

70_G_10 2.8 10.9 9p21.3 No No gene

20_E_9 2.8 2.2 4q26 No L1PA14 (LINE)

87_B_10 2.7 3.1 3q24 No MIRb (SINE)

73_E_4 2.7 2.0 2q32.1 No AluSx (SINE)

51_G_2 2.7 2.6 6p22.1 No LTR6A (LTR)

127_A_11 2.6 4.1 9q34.11 No MER66B (LTR)

98_G_6 2.6 4.0 12q13.11 Yes LTR8 (LTR), Hypothetical

protein MGC5576

NM_024056

98_A_4 2.5 5.0 6p22.2 No AluSx and FRAM (SINE)

78_G_1 2.4 5.5 6p22.1 No L1MD2, L1MB4 (LINE),

tRNA-Ala-GCY (tRNA)

118_C_11 2.4 6.1 1p31.1 No MIRb (SINE), MLT1D(LTR)

27_F_5 2.3 2.4 16p11.2 No L1MB7 (LINE)

119_C_11 2.3 2.1 18q12.1 Yes MIRb (SINE),

123_C_12 2.3 4.5 3q22.3 No MLT1A0 (LTR),

78_H_4 2.3 7.3 2q37.3 No LTR2C (LTR)

88_C_1 2.3 2.9 6q13 No MER55B (LTR), L3 (LINE)

Clones with high H3-K27 tri-methylation in PC3 by CpG microarray Clone ID* K27

mono- Me

K27

Tri- Me


55_H_5 0.6 7.6 20q13.13 Yes MIRb (SINE)

61_F_8 0.8 7.3 Xq21.33 No L1MB8 (LINE)

125_D_6 0.8 6.7 17q25.3 Yes No gene

25_F_2 0.8 6.7 3q24.2 No RAR beta2 NM_016152

14_D_8 0.5 5.6 22q11.21 No MLT1B (LTR)

107_C_8 1.0 5.5 3q22.2 No L2 (LINE)

41_D_9 0.6 5.1 12q13.12 Yes WNT1 NM_005430

74_F_5 0.6 5.1 19q13.32 Yes AluSc (SINE), EML 2 intron NM_012155

87_C_2 0.8 4.4 15q26.2 Yes AluSx (SINE)

25_G_9 1.0 4.3 8q22.1 YES EST fragment

122_B_1 0.6 4.1 15q25.1 Yes CRABP1 intron NM_004378

26_H_10 1.0 4.1 3q25.31 Yes KCNAB1 isoform3 BC043166

121_D_9 0.8 4.0 15q25.1 Yes MIR3 (SINE)

103_H_8 0.6 4.0 6p11.2 No EST fragment

115_G_4 0.8 3.9 3q13.11 Yes ALCAM intron NM_001627

43_C_6 0.5 3.9 5q22.3 Yes TRIM 36 NM_018700

115_G_1 0.6 3.7 3q25.2 No No gene

96_G_5 0.6 3.7 5q14.3 No MER67D (LTR)

96_G_6 0.3 3.4 1p36.33 Yes SAMD11 NM_152486

108_C_8 0.6 3.3 13q31.1 No No gene

5_D_4 0.6 3.1 1q23.3 Yes LMX1A intron NM_177398

119_E_11 0.9 3.1 7p14.3 No LTR2C (LTR)

112_G_4 0.4 3.1 14q31.1 No Neurexin 3 beta (exon10) NM_138970

42_D_1 0.5 3.0 11q22.3 Yes AMPA4 (GRIA4) intron NM_000829

113_H_7 0.8 3.0 14q32.13 No No gene

8_A_5 0.4 3.0 15q26.1 Yes RGMA NM_020211

86_A_7 0.5 2.9 19q13.33 No MIR (SINE)

6_D_4 0.6 2.8 22q12.1 No MIRb (SINE), HPS-4 NM_022081

98_C_9 0.3 2.7 16p12.3 No XYLT1 intron NM_022166

3_H_10 0.5 2.7 10q24.2 Yes NKX2-3 NM_145285

43_B_9 0.4 2.7 10q26.11 Yes No gene

97_B_12 0.6 2.7 17q21.31 Yes MAPT intron NM_016835

122_D_5 0.4 2.6 17q25.1 Yes OTOP3 NM_178233

5_A_8 0.5 2.6 1q32.2 Yes CR2 NM_001877

114_G_1 0.4 2.5 15q24.1 Yes KIAA1465 NM_020851

9_H_6 0.7 2.4 10q24.31 Yes PAX2 splice variant AY153483

99_C_9 0.2 2.4 1p36.33 Yes SAMD11 NM_152486

97_C_9 0.2 2.2 1p36.33 Yes SAMD11 NM_152486

82_C_6 0.6 2.2 12q13.12 Yes Hypothetical protein

FLJ13236

NM_024902

62_E_8 0.6 2.2 17q21.32 No IMP intron NM_006546

94_G_11 0.7 2.1 10q26.12 Yes MER5A1 (DNA)

95_G_12 0.7 2.1 Not available§

18_A_2 0.8 2.1 8q24.12 Yes COL14A1 NM_021110

61_E_2 1.0 2.1 3q26.31 No No gene

103_F_11 0.7 2.1 18q12.1 Yes NOL4 NM_003787

85_F_12 1.0 2.1 5p15.33 Yes IRX1 NM_024337)

96_G_1 0.8 2.1 5p14.3 No MER67D (LTR)

110_H_5 1.8 2.1 Not available


93_C_8 0.7 2.1 5p15.33 Yes IRX4 NM_016358

78_C_11 1.5 2.1 Not available

94_F_7 0.9 2.1 6p22.1 No AluSx (SINE)

94_B_2 1.2 2.1 Not available

123_D_9 0.8 2.1 20p13 Yes SOX12 NM_006943

126_G_9 1.6 2.1 Not available

68_A_1 1.1 2.1 12p13.32 Yes KCNA1 BC043166

102_A_7 1.3 2.1 2q11.1 No AluJo (SINE)

24_A_2 1.0 2.1 8q24.12 Yes COL14A1 NM_021110

28_F_7 1.1 2.0 18q12.2 No L2 (LINE)

68_C_5 0.9 2.0 2p21.3 Yes No gene

78_E_6 0.7 2.0 7q21.12 No No gene

31_F_3 1.1 2.0 2p13.3 No MER63 (DNA)

31_G_3 0.7 2.0 17q25.3 Yes No gene

70_G_5 1.0 2.0 Xq11.2 Yes Hypothetical protein

LOC139886

NM_001012968


100_D_6 1.0 2.0 2q35 Yes Hypothetical protein

MGC50811 3'UTR

NM_198559

70_C_1 1.1 2.0 7p22.1 No No gene

69_C_4 1.9 2.0 2p16.1 Yes No gene

53_B_7 0.5 2.0 2p16.1 Yes No gene


60_A_11 1.0 2.0 14q11.2 Yes RNASE11 variant NM_145250

87_A_8 1.0 2.0 8q23.3 No CSMD3 NM_198123

96_F_7 0.3 2.0 5p14.3 No MER67D (LTR)

121_A_6 1.1 2.0 6q14.1 No L1ME4a (LINE)

102_H_1 0.5 2.0 11q24.1 Yes No gene

107_E_12 0.7 2.0 16p13.3 Yes AluSg (SINE)

97_F_2 1.8 2.0 1q32.3 No No gene

90_F_11 0.8 2.0 2q32.3 No No gene

121_C_2 1.0 2.0 9q34.2 Yes WDR5 NM_017588

101_H_4 2.0 2.0 15q11.2 No L1PA16 (LINE)

86_D_4 0.7 2.0 15q15.1 Yes DLL4 NM_019074

29_C_11 1.3 2.0 18q21.1 No L2 (LINE), MSTA (LTR)

82_H_10 1.3 2.0 4q13.3 Yes Hypothetical protein

DKFZp781I1455

CR933645

54_E_11 1.1 2.0 11q13.1 Yes STIP1 NM_006819


115_C_5 1.4 2.0 6q25.1 No MLT1J (LTR), MER58B (DNA)


88_D_6 1.2 2.0 2p11.1 No MER4D1 (LTR)

21_E_11 1.4 2.0 15q22.1 No MIRb (SINE)

19_E_5 1.4 2.0 15q14 Yes RASGRP1 NM_005739

36_F_7 0.8 2.0 7q36.3 Yes MIR (SINE), EN2 3'-UTR NM_001427


91_C_11 0.9 2.0 Xq22.33 No LTR8 (LTR)

67_H_8 1.2 2.0 11q23.3 Yes IGSF4 NM_014333

30_A_11 1.5 2.0 13q12.2 No MER112 (DNA)

106_E_6 0.7 2.0 20p12.2 No SNAP25 intron NM_130811

79_E_11 1.1 2.0 10p13 Yes Hypothetical protein

LOC221061

NM_001010924

49_C_11 1.2 2.0 12q21.2 Yes Hypothetical protein (gluno)

mRNA

123_F_2 1.3 2.0 20q13.13 No No gene

33_C_4 1.6 2.0 12p12.3 Yes WBP11, hypothetical protein

LOC144608

NM_016312,

NM_175874

80_A_5 1.9 2.0 9q12 No MSPD2 (LTR)

118_E_11 1.7 2.0 1p31.1 No L1MC2 (LINE)

48_E_11 1.5 2.0 17q23.2 Yes TBX2, Hypothetical protein

LOC440450

NM_005994

77_A_11 1.2 2.0 17q21.31 Yes Hypothetical protein

FLJ32379

AK056941

75_B_3 0.9 2.0 11p11.2 Yes No gene

116_D_3 1.1 2.0 5p13.3 Yes CDH6 NM_004932

60_D_1 0.6 2.0 Not available

3_D_1 0.3 2.0 15q13.2 Yes no gene



47_A_2 1.3 2.0 7q36.3 No no gene

98_E_4 0.9 2.0 7q36.3 Yes no gene


55_F_7 1.1 2.0 14q23.1 Yes LOC387990 NM_207377


128_A_11 1.5 2.0 9q34.11 No MER66B (LTR)



19_F_10 0.4 2.0 7p14.1 No ELMO1 exon2 NM_130442

111_B_7 0.7 2.0 9p21.1 No No gene

76_E_10 1.1 2.0 17q21.33 No L1ME3A (LINE)

108_H_4 0.8 2.0 14q22.1 Yes TXNDC NM_030755

94_D_5 1.4 2.0 6q21 Yes LACE1 NM_145315

10_E_5 1.1 2.0 18p11.32 Yes SMCHD1, L2 (LINE) NM_015295

104_C_11 0.7 2.0 14q24.2 No L2 (LINE)

21_E_4 1.9 2.0 4q35.1 Yes No gene

5_A_1 1.6 2.0 11p15.4 Yes ILK, L2 (LINE) NM_001014794

58_G_3 0.8 2.0 12q11.23 No No gene

114_F_5 1.5 2.0 2q36.1 No L1PB1 (LINE)

77_F_12 1.3 2.0 5q21.1 No MIR(SINE)

68_F_11 1.1 2.0 10q24.2 Yes HPSE2 intron1 NM_021828


66_D_12 0.6 2.0 12q23.1 Yes Hypothetical protein

LOC120935

NM_182496

97_B_10 0.6 2.0 Chr19 No Chr 19 multiple hit

8_G_11 1.7 2.0 9q21.33 Yes HBLD2, L1MB5 (LINE) NM_030940

55_F_4 0.8 2.0 17p12 No TRIM16, AluSx and Alu Yb8

(SINE)

NM_006470

34_H_12 1.3 2.0 4q21.3 No MIR3 (SINE)

18_F_11 1.1 2.0 4q35.1 Yes MIR (SINE)

119_B_8 1.3 2.0 4q13.3 No L2 (LINE)

89_G_9 1.3 2.0 Xq21.3 Yes No gene

76_E_11 0.8 2.0 1p22.2 Yes No gene

40_E_5 1.8 2.0 1p36.12 Yes AOF2 NM_015013

51_H_8 0.6 2.0 3p14.2 Yes ZNF312 NM_018008

27_F_2 0.9 2.0 3p24.2 Yes RAR beta2 NM_016152

94_C_4 1.2 2.0 19q13.42 No AluJb (SINE)

31_F_10 1.0 2.0 2p21 Yes No gene

22_F_6 1.0 2.0 4q12 Yes GSH-2 BC075089

107_B_4 0.9 2.0 9p13.1 No L2 (LINE)

106_B_4 1.0 2.0 19q13.32 No MIRb (SINE)

9_E_3 1.0 2.0 10q24.32 No MIRb (SINE)

11_D_8 0.5 2.0 1q41 Yes MARK1 NM_018650


81_A_5 1.6 2.0 3p21.31 No No gene

17_D_11 0.8 2.0 17q12 Yes TCF2 NM_000458

80_D_10 1.3 2.0 15q21.3 No HAL1 (LINE)

5_B_2 1.6 2.0 1q21.1 No LTR75 (LTR), MER45B

(DNA)

2_B_3 0.9 2.0 5p12 No FGF10 NM_004465

120_E_6 1.4 2.0 4p15.2 No No gene

87_G_12 1.3 2.0 10q23.32 No L1PA13 (LINE)

111_F_7 0.5 2.0 12p12.2 No FRAM (SINE), L3 (LINE)

83_H_1 1.1 2.0 15q11.2 No L1P4 (LINE)

111_G_1 1.8 2.0 9p21.2 No MIRb (SINE)

85_D_5 0.8 2.0 2p13.2 No MIR3 (SINE)

28_D_3 0.6 2.0 6q23.3 No AluJb (SINE)


92_B_7 1.5 2.0 5q31.3 No AluSg (SINE)

36_F_1 0.6 2.0 2q36.2 No MER5B (DNA)

78_F_3 1.5 2.0 4q21.21 No No gene

69_B_8 0.9 2.0 8q23.3 No L1MA10 (LINE)

61_G_10 1.1 2.0 13q14.13 No LTR-38int (LTR)

22_E_4 1.6 2.0 4q35.1 Yes HELT NM_001029887

49_D_12 0.5 2.0 3q13.31 No No gene

97_E_8 1.1 2.0 16q12.2 Yes MIRb (SINE), IRX3 3'UTR NM_024336

56_E_5 0.5 2.0 1q41 No L1Mec (LINE)

98_G_9 1.0 2.0 18q21.32 Yes RAX NM_013435

85_B_9 0.8 2.0 7p21.3 No MIRb (SINE)

116_F_7 1.4 2.0 11q23.3 No MLT1E1 (LTR)

79_E_6 0.9 2.0 9q34.11 Yes PPP2R4 NM_178000


1_F_7 0.5 2.0 11p13 Yes SLC1A2, MIR (SINE) NM_004171

119_H_1 1.0 2.0 1q32.1 Yes No gene


33_A_11 1.0 2.0 7p11.2 No MER63C (DNA)

10_G_12 0.6 2.0 19q13.32 Yes ERCC1, L2 (LINE)

41_D_1 0.5 2.0 8q24.3 No L1ME4a (LINE), MER20

(DNA)

9_G_9 0.8 2.0 10q24.31 Yes PAX2 AY153483

57_B_8 0.6 2.0 4q32.3 No L2 (LINE), LTR50 (LTR)

57_B_7 0.6 2.0 13q21.31 No LTR16A (LTR)

120_C_5 1.5 2.0 11q13.3 No AluSx (SINE)

76_G_12 1.3 2.0 9q33.3 Yes MIR3 (SINE), L2 (LINE)




96_F_9 1.0 2.0 14q21.3 No AluY (SINE)


18_E_8 1.0 2.0 15q21.3 Yes No gene

47_F_12 1.5 2.0 2q22.1 No HAL1 (LINE)

36_F_5 0.9 2.0 5p15.31 No No gene

118_A_5 0.9 2.0 10p11.23 No L2 (LINE)

95_E_4 1.9 2.0 19q13.41 Yes No gene

30_C_11 1.5 2.0 1p34.3 Yes CGI-94 (UTP11L) NM_016037

28_A_11 0.9 2.0 13q32.3 No No gene

120_H_12 1.5 2.0 15q21.1 Yes FBN1 NM_000138


58_D_5 0.8 2.0 12p12.2 Yes Hypothetical protein,

LOC441762

AY587847

53_B_9 0.5 2.0 12q24.21 Yes TBX5 NM_000192

79_H_6 0.9 2.0 10p11.23 Yes Hypothetical protein

LOC220929

NM_182755

11_F_4 0.6 2.0 1p22.2 No L1HS (LINE)

74_B_6 1.8 2.0 10p14 No No gene


28_G_9 0.8 2.0 4q27 No KIAA1109 intron NM_015312


115_H_9 1.5 2.0 8q24.12 No MLT1D (LTR)

119_A_12 0.9 2.0 5q31.1 Yes QP-C, MIRb (SINE) BC090048


93_B_9 0.8 2.0 13q34 No No gene

26_G_9 1.0 2.0 16p12.3 Yes Hypothetical protein

LOC112479 (EXOD1),

NEF-sp, LTR10C (LTR)

NM_080663,

NM_030941


15_G_8 1.5 2.0 16p13.11 No AluJo (SINE)


76_F_6 1.3 2.0 9q22.2 No AluJo (SINE), L1M4b (LINE)


121_D_6 1.3 2.0 1q22 Yes RHBG BC065218

61_H_2 0.9 2.0 7p22.1 No FLAM_C (SINE)

114_E_9 0.8 2.0 Mix

29_A_11 1.0 2.0 13q32.3 No gene

100_C_12 0.8 2.0 4q28.3 No LTR16B (LTR)

87_A_9 1.0 2.0 20q13.33 No MIRb (SINE)

121_F_7 1.4 2.0 3p14.3 Yes Wnt5a NM_003392


87_F_6 1.6 2.0 17p13.2 Yes ALOX15 NM_001140

6_G_4 0.8 2.0 13q14.2 Yes EBPL delta8-delta7 NM_032565

84_F_2 1.2 2.0 15q25.1 Yes IREB2 NM_004136

35_A_11 1.8 2.0 12q24.13 Yes MIRb (SINE), L2 (LINE)


2_H_6 0.7 2.0 2q31.1 Yes HoxD11 variant NM_021192

34_G_12 1.4 2.0 11q22.2 No MER5a and MER5b (DNA)

63_A_7 1.5 2.0 12q13.13 Yes HoxC5 NM_018953

59_D_2 1.4 2.0 2p13.3 Yes No gene

46_F_12 1.7 2.0 2q22.1 No HAL1 (LINE)

92_C_5 0.8 2.0 8p21.2 No MIRb (SINE)

82_E_6 1.0 2.0 10q22.1 Yes SLC29A NM_004955


28_E_10 1.7 2.0 8q24.12 No MIRm (SINE)

109_D_1 1.1 2.0 7p14.1 No MIR3 (SINE)


67_C_8 1.2 2.0 8p21.2 No L1PA3 (LINE)

84_C_6 1.2 2.0 7q33 Yes Hypothetical protein

HSPC049, L1ME4a (LINE)

NM_014149

103_A_10 1.8 2.0 5q31.3 Yes TAF7 NM_005642

107_C_6 1.1 2.0 11q14.3 No No gene

5_B_9 0.6 2.0 16q24.1 No No gene

47_C_2 1.4 2.0 3p25.1 No L1M4 (LINE)

87_D_1 1.6 2.0 11q13.3 No MIR and AluSc (SINE),

MER113 (DNA)

25_H_9 0.7 2.0 2q34 Yes ERBB4 NM_005235

27_A_6 0.7 2.0 14q32.12 No HERVH (LTR)

40_B_8 1.4 2.0 12p12.1 Yes ST8SIA1 NM_003034

122_G_5 0.9 2.0 1p32.2 No No gene

56_B_9 0.7 2.0 Xq22.2 Yes Hypothetical protein

LOC139231

NM_207318

68_B_3 1.7 2.0 14q11.2 Yes NFATC4 NM_004554

117_D_3 0.7 2.0 6q22.31 No No gene


54_E_12 1.4 2.0 22q13.1 Yes PGEA1 NM_001002880

109_B_7 0.8 2.0 1p36.12 Yes USP48 NM_032236

115_H_6 1.4 2.0 2p25.3 No MIRb (SINE)

98_B_7 0.8 2.0 4q25 Yes LEF1.1 variant NM_016269

22_H_2 0.8 2.0 3q24.2 No No gene

79_C_3 1.5 2.0 4q32.2 Yes NPY1R NM_000909

30_G_8 0.8 2.0 2p21 Yes Hypothetical protein

LOC400951 variant

5_D_2 0.5 2.0 7q36.3 Yes No gene


117_E_11 1.5 2.0 1p31.1 No L1MC2 (LINE)

79_D_8 0.9 2.0 20p12.2 No L1ME3A (LINE)

27_C_8 1.6 2.0 19q13.43 Yes ZNF256 NM_005773

67_D_6 1.6 2.0 3q28 No MIRb (SINE)

68_D_1 1.5 2.0 15q22.2 Yes CA12 isoform 1 precursor NM_001218

124_H_8 0.8 2.0 18q23 Yes ZNF516, FLJ44313 NM_014643,

AK126293

108_H_2 1.8 2.0 11p15.1 No L1MB4 (LINE)

57_F_1

127_G_9

59_B_9

51_F_2

122_D_9

0.9

1.3

2.0

1.3

0.8

2.0

2.0

2.0

2.0

2.0

19p13.3

11q24.1

12q24.21

5q22.1

20p13

No

No

No

No

Yes

TCF3 variant

MIR (SINE)

L2 (LINE)

MIR (SINE)

SOX12

NM_003200

NM_006943

*; Sequence is available from the Der Laboratory CpG Island Microarray Bioinformatics web site (http://derlab.med.utoronto.ca/CpGIslands/CpGIslandsMain.php). ¶; CpG island within 1kb of clone. §; Sequence information with the spot is not available on the web site. †; Accession numbers are not provided for repeats.

Supplement Table 2. Top 200 genes with high H3-K27 tri-methylation in PC3 by 88K microarray

Gene name Loci P value Probe location* CpG island¶ Accession no.

PGR chr11 1.68E-04 chr11:100504830-100504875 Yes NM_000926

KIRREL3 chr11 1.77E-04 chr11:126377038-126377097 Yes NM_032531-NM_173579

OR6X1 chr11 1.79E-04 chr11:123130316-123130376 No NM_001005188

ARG99 chr12 1.83E-04 chr12:029828882-029828942 Yes NM_175861

SLN chr11 1.84E-04 chr11:107087717-107087777 No NM_003063

ARMCX4 chrX 1.86E-04 chrX:100545653-100545713 Yes NM_152583

IFNG chr12 1.90E-04 chr12:066839366-066839426 No NM_000619

C18orf26 chr18 1.91E-04 chr18:050409117-050409177 No NM_173629

MC2R chr18 1.96E-04 chr18:013875386-013875444 No NM_000529

TECTA chr11 1.97E-04 chr11:120477639-120477699 No NM_005422

ENTPD1 chr10 2.03E-04 chr10:097504988-097505048 No NM_001776

AQP4 chr18 2.03E-04 chr18:022699327-022699387 No NM_001650

SAA4 chr11 2.10E-04 chr11:018213797-018213850 No NM_006512

CLEC1B chr12 2.11E-04 chr12:010042994-010043054 No NM_016509

AMACO chr10 2.13E-04 chr10:115988009-115988069 No NM_198496

NOV1 chr11 2.16E-04 chr11:004563674-004563734 No NM_144663-NM_001005170

RNASE12 chr14 2.18E-04 chr14:020128385-020128444 No NM_001024822

GPM6B chrX 2.29E-04 chrX:013594366-013594426 No NM_001001996


ZNFN1A3 chr17 2.35E-04 chr17:035274755-035274815 Yes NM_183232-NM_198844

ZPBP2 chr17 2.35E-04 chr17:035274893-035274953 Yes NM_183232-NM_198844

KLRF1 chr12 2.38E-04 chr12:009871318-009871378 No NM_016523

OR6C6 chr12 2.42E-04 chr12:053974965-053975025 No NM_001005493

FLJ25477 chr13 2.44E-04 chr13:024643476-024643521 Yes NM_152704

PCK1 chr20 2.55E-04 chr20:055568522-055568582 No NM_002591

LIN28B chr6 2.56E-04 chr6:105510621-105510681 No NM_001004317

MGC35212 chr16 2.57E-04 chr16:001850226-001850286 No NM_152764

SLC8A3 chr14 2.59E-04 chr14:069704625-069704678 Yes NM_033262

SPG3A chr14 2.62E-04 chr14:050095702-050095754 Yes NM_015915

ZNF663 chr20 2.67E-04 chr20:044518744-044518804 No NM_173643

GPHB5 chr14 2.69E-04 chr14:062854007-062854067 No NM_145171


FLJ00060 chr19 2.71E-04 chr19:059738959-059739018 No NM_033206

DLGAP1 chr18 2.73E-04 chr18:003835115-003835175 No NM_001003809

KRTAP13-1 chr21 2.74E-04 chr21:030689436-030689496 No NM_181599

USP26 chrX 2.75E-04 chrX:131887448-131887505 No NM_031907

AMICA1 chr11 2.79E-04 chr11:117588512-117588572 No NM_153206

GPR15 chr3 2.80E-04 chr3:099724556-099724601 No NM_019895-NM_005290

ENPP2 chr8 2.85E-04 chr8:120719943-120720003 No NM_006209

SPIC chr12 2.86E-04 chr12:100372102-100372162 No NM_152323

OR2AG1 chr11 2.91E-04 chr11:006761992-006762052 No NM_001004489

ASB15 chr7 2.92E-04 chr7:122842184-122842244 No NM_080928

MUM1L1 chrX 2.93E-04 chrX:105217622-105217682 No NM_152423

TNIP3 chr4 2.94E-04 chr4:122442723-122442783 No NM_024873

CRNKL1 chr20 2.98E-04 chr20:019981360-019981405 No NM_016652

CD1D chr1 2.99E-04 chr1:154961900-154961960 No NM_001766

POSTN chr13 3.02E-04 chr13:037070547-037070607 No NM_006475

SLC30A8 chr8 3.03E-04 chr8:118215524-118215584 No NM_173851


TRIM36 chr5 3.11E-04 chr5:114543356-114543407 Yes NM_001017398

NRG4 chr15 3.15E-04 chr15:074090529-074090589 No NM_138573

LOC283514 chr13 3.20E-04 chr13:045323680-045323735 No NM_198849

TPH1 chr11 3.23E-04 chr11:018018701-018018761 No NM_004179

ABCA9 chr17 3.27E-04 chr17:064568429-064568489 No NM_080283

ABCB5 chr7 3.28E-04 chr7:020459504-020459564 No NM_178559

ICA1 chr7 3.31E-04 chr7:008075444-008075489 Yes NM_004968

HABP2 chr10 3.33E-04 chr10:115301828-115301874 No NM_004132

LILRB5 chr19 3.33E-04 chr19:059452739-059452789 No NM_006840

ACADL chr2 3.34E-04 chr2:210915664-210915709 Yes NM_001608

C4BPA chr1 3.36E-04 chr1:203664983-203665043 No NM_000715

OR10A7 chr12 3.36E-04 chr12:053900154-053900214 No NM_001005280

TFEC chr7 3.40E-04 chr7:115264490-115264550 No NM_001018058

OR6C74 chr12 3.40E-04 chr12:053926625-053926685 No NM_001005490

NALP14 chr11 3.42E-04 chr11:007015885-007015945 No NM_176822

MOBP chr3 3.45E-04 chr3:039483116-039483176 No NM_182935

SULF1 chr8 3.48E-04 chr8:070540623-070540683 No NM_015170

LONRF2 chr2 3.57E-04 chr2:100383827-100383887 No NM_198461

OR4D10 chr11 3.57E-04 chr11:059000644-059000699 No NM_001004705

HOXB9 chr17 3.60E-04 chr17:044058589-044058642 Yes NM_024017

G6PC2 chr2 3.61E-04 chr2:169582526-169582585 No NM_021176

FLJ40919 chr13 3.63E-04 chr13:042252814-042252874 No NM_182508

ATP1B4 chrX 3.64E-04 chrX:119276985-119277045 No NM_012069

CSMD3 chr8 3.68E-04 chr8:114457960-114458020 No NM_198124

VAX1 chr10 3.71E-04 chr10:118887337-118887386 Yes NM_199131

ATOH1 chr4 3.76E-04 chr4:095106523-095106583 Yes NM_005172

GAS2 chr11 3.77E-04 chr11:022645244-022645296 No NM_177553

PTH chr11 3.78E-04 chr11:013473823-013473883 No NM_000315

hsa-mir-106a chrX 3.81E-04 chrX:133029728-133029788 No hsa-mir-106a

CDH20 chr18 3.84E-04 chr18:057307739-057307798 No NM_031891

C1QTNF7 chr4 3.84E-04 chr4:015017726-015017786 No NM_031911

LEMD1 chr1 3.85E-04 chr1:202122530-202122590 No NM_001001552

RUNX1T1 chr8 3.85E-04 chr8:093144469-093144529 No NM_004349

OR10P1 chr12 3.87E-04 chr12:054316241-054316301 No NM_206899

MGC35118 chr15 3.98E-04 chr15:036013967-036014025 No NM_152453

PHACTR1 chr6 4.01E-04 chr6:012824852-012824912 No NM_030948

ACF chr10 4.06E-04 chr10:052315557-052315617 No NM_138933

ENPP5 chr6 4.07E-04 chr6:046247328-046247388 No NM_021572

IGFL3 chr19 4.08E-04 chr19:051319499-051319550 No NM_207393

DCAL1 chr12 4.13E-04 chr12:009776941-009777001 No NM_172004

NR5A2 chr1 4.14E-04 chr1:196727827-196727887 No NM_003822

ABCA6 chr17 4.16E-04 chr17:064649280-064649340 No NM_080284

NALP9 chr19 4.20E-04 chr19:060941432-060941492 No NM_176820

DRD3 chr3 4.21E-04 chr3:115373204-115373257 No NM_000796

NR1H4 chr12 4.22E-04 chr12:099369679-099369739 No NM_005123

KCNA10 chr1 4.24E-04 chr1:110774023-110774075 No NM_005549

OR1D2 chr17 4.29E-04 chr17:002943850-002943910 No NM_002548

CLCA1 chr1 4.31E-04 chr1:086645752-086645812 No NM_001285

STOML3 chr13 4.33E-04 chr13:038462699-038462759 No NM_145286

SDR-O chr12 4.33E-04 chr12:055614599-055614656 No NM_148897

OR52K1 chr11 4.36E-04 chr11:004465740-004465800 No NM_001005171

OR9Q2 chr11 4.41E-04 chr11:057713810-057713870 No NM_001005283

COL14A1 chr8 4.42E-04 chr8:121331699-121331759 No NM_021110

PIK3CG chr7 4.52E-04 chr7:106098725-106098785 No NM_002649

FLJ44881 chr18 4.54E-04 chr18:072530354-072530412 No NM_207461

OR4D11 chr11 4.54E-04 chr11:059027051-059027111 No NM_001004706

UNQ9356 chr6 4.60E-04 chr6:055299771-055299831 No NM_207410

ALB chr4 4.63E-04 chr4:074634805-074634865 No NM_000477

PRSS7 chr21 4.65E-04 chr21:018697980-018698040 No NM_002772

ASCL4 chr12 4.66E-04 chr12:106670284-106670342 Yes NM_203436

GIMAP7 chr7 4.67E-04 chr7:149649012-149649072 No NM_153236

TAT chr16 4.69E-04 chr16:070167585-070167639 No NM_000353

OR2AT4 chr11 4.70E-04 chr11:074478377-074478426 No NM_001005285

HLA-DQA2 chr6 4.74E-04 chr6:032816451-032816511 No NM_020056

F11 chr4 4.76E-04 chr4:187561422-187561470 No NM_000128

LOXHD1 chr18 4.77E-04 chr18:042435607-042435667 No NM_144612

DEFB126 chr20 4.78E-04 chr20:000070321-000070381 No NM_030931

OR8D1 chr11 4.79E-04 chr11:123685609-123685664 No NM_001002917

CXorf1 chrX 4.83E-04 chrX:144613545-144613605 No NM_004709

AFP chr4 4.87E-04 chr4:074666405-074666465 No NM_001134

OR6C70 chr12 4.88E-04 chr12:054149628-054149688 No NM_001005499

ITK chr5 4.92E-04 chr5:156539587-156539647 No NM_005546

WNT8B chr10 4.98E-04 chr10:102211898-102211958 No NM_003393

IL9 chr5 5.00E-04 chr5:135259614-135259674 No NM_000590

ALDH8A1 chr6 5.02E-04 chr6:135312593-135312653 No NM_022568

GJB6 chr13 5.03E-04 chr13:019702769-019702829 No NM_006783

OR5K4 chr3 5.05E-04 chr3:099554381-099554441 No NM_001005517

LAMB4 chr7 5.15E-04 chr7:107364493-107364553 No NM_007356

NTS chr12 5.16E-04 chr12:084769542-084769602 No NM_006183

TEX15 chr8 5.24E-04 chr8:030825798-030825858 No NM_031271

OR8A1 chr11 5.24E-04 chr11:123944152-123944212 No NM_001005194

CD1A chr1 5.25E-04 chr1:155036133-155036193 No NM_001763

LALBA chr12 5.26E-04 chr12:047249800-047249860 No NM_002289

FGF9 chr13 5.33E-04 chr13:021142921-021142971 No NM_002010

ELMOD1 chr11 5.34E-04 chr11:106966526-106966585 Yes NM_018712

UBD chr6 5.34E-04 chr6:029635480-029635537 No NM_006398

GABRA1 chr5 5.39E-04 chr5:161205977-161206037 No NM_000806

CTLA4 chr2 5.43E-04 chr2:204557288-204557348 No NM_005214

CD86 chr3 5.43E-04 chr3:123257118-123257178 No NM_175862

ASAH2 chr10 5.59E-04 chr10:051678053-051678113 No NM_019893

MBD3L1 chr19 5.63E-04 chr19:008813590-008813650 No NM_145208

MGC50104 chr11 5.66E-04 chr11:110631368-110631428 No NM_198498

GAP43 chr3 5.70E-04 chr3:116824160-116824220 No NM_002045

TFAP2D chr6 5.72E-04 chr6:050788798-050788858 No NM_172238

OR9A2 chr7 5.75E-04 chr7:142240764-142240816 No NM_001001658

GZMH chr14 5.80E-04 chr14:024148431-024148491 No NM_033423

OR52B4 chr11 5.86E-04 chr11:004345840-004345885 No NM_001005161

OR11G2 chr14 5.88E-04 chr14:019734462-019734522 No NM_001005503

OTOR chr20 5.88E-04 chr20:016675988-016676042 No NM_020157

LOC387601 chr11 5.91E-04 chr11:062753585-062753645 No NM_199352

CHAT chr10 5.93E-04 chr10:050486514-050486559 Yes NM_020984

PRG2 chr11 5.95E-04 chr11:056913701-056913759 No NM_002728



OVCH2 chr11 6.07E-04 chr11:007684468-007684528 No NM_198185

ANXA13 chr8 6.11E-04 chr8:124818605-124818665 No NM_001003954

FGF23 chr12 6.29E-04 chr12:004358928-004358973 No NM_020638

TAC1 chr7 6.33E-04 chr7:097005078-097005138 Yes NM_003182

ZIC4 chr3 6.37E-04 chr3:148607180-148607237 No NM_032153-NM_003412

OR2G3 chr1 6.38E-04 chr1:244094123-244094183 No NM_001001914


GYS2 chr12 6.43E-04 chr12:021648901-021648960 No NM_021957

FAM5B chr1 6.44E-04 chr1:173872174-173872219 No NM_207108-NM_021165

ASTN chr1 6.44E-04 chr1:173865863-173865923 Yes NM_207108-NM_021165

GRM3 chr7 6.46E-04 chr7:085917000-085917060 No NM_000840

MGC39827 chr12 6.48E-04 chr12:118235230-118235275 Yes NM_178499

GPR88 chr1 6.49E-04 chr1:100715323-100715383 Yes NM_022049

BLNK chr10 6.59E-04 chr10:098020815-098020875 No NM_013314

RGSL2 chr1 6.61E-04 chr1:179150077-179150137 No NM_032267

EYA1 chr8 6.62E-04 chr8:072430949-072431009 No NM_172059

OR1N2 chr9 6.65E-04 chr9:122394045-122394105 No NM_001004457

IAPP chr12 6.71E-04 chr12:021416414-021416474 No NM_000415

SIGLEC6 chr19 6.71E-04 chr19:056726430-056726475 No NM_001245

MARCO chr2 6.82E-04 chr2:119415372-119415427 No NM_006770

EPB42 chr15 6.85E-04 chr15:041300664-041300714 No NM_000119

CXCR4 chr2 6.88E-04 chr2:136709188-136709242 Yes NM_001008540

IL16 chr15 6.89E-04 chr15:079262237-079262283 No NM_172217

SPRR2G chr1 6.89E-04 chr1:149935346-149935392 No NM_001014291

OR5V1 chr6 6.98E-04 chr6:029431817-029431877 No NM_030876

MGC45562 chr17 6.98E-04 chr17:036074548-036074608 No NM_152349


ERG chr21 7.00E-04 chr21:038955535-038955581 Yes NM_004449

SIGLEC7 chr19 7.02E-04 chr19:056336425-056336470 No NM_014385

ELMO1 chr7 7.12E-04 chr7:037261780-037261825 Yes NM_014800

C1orf164 chr1 7.14E-04 chr1:044540053-044540101 Yes NM_018150

IMP-1 chr17 7.14E-04 chr17:044428936-044428981 Yes NM_006546

SMR3B chr4 7.17E-04 chr4:071428683-071428743 No NM_006685

TREM1 chr6 7.23E-04 chr6:041362081-041362135 No NM_018643

ARPP-21 chr3 7.25E-04 chr3:035656656-035656708 No NM_016300

ATOH7 chr10 7.25E-04 chr10:069661239-069661284 Yes NM_145178

TAS2R1 chr5 7.26E-04 chr5:009682915-009682975 No NM_019599

OTC chrX 7.29E-04 chrX:037966658-037966718 No NM_000531

CHRM2 chr7 7.32E-04 chr7:136010234-136010294 Yes NM_001006627

EN2 chr7 7.43E-04 chr7:154749041-154749086 Yes NM_001427

C1orf114 chr1 7.47E-04 chr1:166128095-166128149 Yes NM_021179

KRTAP13-2 chr21 7.52E-04 chr21:030666434-030666494 No NM_181621

CD40LG chrX 7.54E-04 chrX:135454835-135454895 No NM_000074


TMPRSS11A chr4 7.59E-04 chr4:068657690-068657750 No NM_182606

SEMG2 chr20 7.60E-04 chr20:043282999-043283059 No NM_003008

FPRL1 chr19 7.65E-04 chr19:056956256-056956303 No NM_001462

*; Probe location is available from the UCSC genome Bioinformatics web site (http://genome.ucsc.edu/). ¶; CpG island within 1kb of clone.

Supplement Table 3. Clones with high H3-K27 mono-methylation and/or high H3-K27 tri-methylation in SW48 by CpG microarray Clones with high H3-K27 mono-methylation in SW48 by CpG microarray Clone ID* 1Me

average

3Me

average


111_C_8 8.6 1.6 Xq21.3 No L1MC1(LINE)

111_C_6 7.7 0.9 Not available§

106_E_7 6.4 2.9 2q33.1 No AluJb (SINE), L1PA5 (LINE)

93_E_5 5.2 0.9 5p15.33 Yes No gene

39_C_11 5.0 0.9 4p25 Yes DKK-2 AF177395

70_E_12 4.7 1.4 1q23.2 Yes IGSF4B NM_021189

94_E_5 4.6 1.1 5q15.33 Yes No gene

100_C_3 4.5 0.8 4p15.2 Yes LGI-2 NM_018176

58_H_1 4.2 0.8 13q13.3 Yes Cyclin A1 NM_003914


93_E_6 4.1 0.9 5p15.33 Yes No gene

102_G_2 3.9 2.3 2q33.1 No AluJb (SINE), L1PA5 (LINE)

104_G_3 3.6 0.9 Xp11.23 Yes PCSK1N NM_013271

110_C_8 3.5 1.2 Xp21.3 No L1MC1 (LINE)

6_F_8 3.5 0.7 5q23.1 Yes p49/STRAP BC031222


25_F_6 3.4 0.7 1q31.1 Yes TPR, C1orf 27 NM_003292, NM_017847


50_A_5 3.1 0.5 6p22.1 No tRNA-Asp-GAY

8_F_8 3.0 1.0 5p21.3 Yes Ephrin-A5(EFNA5) NM_001962



84_A_12 2.8 0.7 1q24.2 Yes No gene

96_B_5 2.8 0.6 5q11.1 No No gene

50_H_9 2.7 0.5 4q35.1 No No gene

60_B_10 2.6 0.4 6p22.1 No tRNA-Val-GTY

100_A_2 2.6 0.6 6p22.1 No tRNA-Ile-ATT

114_G_12 2.6 0.7 6q14.3 Yes hypothetical protein LOC112609 NM_138409



75_A_10 2.5 0.8 7q36.1 Yes Splice EST

19_E_1 2.4 0.9 1q21.1 No AluY (SINE)

121_H_12 2.4 0.7 Chr.7 random RNU2 (U2 small nuclear RNA)

23_B_2 2.4 0.8 17q21.33 Yes MRPL27 NM_016504


119_G_6 2.4 0.9 12q23.1 Yes FLJ44867(spliced EST),

tRNA-Asp-GAY, AluSx (SINE)

AK126817

57_H_11 2.3 0.7 1p36.11 No AluSx (SINE)

59_G_4 2.3 0.4 6q13 Yes COL9A1 NM_001851

100_G_8 2.3 0.3 2q35 Yes USP37, RQCD1 protein NM_020935, NM_005444

112_G_3 2.3 0.8 11q23.3 No MIR3 (SINE)

89_A_6 2.3 0.6 13q22.3 No MLT1H-int (LTR)


29_B_8 2.2 0.9 1q41 Yes HLX-1 intron2 NM_021958

101_G_8 2.2 0.2 11q13.1 Yes SIPA-1 NM_153253



88_F_1 2.2 0.5 Chr.7 random RNU2 (U2 small nuclear RNA)

60_D_9 2.2 0.5 1p36.13 No MIRb (SINE), L2(LINE)

43_C_5 2.2 0.5 2q12.3 No AluSg (SINE)

93_E_10 2.2 0.6 2q31.3 No MER119 (SINE)

103_C_3 2.2 0.4 18q21.32 Yes No gene

97_H_1 2.2 0.6 6p22.1 No tRNA-Ile-ATT

44_C_5 2.2 0.8 2q12.3 AluSg (SINE)

85_A_12 2.2 0.5 6q27 Yes RNASET2 NM_003730


60_G_11 2.2 0.4 15q15.1 Yes MAPKBP1, PLA2G4 NM_014994, NM_024420

101_F_1 2.2 0.4 2p21.3 Yes CXCR4 NM_003467

47_D_6 2.1 0.7 12q13.2 No AluSx (SINE)

90_B_5 2.1 0.7 1q32.2 Yes DAF (CD55) NM_213815

94_F_4 2.1 0.8 2q21.3 No ZRANB3 NM_032143

72_B_1 2.1 0.3 10q11.21 Yes hypothetical protein MGC16291 NM_032770

99_H_2 2.1 0.6 6p22.1 No tRNA-Ile-ATT

119_F_12 2.1 0.6 Chr.7 random RNU2 (U2 small nuclear RNA)



102_A_2 2.1 0.5 6p22.1 No tRNA-Ile-ATT

64_G_4 2.1 0.4 Chr.7 random RNU2 (U2 small nuclear RNA)

85_C_6 2.1 0.7 2q36.1 No ACSL3 intron NM_004457

94_F_11 2.1 0.9 6p22.1 No tRNA-Ile-ATT

40_C_11 2.1 0.8 8q24.21 No L1MEe (LINE)


117_B_12 2.0 0.5 8q23.3 Yes CSMD3 intron NM_198123

125_E_5 2.0 0.8 13q33.1 Yes TPP2 NM_003291

115_B_8 2.0 0.4 Xq26.3 Yes No gene


95_F_4 2.0 0.9 1q24.2 Yes hypothetical protein LOC57821 NM_021179

Clones with high H3-K27 tri-methylation in SW48 by CpG microarray Clone ID* K27

mono- Me

K27 Tri- Me Loci CpG¶ Gene name Accession no.†

106_E_7 6.4 2.9 2q33.1 No AluJb (SINE), L1PA5 (LINE)

100_H_4 1.0 2.7 15q11.2 No L1P4 (LINE)

2_F_4 1.0 2.7 13q14.2 No AluSg (SINE)

102_H_4 1.0 2.4 Not

available§


116_D_12 0.8 2.2 14q32.3 No Intron of IGHG BC067091

121_A_6 0.8 2.2 Not

available

24_H_5 1.1 2.2 21q22.13 No No gene

101_H_4 0.9 2.1 15q11.2 No L1P4 (LINE)

96_G_6 0.8 2.1 5p14.3 No MER67D (LTR)

74_A_1 0.5 2.1 Not

available

19_D_11 0.9 2.1 6p12.3 Yes No gene


27_A_12 0.4 2.1 5p11 No Satellite

96_H_4 0.8 2.0 5p14.3 No MER67D (LTR)

32_D_8 0.8 2.0 15q25.1 Yes Cervical cancer suppressor-1 AF249277

25_F_2 0.9 2.0 3p24.2 Yes RARb2 NM_016152

34_A_8 0.7 2.0 4p11 No MER5A (DNA)

31_D_8

6_D_12

35_C_2

109_C_6

0.7

0.9

0.8

0.8

2.0

2.0

2.0

2.0

4p11

3p22.1

14q32.33

17p13.1

No

Yes

No

Yes

MER5A (DNA)

Copine IV

MLT1B (LTR), IGHV4-31and

IGHV3-30-2andIGHV3-30.1

YBX2, AluSq(SINE)

NM_130808

BC053984,

AJ298612

NM_015982

*; Sequence is available from the Der Laboratory CpG Island Microarray Bioinformatics web site (http://derlab.med.utoronto.ca/CpGIslands/CpGIslandsMain.php). ¶; CpG island within 1kb of clone. §; Sequence information with the spot is not available on the web site. †; Accession numbers are not provided for repeats.

Supplement Table 4. Gene list with increasing of expression in 2-fold or more after EZH2 knockdown in PC3 cells

Gene Title Gene Symbol Accesion no. Signal on

control

Signal on

EZH2 KD

fold

change

EGF-like repeats and discoidin I-like domains 3 EDIL3 AA053711 214.81 2903.42 13.52 secreted protein, acidic, cysteine-rich (osteonectin) /// secreted protein, acidic, cysteine-rich (osteonectin)

SPARC NM_003118 63.23 675.64 10.69

mesenchymal stem cell protein DSC54 /// mesenchymal stem cell protein DSC54

LOC51334 NM_016644 47.25 455.47 9.64

insulin-like growth factor binding protein 5 IGFBP5 R73554 45.73 417.93 9.14 retinol binding protein 4, plasma /// retinol binding protein 4, plasma

RBP4 NM_006744 164.53 1101.52 6.69

matrix metalloproteinase 1 (interstitial collagenase) /// matrix metalloproteinase 1 (interstitial collagenase)

MMP1 NM_002421 58.27 351.92 6.04

adaptor-related protein complex 3, beta 2 subunit AP3B2 BC035640 174.21 1000.17 5.74 KIAA1276 protein KIAA1276 AI627532 192.98 1065.92 5.52 connective tissue growth factor /// connective tissue growth factor

CTGF M92934 237.11 1246.89 5.26

transmembrane 4 superfamily member 3 /// transmembrane 4 superfamily member 3

TM4SF3 NM_004616 292.33 1494 5.11

stathmin-like 3 STMN3 AL353715 288.38 1406.11 4.88 cytochrome P450, family 19, subfamily A, polypeptide 1 CYP19A1 BC035714 48.91 227.68 4.66 nebulette NEBL AL157398 107.14 469.7 4.38 thymosin, beta, identified in neuroblastoma cells /// thymosin, beta, identified in neuroblastoma cells

TMSNB NM_021992 225.34 982.13 4.36

nipsnap homolog 3A (C. elegans) /// nipsnap homolog 3A (C. elegans)

NIPSNAP3A BC005935 110.72 455.72 4.12

Kallmann syndrome 1 sequence /// Kallmann syndrome 1 sequence

KAL1 NM_000216 149.48 602.06 4.03

zinc finger protein 37a (KOX 21) ZNF37A AK026980 78.65 307.22 3.91 chromosome 6 open reading frame 158 C6orf158 AL574912 44.27 172.47 3.9 ribonuclease, RNase A family, 4 RNASE4 NM_002937 134.09 521.65 3.89 interleukin 9 receptor IL9R L39064 224.59 855.82 3.81 serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3 /// serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3

SERPINB3 U19556 103.76 394.19 3.8

target of Nesh-SH3 TARSH AB056106 219.35 828.92 3.78 collagen, type VIII, alpha 1 COL8A1 AL359062 52.78 199.07 3.77 amyloid beta (A4) precursor protein-binding, family B, member 2 (Fe65-like)

APBB2 AK024871 85.38 321.4 3.76

HRAS-like suppressor 2 HRASLS2 NM_017878 262.07 957.66 3.65 hydroxysteroid (17-beta) dehydrogenase 2 /// hydroxysteroid (17-beta) dehydrogenase 2

HSD17B2 NM_002153 65.39 234.53 3.59

ubiquitin specific protease 34 USP34 AK023845 473.68 1648.24 3.48 hepatic leukemia factor HLF AI810712 79.13 272.27 3.44 myosin, light polypeptide kinase MYLK AA526844 160.09 546.34 3.41 four and a half LIM domains 1 FHL1 AF220153 252.97 861 3.4 serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1

SERPINE1 AL574210 239.96 816.64 3.4

matrilin 3 /// matrilin 3 MATN3 NM_002381 47.49 159.49 3.36 membrane-spanning 4-domains, subfamily A, member 1 MS4A1 AW474852 67.98 226.79 3.34

homeo box C8 /// homeo box C8 HOXC8 NM_022658 288.42 950.66 3.3 potassium large conductance calcium-activated channel, subfamily M, alpha member 1 /// potassium large conductance calcium-activated channel, subfamily M, alpha member 1

KCNMA1 AI129381 599.4 1962.58 3.27

G protein-coupled receptor kinase 4 GRK4 AW269179 271.57 883.49 3.25 collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)

COL3A1 AU144167 81.35 262.28 3.22

hydroxyprostaglandin dehydrogenase 15-(NAD) /// hydroxyprostaglandin dehydrogenase 15-(NAD)

HPGD AL574184 118.71 380.8 3.21

chromosome 14 open reading frame 45 C14orf45 NM_025057 382.25 1223.11 3.2 tyrosinase-related protein 1 /// tyrosinase-related protein 1 TYRP1 NM_000550 240.94 771.86 3.2 Kruppel-like factor 3 (basic) /// Kruppel-like factor 3 (basic) KLF3 NM_016531 430.9 1364.43 3.17 RNA binding motif protein, X-linked RBMX AA460960 294.15 931.88 3.17 putative G-protein coupled receptor GPCR41 FLJ11856 BC026857 563.63 1775.28 3.15 interferon-induced protein with tetratricopeptide repeats 2 IFIT2 AA131041 123.06 387.22 3.15 a disintegrin and metalloproteinase domain 12 (meltrin alpha) ADAM12 AA147933 98.8 310.64 3.14 phospholipase A2, group XIIB PLA2G12B BF939574 168.28 527.12 3.13 monoglyceride lipase MGLL BC006230 171.7 535.02 3.12 5'-nucleotidase, ecto (CD73) NT5E NM_002526 73.6 227.33 3.09 tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) /// tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)

TFPI AF021834 74.88 228.99 3.06

adenylate cyclase 7 /// adenylate cyclase 7 ADCY7 NM_001114 90.99 277.05 3.04 NCAG1 NCAG1 AK021539 68.32 207.6 3.04 ARG99 protein ARG99 BF109231 98.56 297.27 3.02 Kruppel-like factor 2 (lung) /// Kruppel-like factor 2 (lung) KLF2 NM_016270 283.35 856.97 3.02 Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)

MJD U63332 70.62 212.64 3.01

hypothetical protein FLJ22527 FLJ22527 BC008085 82.59 247.39 3 synaptotagmin VI SYT6 AI863338 248.74 744.41 2.99 basic transcription element binding protein 1 BTEB1 AI458659 255.81 761.93 2.98 insulin-like growth factor binding protein 3 /// insulin-like growth factor binding protein 3

IGFBP3 BF340228 442.04 1309.19 2.96

kidney associated antigen 1 KAAG1 AF181722 410.61 1207.49 2.94 implantation-associated protein DKFZp564K142 AF130104 442.66 1298.11 2.93 annexin A10 /// annexin A10 ANXA10 AF196478 376.5 1097.53 2.92 interferon-induced protein with tetratricopeptide repeats 4 IFIT4 AI075407 91.41 266.05 2.91 GULP, engulfment adaptor PTB domain containing 1 GULP1 AF200715 401.7 1164.74 2.9 integrin, alpha 6 ITGA6 NM_000210 478.7 1388.63 2.9 hypothetical protein LOC285224 LOC285224 AK097457 103.87 298 2.87 CD59 antigen p18-20 (antigen identified by monoclonal antibodies 16.3A5, EJ16, EJ30, EL32 and G344)

CD59 BF983379 1468.7 4196.96 2.86

Rho GTPase activating protein 5 ARHGAP5 AW044631 298.22 850.46 2.85 myelin expression factor 2 MYEF2 AK023133 78.52 223.64 2.85 nicotinamide N-methyltransferase /// nicotinamide N-methyltransferase

NNMT AV650983 1419.23 4022.39 2.83

iroquois homeobox protein 5 /// iroquois homeobox protein 5 IRX5 U90304 187.72 528.1 2.81 t-complex-associated-testis-expressed 3 TCTE3 AF519569 245.13 688.22 2.81 complement component 1, s subcomponent /// complement component 1, s subcomponent

C1S M18767 157.47 440.36 2.8

hypothetical protein FLJ90022 FLJ90022 AW264102 375.14 1051.19 2.8 lymphocyte antigen 9 LY9 AI524095 177.48 497.2 2.8

chemokine (C-C motif) ligand 20 /// chemokine (C-C motif) ligand 20

CCL20 NM_004591 173.94 483.28 2.78

msh homeo box homolog 2 (Drosophila) MSX2 D89377 113.75 315.17 2.77 hyaluronan synthase 2 /// hyaluronan synthase 2 HAS2 NM_005328 121.58 334.23 2.75 chromosome 20 open reading frame 56 C20orf56 AL121722 531.44 1458.2 2.74 contactin associated protein-like 3 CNTNAP3 AF333769 119.84 328.87 2.74 dedicator of cytokinesis 4 DOCK4 NM_014705 133.09 362.93 2.73 neuron navigator 2 NAV2 AK001892 206.81 564.04 2.73 UBX domain containing 3 UBXD3 AA382425 589.3 1607.98 2.73 tripartite motif-containing 2 TRIM2 BC005016 115.47 313.55 2.72 netrin 4 NTN4 AF278532 112.07 300.8 2.68 aldehyde oxidase 1 AOX1 NM_001159 177.63 473.42 2.67 anthrax toxin receptor 2 ANTXR2 AU152178 184.2 490.08 2.66 KIAA1648 protein KIAA1648 AW195681 623.27 1659.78 2.66 mab-21-like 2 (C. elegans) MAB21L2 AF262032 367.04 975.6 2.66 neutrophil cytosolic factor 4, 40kDa /// neutrophil cytosolic factor 4, 40kDa

NCF4 NM_013416 88.88 235.84 2.65

tumor necrosis factor, alpha-induced protein 6 /// tumor necrosis factor, alpha-induced protein 6

TNFAIP6 NM_007115 163.16 431.95 2.65

syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)

SNTB2 AI695684 203.23 535.73 2.64

hypothetical protein LOC90321 LOC90321 AA081007 351.09 924 2.63 melanoma antigen, family E, 1, cancer/testis specific MAGEE1 AL031073 168.98 445.18 2.63 craniofacial development protein 1 /// craniofacial development protein 1

CFDP1 NM_006324 606.5 1585.73 2.61

myosin heavy chain Myr 8 MYR8 AI522028 249.36 651.21 2.61 spastic paraplegia 20, spartin (Troyer syndrome) SPG20 AA226334 470.2 1229.12 2.61 transcription factor 8 (represses interleukin 2 expression) TCF8 U12170 73.25 191.4 2.61 hypothetical protein FLJ38993 FLJ38993 AF070524 83.81 217.57 2.6 neuronal growth regulator 1 NEGR1 AI123532 71.35 185.46 2.6 hypothetical protein DKFZp761C1711 DKFZP761C1711 AL137340 125.46 324.39 2.59 glucagon-like peptide 1 receptor /// glucagon-like peptide 1 receptor

GLP1R U01157 284.1 735.05 2.59

RAB3B, member RAS oncogene family RAB3B BE552383 218.93 567.1 2.59 uronyl-2-sulfotransferase /// uronyl-2-sulfotransferase UST NM_005715 135.59 351.83 2.59 neuropeptide Y receptor Y6 (pseudogene) NPY6R BF968482 245.28 633.58 2.58 piccolo (presynaptic cytomatrix protein) PCLO AB011131 103.34 266.95 2.58 SUMO1/sentrin specific protease 1 SENP1 BF056555 80.31 207.09 2.58 urotensin 2 UTS2 NM_021995 106.49 274.21 2.58 mitogen-activated protein kinase kinase kinase kinase 4 MAP4K4 AL561281 164.28 421.93 2.57 olfactory receptor, family 2, subfamily I, member 6 OR2I6 AI694413 320.99 824.61 2.57 hypothetical protein FLJ22028 FLJ22028 AI554909 226.48 580.05 2.56 delta-notch-like EGF repeat-containing transmembrane DNER BF059512 72.01 183.51 2.55 cathepsin B CTSB W47179 124.55 315.96 2.54 epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)

EGFR AF277897 165.16 419.89 2.54

elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2

ELOVL2 BF508639 131.54 333.61 2.54

fatty acid binding protein 4, adipocyte FABP4 AI766029 266.26 675.53 2.54 hemogen HEMGN AF322875 95.61 243.05 2.54 keratin associated protein 4-12 KRTAP4-12 BC004180 194.07 493.3 2.54 neuronal PAS domain protein 2 NPAS2 AI743090 254.58 644.84 2.53

Friend leukemia virus integration 1 FLI1 NM_002017 67.43 169.2 2.51 RNA binding motif, single stranded interacting protein RBMS3 AA428240 70.87 178.01 2.51 ELYS transcription factor-like protein TMBS62 ELYS AL080144 697.67 1740.91 2.5 interferon, alpha-inducible protein (clone IFI-6-16) /// interferon, alpha-inducible protein (clone IFI-6-16)

G1P3 NM_022873 238 595.12 2.5

inhibitor of DNA binding 2, dominant negative helix-loop-helix protein

ID2 D13891 67.58 168.86 2.5

erythrocyte membrane protein band 4.1-like 3 EPB41L3 AI770004 325.75 809.5 2.49 galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio syndrome, mucopolysaccharidosis type IVA)

GALNS AA884446 695.78 1729.59 2.49

MADS box transcription enhancer factor 2, polypeptide D (myocyte enhancer factor 2D)

MEF2D NM_005920 521.97 1300.29 2.49

KIAA0738 gene product KIAA0738 BF030508 94.31 233.91 2.48 phosphoenolpyruvate carboxykinase 1 (soluble) /// phosphoenolpyruvate carboxykinase 1 (soluble)

PCK1 NM_002591 69.34 171.89 2.48

solute carrier family 12 (sodium/potassium/chloride transporters), member 2

SLC12A2 AK025062 308.82 764.35 2.48

tumor necrosis factor receptor superfamily, member 21 TNFRSF21 BE568134 851.73 2108.97 2.48 hypothetical protein LOC142893 LOC142893 AU159465 673.65 1666.05 2.47 primase, polypeptide 2A, 58kDa /// primase, polypeptide 2A, 58kDa

PRIM2A NM_000947 468.06 1157.12 2.47

sialic acid binding Ig-like lectin 5 /// sialic acid binding Ig-like lectin 5

SIGLEC5 NM_003830 622.49 1540.07 2.47

zinc finger protein, X-linked ZFX R51161 72.62 179.75 2.47 interleukin 6 receptor IL6R S72848 401.43 986.69 2.46 tachykinin receptor 1 TACR1 M81797 395.04 968.03 2.45 CD164 antigen, sialomucin CD164 AF263279 675.84 1646.36 2.44 chondroitin sulfate GalNAcT-2 GALNACT-2 NM_018590 124.22 303.56 2.44 lectin, mannose-binding, 1 LMAN1 U09716 347.51 849.11 2.44 hypothetical protein LOC285705 LOC285705 AL117590 831.2 2032.2 2.44 N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2 /// N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2

NDST2 NM_003635 725.09 1767.03 2.44

chromosome 20 open reading frame 160 C20orf160 BC019892 693.99 1687.61 2.43 recombination protein REC14 REC14 BF791874 939.02 2285.7 2.43 Ras-related GTP binding D RRAGD AF272036 272.22 662.82 2.43 sorting nexin 13 SNX13 T88880 187.28 453.58 2.42 yippee protein CGI-127 NM_016061 358.72 862.99 2.41 comparative gene identification transcript 37 CGI-37 AF161528 304.98 735.61 2.41 solute carrier family 2 (facilitated glucose transporter), member 10 /// solute carrier family 2 (facilitated glucose transporter), member 10 /// solute carrier family 2 (facilitated glucose transporter), member 10

SLC2A10 NM_030777 191.75 462.74 2.41

sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) /// sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)

SPOCK AF231124 1218.04 2929.62 2.41

interleukin 13 receptor, alpha 1 IL13RA1 U81379 182.6 437.33 2.4 KIAA0241 protein KIAA0241 AI797458 187.3 450.34 2.4 COMM domain containing 10 COMMD10 BC005179 154.5 368.69 2.39 carboxypeptidase E /// carboxypeptidase E CPE NM_001873 129.44 309.46 2.39 epithelial membrane protein 1 EMP1 NM_001423 564.18 1345.62 2.39 galactose-3-O-sulfotransferase 1 /// galactose-3-O-sulfotransferase 1

GAL3ST1 NM_004861 262.49 627.16 2.39

scavenger receptor class B, member 1 SCARB1 AV708130 832.87 1991.1 2.39 KIAA1970 protein KIAA1970 AA833716 313.04 745.68 2.38 transition protein 2 (during histone to protamine replacement) /// transition protein 2 (during histone to protamine replacement)

TNP2 NM_005425 256.3 610.94 2.38

chromosome 6 open reading frame 89 C6orf89 AL119182 624.73 1481.12 2.37 hypothetical protein FLJ11171 FLJ11171 AK023183 121.57 287.95 2.37 lysyl oxidase-like 4 LOXL4 AW190565 323.76 767.06 2.37 mitogen-activated protein kinase kinase kinase kinase 3 /// mitogen-activated protein kinase kinase kinase kinase 3

MAP4K3 NM_003618 268.38 633.45 2.36

tropomyosin 3 TPM3 AY004867 238.93 563.95 2.36 zinc finger protein 567 ZNF567 BF435183 77.85 183.76 2.36 hypothetical protein FLJ13105 FLJ13105 NM_025001 85.68 201.2 2.35 CocoaCrisp LOC83690 AF142573 111.09 260.7 2.35 hypothetical protein MGC33424 MGC33424 AL548941 413.92 972.86 2.35 vesicle-associated membrane protein 4 /// vesicle-associated membrane protein 4

VAMP4 BC005974 99.27 233.33 2.35

sterile alpha motif domain containing 4 SAMD4 AL117523 189.45 442.96 2.34 sialyltransferase 10 (alpha-2,3-sialyltransferase VI) /// sialyltransferase 10 (alpha-2,3-sialyltransferase VI)

SIAT10 AB022918 131.6 307.74 2.34

DNA2 DNA replication helicase 2-like (yeast) DNA2L AI305170 255.12 595.5 2.33 hypothetical protein FLJ12847 FLJ12847 BC030702 122.88 286.47 2.33 mitogen-activated protein kinase kinase kinase 8 /// mitogen-activated protein kinase kinase kinase 8

MAP3K8 NM_005204 77.77 181.5 2.33

nicotinamide nucleotide adenylyltransferase 1 NMNAT1 AW779092 112.04 261.57 2.33 SLAM family member 6 SLAMF6 NM_052931 948 2205.04 2.33 hypothetical protein FLJ11783 FLJ11783 NM_024891 483.34 1121.33 2.32 transmembrane protein 16A TMEM16A NM_018043 141.97 329.98 2.32 collagen, type I, alpha 1 COL1A1 BE221212 190.46 439.65 2.31 protein kinase, cAMP-dependent, regulatory, type I, beta PRKAR1B AU148827 326.26 753.96 2.31 sortilin-related receptor, L(DLR class) A repeats-containing SORL1 AV728268 261.37 603.49 2.31 tuberous sclerosis 1 /// tuberous sclerosis 1 TSC1 AF013168 365.09 844.51 2.31 vacuolar protein sorting 13C (yeast) VPS13C NM_018080 216.46 500.95 2.31 ATPase, Class I, type 8B, member 1 ATP8B1 BG290908 118.46 272.17 2.3 hypothetical protein FLJ25070 FLJ25070 BF116157 466.76 1071.62 2.3 transcriptional co-activator with PDZ-binding motif (TAZ) TAZ BF674349 1231.76 2834.87 2.3 zinc finger protein 76 (expressed in testis) /// zinc finger protein 76 (expressed in testis)

ZNF76 NM_003427 770.1 1769.91 2.3

ATP-binding cassette, sub-family A (ABC1), member 5 ABCA5 BF693921 163.56 374.62 2.29 ceruloplasmin (ferroxidase) CP AI922198 124.16 284.41 2.29 G2 protein G2 H08993 88.85 203.79 2.29 vesicle transport through interaction with t-SNAREs homolog 1A (yeast)

VTI1A AA333161 273.06 625.98 2.29

BCL2-related protein A1 /// BCL2-related protein A1 BCL2A1 NM_004049 288.32 658.43 2.28 gap junction protein, alpha 1, 43kDa (connexin 43) /// gap junction protein, alpha 1, 43kDa (connexin 43)

GJA1 NM_000165 2221.63 5069.55 2.28

myosin ID MYO1D AA621962 86.97 197.97 2.28 purinergic receptor P2Y, G-protein coupled, 5 /// purinergic receptor P2Y, G-protein coupled, 5

P2RY5 NM_005767 151.57 344.99 2.28

solute carrier family 4, sodium bicarbonate cotransporter, member 8

SLC4A8 BC025994 597 1361.11 2.28

ubiquitin-like, containing PHD and RING finger domains, 2 UHRF2 BF511410 389.23 888.93 2.28 chromosome 9 open reading frame 116 C9orf116 AU160041 388.19 881.91 2.27

neuropilin 1 NRP1 AF145712 940.16 2136.68 2.27 sprouty homolog 4 (Drosophila) SPRY4 W48843 729.52 1652.4 2.27 integrin, beta-like 1 (with EGF-like repeat domains) /// integrin, beta-like 1 (with EGF-like repeat domains)

ITGBL1 NM_004791 172.79 390.75 2.26

hypothetical protein LOC339529 LOC339529 AW072559 363.02 820.84 2.26 odd-skipped homolog (Drosophila) ODD AI569974 217.98 493.27 2.26 spermidine/spermine N1-acetyltransferase /// spermidine/spermine N1-acetyltransferase

SAT BE326919 510.56 1152.39 2.26

chromosome 10 open reading frame 6 C10orf6 BF509267 324.61 729.04 2.25 CAP, adenylate cyclase-associated protein, 2 (yeast) /// CAP, adenylate cyclase-associated protein, 2 (yeast)

CAP2 N90755 270.87 609.03 2.25

chemokine binding protein 2 /// chemokine binding protein 2 CCBP2 NM_001296 338.35 760.13 2.25 hypothetical protein LOC146443 LOC146443 AI637729 378.02 849.42 2.25 protocadherin alpha 6 PCDHA6 AI268404 276.12 620.64 2.25 A kinase (PRKA) anchor protein 13 AKAP13 AF126008 222.84 500.01 2.24 aldehyde dehydrogenase 3 family, member B1 ALDH3B1 AL137634 866.82 1938.05 2.24 distal-less homeo box 2 DLX2 BE792224 468.49 1050.98 2.24 histone 1, H4h HIST1H4H NM_003543 105.97 237.83 2.24 KIAA0157 KIAA0157 D63877 692.18 1547.45 2.24 LIM and cysteine-rich domains 1 LMCD1 AA045042 231.46 518.01 2.24 NIMA (never in mitosis gene a)-related kinase 3 /// NIMA (never in mitosis gene a)-related kinase 3

NEK3 Z25434 142.29 319.37 2.24

hypothetical protein FLJ25056 FLJ25056 AK057785 381.78 852.45 2.23 KIAA1093 protein KIAA1093 N64803 462.01 1029.48 2.23 retinoblastoma-associated protein 140 RAP140 AW138775 538.77 1203.36 2.23 Rho guanine nucleotide exchange factor (GEF) 3 /// Rho guanine nucleotide exchange factor (GEF) 3

ARHGEF3 NM_019555 220.57 489.56 2.22

chromosome 18 open reading frame 25 C18orf25 BE783279 239.9 533.4 2.22 D4, zinc and double PHD fingers, family 3 DPF3 AI125562 188.09 418.04 2.22 chemokine (C-X-C motif) ligand 5 /// chemokine (C-X-C motif) ligand 5

CXCL5 NM_002994 143.21 316.78 2.21

hypothetical protein BC012029 LOC152573 AI735586 916.58 2028.57 2.21 hypothetical protein LOC286044 LOC286044 NM_024607 161.33 357.14 2.21 hypothetical protein BC000282 LOC89894 AK021528 472.48 1045.8 2.21 sodium channel, voltage-gated, type II, alpha 2 /// sodium channel, voltage-gated, type II, alpha 2

SCN2A2 NM_021007 176.64 391.03 2.21

ASCL830 UNQ830 AI871385 383.88 850.12 2.21 guanine nucleotide binding protein (G protein), alpha 14 /// guanine nucleotide binding protein (G protein), alpha 14

GNA14 NM_004297 347.69 764.88 2.2

sarcospan (Kras oncogene-associated gene) /// sarcospan (Kras oncogene-associated gene)

SSPN AL136756 417.65 920.38 2.2

hypothetical protein FLJ10052 FLJ10052 BC004888 98.6 215.73 2.19 acyl-Coenzyme A dehydrogenase family, member 8 /// acyl-Coenzyme A dehydrogenase family, member 8

ACAD8 BC001964 236.57 514.85 2.18

engulfment and cell motility 1 (ced-12 homolog, C. elegans) ELMO1 NM_014800 220.48 481.18 2.18 hypothetical protein FLJ10134 FLJ10134 NM_018004 709.4 1544.3 2.18 hypothetical protein LOC338862 LOC338862 BC042673 442.85 966.5 2.18 zinc finger protein 175 /// zinc finger protein 175 ZNF175 NM_007147 513.94 1119.03 2.18 amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease)

APP X06989 1010.36 2195.96 2.17

glypican 6 GPC6 AF111178 865.88 1881.43 2.17 HSPC009 protein HSPC009 AI056409 986.9 2138 2.17 nucleolar protein 3 (apoptosis repressor with CARD domain) NOL3 BU785956 158.55 343.38 2.17

proline-rich protein BstNI subfamily 3 /// proline-rich protein BstNI subfamily 3

PRB3 NM_006249 724.75 1571.02 2.17

serum/glucocorticoid regulated kinase /// serum/glucocorticoid regulated kinase

SGK NM_005627 183.21 397.8 2.17

sialyltransferase 7D ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)

SIAT7D BE858453 509.69 1105.59 2.17

IBR domain containing 2 IBRDC2 AI953847 407.97 880.25 2.16 chromosome 19 open reading frame 29 C19orf29 AI200896 658.72 1417.28 2.15 EphA5 EPHA5 BE218107 133.09 285.57 2.15 hypothetical protein FLJ38149 FLJ38149 AK095468 137.22 294.66 2.15 hyaluronan synthase 3 HAS3 AF232772 2520.95 5406.42 2.14 male sterility domain containing 1 MLSTD1 NM_018099 339.99 727.29 2.14 ATPase, Class II, type 9A ATP9A AB014511 1107.71 2363.79 2.13 glucosidase, beta (bile acid) 2 GBA2 AB046825 705.53 1505.69 2.13 nuclear DNA-binding protein /// nuclear DNA-binding protein /// nuclear DNA-binding protein

C1D NM_006333 618.09 1303.22 2.11

endothelin 1 EDN1 J05008 1178.03 2488.41 2.11 KIAA1554 protein KIAA1554 AF318359 592.18 1251.49 2.11 olfactory receptor, family 12, subfamily D, member 2 /// olfactory receptor, family 12, subfamily D, member 2

OR12D2 NM_013936 335.95 708.36 2.11

hypothetical protein LOC286167 LOC286167 AV721528 1242.62 2613.73 2.1 chromosome 3 open reading frame 6 C3orf6 BF941088 760.94 1590.02 2.09 GABA(A) receptor-associated protein-like 2 /// GABA(A) receptor-associated protein-like 2

GABARAPL2 AB030710 1188.58 2463.07 2.07

Supplementary Table 5. Primer sequences and target sequences of shRNA

The primers for pyrosequencing methylation analysis Region Primer sequences and annealing temperature Product

length (bp) Sequencing primers No. of

CpGs Sequence Length

p16 (+263-+95)

Forward GGTTGTTTTYGGTTGGTGTTTT Reverse (5’-Biotin) ACCCTATCCCTCAAATCCTCTAAAA 58/56/54/52°C

175

TTTTTGTTTGGAAAGAT

2

5

RASSF1A Forward GGGGGAGTTTGAGTTTATTGA Reverse (5’-Biotin) CTACCCCTTAACTACCCCTTCC 55°C

298

Seq1: GGGTAGTATTAGGTTGGAGSeq2: GATTTTATTTGGGG Seq3: GTAAAGGTTTGTAGTG

5

3

6

22

9

24 PGR Forward

TGATTGAGTTGAAGGTAAAG Reverse-Universal GGGACACCGCTGATCGTTTAAAATCCTATCCCTAACAAAA Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 58/56/54/52°C

225

Seq1: GGATTTTTATTGTTGTGT Seq2: GGGGAGTTAGATTT Seq3: GGATATTTTGTTTGAAGTTT

2

1

1

10

10

8 RARß1 Forward

GGAYGTTAGGGGTTTGGATAGTA Reverse-Universal GGGACACCGCTGATCGTTTAAACTCCCRCTATCTACTCTCAAC Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 55°C

180

GGGTTGTTTTGGAGT

6

17

RARß2 ForwardTTTTGTTAAAGGGGGGATTAG Reverse-Universal GGGACACCGCTGATCGTTTAAATTCTCCTTCCAAATAAATACTTAC Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 55°C

181

TGTTTGAGGATTGGGAT

5

21

OTOP3 ForwardGGGATTAATGAGATTTTTAAAGTTAATA Reverse-Universal

281

TTTAAAGTTAATAGAAAAAT

6

27

GGGACACCGCTGATCGTTTAAACCCCCCTTTTAAAAAAATAAATA Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 50°C

SAMD11 ForwardGTGTTTAGGTTGGGTTTTAGTT Reverse-Universal GGGACACCGCTGATCGTTTAACCAATCTCCAAACTACCTCTCT Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 55°C

199

TTTTTTATTTTTATATTTAG

5

32

Trim36 ForwardGAGATGGGGTTTTTTTTTAGA Reverse-Universal GGGACACCGCTGATCGTTTAACCCCAACTAAACATTCCC Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 50°C

113

GGGGTTTTTTTTTAGATT

5

23

WNT1 ForwardTTTTAGGGTTGTTAAAGTTAGATTG Reverse-Universal GGGACACCGCTGATCGTTTACAAAACCCCATAACCTACCT Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 55°C

160

AGGGTTGTTAAAGTTAGATT

6

31

CR2 ForwardGGTTTATAGTTGTTTGTTGTTTTAGTT Reverse-Universal GGGACACCGCTGATCGTTTATTTTAACCCCCTACTTTACATC Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 50°C

262

TAGTTTTGTTTTTTTAGAGT

5

23

KCNAB1 ForwardGAGGGGTTTTGAGGAGTTT Reverse-Universal GGGACACCGCTGATCGTTTACCAACATCCCCTAAACCA Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 58/56/54/52°C

188

GGGTTTTGAGGAGTTTTTA

4

23

NKX2-3 Forward

TTGTAGTGGTTGTAATAAAATTTAGA Reverse-Universal GGGACACCGCTGATCGTTTATCATCAAAACCACTTAATTATCC Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 50°C

218 GATTTAGATTGGAGTGGG 5 34

RGMA ForwardTTGGGTAGGGGAAGTATTG Reverse-Universal GGGACACCGCTGATCGTTTATCCTACTCCCCAACTACATACCT Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 50°C

99

TGGGTAGGGGAAGTATT

7

38

ER-α Forward TTTTTGGGTTATTTTTAGTAGATT Reverse-Universal GGGACACCGCTGATCGTTTACAAAAAACAACTTCCCTAAACTT Universal (5’-Biotin) GGGACACCGCTGATCGTTTA 58/56/54/52°C

133

Seq1: GGTTATTTTTAGTAGATTTT Seq2: AATTTAGTTTTTATTTAGTA

4

2

25

14

RARß2-SEAP reporter

Forward GGAAYGTATTYGGAAGGT Reverse CAACAACATAATAAACRAATTC 60/58/56/52°C

The primers for ChIP-PCR Region Primer sequences and annealing temperature Q-PCR probe SAMD11 (Q-PCR)

Forward: CTTTTCCCGGTCTCGTTCTG Reverse: CGGTGGACGCTGGATATGA 60°C

CGGCAACCTTCCCAC

TRIM36 (Q-PCR)

Forward: GCCCGCTTCTTGCTTTCC Reverse: CCGCCCATAAGCTGTTAACC 60°C

CGCTTCCCCTCTTT

WNT1 (Q-PCR)

Forward: TGTTAAAGCCAGACTGCGAACTC Reverse: GGCTTTGCCCGCTCTGT 60°C

CAACAACCAAAGTCG

OTOP3 (Q-PCR)

Forward: TTCAGCAAGCCAGTCACAGAGT Reverse: GCTTATGCCGCGGAACAC

CCCAGCTTGATCACCAA

60°C NKX2-3 (Q-PCR)

Forward: CCCTGCAGTGGCTGTAACAA Reverse: CAGTCTAAATCGCCTCCATTGG 60°C

ACCCAGACCCCCAGGT

KCNAB1 (Q-PCR)

Forward: TTCAGCAAGCCAGTCACAGAGT Reverse: GCTTATGCCGCGGAACAC 60°C

TCACGTGTTAATTCAC

RARß1 (Q-PCR)

Forward: GCATTTGCATGGCATCCA Reverse: CCGCGGTACACGCAAAA 60°C

CCGGCTGCCTAGCA

RARß2 (Q-PCR)

Forward: GCACGTAGGCTGTTGGTCTTT Reverse: GCTGGCTTGTCTGTCATAATTCA 60°C

CCAGCCCCGAATC

MGMT (Q-PCR)

Forward: AAAGGTACGGGCCATTTGG Reverse: GGCGCCTTCCCAGCTT 60°C

TAAGGCACAGAGCCTC

PGR (Q-PCR)

Forward: GAGCCGCGTGTCACTAAATTG Reverse: TCACAAGTCCGGCACTTGAG 60°C

CGTCGCAGCCGCA

RASSF1a (Q-PCR)

Forward: GGACCCTCTTCCTCTAGCACAGT Reverse: GCACCACGCGGAGATACC 60°C

TGGCCTCCAGAAAC

p21 (Q-PCR)

Forward: GCCAACTCATTCTCCAAGTAAAAAA Reverse: GTGCGCTGGACACATTTCC 60°C

CCAGATTTGTGGCTCACT

p16 (Q-PCR)

Forward: GGGCGGATTTCTTTTTAACAGA Reverse: CGCCTGCCAGCAAAGG 60°C

TGAACGCACTCAAAC

ERα (Q-PCR)

Forward: CCCTGACATTGGCTTAAACATCA Reverse: TCTTTGGGATCGCTCCAAAT 60°C

TCCAGGCACAACTC

SAMD11

Forward: TTTGAGGCAGGGAGTGAGAT Reverse: CACGCAGCACCCGAGTC 62/58/56/52°C

TRIM36

Forward: CTCGATGGCCTTCATTTCAC Reverse: GCGGGTGTATCGAATTTGTC 62/58/56/52°C

WNT1 Forward: CCAGGGTTGTTAAAGCCAGAC Reverse: AGGCAACAGCGCCCA

62/58/56/52°C OTOP3 Forward: CCATTCCCAGCTTGATCACC

Reverse: GCTGAGGGCTGTGCAGG 62/58/56/52°C

NKX2-3

Forward: CCAACGTGACGCAAATCTCC Reverse: TGCCGAGTCGGGCTTTT 62/58/56/52°C

KCNAB1 Forward: AGAAAAGGAACTCTGACAAGGCReverse: TGCAGCACAACAGTTGGAAC 62/58/56/52°C

CR2 Forward: TAGTAAGAGAAACAAGTGAGTGTAGTGG Reverse: CGGTGAGGGTGGGACAAG 62/58/56/52°C

RGMA Forward: CTCCACCGCAACCCTGCReverse: CCCGCATCAGCACCG 62/58/56/52°C

GAS2 (Q-PCR)

Forward: CACAGAGGCAAGGCAGAGAAC Reverse: TGTCCACACTGCTAAGAGTTTGG 60°C

AGACCTGTGCTTCTTTA

PIK3-CG (Q-PCR)

Forward: TCTGACTCGGAATAGTGGCACTT Reverse: CTCAAGAACCGACAACAGTTTCA 60°C

CTTCTCGGCTAGATTAT

RARß2-SEAP reporter

Forward: AAGCTTCGAATCGCGAATTC Reverse: TCGCGGTTCCAGAAGTCC 60°C

The primers for RT-PCR Region Primer sequences and annealing temperature Q-PCR probe RASSF1a (Q-PCR)

Forward: CCTCTGTGGCGACTTCATCTG Reverse: TAGTGGCAGGTGAACTTGCAA 60°C

CCTGCAGTGCGCGC

p16 (Q-PCR)

Forward: CGCTGCCCATCATCATGA Reverse: CCAACGCACCGAATAGTTACG 60°C

CTGGATCGGCCTCC

RARß1 (Q-PCR)

Forward: CATCTTGACTTTGGCCCAGA Reverse: AAAGTGAGGGAGGCAAATGC 60°C

CACAGCTCAGCCTCAACTCCTGCAG

RARß2 Forward: GCTTCAGTGGATTGACCCAA

(Q-PCR) Reverse: CGAGTTCCTCAGAGCTGGTG60°C

CCGAATGGCAGCATCGGCAC

PGR Forward: CGCCCTATCTCAACTACCTGAReverse: TGCGGATTTTATCAACGATG 60°C

RARß1

Forward: TGACGTCAGCAGTGACTACTG Reverse: GTGGTTGAACTGCACATTCAGA 60°C

RARß2

Forward: TCTGTCAGTGAGTCCTGGGC Reverse: GCTTGGGACGAGTTCCTCAG 60°C

ERα

Forward: CCGCAGCTGTCGCCTTT Reverse: CTGGCAGCTCTTCCTCCTGT 60°C

KCNAB Forward: CGCCTCAGCATCACATTTCT Reverse: CCACTTTCATAGGCGATGGTC 60°C

SAMD11 Forward: CAACCTTCCCACCCTCATATC Reverse: TCTTCTCTGAAAAGCAGTCGC 60°C

TRIM36 Forward: GGGAGATGAGTGAATTTGGC Reverse: TCGAGAGTCAGCAGGAGTTCT 60°C

RGMA Forward: ATGCAGCCGCCAAGGG Reverse: CGCTCCAGAACTCAGAGTTGC 60°C

CR2

Forward: GAAAATGGAGTGCTGTCCCC Reverse: TGTCCAGCAATTACACACCG 60°C

WNT1 Forward: GCTGGGTTTCTGCTACGCTG Reverse: CGCTGTTTGCGGCTCAAC 60°C

OTOP3 Forward: GAAGGTCCTCTCCCTGCTTTReverse: GATGTGGCTCACATCGTAGC 60°C

NKX2-3 Forward: TGAACTCACTAGCCGCAGCA Reverse: TCTCCGGCCGTCTCTAGAG 60°C

GAPDH Forward: TCGGTGCGTGCCCAGTTGAACC

Reverse: ATGCGGCTGACTGTCGAACAGGAG 60°C

Target sequences of shRNA against EZH2

shRNA† Target sequences

EZH2 version A GACTCTGAATGCAGTTGCT

EZH2 version B ATATGACTGCTTCCTACAT

EZH2 version C CATGTAGACAGGTGTATGA

†, We designed three different retrovirus vectors.

gene silencing in cancer by histone h3 lysine 27 tri ......gene silencing in cancer by histone h3...

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