Table S2. Sequences immunoprecipitating with anti-hif-1α

Transcript

1 Genome-wide analysis of HIF DNA-bdg-supplemental material Table S2. Sequences immunoprecipitatg with anti-α The table gives the chromosomal co-ordates of each anti-α immunoprecipitated locus meetg criteria of an MA Z of > 4, a width of > 100bp or > 5 probes, and a false discovery rate of < 5%, together with the maximum Z anti-α and anti-α at that gene locus. The presence or absence, and position of any HRE core motif with these sequences is given. The table also specifies whether the nearest gene to the immunoprecipitated locus was significantly regulated by exposure of cells to 1% hypoxia or 2mM DMOG or by transfection of sirnas directed agast α, α or both sirnas the Affymetrix s. Note that at a of loci several sequences were immunoprecipitated that shared proximity to a common transcriptional start site. These loci are listed order with the most strongly enriched site dicated black type and others grey type. Name chromosome start end Strand Coordates of 1 ASMT ACETYLSEROTONIN O-METHYLTRANSFERASE NM_ No chrx Yes , PLS3 PLASTIN 3 (T ISOFORM) NM_ No chrx Yes , , , , , , , GPI GLUCOSE PHOSPHATE ISOMERASE NM_ No chr Yes , , , , chr No 4 DARS ASPARTYL-TRNA SYNTHETASE NM_ Yes chr Yes , , , , , SNAPC1 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_ No chr No 1, 43KDA 6 SEC61G SEC61 GAMMA SUBUNIT NM_ No chr Yes GTF2IRD2B GTF2I REPEAT DOMAIN CONTAINING 2B NM_ No chr No chr No chr No 8 SAP30 SIN3A-ASSOCIATED PROTEIN, 30KDA NM_ Yes chr Yes , , ZMYND8 PROTEIN KINASE C BINDING PROTEIN 1 NM_ Yes chr Yes chr Yes , chr No chr Yes chr No chr No chr No chr No 10 RSBN1 ROUND SPERMATID BASIC PROTEIN 1 NM_ Yes chr Yes , , chr Yes chr No 11 BNIP3L BCL2/ADENOVIRUS E1B 19KDA INTERACTING PROTEIN 3-LIKE NM_ Yes chr Yes , , , , FAM139A HYPOTHETICAL PROTEIN FLJ40722 NM_ Yes chr Yes , Supplemental material Page 2

2 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of GTF2IRD2 GTF2I REPEAT DOMAIN CONTAINING 2 NM_ No chr Yes chr No 14 C3ORF28 CHROMSOME 3 OPEN READING FRAME 28 NM_ Yes chr No chr No chr No 15 STC2 STANNIOCALCIN 2 NM_ Yes chr Yes chr Yes NARF NUCLEAR PRELAMIN A RECOGNITION FACTOR NM_ Yes chr No 17 TF TRANSFERRIN NM_ No chr Yes HK2 HEXOKINASE 2 NM_ Yes chr Yes , chr No 19 INHA INHIBIN, ALPHA NM_ Yes chr Yes , chr No 20 PCF11 KIAA0824 PROTEIN NM_ No chr Yes , , C9ORF30 CHROMOSOME 9 OPEN READING FRAME 30 NM_ No chr Yes , chr Yes CBWD3 COBW DOMAIN CONTAINING 3 NM_ No chr Yes , , , , , , RAD51L1 RAD51-LIKE 1 (S. CEREVISIAE) NM_ Yes chr Yes , , , KIAA0195 KIAA0195 NM_ No chr Yes S100P S100 CALCIUM BINDING PROTEIN P NM_ Yes chr Yes CDKN1B CYCLIN-DEPENDENT KINASE INHIBITOR 1B (P27, KIP1) NM_ No chr Yes , chr No 27 NFE2L1 NUCLEAR FACTOR (ERYTHROID-DERIVED 2)-LIKE 1 NM_ No chr Yes , HIG2 HYPOXIA-INDUCIBLE PROTEIN 2 NM_ Yes chr Yes , , , , , QSOX1 QUIESCIN Q6 NM_ Yes chr No 30 INSIG2 INSULIN INDUCED GENE 2 NM_ Yes chr Yes , , chr No chr Yes ARRDC3 ARRESTIN DOMAIN CONTAINING 3 NM_ No chr Yes , , ALKBH5 ALKB, ALKYLATION REPAIR HOMOLOG 5 (E. COLI) NM_ No chr Yes , chr No 33 FLJ16641 FLJ16641 PROTEIN NM_ No chr Yes , , chr Yes , , , , , chr Yes MAX MYC ASSOCIATED FACTOR X NM_ No chr Yes ZNF398 ZINC FINGER PROTEIN 398 NM_ No chr Yes PAICS PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE, PHOSPHORIBOSYLAMINOIMIDAZOLE SUCCINOCARBOXAMIDE SYNTHETASE NM_ No chr No Supplemental material Page 3

3 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 37 CBWD2 COBW DOMAIN CONTAINING 2 NM_ No chr Yes , , , , , , , GNAI3 GUANINE NUCLEOTIDE BINDING PROTEIN (G PROTEIN), NM_ No chr Yes ALPHA INHIBITING ACTIVITY POLYPEPTIDE 3 39 PPP1R3C PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 3C NM_ Yes chr No chr Yes BBX BOBBY SOX HOMOLOG (DROSOPHILA) NM_ Yes chr Yes , PNPLA8 INTRACELLULAR MEMBRANE-ASSOCIATED CALCIUM- INDEPENDENT PHOSPHOLIPASE A2 GAMMA 42 PFKFB3 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BIPHOSPHATASE 3 NM_ No chr Yes , , NM_ Yes chr Yes , , chr No 43 C5ORF15 HYPOTHETICAL PROTEIN NM_ No chr Yes BACE2 BETA-SITE APP-CLEAVING ENZYME 2 NM_ Yes chr Yes , UPK1B UROPLAKIN 1B NM_ No chr Yes FAM13A1 FAMILY WITH SEQUENCE SIMILARITY 13, MEMBER A1 NM_ Yes chr Yes , CCNG2 CYCLIN G2 NM_ Yes chr No 48 CYP27C1 FLJ16008 PROTEIN NM_ No chr Yes OXSM 3-OXOACYL-ACP SYNTHASE, MITOCHONDRIAL NM_ No chr Yes CBWD5 COBW DOMAIN CONTAINING 5 NM_ No chr Yes , , , CITED2 CBP/P300-INTERACTING TRANSACTIVATOR, WITH GLU/ASP- RICH CARBOXY-TERMINAL DOMAIN, 2 NM_ Yes chr Yes , , , C12ORF36 CHROMOSOME 12 OPEN READING FRAME 36 NM_ No chr Yes RAPGEF6 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 6 NM_ No chr Yes LOC HCV F-TRANSACTIVATED PROTEIN 1 NM_ Yes chr Yes , chr Yes chr No 55 JMJD1A JUMONJI DOMAIN CONTAINING 1A NM_ Yes chr Yes , , , , TFRC TRANSFERRIN RECEPTOR (P90, CD71) NM_ No chr Yes CRKL V-CRK SARCOMA VIRUS CT10 ONCOGENE HOMOLOG (AVIAN)-LIKE NM_ No chr No chr Yes chr No 58 TRIM37 TRIPARTITE MOTIF-CONTAINING 37 NM_ No chr No chr No 59 FOXN3 CHECKPOINT SUPPRESSOR 1 NM_ No chr No 60 PIK3C2G PHOSPHOINOSITIDE-3-KINASE, CLASS 2, GAMMA POLYPEPTIDE NM_ No chr Yes , , FOXO3 FORKHEAD BOX O3A NM_ No chr Yes , 62 SLC2A1 SOLUTE CARRIER FAMILY 2 (FACILITATED GLUCOSE TRANSPORTER), MEMBER 1 63 GBE1 GLUCAN (1,4-ALPHA-), BRANCHING ENZYME 1 (GLYCOGEN BRANCHING ENZYME, ANDERSEN DISEASE, GLYCOGEN STORAGE DISEASE TYPE IV) NM_ Yes chr No NM_ Yes chr Yes , , , , DTNA DYSTROBREVIN, ALPHA NM_ Yes chr Yes , , Supplemental material Page 4

4 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 65 CHD1L CHROMODOMAIN HELICASE DNA BINDING PROTEIN 1-LIKE NM_ No chr Yes , , CARD14 CASPASE RECRUITMENT DOMAIN FAMILY, MEMBER 14 NM_ No chr No 67 UBC UBIQUITIN C NM_ No chr No chr No chr No 68 IVNS1ABP INFLUENZA VIRUS NS1A BINDING PROTEIN NM_ No chr Yes , , , , ILVBL ILVB (BACTERIAL ACETOLACTATE SYNTHASE)-LIKE NM_ Yes chr Yes CBWD1 COBW DOMAIN CONTAINING 1 NM_ No chr Yes , LDHA LACTATE DEHYDROGENASE A NM_ No chr Yes , FAM110C TRANSFERRIN NM_ No chr Yes 37109, BAMBI BMP AND ACTIVIN MEMBRANE-BOUND INHIBITOR HOMOLOG (XENOPUS LAEVIS) NM_ No chr Yes , , IARS2 ISOLEUCINE-TRNA SYNTHETASE 2, MITOCHONDRIAL NM_ No chr Yes DYNLL1 DYNEIN, LIGHT CHAIN, LC8-TYPE 1 NM_ No chr Yes RASEF RAS AND EF-HAND DOMAIN CONTAINING NM_ No chr Yes IQCG HYPOTHETICAL PROTEIN FLJ23571 NM_ No chr No 78 HIST2H3PS2 HISTONE 1, H2BD NM_ Yes chr Yes , , MTP18 MITOCHONDRIAL PROTEIN 18 KDA NM_ No chr No chr Yes SFRS18 CHROMOSOME 6 OPEN READING FRAME 111 NM_ No chr Yes , , , , , HSPA9 HEAT SHOCK 70KDA PROTEIN 9B (MORTALIN-2) NM_ No chr No 82 HIST2H4B H4 HISTONE, FAMILY 2 NM_ Yes chr No chr No chr No 83 CDC73 CELL DIVISION CYCLE 73, PAF1/RNA POLYMERASE II NM_ No chr No COMPLEX COMPONENT, HOMOLOG (S. CEREVISIAE) 84 CARHSP1 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_ No chr Yes , 50KDA 85 USP32 UBIQUITIN SPECIFIC PEPTIDASE 32 NM_ No chr No chr No 86 TRIM16 TRIPARTITE MOTIF-CONTAINING 16 NM_ No chr Yes C1ORF192 CHROMOSOME 1 OPEN READING FRAME 192 NM_ No chr Yes MS4A7 MEMBRANE-SPANNING 4-DOMAINS, SUBFAMILY A, MEMBER NM_ No chr No 7 89 DDB2 DAMAGE-SPECIFIC DNA BINDING PROTEIN 2, 48KDA NM_ No chr Yes , FBXO42 F-BOX PROTEIN 42 NM_ No chr No chr No 91 C1ORF161 CHROMOSOME 1 OPEN READING FRAME 161 NM_ No chr Yes , chr No 92 TMEM97 TRANSMEMBRANE PROTEIN 97 NM_ No chr Yes SNAPC3 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE 3, 50KDA NM_ No chr Yes , TMEM48 TRANSMEMBRANE PROTEIN 48 NM_ No chr No 95 SCYL1 SCY1-LIKE 1 (S. CEREVISIAE) NM_ No chr Yes , chr Yes CGA GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE NM_ No chr No chr Yes TMEM107 TRANSMEMBRANE PROTEIN 107 NM_ Yes chr No 98 PDLIM2 PDZ-LIM PROTEIN MYSTIQUE NM_ Yes chr No 99 SMG1 PI-3-KINASE-RELATED KINASE SMG-1 NM_ No chr Yes , , DNASE1 DEOXYRIBONUCLEASE I NM_ Yes chr Yes , Supplemental material Page 5

5 Genome-wide analysis of HIF DNA-bdg-supplemental material Name Supplemental material Page 6 chromosome start end Strand Coordates of DHRS13 HYPOTHETICAL PROTEIN MGC23280 NM_ Yes chr Yes , , TEX14 TESTIS EXPRESSED SEQUENCE 14 NM_ No chr No 103 HIST1H1C HISTONE 1, H1C NM_ No chr Yes SOSTDC1 SCLEROSTIN DOMAIN CONTAINING 1 NM_ No chr Yes , RBPJ RECOMBINING BINDING PROTEIN SUPPRESSOR OF HAIRLESS NM_ Yes chr Yes (DROSOPHILA) 106 C11ORF30 CHROMOSOME 11 OPEN READING FRAME 30 NM_ No chr Yes , , , , POM121 POM121 MEMBRANE GLYCOPROTEIN (RAT) NM_ No chr No chr No 108 IER3 IMMEDIATE EARLY RESPONSE 3 NM_ No chr No 109 CP CERULOPLASMIN (FERROXIDASE) NM_ No chr Yes RNF183 RING FINGER PROTEIN 183 NM_ Yes chr Yes , PNRC1 PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 1 NM_ Yes chr No 112 C8ORF44 CHROMOSOME 8 OPEN READING FRAME 44 NM_ No chr No 113 BCL2L2 BCL2-LIKE 2 NM_ No chr No 114 TTLL2 TUBULIN TYROSINE LIGASE-LIKE FAMILY, MEMBER 2 NM_ No chr Yes , FLJ10292 MAGO-NASHI HOMOLOG NM_ No chr No 116 PDE4DIP PHOSPHODIESTERASE 4D INTERACTING PROTEIN NM_ No chr No (MYOMEGALIN) chr No 117 SMC2 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE 3, 50KDA NM_ No chr Yes , PPP1R15B PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) NM_ No chr No SUBUNIT 15B 119 C6ORF170 CHROMOSOME 6 OPEN READING FRAME 170 NM_ No chr No 120 LOC SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_ No chrx No 3, 50KDA 121 HLA-G HLA-G HISTOCOMPATIBILITY ANTIGEN, CLASS I, G NM_ No chr No 122 MYC V-MYC MYELOCYTOMATOSIS VIRAL ONCOGENE HOMOLOG NM_ No chr No (AVIAN) chr No 123 SERGEF SECRETION REGULATING GUANINE NUCLEOTIDE EXCHANGE NM_ No chr No FACTOR 124 RPL10 RIBOSOMAL PROTEIN L10 NM_ No chrx Yes , , TRIM33 KIAA1113 PROTEIN NM_ No chr Yes chr No 126 SOS1 SON OF SEVENLESS HOMOLOG 1 (DROSOPHILA) NM_ No chr No 127 UPK3B UROPLAKIN 3B NM_ No chr No chr No 128 STIM2 STROMAL INTERACTION MOLECULE 2 NM_ No chr Yes RAP2B RAP2B, MEMBER OF RAS ONCOGENE FAMILY NM_ No chr Yes , , ECE2 ENDOTHELIN CONVERTING ENZYME 2 NM_ No chr Yes TCP11L2 T-COMPLEX 11 (MOUSE) LIKE 2 NM_ No chr Yes , PEX13 PEROXISOME BIOGENESIS FACTOR 13 NM_ No chr Yes RAPGEF1 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 1 NM_ No chr Yes , , SEPSECS SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN NM_ No chr Yes NFIL3 NUCLEAR FACTOR, INTERLEUKIN 3 REGULATED NM_ Yes chr No 136 TRPM7 TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL, NM_ No chr Yes SUBFAMILY M, MEMBER ENO3 ENOLASE 1, (ALPHA) NM_ No chr No 138 LOC90342 TRANSFERRIN NM_ No chr Yes LOC HYPOTHETICAL GENE SUPPORTED BY AK NM_ No chr Yes GPRC5A G PROTEIN-COUPLED RECEPTOR, FAMILY C, GROUP 5, NM_ Yes chr Yes MEMBER A 141 C1ORF51 CHROMOSOME 1 OPEN READING FRAME 51 NM_ Yes chr Yes , , , , ,

6 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of , , , PGK1 PHOSPHOGLYCERATE KINASE 1 NM_ Yes chrx No 143 S100A10 S100 CALCIUM BINDING PROTEIN A10 (ANNEXIN II LIGAND, NM_ Yes chr No CALPACTIN I, LIGHT POLYPEPTIDE (P11)) 144 PVRL4 POLIOVIRUS RECEPTOR-RELATED 4 NM_ Yes chr Yes , CABLES1 CDK5 AND ABL ENZYME SUBSTRATE 1 NM_ No chr Yes , ZNF432 ZINC FINGER PROTEIN 432 NM_ Yes chr No 147 LOXL2 LYSYL OXIDASE-LIKE 2 NM_ Yes chr No chr No 148 UGP2 UDP-GLUCOSE PYROPHOSPHORYLASE 2 NM_ No chr Yes , , EAPP CHROMOSOME 14 OPEN READING FRAME 11 NM_ No chr Yes EIF2C4 ARGONAUTE 4 NM_ Yes chr Yes FLJ39743 HYPOTHETICAL PROTEIN FLJ39743 NM_ No chr Yes , REXO1L1 REX1, RNA EXONUCLEASE 1 HOMOLOG (S. CEREVISIAE)-LIKE 1 NM_ No chr Yes chr Yes chr Yes chr No chr No chr Yes chr No chr Yes chr Yes chr No chr Yes , , chr No chr Yes chr No chr Yes , chr Yes chr No chr Yes chr No chr No chr No chr Yes chr No chr Yes RSPH10B HYPOTHETICAL PROTEIN LOC NM_ No chr No 154 HIST2H3C HISTONE 2, H3C NM_ No chr Yes , chr Yes , chr Yes , , , chr Yes BASP1 BRAIN ABUNDANT, MEMBRANE ATTACHED SIGNAL PROTEIN 1 NM_ No chr Yes , , chr No chr Yes chr Yes , , chr Yes , , chr Yes , , , Supplemental material Page 7

7 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of chr No chr Yes chr Yes chr No chr No chr Yes , , chr No chr No chr No 156 ATP8B4 ATPASE, CLASS I, TYPE 8B, MEMBER 4 NM_ No chr No 157 RP11-191L9.1 FLJ46257 PROTEIN NM_ No chr No 158 TMEM45A TRANSMEMBRANE PROTEIN 45A NM_ Yes chr Yes , chr Yes MTERFD2 MTERF DOMAIN CONTAINING 2 NM_ No chr No 160 RAB24 RAB24, MEMBER RAS ONCOGENE FAMILY NM_ No chr Yes , TTC26 HYPOTHETICAL PROTEIN FLJ12571 NM_ No chr No 162 RNF145 HYPOTHETICAL PROTEIN FLJ31951 NM_ No chr No 163 SAP18 SIN3A-ASSOCIATED PROTEIN, 18KDA NM_ No chr Yes BCAS3 BREAST CARCINOMA AMPLIFIED SEQUENCE 3 NM_ No chr Yes , chr No chr No 165 SRGAP2 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_ No chr No 3, 50KDA 166 WDR89 CHROMOSOME 14 OPEN READING FRAME 150 NM_ No chr No 167 LOC DEUBIQUITINATING ENZYME 3 NM_ No chr Yes , chr Yes , chr Yes , , , chr Yes , , chr Yes chr Yes , , , chr Yes , chr Yes , chr No chr Yes , , chr Yes , , chr No chr Yes , , chr No chr No 168 PARD6B PAR-6 PARTITIONING DEFECTIVE 6 HOMOLOG BETA (C. NM_ No chr No ELEGANS) chr No chr Yes STARD4 START DOMAIN CONTAINING 4, STEROL REGULATED NM_ No chr No 170 LOC SIMILAR TO NUCLEAR PORE COMPLEX INTERACTING NM_ No chr Yes PROTEIN chr No 171 GAGE1 G ANTIGEN 1 NM_ No chrx No 172 DHX35 DEAH (ASP-GLU-ALA-HIS) BOX POLYPEPTIDE 35 NM_ No chr No Supplemental material Page 8

8 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 173 ALDOC ALDOLASE C, FRUCTOSE-BISPHOSPHATE NM_ Yes chr No 174 NCOA5 NUCLEAR RECEPTOR COACTIVATOR 5 NM_ No chr Yes , MINK1 MISSHAPEN-LIKE KINASE 1 (ZEBRAFISH) NM_ No chr No 176 NLRP4 NACHT, LEUCINE RICH REPEAT AND PYD CONTAINING 4 NM_ No chr No 177 GPR1 G PROTEIN-COUPLED RECEPTOR 1 NM_ No chr Yes , C3ORF14 CHROMOSOME 3 OPEN READING FRAME 14 NM_ No chr No 179 SYTL2 SYNAPTOTAGMIN-LIKE 2 NM_ Yes chr Yes NACA2 NASCENT-POLYPEPTIDE-ASSOCIATED COMPLEX ALPHA POLYPEPTIDE-LIKE NM_ No chr No chr Yes FLJ39739 FLJ39739 PROTEIN NM_ Yes chr Yes , chr Yes , , , ZNF107 ZINC FINGER PROTEIN 588 NM_ No chr No 183 IRF2BP2 TRANSFERRIN NM_ No chr No 184 PDGFB PLATELET-DERIVED GROWTH FACTOR BETA POLYPEPTIDE NM_ Yes chr No (SIMIAN SARCOMA VIRAL (V-SIS) ONCOGENE HOMOLOG) 185 AMAC1L2 ACYL-MALONYL CONDENSING ENZYME 1-LIKE 2 NM_ No chr No 186 RABL2A RAB, MEMBER OF RAS ONCOGENE FAMILY-LIKE 2A NM_ No chr No chr No chr No 187 NBPF1 3-OXOACYL-ACP SYNTHASE, MITOCHONDRIAL NM_ No chr No chr No 188 ANKZF1 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE 3, 50KDA NM_ Yes chr Yes , , JARID1B JUMONJI, AT RICH INTERACTIVE DOMAIN 1B (RBP2-LIKE) NM_ No chr No 190 SORT1 SORTILIN 1 NM_ No chr Yes WDR54 WD REPEAT DOMAIN 54 NM_ Yes chr No 192 CSTF1 CLEAVAGE STIMULATION FACTOR, 3' PRE-RNA, SUBUNIT 1, NM_ No chr No 50KDA 193 ATP9A ATPASE, CLASS II, TYPE 9A NM_ No chr No 194 WISP2 WNT1 INDUCIBLE SIGNALING PATHWAY PROTEIN 2 NM_ Yes chr No 195 BMP7 BONE MORPHOGENETIC PROTEIN 7 (OSTEOGENIC PROTEIN 1) NM_ No chr No 196 ENO2 ENOLASE 2 (GAMMA, NEURONAL) NM_ Yes chr No 197 PFKFB4 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BIPHOSPHATASE NM_ Yes chr No PPP2R1A PROTEIN PHOSPHATASE 2 (FORMERLY 2A), REGULATORY NM_ No chr No SUBUNIT A (PR 65), ALPHA ISOFORM 199 TMOD3 TROPOMODULIN 3 (UBIQUITOUS) NM_ No chr Yes ID2 INHIBITOR OF DNA BINDING 2, DOMINANT NEGATIVE HELIX- NM_ No chr No LOOP-HELIX PROTEIN 201 PSMA1 PROTEASOME (PROSOME, MACROPAIN) SUBUNIT, ALPHA NM_ No chr No TYPE, PGAM1 PHOSPHOGLYCERATE MUTASE 1 (BRAIN) NM_ No chr Yes , GIYD2 GIY-YIG DOMAIN CONTAINING 2 NM_ No chr No chr No 204 PPIAL4 PEPTIDYLPROLYL ISOMERASE A (CYCLOPHILIN A)-LIKE 4 NM_ No chr No chr Yes chr No chr No chr No 205 TGIF1 TGFB-INDUCED FACTOR (TALE FAMILY HOMEOBOX) NM_ No chr No 206 SPAG9 SPERM ASSOCIATED ANTIGEN 9 NM_ No chr Yes , , HIST2H2BF HISTONE 2, H2BF NM_ No chr No 208 RIT1 RAS-LIKE WITHOUT CAAX 1 NM_ No chr No 209 SULT1A4 SULFOTRANSFERASE FAMILY, CYTOSOLIC, 1A, PHENOL- NM_ No chr No PREFERRING, MEMBER MYNN MYONEURIN NM_ No chr Yes , , AKAP13 LYMPHOID BLAST CRISIS ONCOGENE NM_ No chr Yes ZNF318 ZINC FINGER PROTEIN 318 NM_ No chr No 213 RELT TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY, MEMBER 19-LIKE NM_ No chr Yes Supplemental material Page 9

9 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 214 GRB2 GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 NM_ No chr No 215 ESM1 ENDOTHELIAL CELL-SPECIFIC MOLECULE 1 NM_ No chr No 216 SMURF2 SMAD SPECIFIC E3 UBIQUITIN PROTEIN LIGASE 2 NM_ No chr No 217 AXUD1 AXIN1 UP-REGULATED 1 NM_ No chr Yes , , , IPMK INOSITOL POLYPHOSPHATE MULTIKINASE NM_ No chr Yes , UQCRC2 UBIQUINOL-CYTOCHROME C REDUCTASE CORE PROTEIN II NM_ No chr Yes , chr No 220 KIAA1715 KIAA1715 NM_ Yes chr Yes , , COX7C CYTOCHROME C OXIDASE SUBUNIT VIIC NM_ No chr No 222 SMEK2 KIAA1387 PROTEIN NM_ No chr Yes , PODXL PODOCALYXIN-LIKE NM_ No chr No 224 CCT8L2 T-COMPLEX PROTEIN 1 NM_ No chr Yes PSMD6 PROTEASOME (PROSOME, MACROPAIN) 26S SUBUNIT, NON- ATPASE, SPRY1 SPROUTY HOMOLOG 1, ANTAGONIST OF FGF SIGNALING (DROSOPHILA) NM_ No chr Yes , chr No NM_ Yes chr Yes , , SMAP1L STROMAL MEMBRANE-ASSOCIATED PROTEIN 1-LIKE NM_ No chr No 228 TNIP1 TNFAIP3 INTERACTING PROTEIN 1 NM_ No chr No 229 FBL FIBRILLARIN NM_ No chr No 230 RAD51C RAD51 HOMOLOG C (S. CEREVISIAE) NM_ No chr No 231 OPN1MW OPSIN 1 (CONE PIGMENTS), MEDIUM-WAVE-SENSITIVE NM_ No chrx No (COLOR BLINDNESS, DEUTAN) 232 FAM103A1 FAMILY WITH SEQUENCE SIMILARITY 103, MEMBER A1 NM_ No chr No 233 C10ORF28 CHROMOSOME 10 OPEN READING FRAME 28 NM_ No chr Yes FER1L3 FER-1-LIKE 3, MYOFERLIN (C. ELEGANS) NM_ No chr Yes ATXN1 ATAXIN 1 NM_ Yes chr No 236 KIAA0460 KIAA0460 NM_ No chr Yes GAGE6 G ANTIGEN 6 NM_ No chrx No chrx No chrx Yes , chrx Yes , chrx Yes chrx No 238 BCKDHA BRANCHED CHAIN KETO ACID DEHYDROGENASE E1, ALPHA NM_ No chr Yes POLYPEPTIDE 239 GREB1 GREB1 PROTEIN NM_ No chr No 240 TARS THREONYL-TRNA SYNTHETASE NM_ No chr Yes , FANK1 FIBRONECTIN TYPE III AND ANKYRIN REPEAT DOMAINS 1 NM_ Yes chr No 242 PLA2G10 PHOSPHOLIPASE A2, GROUP X NM_ No chr No chr No 243 DAAM1 DISHEVELLED ASSOCIATED ACTIVATOR OF MORPHOGENESIS NM_ Yes chr No ATP11A ATPASE, CLASS VI, TYPE 11A NM_ No chr No 245 NDUFB9 NADH DEHYDROGENASE (UBIQUINONE) 1 BETA NM_ No chr No SUBCOMPLEX, 9, 22KDA 246 HEATR6 AMPLIFIED IN BREAST CANCER 1 NM_ No chr No chr Yes TPT1 TUMOR PROTEIN, TRANSLATIONALLY-CONTROLLED 1 NM_ No chr No 248 ZNF323 ZINC FINGER PROTEIN 323 NM_ No chr Yes PAK7 P21(CDKN1A)-ACTIVATED KINASE 7 NM_ No chr No 250 MXI1 MAX INTERACTOR 1 NM_ Yes chr Yes ANLN ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, NM_ No chr No DROSOPHILA) 252 TUBD1 TUBULIN, DELTA 1 NM_ No chr Yes TBX4 T-BOX 4 NM_ No chr No 254 MTMR11 MYOTUBULARIN RELATED PROTEIN 11 NM_ No chr Yes RASSF3 RAS ASSOCIATION (RALGDS/AF-6) DOMAIN FAMILY 3 NM_ No chr No 256 HFE2 HEMOCHROMATOSIS TYPE 2 (JUVENILE) NM_ No chr Yes chr Yes , Supplemental material Page 10

10 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of chr Yes chr Yes chr No 257 ZNF250 ZINC FINGER PROTEIN 250 NM_ No chr No 258 HIPK1 KIAA0630 PROTEIN NM_ Yes chr No 259 BCAS4 BREAST CARCINOMA AMPLIFIED SEQUENCE 4 NM_ No chr No 260 METTL9 TRANSFERRIN NM_ No chr No 261 BRIP1 BRCA1 INTERACTING PROTEIN C-TERMINAL HELICASE 1 NM_ No chr No 262 PPM1D PROTEIN PHOSPHATASE 1D MAGNESIUM-DEPENDENT, DELTA NM_ No chr No ISOFORM 263 LOC BA299N6.3 NM_ No chr No 264 CCRL1 CHEMOKINE (C-C MOTIF) RECEPTOR-LIKE 1 NM_ No chr No 265 ANXA2 ANNEXIN A2 NM_ No chr Yes , TRIM27 RET FINGER PROTEIN NM_ No chr No 267 ITFG2 UNCHARACTERIZED HEMATOPOIETIC STEM/PROGENITOR NM_ No chr No CELLS PROTEIN MDS CLK2 CDC-LIKE KINASE 2 NM_ No chr No 269 CTGLF1 CENTAURIN, GAMMA-LIKE FAMILY, MEMBER 1 NM_ No chr No 270 LOC FKSG73 PROTEIN NM_ No chr No chr No chr No 271 FLJ44005 FLJ44005 PROTEIN NM_ No chr No 272 CDK2AP1 CDK2-ASSOCIATED PROTEIN 1 NM_ No chr Yes ZFHX3 AT-BINDING TRANSCRIPTION FACTOR 1 NM_ No chr No 274 GOLGA GOLGIN-LIKE PROTEIN NM_ No chr Yes KIAA1920 KIAA1920 PROTEIN NM_ No chr No chr No 276 HNRPD HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D (AU- NM_ No chr No RICH ELEMENT RNA BINDING PROTEIN 1, 37KDA) 277 BTBD3 BTB (POZ) DOMAIN CONTAINING 3 NM_ No chr No 278 C5ORF36 HYPOTHETICAL PROTEIN MGC34713 NM_ No chr No 279 RAB6IP1 RAB6 INTERACTING PROTEIN 1 NM_ No chr Yes HJURP HYPOTHETICAL PROTEIN DKFZP762E1312 NM_ No chr No 281 CLASP1 CYTOPLASMIC LINKER ASSOCIATED PROTEIN 1 NM_ No chr No 282 C1ORF147 CHROMOSOME 1 OPEN READING FRAME 147 NM_ No chr No 283 CLTC CLATHRIN, HEAVY POLYPEPTIDE (HC) NM_ No chr No 284 DOK5 DOCKING PROTEIN 5 NM_ No chr Yes FEZF2 ZINC FINGER PROTEIN 312 NM_ No chr No 286 PKM2 PYRUVATE KINASE, MUSCLE NM_ No chr No 287 PRICKLE3 LIM DOMAIN ONLY 6 NM_ No chrx No 288 TREM1 TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 1 NM_ No chr No 289 EDEM1 ER DEGRADATION ENHANCER, MANNOSIDASE ALPHA-LIKE 1 NM_ No chr Yes OR4A47 OLFACTORY RECEPTOR, FAMILY 4, SUBFAMILY A, MEMBER NM_ No chr No YEATS2 YEATS DOMAIN CONTAINING 2 NM_ Yes chr No 292 LOC SECRETORY PROTEIN LOC NM_ No chr No 293 AP4B1 ADAPTOR-RELATED PROTEIN COMPLEX 4, BETA 1 SUBUNIT NM_ No chr No 294 SLN SARCOLIPIN NM_ No chr Yes LOC HYPOTHETICAL LOC NM_ No chr Yes chr Yes NDUFA5 NADH DEHYDROGENASE (UBIQUINONE) 1 ALPHA NM_ No chr No SUBCOMPLEX, 5, 13KDA 297 OR4F3 OLFACTORY RECEPTOR, FAMILY 4, SUBFAMILY F, MEMBER 3 NM_ No chr No 298 PLOD3 PROCOLLAGEN-LYSINE, 2-OXOGLUTARATE 5-DIOXYGENASE NM_ No chr No HSPBAP1 HSPB (HEAT SHOCK 27KDA) ASSOCIATED PROTEIN 1 NM_ No chr No 300 NBPF15 NEUROBLASTOMA BREAKPOINT FAMILY, MEMBER 14 NM_ No chr No chr Yes chr No 301 GUSBP1 HYPOTHETICAL PROTEIN LOC NM_ Yes chr No 302 OR7A17 OLFACTORY RECEPTOR, FAMILY 7, SUBFAMILY A, MEMBER NM_ No chr Yes NFATC4 NUCLEAR FACTOR OF ACTIVATED T-CELLS, CYTOPLASMIC, NM_ No chr No CALCINEURIN-DEPENDENT AZI2 5-AZACYTIDINE INDUCED 2 NM_ Yes chr Yes PLEKHA6 PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY A NM_ No chr Yes MEMBER CDR2 CEREBELLAR DEGENERATION-RELATED PROTEIN 2, 62KDA NM_ No chr No chr No chr Yes MAP3K13 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 13 NM_ Yes chr Yes , Supplemental material Page 11

11 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 308 TBXAS1 THROMBOXANE A SYNTHASE 1 (PLATELET, CYTOCHROME NM_ No chr Yes P450, FAMILY 5, SUBFAMILY A) 309 ELMO2 ENGULFMENT AND CELL MOTILITY 2 NM_ No chr No 310 TFB1M TRANSCRIPTION FACTOR B1, MITOCHONDRIAL NM_ No chr No 311 GAGE8 G ANTIGEN 8 NM_ No chrx No 312 NBN NIBRIN NM_ No chr No chr No 313 TMEM121 TRANSMEMBRANE PROTEIN 121 NM_ No chr No chr Yes , chr No 314 CCDC47 COILED-COIL DOMAIN CONTAINING 47 NM_ No chr No 315 GGT3 GAMMA-GLUTAMYLTRANSFERASE 2 NM_ No chr No 316 PAIP2 POLY(A) BINDING PROTEIN INTERACTING PROTEIN 2 NM_ No chr Yes , NCOA7 NUCLEAR RECEPTOR COACTIVATOR 7 NM_ No chr Yes SLC45A3 SOLUTE CARRIER FAMILY 45, MEMBER 3 NM_ Yes chr No 319 VAC14 TAX1 (HUMAN T-CELL LEUKEMIA VIRUS TYPE I) BINDING NM_ No chr No PROTEIN GAPDH GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE NM_ Yes chr Yes DHX40 DEAH (ASP-GLU-ALA-HIS) BOX POLYPEPTIDE 40 NM_ No chr No 322 DSP DESMOPLAKIN NM_ Yes chr Yes C1QTNF3 COMPLEMENT-C1Q TUMOR NECROSIS FACTOR-RELATED NM_ No chr Yes PROTEIN; LIKELY ORTHOLOG OF MOUSE CORS26 (COLLAGENOUS REPEAT-CONTAINING SEQUENCE OF 26-KDA PROTEIN) chr No 324 LOC HYPOTHETICAL PROTEIN LOC NM_ No chr No 325 PLOD2 PROCOLLAGEN-LYSINE, 2-OXOGLUTARATE 5-DIOXYGENASE NM_ Yes chr No 2 chr Yes , RUNX1 RUNT-RELATED TRANSCRIPTION FACTOR 1 (ACUTE MYELOID NM_ Yes chr No LEUKEMIA 1; AML1 ONCOGENE) 327 GLRX GLUTAREDOXIN (THIOLTRANSFERASE) NM_ Yes chr No 328 HSDL2 HYDROXYSTEROID DEHYDROGENASE LIKE 2 NM_ No chr Yes PSMD7 PROTEASOME (PROSOME, MACROPAIN) 26S SUBUNIT, NON- NM_ No chr No ATPASE, 7 (MOV34 HOMOLOG) 330 TEX2 TESTIS EXPRESSED SEQUENCE 2 NM_ No chr No 331 CYP24A1 CYTOCHROME P450, FAMILY 24, SUBFAMILY A, POLYPEPTIDE NM_ No chr No RPS17 RIBOSOMAL PROTEIN S17 NM_ No chr No 333 CA9 CARBONIC ANHYDRASE IX NM_ Yes chr No 334 NCBP1 NUCLEAR CAP BINDING PROTEIN SUBUNIT 1, 80KDA NM_ No chr No 335 DGKH DIACYLGLYCEROL KINASE, ETA NM_ No chr No 336 KRTCAP3 KERATINOCYTE ASSOCIATED PROTEIN 3 NM_ No chr No 337 TRAF7 TNF RECEPTOR-ASSOCIATED FACTOR 7 NM_ No chr Yes , FAM84B FAMILY WITH SEQUENCE SIMILARITY 84, MEMBER B NM_ No chr No 339 ZNF217 ZINC FINGER PROTEIN 217 NM_ No chr No chr No 340 KRTAP5-7 KERATIN ASSOCIATED PROTEIN 5-7 NM_ No chr Yes , , , , , SMCR7 SMITH-MAGENIS SYNDROME CHROMOSOME REGION, NM_ No chr No CANDIDATE BCAS1 BREAST CARCINOMA AMPLIFIED SEQUENCE 1 NM_ No chr Yes chr No chr No 343 C17ORF64 CHROMOSOME 17 OPEN READING FRAME 64 NM_ No chr No 344 RIPK4 RECEPTOR-INTERACTING SERINE-THREONINE KINASE 4 NM_ Yes chr No 345 MPV17L MPV17-LIKE PROTEIN TYPE 2 NM_ No chr No 346 TMTC2 TRANSMEMBRANE AND TETRATRICOPEPTIDE REPEAT CONTAINING 2 NM_ Yes chr Yes , RLF REARRANGED L-MYC FUSION NM_ Yes chr No 348 ZFP14 MOUSE ZINC FINGER PROTEIN 14-LIKE NM_ No chr Yes FOXD4 FORKHEAD BOX D4 NM_ No chr No 350 PFDN4 PREFOLDIN SUBUNIT 4 NM_ No chr No 351 C15ORF39 DKFZP434H132 PROTEIN NM_ No chr No chr No Supplemental material Page 12

12 Genome-wide analysis of HIF DNA-bdg-supplemental material Name chromosome start end Strand Coordates of 352 HSD17B3 HYDROXYSTEROID (17-BETA) DEHYDROGENASE 3 NM_ No chr Yes ERGIC2 ERGIC AND GOLGI 2 NM_ No chr No 354 TP53 TUMOR PROTEIN P53 (LI-FRAUMENI SYNDROME) NM_ No chr No 355 DKFZP434K191 HYPOTHETICAL PROTEIN DKFZP434K191 NM_ No chr No 356 RUNDC2B RUN DOMAIN CONTAINING 2A NM_ No chr Yes , NOMO3 NODAL MODULATOR 3 NM_ No chr No chr No 358 TUBA3C TUBULIN, ALPHA 2 NM_ No chr No 359 FOXD4L1 FORKHEAD BOX D4-LIKE 1 NM_ No chr No chr No 360 FLJ22795 HYPOTHETICAL PROTEIN FLJ22795 NM_ No chr No 361 ZNF295 ZINC FINGER PROTEIN 295 NM_ No chr No 362 NBPF10 SMALL NUCLEAR RNA ACTIVATING COMPLEX, POLYPEPTIDE NM_ No chr No 3, 50KDA 363 LOC51136 PTD016 PROTEIN NM_ No chr No chr No 364 MOV10 MOV10, MOLONEY LEUKEMIA VIRUS 10, HOMOLOG (MOUSE) NM_ No chr No 365 PRICKLE2 PRICKLE-LIKE 2 (DROSOPHILA) NM_ No chr No 366 PARN POLY(A)-SPECIFIC RIBONUCLEASE (DEADENYLATION NM_ No chr No NUCLEASE) 367 FLJ42953 FLJ42953 PROTEIN NM_ No chr No 368 C11ORF71 HYPOTHETICAL PROTEIN FLJ20010 NM_ No chr No 369 LAT LINKER FOR ACTIVATION OF T CELLS NM_ No chr No 370 VIM VIMENTIN NM_ No chr No 371 CRIPAK HYPOTHETICAL PROTEIN FLJ34443 NM_ Yes chr No chr No 372 LOC SIMILAR TO WILLIAMS BEUREN SYNDROME CHROMOSOME NM_ No chr No REGION PPAT PHOSPHORIBOSYL PYROPHOSPHATE AMIDOTRANSFERASE NM_ No chr No 374 KNDC1 KINASE NON-CATALYTIC C-LOBE DOMAIN (KIND) NM_ No chr No CONTAINING THOC7 NGG1 INTERACTING FACTOR 3 LIKE 1 BINDING PROTEIN 1 NM_ No chr No 376 COX11 COX11 HOMOLOG, CYTOCHROME C OXIDASE ASSEMBLY NM_ No chr No PROTEIN (YEAST) 377 DAPL1 SIMILAR TO DEATH-ASSOCIATED PROTEIN NM_ No chr No 378 SERF1A SMALL EDRK-RICH FACTOR 1A (TELOMERIC) NM_ No chr No 379 C3ORF10 CHROMOSOME 3 OPEN READING FRAME 10 NM_ No chr Yes , , SQLE SQUALENE EPOXIDASE NM_ No chr Yes NA NA NM_ Yes chr No 382 TUBB8 TUBULIN, BETA 8 NM_ No chr No 383 C6ORF126 AAAL3045 NM_ No chr No 384 PILRB PAIRED IMMUNOGLOBIN-LIKE TYPE 2 RECEPTOR BETA NM_ No chr No 385 CCDC107 HYPOTHETICAL PROTEIN MGC31967 NM_ No chr No 386 OR4F17 OLFACTORY RECEPTOR, FAMILY 4, SUBFAMILY F, MEMBER NM_ No chr No WSB1 WD REPEAT AND SOCS BOX-CONTAINING 1 NM_ Yes chr No 388 CASR CALCIUM-SENSING RECEPTOR (HYPOCALCIURIC NM_ No chr No HYPERCALCEMIA 1, SEVERE NEONATAL HYPERPARATHYROIDISM) 389 OR2V2 OLFACTORY RECEPTOR, FAMILY 2, SUBFAMILY V, MEMBER 2 NM_ No chr No 390 PTPRG PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, G NM_ No chr Yes RGS20 REGULATOR OF G-PROTEIN SIGNALLING 20 NM_ No chr No 392 CDH26 CADHERIN-LIKE 26 NM_ No chr Yes FAM129B CHROMOSOME 9 OPEN READING FRAME 88 NM_ No chr No 394 CHMP2B CHROMATIN MODIFYING PROTEIN 2B NM_ No chr No Supplemental material Page 13

13 Genome-wide analysis of HIF DNA-bdg-supplemental material Table S3. Sequences immunoprecipitatg with anti-α The table gives the chromosomal co-ordates of each anti-α immunoprecipitated locus meetg criteria of an MA Z of > 4, a width of > 100bp or > 5 probes, and a false discovery rate of < 5%, together with the maximum Z anti-α and anti-α at that gene locus. The presence or absence, and position of any HRE core motif with these sequences is given. The table also specifies whether the nearest gene to the immunoprecipitated locus was significantly regulated by exposure of cells to 1% hypoxia or 2mM DMOG or by transfection of sirnas directed agast α, α or both sirnas the Affymetrix s. Note that at a of loci several sequences were immunoprecipitated that shared proximity to a common transcriptional start site. These loci are listed order with the most strongly enriched site dicated black type and others grey type. Name chromosome start end strand Coordates of 1 ASMT ACETYLSEROTONIN O-METHYLTRANSFERASE NM_ No chrx Yes , PLS3 PLASTIN 3 (T ISOFORM) NM_ No chrx Yes , , , , , , , ZMYND8 PROTEIN KINASE C BINDING PROTEIN 1 NM_ Yes chr Yes chr Yes , FAM139A HYPOTHETICAL PROTEIN FLJ40722 NM_ Yes chr Yes , TF TRANSFERRIN NM_ No chr Yes DHX35 DEAH (ASP-GLU-ALA-HIS) BOX POLYPEPTIDE 35 NM_ No chr No 7 SEC61G SEC61 GAMMA SUBUNIT NM_ No chr No 8 HIG2 HYPOXIA-INDUCIBLE PROTEIN 2 NM_ Yes chr Yes , , , , CITED2 CBP/P300-INTERACTING TRANSACTIVATOR, WITH GLU/ASP-RICH CARBOXY-TERMINAL DOMAIN, 2 10 RAPGEF1 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 1 11 CHD1L CHROMODOMAIN HELICASE DNA BINDING PROTEIN 1-LIKE NM_ Yes chr Yes , , , , NM_ No chr Yes , , NM_ No chr Yes , , UPK1B UROPLAKIN 1B NM_ No chr Yes KIAA0195 KIAA0195 NM_ No chr Yes BACE2 BETA-SITE APP-CLEAVING ENZYME 2 NM_ Yes chr Yes , C1ORF161 CHROMOSOME 1 OPEN READING FRAME 161 NM_ No chr Yes , GPRC5A G PROTEIN-COUPLED RECEPTOR, FAMILY C, NM_ Yes chr Yes GROUP 5, MEMBER A 17 UBC UBIQUITIN C NM_ No chr No 18 S100A4 S100 CALCIUM BINDING PROTEIN A4 (CALCIUM PROTEIN, CALVASCULIN, METASTASIN, MURINE PLACENTAL HOMOLOG) NM_ Yes chr Yes , , , , FLJ16641 FLJ16641 PROTEIN NM_ No chr Yes , Supplemental material Page 14