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Supplementary Tables S1-S4 SUPPLEMENTAL INFORMATION Tables S1–S4 FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells Biswajyoti Sahu1, Marko Laakso1,2, Päivi Pihlajamaa1, Kristian Ovaska1,2, Ievgenii Sinielnikov1, Sampsa Hautaniemi1,2, and Olli A. Jänne1,3 1Institute of Biomedicine and 2Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland, and 3Department of Clinical Chemistry, Helsinki University Central Hospital, FI-00290 Helsinki, Finland. Table S1. Sequences of the primers used in direct ChIP assays and qRT-PCR. Primer name Primer sequence (5’→3’) LNCaP-1F5 unique sites LU1+ GTTGAGGTTGCCCCAATTTA LU1- TTCATTGAAGGTGCTGATGC LU2+ TTACCATGATGCACCGAAGA LU2- TGCCTCTCACACTGTCAATACC LU3+ GGTGTGCAGCCTTCTGAGAT LU3- GCTGCAGATCCACAAGTCAA LU4+ GGCAGCTTTCCTTTCTGATG LU4- AGATAGAGGGCAAAAGCAAGC LU5+ ATGTCAGGCAAACTGGGTCT LU5- CCTAACCAGATCCTGCTGTCA LU6+ GATTCAGCAAATGGAAAATGC LU6- CTAGTTGAACTGAGCCAACGTG LU7- GGAATGCAAACATGGTACACAG LU7+ AGGAGCCTGACTGCTGGAT LU8- ATCTCACAGCCCTGCTGACT LU8+ GCCAGGAATTGATTTTTCCA LU9- GGAGTTTCCAGAGTGCAAGG LU9+ CCTCTGTTCCCAGGTGTGAT LU10- CGTGATGTTTCCTGCTGAGA LU10+ ATTTCCTGTTCCGCAGTGTT Overlapping AR/GR sites AG1+ TCCCTTCAAGGAAGAAACGA AG1- GGGAGGATGTGAGGAAAGAAC AG2+ CTTTACTGCCAGCCTTCTTAGG AG2- GGAGGAAAGACAGAGGACAGG AG3+ GCTGGTCCACAGTCAGGAA AG3- CACTTTCCCTTCCGTCTTTTT AG4+ GAACATTGTGTTCTGGCTGAGA AG4- GGCTAGGTAAGAGGCAGCACT AG5+ CAGGCACGTGTACACACACA AG5- TGGTTAGGACTGTTTGGTTGC AG6+ CCAGTAATTGCCCCCATAAA AG6- TAAAAAGCAGGCAGGACTGG Unique GR sites UG1+ AGAAGAGGGTGAGCCCAGA UG1- GGAAACACACTGGTCGCTTT UG2+ CTGTCCTTCTCCACCCTCAC UG2- ATCTGAAGGCCCTGAGTGG UG3+ AAGCTGCTTCCTCAGCAGAA UG3- GGTCACAACCTGATGACTGGT UG4+ AGAACCAGGCCAGAGGCTA UG4- ATCGCAGCACAGAAAGTCCT UG5+ GCTGAGCTTCCTGTCACCTC UG5- CTGCTAAGATCCCCAGAGACC UG6+ AGACGGCTGGATCAGAACAG UG6- CCTGTCCCTTCTCTGGTGAC Unique AR sites UA1+ GTGGGGATTGTGATGTCTCC UA1- AAGTTCATCCGGGCTCAAG UA2+ CACAGACAGAGCAGGGAGTG UA2- GGCTCACTCGACAGTTCTCC UA3+ GAGAACACGGATGGGTTCC UA3- AAGGTTGGTTTGGCAGAAGA UA4+ CTGAACACGGAGGGGATTAG UA4- AGTCTCCAAGGGTGAAAGCA UA5+ TTTGTCAGCTCTTTCCATTGC UA5- CGATGCAAAAGTGAGGCTTT UA6+ TCCCTCTGTGAACAAACACG UA6- GGCTCAGAGTCAGGATGAGG PSA enhancer+ (Wang et al. 2005) TGGGACAACTTGCAAACCTG PSA enhancer- (Wang et al. 2005) CCAGAGTAGGTCTGTTTTCAATCCA FKBP5 enhancer+ CTCTCCAACCTGCACTCCAT FKBP5 enhancer- TAAAAGCACACAGGCGTGAA PGC promoter+ AGGCAGAGTGCTGGGATAGA PGC promoter- GGGCCCACAACAAAGAACTA VCaP Unique GR sites VU1+ GGGGGTGGAATAAAGCATCT VU1- AGAGCAATCAGGGACTGCAT VU2+ TCTTGCCTCAGCGTTGACT VU2- TTGGCAATTTGACAGATCCA VU3+ AACTCCCCGAGTCCAAAGTT VU3- CTGAAGCACAGGACATGGAA VU4+ ATGCCTACCTCCTCCATCCT VU4- ATTGGCTCCCTGTGAACTTG VU5+ ACATCGGGTGACTGGAGTTC VU5- AGCGGTCTCTGCATCTAAGC VU6+ CCACCTCCATCAGATAAGCAC VU6- CAAGAGCACCAGGGCTGTA VU7+ GCAAAGTGGACAGACAGCAA VU7- CTTTGCATCCGTTTCATTCC VU8+ GTGAAGGCTTCTGGAGTTGC VU8- GCCTCAGCACATTCCTGTCT VU9+ GACAGCCAGAATTCCTCCAA VU9- ACCGACAAGAGATGCTCAGG VU10+ ATACCAAATTGCCTGGCATC VU10- TCTGCAGTGACAGCTTTGTGT LNCaP-1F5 Unique GR sites LG1+ GCTTCCCACTCCTTCTCCA LG1- TGACCCTGTGTTTCCCTTTC LG2+ TGGTTGTAACACCCCATTAGG LG2- TTGTTGAGCCACTCCGTAATC LG3+ AAGACTCCTTGGGAGGCACT LG3- CGGGATATGGAGAGAAACCA LG4+ AGCACCAGTGCCATAATTCC LG4- GGGAGCTGACTATGCTCCAG LG5+ TTCTGGAGCGCTAAGAGAGC LG5- TCTTTGTGCCCCAAGACTTC LG6+ ACAGCAGCCACCTCACAAC LG6- GGAGTTCCACCAGCACCTAA LG7+ GGTTTGCCAAGGGTCCTAA LG7- TCCCAGGTACCAGTGCTTCT LG8+ CACCATCCAGTGACAGTTGG LG8- TGTCTGTGGAATTGCCATGT LG9+ TAACCACATCAAGCGAGCTG LG9- AGGGTGTTCTGTGCTCTTCAA LG10+ TGCCCTTCCCATACTAGGTG LG10- AGAAAGCCACTGGGCACTAA LG11+ AGGAATGAGGAGCCTTGGA LG11- AGAACCTGCCCTTCCTTACC LG12+ TCCTGGGCATAGATGAATGAG LG12- GGAAGTGAGGCTCAGCGTAG LG13+ TGGGTATCCTCAGTGCTCCT LG13- GCCCTGGGGAATGATAAGTT LG14+ AGTCGCCTGACCTGTACCTG LG14- GGTGTTAGGAACTGTCCTGAGC mRNA qRT-PCR primer name KLK3 mRNA+ (Wang et al. 2007) TGTGTGCTGGACGCTGGA KLK3 mRNA- (Wang et al. 2007) CACTGCCCCATGACGTGAT TMPRSS2 mRNA+ (Wang et al. 2007) GGACAGTGTGCACCTCAAAGAC TMPRSS2 mRNA- (Wang et al. 2007) TCCCACGAGGAAGGTCCC NFKBIA mRNA+ (Sahu et al. 2011) GGGACTCGTTCCTGCACTT NFKBIA mRNA- (Sahu et al. 2011) GTCTGCTGCAGGTTGTTCTG SPDEF mRNA+ (Sahu et al. 2011) AAGTGCTCAAGGACATCGAGA SPDEF mRNA- (Sahu et al. 2011) AGGAGCCACTTCTGCACATT LPAR3 mRNA+ (Sahu et al. 2011) CTCATGGCCTTCCTCATCAT LPAR3 mRNA- (Sahu et al. 2011) TACCACAAACGCCCCTAAGA EXTL2 mRNA+ (Sahu et al. 2011) CCTGAACTGGAAACCAATGC EXTL2 mRNA- (Sahu et al. 2011) TCAGGAAATTGCTGCCAAA ERRFI1 mRNA+ GACCTACTGGAGCAGTCGCAGTGA ERRFI1 mRNA- GCAGTGGCCATTCATCGGAGCA ELL2 mRNA+ GCTCACCGAGACGGCGATCC ELL2 mRNA- ACAAGCCCGTGGAGTCCTTGGAA JAG1 mRNA+ TCGGGTCAGTTCGAGTTGGA JAG1 mRNA- AGGCACACTTTGAAGTATGTGTC NDRG1 mRNA+ CCACCTTTTTGGGAAGGAA NDRG1 mRNA- GCATTGATGAACAGGTGCAG SNAI2 mRNA+ TGCGGCAAGGCGTTTTCCAGA SNAI2 mRNA- GGGTCTGCAGATGAGCCCTCAGA S100P mRNA+ GCAGACCCTGACCAAGGGGGA S100P mRNA- CTGGGCATCTCCATTGGCGTCC Table S2. ChIP-sequencing aligned read statistics. The ChIP-sequencing data for AR-DHT in LNCaP-1F5 and IgG controls are described in Sahu et al. (2011), and can be retrieved with accession number GSE30623. The remaining datasets are deposited to Gene Expression Omnibus with accession number GSE39880. Sample Yield (kbases) % PF clusters % Align AR DHT LNCaP-1F5 (rep1) 626712 81.8 73.7 AR DHT LNCaP-1F5 (rep2) 628314 80.08 73.9 AR CPA LNCaP-1F5 (rep1) 632634 78.8 73.5 AR CPA LNCaP-1F5 (rep2) 570026 70.7 75.2 AR RU486 LNCaP-1F5 (rep1) 721204 79.2 73.8 AR RU486 LNCaP-1F5 (rep2) 606607 72.9 75.04 AR Vehicle LNCaP-1F5 475392 49.5 77.8 LNCaP-1F5 rIgG 743283 80.59 75.27 RNA PolII DHT LNCaP-1F5 209815 51.95 74.78 RNA PolII Dex LNCaP-1F5 361153 76.73 73.12 GR Dex LNCaP-1F5 (rep 1) 1077706 82.15 75.70 GR Dex LNCaP-1F5 (rep 2) 801000 84.61 73.35 LNCaP-1F5 mIgG 1363000 76.54 75.92 AR DHT VCaP (rep 1) 1392000 84.04 79.46 AR DHT VCaP (Recent) 3013000 75.50 79.11 AR DHT LNCaP-1F5 (Recent) 1217000 85.87 77.44 VCaP rIgG 1433000 80.28 75.51 GR Dex VCaP 1187000 79.14 73.89 VCaP mIgG 1099000 77.19 66.85 Table S3. Fold-change levels of top 100 transcripts up-regulated by DHT in LNCaP- 1F5 cells grouped according to the response to concomitant DHT and Dex exposure. The numbers are from LNCaP-1F5 microarray experiments with three biological replicates and are expressed on a log2 scale (mean). Transcript DHT alone Dex alone DHT + Dex Dex-dominant genes FKBP5 3.76 4.02 4.64 PGC 3.38 6.41 7.26 ELL2 2.76 3.36 3.87 TUBA3D 2.76 6.16 6.91 SNAI2 2.62 4.16 4.52 ERRFI1 2.23 3.82 4.70 S100P 1.98 6.17 6.01 STK39 2.05 2.64 3.17 ZBTB16 1.86 2.08 2.53 PTGER4 1.73 3.18 4.56 AC061975.4 1.60 1.91 3.04 PHGR1 1.72 2.72 2.99 GLRX 1.71 2.30 2.44 TUBA3E 1.62 5.38 6.25 IRS2 1.55 2.66 3.44 RGS2 1.45 3.88 4.14 TIPARP 1.45 5.27 6.24 GNMT 1.47 3.31 4.10 LCP1 1.45 1.49 2.18 JAG1 1.52 1.94 2.43 KRT8 1.40 2.67 3.37 MUM1L1 1.34 2.24 3.56 ATAD2 1.37 1.90 2.58 NFKBIA 1.25 1.80 2.32 C9orf152 1.30 1.41 2.02 CEBPD 1.42 3.63 3.92 SGK1 1.26 3.80 4.04 DHT-dominant genes SLC45A3 3.63 0.30 2.04 TMEFF2 3.05 0.07 0.77 NDRG1 2.98 1.35 2.65 SAT1 2.97 1.36 2.66 ST6GALNAC1 2.97 0.56 2.10 EAF2 2.68 0.83 2.31 UGT2B28 2.94 -0.48 1.46 TMPRSS2 2.67 0.41 0.98 MICAL1 2.43 1.05 1.95 PCDH20 2.18 0.17 0.77 TM4SF1 2.17 -0.12 0.04 INPP4B 2.17 0.15 1.36 PMEPA1 2.11 0.66 1.22 ABCC4 2.08 0.61 1.71 SORD 2.13 0.49 2.27 NCAPD3 2.04 -0.11 1.24 ZNF385B 2.04 0.13 1.20 HERC5 2.07 0.54 1.46 NBL1 1.98 0.85 2.17 UGT2B11 1.82 -0.66 0.31 SLC41A1 1.90 0.20 1.17 SPDEF 1.97 -0.30 0.82 TMEM79 1.83 0.63 1.15 LPAR3 1.98 0.50 1.40 ELOVL2 1.93 0.29 1.33 C3orf58 1.70 0.48 1.63 ALDH1A3 1.73 0.59 0.67 C1orf116 1.78 -0.46 0.48 CYP11A1 1.58 0.64 1.46 ECI2 1.47 0.17 1.00 RAB3B 1.62 0.67 1.68 KLK3 1.63 0.64 0.91 ANKRD37 1.67 0.75 1.40 EXTL2 1.43 0.28 0.67 SLC35F2 1.42 -0.10 0.56 HERC3 1.42 0.08 1.01 RP11-312J18 1.42 -0.39 0.47 SMS 1.43 -0.42 0.54 TBC1D4 1.34 0.58 1.29 CREB3L4 1.46 -0.20 0.65 SLC2A12 1.38 -0.53 0.11 DBI 1.41 0.99 1.83 ADAMTS1 1.40 -0.61 -0.54 KCNN2 1.32 -0.05 0.81 ZBTB24 1.34 0.90 1.17 KLK4 1.23 0.14 0.41 MAPK6 1.30 0.51 0.80 CLDN8 1.37 0.03 0.32 SLC16A6 1.40 0.22 1.01 CROT 1.27 -0.17 0.43 UAP1 1.24 0.03 0.53 SASH1 1.26 -0.29 0.11 FZD5 1.23 0.09 0.71 Table S4. Core set of genes up-regulated by Dex in LNCaP-1F5 cells and expressed in GR+ vs. GR– prostate adenocarcinomas (Tomlins et al. 2007). The numbers are from LNCaP-1F5 microarray experiments with three biological replicates and are expressed on a log2 scale (mean). Transcript Dex DHT DHT+Dex Description LONRF1 3.52 1 4.12 LON peptidase N-terminal domain and ring finger 1 KRT6A 3.03 0.08 2.6 keratin 6A SLC22A23 2.38 0.52 2.92 solute carrier family 22, member 23 LRIG1 2.12 1.97 2.89 leucine-rich repeats and immunoglobulin-like domains 1 ATP1A1 2 1 2.33 ATPase, Na+/K+ transporting, alpha 1 polypeptide MBOAT2 1.93 1.72 2.46 membrane bound O-acyltransferase domain containing 2 (RAB4A, member RAS oncogene FBXO31 1.67 0.5 2.3 F-box protein 31 STAT3 1.43 0.14 1.4 signal transducer and activator of transcription 3 (acute-phase response factor) VCL 1.46 0.4 1.89 vinculin ACSL3 1.31 1.66 1.88 acyl-CoA synthetase long-chain family member 3 DOCK5 1.27 -0.18 1.6 dedicator of cytokinesis 5 ELF1 1.03 0.18 1.47 E74-like factor 1 (ets domain transcription factor) PDIA5 1.2 1.06 1.5 protein disulfide isomerase family A, member 5 LIFR 1.2 0.2 2.05 leukemia inhibitory factor receptor alpha NFIB 0.7 1 1.3 nuclear factor I/B ARPC5 0.93 0.08 1.2 ral guanine nucleotide dissociation stimulator- like 1///actin related protein 2/3 complex, HSD17B4 0.9 0.5 0.9 hydroxysteroid (17-beta) dehydrogenase 4 HSD17B11 0.81 0.76 1.25 hydroxysteroid (17-beta) dehydrogenase 11 BTG1 0.86 0.75 1 B-cell translocation gene 1, anti-proliferative KIF13B 0.87 0.35 0.92 kinesin family member 13B RAB3B 0.67 1.62 1.67 RAB3B, member RAS oncogene family .
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