1. *** * * * Figure S1 Supplementary Figure 1. Analysis of JARID1A–D mRNA levels showed that JARID1D knockdown had insignificant or weak effects on expression levels of JARID1A–C. Three shRNAs (shJARID1D-N1, shJARID1D-N4 and shJARID1D-4) were used to deplete JARID1D in DU145 prostate cancer cells. Total RNAs were isolated and analyzed using quantitative RT-PCR. The relative fold represents the expression levels in individual samples over those in control shLuciferase (shLuc) samples.

2. Figure S2 P value Genes down-regulated by JARID1D knockdown 3.31E-05 8.97E-05 1.49E-04 1.70E-04 9.91E-04 1.73E-03 4.07E-03 Supplementary Figure 2. Gene ontology analysis for genes down-regulated in JARID1D-depleted cells. Gene expression levels were measured by the gene expression microarray Affymetrix U133P. Gene ontology analysis was performed for 378 genes that were down-regulated at least 2 fold in shJARID1D group compared with shLuciferase group (shJARID1d/shLuciferase <0.5).

3. TSS H3K4me3 (shLuc) H3K4me3 (shJARID1D) -2K 2K -2K 2K TSS 312 0 202 102 All human genes in DU145 cells Figure S3 Supplementary Figure 3. Heatmap for H3K4me3 ChIP-Seq signals of all the gene- regulatory regions spanning − 2kb to +2kb suggested that many H3K4me3 signals were slightly increased by JARID1D knockdown.

4. Figure S4 Prostate tissues, primary tumors and metastatic tumors JARID1D JARID1B JARID1A JARID1C P value 3.43E-4 0.736 2.76E-6 9.96E-15 Fold Change −1.92 1.06 1.53 3.39 Gene Normal (28) Primary (59) Metastasis (35) Lowest highest Not measured Supplementary Figure 4. Of JARID1A–1D, only JARID1D mRNA levels were downregulated in metastasis tumors compared to primary tumors. The mRNA levels of JARID1A–1D in normal prostate tissues, primary prostate tumors and metastatic prostate tumors are presented using datasets called Grasso prostate cancer (A) and Yu prostate cancer (B) from Oncomine database. The P values and fold changes were calculated between primary and metastasis tumors. The sign “−” in fold change indicates “down-regulation”. JARID1D JARID1B JARID1A JARID1C P value 6.18E-8 0.053 0.007 1.18E-6 Fold Change −1.22 -1.05 1.11 1.29 Gene Normal (24) Primary (64) Metastasis (24) Prostate tissues, primary tumors and metastatic tumors A B

5. Figure S5 Supplementary Figure 5. JARID1D mRNA levels were not correlated with MMP2 (A), MMP7 (B), MMP10 (C), MMP13 (D), Slug (E) and N-Cadherin (F) mRNA levels. A dataset from the publicly available database cBioPortal (NCBI GEO Database #GSE21032) were analyzed. A B CD E F