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Differential Regulation of Estrogen Receptor Α Expression in Breast Cancer Cells by Metastasis-Associated Protein 1

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Differential Regulation of Estrogen Receptor Α Expression in Breast Cancer Cells by Metastasis-Associated Protein 1 CAN-13-2020R Supplementary Materials Differential Regulation of Estrogen Receptor α Expression in Breast Cancer Cells by Metastasis-Associated Protein 1 Hyun-Jin Kang1, Min-Ho Lee1, Hae-Lim Kang1, Sung-Hae Kim1, Jung-Ranh Ahn1, Hyelin Na1, Tae-Young Na1, Yona Kim2, Je Kyung Seong2, and Mi-Ock Lee1 1College of Pharmacy and Bio-MAX institute, Research Institute of Pharmaceutical Sciences; and 2College of Veterinary Medicine, BK21 Plus Program for Veterinary Science, Seoul National University, Seoul, Korea; Abbreviations ERα, Estrogen receptor alpha; MTA1, Metastasis-associated protein 1; TFAPT2C, Transcription factor AP-2 gamma; IFI16, interferon inducible protein 16; HDAC, Histone deacetylases; shRNA, small hairpin RNA Supplementary Tables Supplementary Table 1. The sequences of RT-PCR, ChIP, siRNA, and shRNA Oligonucleotide Nucleotide sequence Reference RT-PCR sense 5'-ACTGTAGCAGAGTATCTGGTGA-3' NM_001122742 ERα antisense 5'-GGTCTGCAAGGAATGTTCCTA-3' sense 5'-CACGCACATCAGGGGCAA-3' Lee et al., 2012 MTA1 antisense 5'-GTGCGAAGGTGCCCACA-3' sense 5'-CGTGGGCCGCCCTAGGCACCA-3' Yoo et al., 2006 β-actin antisense 5'-TTGGCTTAGGGTTCAGGGGGG-3' ChIP sense 5'-TTAATCTGGGTGGCTGGA-3' ERα promoter (-3849 ~ -3612) I antisense 5'-TACCCTCTCCTGCTGGA-3' sense 5'-AGGAGCTGGCGGAGGGCGTTCG-3' ERα promoter (+1 ~ +127), II antisense 5'-AGCGCATGTCCCGCCGACACGC-3' Macaluso et al., 2007 sense 5'-GCTGTGCTCTTTTTCCAGGT-3' ERα promoter (+146 ~ +377), III antisense 5'-TTGCTGCTGTCCAGGTACAC-3' Woodfield et al., 2009 sense 5'-TGAACCGTCCGCAGCTCAAGATC-3' ERα promoter (+310 ~ +461), IV antisense 5'-GTCTGACCGTAGACCTGCGCGTTG-3' Zhou et al., 2007 sense 5'-GCTGTGCTCTTTTTCCAGGT-3' ERα promoter (+146 ~ +461) ERpro315 antisense 5'-GTCTGACCGTAGACCTGCGCGTTG-3' siRNA sense 5'-GUUCAGCGUGUCCGGCGAGTT-3' Seo et al., 2009 siGFP antisense 5'-CUCGCCGGACACGCUGAACTT-3' sense 5'-AAGACCCUGCUGGCAGAUAAATT-3' Yoo et al., 2006 siMTA1 antisense 5'-UUUAUCUGCCAGCAGGGUCUUTT-3' sense 5'-CCACACUGGAGUCGCCGAAUATT-3' Williams et al., 2009 siTFAP2C antisense 5'-UAGUCGGCGACUGUGUGGTT-3' sense 5'- GCUGGUCCUAACCAAACGUTT-3' Fujiuchi et al., 2004 siIFI16 antisense 5'-ACGUUUGGUUAGGACCAGCTT-3' sense 5'-GCCUCACCGAAUCCGCAUGTT-3' NM_004964.2 siHDAC1 antisense 5'-CAUGCGGAUUCGGUGAGGCTT-3' sense 5'-AAAUUACGGUCCAGGCUAATT-3' NM_006037.3 siHDAC4 antisense 5'-UUAGCCUGGACCGUAAUUUTT-3' sense 5'-GACUGUUAUUAGCACCUUUTT-3' NM_001015053.1 siHDAC5 antisense 5'-AAAGGUGCUAAUAACAGUCTT-3' sense 5'-CCAUUGCCUACGAGUUUAATT-3' NM_006044.2 siHDAC6 antisense 5'-UUAAACUCGUAGGCAAUGGTT-3' shRNA shGFP 5’-GCAAGCTGACCCTGAAGTTCAT-3’ aAddgene (#30323) shMTA1 5’-GCGCATCTTGTTGGACATATT-3’ bTRCN000001336 shTFAP2C 5’-CCTATGTCTGTGAAGCCGAAT-3’ bTRCN0000019747 shIFI16 5’-ACGTTTGAGGTTCCAAATAAA-3’ bTRCN0000369343 aAddgene (http://www.addgene.org/) bTRCN (The shRNA consortium number) Supplementary Table 2. The common target genes of TFAP2C and MTA1. Gene Regulated Regulated by Refseq Description a b Symbol by MTA1 TFAP2C Slc38a1 BF663461 solute carrier family 38, member 10 ↑ ↑ Ociad2 BG291649 OCIA domain containing 2 ↑ ↑ NPR3 NM_000908 natriuretic peptide receptor C/guanylate cyclase C ↑ ↑ Tnfrsf19 AF246998 tumor necrosis factor receptor superfamily, member 19 ↑ ↑ Depdc6 NM_022783 DEP domain containing 6 ↑ ↑ Plcb4 NM_000933 Phospholipase C, beta 4 ↑ ↑ Tspan5 AF065389 tetraspanin 5 ↑ ↑ Tspan15 NM_012339 tetraspanin 15 ↑ ↑ Itga6 NM_000210 integrin, alpha 6 ↓ ↓ Ppap2b AB000889 phosphatidic acid phosphatase type 2B ↓ ↓ Lpin1 AA813260 lipin 1 ↓ ↓ Nagk NM_017567 N-acetylglucosamine kinase ↓ ↓ Trim56 AL512757 tripartite motif-containing 56 ↓ ↓ Nedd9 AW291077 neural precursor cell expressed, developmentally down-regulated ↓ ↓ 9 Svil NM_003174 supervillin ↓ ↓ Sytl2 NM_017695 synaptotagmin-like 2 ↑ ↓ Slc24a3 NM_020689 solute carrier family 24 (sodium/potassium/calcium exchanger), ↑ ↓ member 3 Gpr126 NM_020455 G protein-coupled receptor 126 ↑ ↓ Pqlc3 AL161956 PQ loop repeat containing 3 ↓ ↑ Rgl1 AF186779 ral guanine nucleotide dissociation stimulator-like 1 ↓ ↑ Kal1 AI432167 Kallmann syndrome 1 sequence ↓ ↑ Sulf2 AL034418 sulfatase 2 ↓ ↑ Micall2 AI821474 MICAL-like 2 ↓ ↑ Gprc5b NM_016235 G protein-coupled receptor, family C, group 5, member B ↓ ↑ Stom M81635 stomatin ↓ ↑ Sulf1 AW043713 sulfatase 1 ↓ ↑ a Woodfield et al (2010) b Ghanta et al (2011): 1123 genes varied by 2 ≥ fold, 0.05 ≤ p-value Supplementary Figures Supplementary Figure 1. Epigenetic control of ERpro315 region by MTA1. MCF7 or MDA-MB- 231 cells were transfected with siMTA1 for 48 h. DNA fragments that immunoprecipitated by anti- H3K4me3 and H3K27me3 antibodies were amplified by PCR using primers for ERpro315. Supplementary Fig. 2. Class II HDACs interact with p300 in the presence of TFAP2C. A. Whole cell lysates were immunoprecipitated (IP) with normal IgG, anti-HDAC4, or anti-HDAC5 antibodies, and immunoprecipitates were fractionated and probed by western blotting (WB) using anti-p300, anti- HDAC4 or anti-HDAC5 antibodies. B. MCF7 cells were transfected with siTFAP2C (300 pmol) for 72 h. Whole cell lysates were immunoprecipitated (IP) with normal IgG, anti-HDAC4, or anti- HDAC5 antibodies, and immunoprecipitates were fractionated and probed by western blotting (WB) using anti-p300, anti-HDAC4 or anti-HDAC5 antibodies. Supplementary References Lee MH, Na H, Kim EJ, Lee HW, Lee MO. Poly(ADP-ribosyl)ation of p53 induces gene-specific transcriptional repression of MTA1. Oncogene 2012;31:5099-107. Yoo YG, Kong G, Lee MO. Metastasis-associated protein 1 enhances stability of hypoxia-inducible factor-1alpha protein by recruiting histone deacetylase 1. EMBO J 2006;25:1231-41. Macaluso M, Montanari M, Noto PB, Gregorio V, Bronner C, Giordano A. Epigenetic modulation of estrogen receptor-alpha by pRb family proteins: a novel mechanism in breast cancer. Cancer Res. 2007;67:7731-7. Woodfield GW, Hitchler MJ, Chen Y, Domann FE, Weigel RJ. Interaction of TFAP2C with the estrogen receptor-alpha promoter is controlled by chromatin structure. Clin Cancer Res. 2009;15:3672-9. Zhou Q, Atadja P, Davidson NE. Histone deacetylase inhibitor LBH589 reactivates silenced estrogen receptor alpha (ER) gene expression without loss of DNA hypermethylation. Cancer Biol Ther. 2007;6:64-9. Seo HW, Kim EJ, Na H, Lee MO. Transcriptional activation of hypoxia-inducible factor-1alpha by HDAC4 and HDAC5 involves differential recruitment of p300 and FIH-1. FEBS Lett 2009;583:55-60. Williams CM, Scibetta AG, Friedrich JK, Canosa M, Berlato C, Moss CH, et al. AP-2gamma promotes proliferation in breast tumour cells by direct repression of the CDKN1A gene. EMBO J 2009;28:3591-601. Fujiuchi N, Aglipay JA, Ohtsuka T, Maehara N, Sahin F, Su GH, et al. Requirement of IFI16 for the maximal activation of p53 induced by ionizing radiation. J Biol Chem 2004;279:20339-44. Woodfield GW, Chen Y, Bair TB, Domann FE, Weigel RJ. Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells. Genes Chromosomes Cancer 2010 ;49:948- 62. Ghanta KS, Li DQ, Eswaran J, Kumar R. Gene profiling of MTA1 identifies novel gene targets and functions. PLoS One 2011;6:e17135. Cicatiello L, Mutarelli M, Grober OM, Paris O, Ferraro L, Ravo M et al. Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Am J Pathol 2010;176:2113-30. .
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