TABLE 1.
Anti-HIF-1α chromatin immunoprecipitation (top 25 gene loci)
The table gives the chromosomal coordinates of each anti-HIF-1α immunoprecipitated locus meeting criteria of an MA Z score of >4, a width of >100 bp or >5 probes, and a false discovery rate of <5%, together with the maximum Z score for anti-HIF-1α and anti-HIF-2α at that gene locus. The presence or absence, and position of any HRE core motif RCGTG within 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 2 mm DMOG or by transfection of siRNAs directed against HIF-1α, HIF-2α, or both siRNAs in the Affymetrix expression arrays. Note that at a number of loci several sequences were immunoprecipitated that shared proximity to a common transcriptional start site. These loci are listed in order with the most strongly enriched site indicated in bold type and others in normal type.
| HIF-1 | Gene Annotation | Gene name | RefSEQ number | Regulated in expression array | Chromosome | Start | End | Strand | Max Z-score |
RCGTG | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| HIF-1 | HIF-2 | ||||||||||
| 1 | ASMT | Acetylserotonin o-methyltransferase | NM_004043 | No | chrX | 1,842,483 | 1,844,214 | + | 17.9 | 21.9 | Yes |
| 2 | PLS3 | Plastin 3 (t isoform) | NM_005032 | No | chrX | 114,898,432 | 114,899,202 | + | 15.8 | 17.4 | Yes |
| 3 | GPI | Glucose-phosphate isomerase | NM_000175 | No | chr19 | 39,541,340 | 3,9542,126 | + | 15.7 | 9.6 | Yes |
| chr19 | 39,540,468 | 39,540,783 | + | 7.4 | No | ||||||
| 4 | DARS | Aspartyl-tRNA synthetase | NM_001349 | Yes | chr2 | 136,458,510 | 136,459,327 | − | 15.5 | 9.8 | Yes |
| 5 | SNAPC1 | Small nuclear RNA activating complex, polypeptide 1, 43 kDa | NM_003082 | No | chr14 | 61,291,513 | 61,291,955 | + | 13.9 | 6.0 | No |
| 6 | SEC61G | Sec61 γ-subunit | NM_001012456 | No | chr7 | 54,794,557 | 54,794,993 | − | 13.4 | 12.2 | Yes |
| 7 | GTF2IRD2B | Gtf2i repeat domain containing 2b | NM_001003795 | No | chr7 | 74,146,820 | 74,147,110 | + | 12.7 | 7.1 | No |
| chr7 | 74,145,407 | 74,145,716 | + | 6.1 | No | ||||||
| chr7 | 74,147,633 | 74,147,933 | + | 5.4 | No | ||||||
| 8 | SAP30 | Sin3a-associated protein, 30 kDa | NM_003864 | Yes | chr4 | 174,527,153 | 174,528,353 | + | 12.6 | 9.3 | Yes |
| 9 | ZMYND8 | Protein kinase C-binding protein 1 | NM_012408 | Yes | chr20 | 45,422,559 | 45,423,749 | − | 12.1 | 15.2 | Yes |
| chr20 | 45,421,122 | 45,421,975 | − | 9.3 | Yes | ||||||
| chr20 | 45,416,738 | 45,416,961 | − | 5.4 | No | ||||||
| chr20 | 45,324,234 | 45,324,808 | − | 5.3 | Yes | ||||||
| chr20 | 45,382,266 | 45,382,561 | − | 5.2 | No | ||||||
| chr20 | 45,381,728 | 45,381,912 | − | 5.0 | No | ||||||
| chr20 | 45,322,893 | 45,323,036 | − | 4.8 | No | ||||||
| chr20 | 45,380596 | 45,380,865 | − | 4.7 | No | ||||||
| 10 | RSBN1 | Round spermatid basic protein 1 | NM_018364 | Yes | chr1 | 114,156,633 | 114,157,374 | − | 11.9 | 6.0 | Yes |
| chr1 | 114,154,609 | 114,155,069 | − | 5.4 | Yes | ||||||
| chr1 | 114,154,093 | 114,154,264 | − | 5.1 | No | ||||||
| 11 | BNIP3L | Bcl2/adenovirus e1b 19-kDa interacting protein 3-like | NM_004331 | Yes | chr8 | 26,297,111 | 26,297,957 | + | 11.9 | 7.9 | Yes |
| 12 | FAM139A | Hypothetical protein flj40722 | NM_173678 | Yes | chr7 | 143,028,228 | 143,029,042 | + | 11.8 | 14.0 | Yes |
| 13 | GTF2IRD2 | Gtf2i repeat domain containing 2 | NM_173537 | No | chr7 | 73,904,992 | 73,905,289 | − | 11.6 | Yes | |
| chr7 | 73,906,359 | 73,906,641 | − | 6.5 | No | ||||||
| 14 | C3ORF28 | Chromsome 3 open reading frame 28 | NM_014367 | Yes | chr3 | 123,584,923 | 123,585,595 | + | 11.6 | 4.9 | No |
| chr3 | 123,586,518 | 123,586,736 | + | 4.7 | No | ||||||
| chr3 | 123,585,892 | 123,586,061 | + | 4.6 | No | ||||||
| 15 | STC2 | Stanniocalcin 2 | NM_003714 | Yes | chr5 | 172,688,209 | 172,689,013 | − | 11.2 | 8.8 | Yes |
| chr5 | 172,689,765 | 172,690,086 | − | 6.0 | Yes | ||||||
| 16 | NARF | Nuclear prelamin a recognition factor | NM_001038618 | Yes | chr17 | 78,008,958 | 78,009,355 | + | 10.9 | No | |
| 17 | TF | Transferrin | NM_001063 | No | chr3 | 134,944,094 | 134,944,856 | + | 10.7 | 13.6 | Yes |
| 18 | HK2 | Hexokinase 2 | NM_000189 | Yes | chr2 | 74,914,233 | 74,914,441 | + | 10.5 | 5.6 | Yes |
| chr2 | 74,912,970 | 74,913,723 | + | 6.9 | No | ||||||
| 19 | INHA | Inhibin, α | NM_002191 | Yes | chr2 | 220,149,206 | 220,150,032 | + | 10.4 | 9.1 | Yes |
| chr2 | 220,150,797 | 220,151,070 | + | 5.2 | No | ||||||
| 20 | PCF11 | Kiaa0824 protein | NM_015885 | No | chr11 | 82,544,764 | 82,545,226 | + | 10.3 | 8.1 | Yes |
| 21 | C9ORF30 | Chromosome 9 open reading frame 30 | NM_080655 | No | chr9 | 102,228,622 | 10,2228,900 | + | 10.3 | 9.7 | Yes |
| chr9 | 102,231,225 | 102,231,536 | + | 5.9 | Yes | ||||||
| 22 | CBWD3 | Cobw domain containing 3 | NM_201453 | No | chr9 | 70,046,581 | 70,047,378 | + | 10.2 | 5.1 | Yes |
| 23 | RAD51L1 | Rad51-like 1 (Saccharomyces cerevisiae) | NM_133510 | Yes | chr14 | 67,356,360 | 67,357,875 | + | 9.8 | 8.2 | Yes |
| 24 | KIAA0195 | Kiaa0195 | NM_014738 | No | chr17 | 70,960,840 | 70,961,202 | + | 9.7 | 11.6 | Yes |
| 25 | S100P | S100 calcium-binding protein p | NM_005980 | Yes | chr4 | 6,721,070 | 6,721,680 | + | 9.7 | 9.4 | Yes |