Page 1
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
Page 2
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.
Page 3
-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.
Page 4
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.
Page 5
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)
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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)
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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
Page 8
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)
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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)
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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
Loci CpG¶ Gene name Accession no.†
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)
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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
Loci CpG¶ Gene name Accession no.†
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
Page 12
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)
Page 13
96_G_1 0.8 2.1 5p14.3 No MER67D (LTR)
110_H_5 1.8 2.1 Not available
111_E_8 0.9 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
108_E_8 0.8 2.0 Not available
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
34_F_8 1.0 2.0 Not available
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)
Page 14
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
93_H_12 1.6 2.0 Not available
115_C_5 1.4 2.0 6q25.1 No MLT1J (LTR), MER58B (DNA)
95_F_7 1.3 2.0 Not available
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
75_E_6 0.9 2.0 Not available
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
22_E_11 1.1 2.0 Not available
120_C_2 1.5 2.0 Not available
Page 15
47_A_2 1.3 2.0 7q36.3 No no gene
98_E_4 0.9 2.0 7q36.3 Yes no gene
75_G_12 1.1 2.0 Not available
55_F_7 1.1 2.0 14q23.1 Yes LOC387990 NM_207377
75_H_12 1.0 2.0 Not available
128_A_11 1.5 2.0 9q34.11 No MER66B (LTR)
108_C_6 0.7 2.0 Not available
80_D_12 0.7 2.0 Not available
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
107_A_8 0.7 2.0 Not available
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
Page 16
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
120_F_11 0.9 2.0 Not available
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)
123_E_11 0.9 2.0 Not available
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
99_E_4 0.8 2.0 Not available
Page 17
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
62_C_11 1.4 2.0 Not available
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)
100_G_6 0.4 2.0 Not available
83_E_5 1.3 2.0 Not available
114_G_4 1.1 2.0 Not available
96_F_9 1.0 2.0 14q21.3 No AluY (SINE)
104_G_5 0.6 2.0 Not available
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
77_E_11 0.9 2.0 Not available
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
127_G_2 1.4 2.0 Not available
28_G_9 0.8 2.0 4q27 No KIAA1109 intron NM_015312
83_A_9 1.6 2.0 Not available
Page 18
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
99_G_9 1.0 2.0 Not available
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
122_F_3 1.8 2.0 Not available
15_G_8 1.5 2.0 16p13.11 No AluJo (SINE)
120_H_10 1.8 2.0 Not available
76_F_6 1.3 2.0 9q22.2 No AluJo (SINE), L1M4b (LINE)
67_C_12 1.1 2.0 Not available
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
96_H_8 0.9 2.0 Not available
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)
85_F_7 1.1 2.0 Not available
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
99_A_4 1.9 2.0 Not available
28_E_10 1.7 2.0 8q24.12 No MIRm (SINE)
109_D_1 1.1 2.0 7p14.1 No MIR3 (SINE)
106_H_12 1.1 2.0 Not available
Page 19
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
96_A_4 2.0 2.0 Not available
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
127_D_11 1.3 2.0 Not available
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)
Page 20
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.
Page 21
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
C16orf47 chr16 2.34E-04 chr16:071735012-071735069 No NM_207385
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
C7orf9 chr7 2.70E-04 chr7:025041069-025041129 No NM_022150
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
Page 22
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
C14orf105 chr14 3.10E-04 chr14:057029943-057030003 No NM_018168
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
Page 23
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
Page 24
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
SLC17A6 chr11 6.01E-04 chr11:022315628-022315688 No NM_020346
RNASE9 chr14 6.02E-04 chr14:020094785-020094845 No NM_001001673
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
SLC26A9 chr1 6.43E-04 chr1:202644020-202644065 No NM_052934
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
Page 25
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
RNASE6 chr14 6.98E-04 chr14:020319098-020319158 No NM_005615
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
SLC26A3 chr7 7.57E-04 chr7:107037391-107037451 No NM_000111
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.
Page 26
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
Loci CpG¶ Gene name Accession no.†
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
100_F_1 4.1 0.8 Not available
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
112_C_6 3.4 1.0 Not available
25_F_6 3.4 0.7 1q31.1 Yes TPR, C1orf 27 NM_003292, NM_017847
103_G_2 3.1 2.1 21q22.13 No AluJb (SINE), L1PA5 (LINE)
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
101_C_3 3.0 0.8 Not available
46_H_12 2.9 1.1 Not available
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
80_C_7 2.6 1.0 Not available
83_A_12 2.6 0.6 Not available
75_A_10 2.5 0.8 7q36.1 Yes Splice EST
Page 27
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
61_B_10 2.4 0.8 Not available
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)
104_G_2 2.2 0.9 2q33.1 No AluJb (SINE), L1PA5 (LINE)
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
48_C_5 2.2 0.9 Not available
47_H_12 2.2 1.0 Not available
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
91_B_5 2.2 0.6 Not available
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)
39_F_3 2.1 0.5 Not available
82_B_6 2.1 0.5 Not available
102_A_2 2.1 0.5 6p22.1 No tRNA-Ile-ATT
Page 28
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)
100_E_7 2.0 0.4 Not available
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
51_D_3 2.0 0.4 Not available
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§
102_G_2 3.9 2.3 2q33.1 No AluJb (SINE), L1PA5 (LINE)
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
103_G_2 3.1 2.1 21q22.13 No AluJb (SINE), L1PA5 (LINE)
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)
Page 29
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.
Page 30
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
Page 31
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
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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
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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
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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
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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
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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
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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
Page 38
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
Page 39
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
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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
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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
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(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
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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.