Supplementary Figure 4: ARLNC1 expression is regulated by AR and FOXA1.

(a) ChIP-seq peaks of H3K4me1, MED1, BRD4, FOXA1, and NKX3-1 from LNCaP cells at the ARLNC1 promoter region. AR ChIP-seq tracks from normal prostate and prostate cancer are also shown. Motif analysis results are summarized at the bottom, suggesting possible binding of AR, FOXA1, NKX3-1, IRF1 and POU1F1 at the ARLNC1 promoter region. (b) Top panel: qPCR analysis of ARLNC1 expression in LNCaP cells, following treatment with siRNAs targeting AR, FOXA1, NKX3-1, BRD4, EZH2, LSD1, IRF1, and POU1F1. Mean ± s.e.m. are shown, n = 3. *Adjusted P = 0.0436, **Adjusted P = 0.0264, ****Adjusted P = 0.0001, compared to control siRNA (si-NT) by ANOVA analysis with Dunnett correction. Bottom panel: On-target effect of siRNAs was evaluated by qPCR analysis in the bottom panel. Mean ± s.e.m. are shown, n = 3. **P = 0.006, ***P < 0.001, compared to control siRNA (si-NT) by two-tailed Student’s t-test. (c) ChIP-PCR analysis in MDA-PCa-2b cells showing relative enrichment (ChIP/input) of AR, FOXA1, NKX3-1 or IgG over ARLNC1 promoter region or control region. Error bars represent mean ± s.e.m. (n = 3). ***Adjusted P = 0.0001 compared to negative control, by ANOVA analysis with Dunnett correction for multiple comparisons. (d) Relative expression (TPM) of AR (Left) and FOXA1 (Right) across a panel of normal tissues in GTEx normal tissue RNA-seq cohort (n = 8,745 samples). Box-plot definition: center, median; box limits, 1st and 3rd quartile; whiskers follow the 1.5 rule.