Oligo sequence for shRNA cloningTurboGFP shRNA upper strand

CCGGCGTGATCTTCACCGACAAGATCTCGAGATCTTGTCGGTGAAGATCACGTTTTT

TurboGFP shRNA bottom strand

AATTAAAAACGTGATCTTCACCGACAAGATCTCGAGATCTTGTCGGTGAAGATCACG

Human PHF2 shRNA-I upper strand

GGCCGGGAACGGGAAACTACTCCTTTACTCGAGTAAAGGAGTAGTTTCCCGTTCTTTTTG

Human PHF2 shRNA-I bottom strand

CTAGCAAAAAGAACGGGAAACTACTCCTTTACTCGAGTAAAGGAGTAGTTTCCCGTTCCC

Human PHF2 shRNA-II upper strand

CCGGGGCAAGCGCCTGACGTCAAGCCTCGAGGCTTGACGTCAGGCGCTTGCCTTTTT

Human PHF2 shRNA-II bottom strand

AATTAAAAAGGCAAGCGCCTGACGTCAAGCCTCGAGGCTTGACGTCAGGCGCTTGCC

Primer sequence for Sub-cloningA

PHF2(h)_1-186_FOR CCGGATCCATGGCGACGGTGCCCGTGTAPHF2(h)_1-186_REV GGGAATTCTTATTGCGGTTGGTGCTGTAGTAPHF2(h)_174-607_FOR CCGGATCCCTGAAGGAGTTTGTGGACTATPHF2(h)_174-607_REV GGGAATTCTTATTCTTGTACTTCCACTTGGCPHF2(h)_594-820_FOR CCGGATCCCAAACCAAGAGCAAGTCAGAGPHF2(h)_594-820_REV GGGAATTCTTAGGCCTGGCCAGCTCCCCACGPHF2(h)_808-1097_FOR CCGGATCCGACTCCTGCCTGCAGACCACPHF2(h)_808-1097_REV GGGAATTCTTAAAGGAGTAGTTTCCCGTTp53(h)_D1-90_FOR TGGCCCCTGTCATCTTCTGTp53(h)_D1-90_REV GAATTCTGCGTAATCCGGTAp53(h)_D90-292_FOR AAGAAAGGGGAGCCTCACCAp53(h)_D90-293_REV GGAGGGGGCTGGTGCAGGGGp53(h)_D1-292_FOR AAGAAAGGGGAGCCTCACCAp53(h)_D1-292_REV GAATTCTGCGTAATCCGGTA

Supplemental Table 1

A Restriction sites are underlined

primer sequence for RT-PCR

p21(h)_RT01 -For AGCGATGGAACTTCGACTTTGp21(h)_ RT01-Rev CGAAGTCACCCTCCAGTGGTmdm2(h)_RT01-For CCGGATCTTGATGCTGGTGTmdm2(h)_RT01-Rev CTGATCCAACCAATCACCTGAATBax(h)_RT01_For GTCTTTTTCCGAGTGGCAGCBax(h)_RT01_Rev CCAGTTGAAGTTGCCGTCAGAprimer sequence for ChIP

p21(h)_P1 GGCTGGTGGCTATTTTGTCCp21(h)_P2 TCCCCTTCCTCCCTGAAAACmdm2(h)_P1’ AAACCATGCATTTTCCCAGCmdm2(h)_P2’ CAGGTCTACCCTCCAATCGCp21(h)_NS1 CAGTGTGGCCAAAGGATCTGACGAp21(h)_NS1 TTGGGGCTGCCTATGTAGTGAAmdm2(h)_NS1’ TCTTGACTTTCATGCAAGTCAAACGGmdm2(h)_NS2’ GAAAGGAAAATATAAGAGGACTGGapdh(h)_Fwd ATCGGGCCAATCTCAGTCCCTTCCCGapdh(h)_Rev GCCTGGTTCAACTGGGCACGCACCGA

Supplemental Table 1 cont.

Supplemental table 1. The oligonucleotide sequences used for cloning of shRNA viral vectors, primers for subcloning of plasmid vectors, and primers for RT-qPCR and Chip-PCR are listed.

p53 functionality and p21 vs PHF2 levels in each tumor Supplemental Table 2

Colon cancers with positive p53 function 　 　 　 　

Patient No.

PHF2 level p21 levelSex age TP53 mutation p53

activity normal tumor normal tumor4 F 66 WT 100 1.2 9.5 1.2 3.96 F 64 WT 100 0.5 14 0.6 1.77 M 56 WT 100 10 4.3 0.8 2.19 M 64 WT 100 9.6 2.5 1.6 1.3

10 M 71 A78S (active) 74.94 5.6 3.6 1.6 2.614 M 57 Q104L (active) 52 4.6 8 0.7 4.415 F 41 Q104L (active) 52 2.1 6.2 0.7 5.416 M 62 WT 100 1 7.9 3 4.317 M 60 Q104L (active) 52 1.2 6.8 0.3 1.419 M 79 WT 100 4.6 11 0.8 3.420 M 77 WT 100 2.6 16 1 3.123 M 66 S106R (active) 50.2 0.6 20 0.6 2.226 M 74 WT 100 2.7 3.7 0.5 127 M 64 WT 100 5 5.5 1.4 1.528 F 67 WT 100 11 9.8 1.5 2.3

p53 functionality and p21 vs PHF2 levels in each tumor Supplemental Table 2 cont.

Colon cancers with negative p53 function

Patient No.

PHF2 level p21 levelSex age TP53 mutation p53

activity normal tumor normal tumor2 F 64 R273C (inactive) 0.9 1.3 13 0.7 1.53 M 75 R248Q (inactive) 0 3.9 16 1.5 2.25 F 55 R175H (inactive) 12.4 5.9 2.8 1.1 2.38 F 58 Y234C (inactive) 2.1 2.8 5.4 1.1 2

11 M 68 insertion after S106 n/a 3.3 8 0.6 1.912 M 62 R342STOP n/a 1.5 8.2 0.3 0.513 F 61 V143E (inactive) 9.13 5.7 9.5 0.6 2.118 M 56 insertion after S106 N/A 1.4 3.5 0.2 0.821 F 70 P151H (inactive) 10.7 0.8 3.9 0.9 2.722 F 62 F54I, C141Y (inactive) 71.7, 9.8 0.7 9.2 0.3 2.124 F 62 R248Q (inactive) 0 13 6.2 1.9 2.425 F 57 R337P (inactive) 4.2 1.2 9.9 0.9 1.529 M 62 Y205N (inactive) 9.3 4.6 12 1.6 3.530 F 65 R337P (inactive) 4.2 4.6 1.7 2 2.4

Supplemental table 2. The p53 cDNA was sequenced in 30 colorectal cancer tissues. According to functional status of p53, the cancer tissues are divided into two groups, active p53 and mutant p53. PHF2 and p21 levels shown in Figure 6a are listed together.

Case No Diagnosis AGE SEX T_stage N_stage M_stage DIFF1 Adenocarcinoma 62 F pT3 pN1 . Moderately2 Adenocarcinoma 56 M pT3 pN1 . Moderately3 Adenocarcinoma 64 F pT4b pN2 . Moderately4 Adenocarcinoma 58 F pT3 pN0 . Moderately5 Adenocarcinoma 68 M pT3 pN1 . Moderately6 Adenocarcinoma 79 M pT3 pN0 . Poorly 7 Adenocarcinoma 62 M pT3 pN1b . Moderately8 Adenocarcinoma 61 F pT3 pN2 . Moderately9 Adenocarcinoma 64 F pT3 pN0 . Moderately

10 Adenocarcinoma 57 F pT3 pN0 . Moderately11 Adenocarcinoma 60 M pT4b pN1 . Well12 Adenocarcinoma 57 M pT2 pN0 . Moderately13 Adenocarcinoma 71 M pT3 pN1 . Moderately14 Adenocarcinoma 62 M pT3 pN1 . Well15 Adenocarcinoma 62 M pT3 pN0 . Moderately16 Adenocarcinoma 41 F pT3 pN0 . Moderately17 Adenocarcinoma 64 M pT3 pN0 . Well18 Adenocarcinoma 75 M pT3 pN0 . Moderately19 Adenocarcinoma 66 F pT3 pN2 . Moderately20 Adenocarcinoma 62 F pT3 pN0 . Moderately21 Adenocarcinoma 70 F pT4b pN0 . Moderately22 Adenocarcinoma 77 M pT3 pN1 . Moderately23 Adenocarcinoma 55 F pT3 pN1 . Moderately24 Adenocarcinoma 64 M pT3 pN0 . Moderately25 Adenocarcinoma 74 M pT3 pN0 . Well26 Adenocarcinoma 67 F pT3 pN0 . Moderately27 Adenocarcinoma 62 M pT3 pN1 . Moderately28 Adenocarcinoma 66 M pT3 pN0 . Moderately29 Adenocarcinoma 65 F pT4b pN1 . Moderately30 Adenocarcinoma 56 M pT3 pN2 . Moderately

Supplemental Table 3Patient Demographics for colon cancer tissue array

Case No.

Diagnosis Age Sex T stage N stage Diff

1 adenocarcinoma 40 M pT4a pN3a poorly differentiated2 adenocarcinoma 43 F pT4a pN0 poorly differentiated3 adenocarcinoma 61 F pT3 pN3a moderately differentiated4 signet ring cell carcinoma 45 F pT3 pN3a 　5 adenocarcinoma 67 M pT3 pN1 poorly differentiated6 adenocarcinoma 53 F pT3 pN3a poorly differentiated7 adenocarcinoma 67 M pT4a pN3b moderately differentiated8 adenocarcinoma 72 M pT3 pN3a poorly differentiated9 mucinous adenocarcinoma 61 M pT1b pN2 　

10 adenocarcinoma 65 M pT4a pN0 poorly differentiated11 adenocarcinoma 70 M pT4a pN2 moderately differentiated12 adenocarcinoma 62 M pT3 pN2 well differentiated13 signet ring cell carcinoma 62 F pT3 pN2 　14 papillary adenocarcinoma 52 M pT2 pN0 　15 adenocarcinoma 60 M pT3 pN3a poorly differentiated16 adenocarcinoma 66 M pT4a pN3b poorly differentiated17 signet ring cell carcinoma 41 M pT3 pN3a 　18 adenocarcinoma 60 F pT3 pN3a poorly differentiated19 adenocarcinoma 59 M pT4a pN3b poorly differentiated20 adenocarcinoma 62 M pT3 pN3b poorly differentiated21 adenocarcinoma 49 M pT4b pN3b poorly differentiated22 mucinous adenocarcinoma 64 M pT3 pN1 　23 undifferentiated carcinoma 55 M pT4a pN3b 　24 adenocarcinoma 56 F pT3 pN2 poorly differentiated25 adenocarcinoma 48 M pT3 pN2 poorly differentiated26 mucinous adenocarcinoma 65 F pT4a pN3a 　27 adenocarcinoma 63 M pT3 pN2 well differentiated28 adenocarcinoma 60 M pT3 pN0 well differentiated29 signet ring cell carcinoma 42 M pT3 pN1 　30 mucinous adenocarcinoma 55 M pT30 pN3a 　

Supplemental Table 3 cont.

Patient Demographics for stomach cancer tissue array

31 adenocarcinoma 58 M pT3 pN3b moderately differentiated32 adenocarcinoma 72 F pT1b pN2 moderately differentiated33 adenocarcinoma 53 M pT3 pN0 poorly differentiated34 adenocarcinoma 46 M pT4b pN0 poorly differentiated35 adenocarcinoma 64 M pT2 pN1 moderately differentiated36 adenocarcinoma 65 M pT2 pN1 poorly differentiated37 adenocarcinoma 45 F pT2 pN1 poorly differentiated38 adenocarcinoma 58 F pT3 pN0 well differentiated39 adenocarcinoma 68 F pT3 pN3a poorly differentiated40 adenocarcinoma 66 M pT4a pN3a poorly differentiated41 adenocarcinoma 63 M pT3 pN0 poorly differentiated42 adenocarcinoma 52 F pT3 pN2 moderately differentiated43 adenocarcinoma 35 F pT1a pN0 poorly differentiated44 adenocarcinoma 44 F pT1b pN0 well differentiated45 adenocarcinoma 55 M pT1a pN0 well differentiated46 signet ring cell carcinoma 40 M pT1a pN0 　47 adenocarcinoma 66 M pT1b pN0 moderately differentiated48 adenocarcinoma 65 F pT1b pN0 moderately differentiated49 adenocarcinoma 62 F pT1b pN0 poorly differentiated50 adenocarcinoma 60 F pT1b pN0 moderately differentiated51 adenocarcinoma 70 F pT1b pN1 moderately differentiated52 adenocarcinoma 52 M pT1b pN0 well differentiated53 signet ring cell carcinoma 40 M pT1b pN1 　54 signet ring cell carcinoma 34 F pT1a pN1 　55 adenocarcinoma 60 M pT1b pN0 well differentiated56 adenocarcinoma 68 M pT1b pN1 well differentiated57 adenocarcinoma 52 M pT2 pN0 well differentiated58 signet ring cell carcinoma 62 M pT1a pN0 　59 adenocarcinoma 60 M pT2 pN0 well differentiated

Supplemental Table 3 cont.

Patient Demographics for stomach cancer tissue array

Supplemental table 3. Demographic information on patients, stages and differentiation degree in colon and stomach cancer arrays used for Figure 6e-h is listed.

C. PARPC. Casp 3C. Casp 9

Tubulin

C. PARP

C. Casp 3C. Casp 9

Tubulin

Hep

G2

Hep

3B

DOX PBS Oxa 5-FUSh-Con + - + - + - + -

Sh-PHF2-I - + - + - + - +

DOX PBS Oxa 5-FUSh-Con + - + - + - + -

Sh-PHF2-I - + - + - + - +

C. PARPC. Casp 3

C. Casp 9

Tubulin

DOX PBS Oxa 5-FUSh-Con + - + - + - + -

Sh-PHF2-I - + - + - + - +C. PARP

C. Casp 3

C. Casp 9

Tubulin

DOX PBS Oxa 5-FUSh-Con + - + - + - + -

Sh-PHF2-I - + - + - + - +K

ATO

III

MK

N-7

4

C. PARPC. Casp 3

C. Casp 9

Tubulin

DOX PBS Oxa 5-FUSh-Con + - + - + - + -

Sh-PHF2-I - + - + - + - +

C. PARPC. Casp 3

C. Casp 9

Tubulin

DOX PBS Oxa 5-FUSh-Con + - + - + - + -

Sh-PHF2-I - + - + - + - +

MD

A-M

B23

1

MC

F7Supplemental Fig. 1

Figure S1. Indicated stable cells were treated with PBS, 12.5 mM oxaliplatin, 50 mM 5-FU or 0.5 mM doxorubicin for 16 hours and apoptotic markers were analyzed by Western blotting using indicated antibodies.

Total H3

H3K4-Me2

H3K9-Me2

H3K27-Me2

H3K36-Me2

H3K72-Me2

Sh-Con + - -Sh-PHF2-I - + -Sh-PHF2-II - - +

Supplemental Fig. 2

Figure S2. Histone methylation status in PHF2 knock down cell lines was measured. Protein extract from HCT116 stable cells underwent western blotting with methyl-specific antibodies. .

Sh-Con

Sh-PHF2

OxaPBS

Supplemental Fig. 3

Figure S3. Xenograft tumor sizes after PBS or Oxaliplatin (Oxa) treatment.