Supplementary Table S1: Relative fold change of transcription expression of miR-224 and its associated Xq28 genes between tumor and paired adjacent non-tumor samples from the three HCC patients.

Patient A Patient B Patient C Mean SDMAGEA4 2971.6 406.8 1.0 1126.4 1610.7GABRE 451385.3 3160.6 658.9 151735.0 259507.8MAGEA5 50.0 113.0 0.6 54.5 56.3miR-224 48.8 8.2 17.9 25.0 21.2miR-452 25.5 5.9 9.2 13.5 10.5U6 1.6 0.6 0.8 1.0 0.5

T/NT

Samples from Patient A, B and C were used for chromatin immunoprecipitation as shown in Figure 4 A &B.

Supplementary Figure S1: Testing of antibodies used for chromatin immunoprecipitation

Western blot analysis of EP300, HDAC1, Histone H3, acetylated form of H3 at lysine 9 (H3K9) and lysine 14 (H3K14), normalized against loading control β-Actin, in NeHepLxHT cells treated with blank, 20 µM 5-Aza, 0.5 µM TSA or 5 µM SAHA, for 72 hours.

Supplementary Figure S2: GABRE expression changes in different stages of HCC.

GABRE expression was extracted from a study conducted by Wurmbach et al (Hepatology 2007;45:938-47) using NextBio. Red box indicates the progressive increase in fold change of GABRE expression in liver dysplasia.

Supplementary Figure S3: Representative ChIP assay on NeHepLxHT cells treated with epigenetic drugs

AB

D

E

FG

H

KJ

C

Rn

A

BD

E F

G

H

K

J

C

Rn

I

II

Quantitative PCR amplification plots of ChIP assay to measure enrichment of miR-224 residing GABRE Intron6 region. Samples presented here include input DNA from untreated cells (A), 5-Aza treated cells (B), TSA treated cells (C) and SAHA treated cells (D), anti-H3K9 or anti-H3K14 ChIP enriched DNA from untreated cells (E), 5-Aza treated cells (F), TSA treated cells (G) and SAHA treated cells (H), unrelated anti-EGFP (J) or no antibody (K) enriched DNA.

H3K9 ChIP

H3K14 ChIP