Table 2. Survey of NR binding enrichment near ligand-responsive genes.
Summary of studies in which NR binding and ligand-dependent transcriptional changes were both measured in the same experimental system. Many of these studies demonstrate that NRs can be associated with both gene activation and repression in response to the same ligand treatment. The table is organized by NR and cell type, as in Table 1. The 3rd column briefly explains the criteria for assigning NR sites to target genes. The proportions of ligand-activated and ligand-repressed genes bound by the NR are shown in columns 4 and 5, respectively.
| % of Regulated Genes w/ Assoc. Binding Site | ||||
|---|---|---|---|---|
| NR | Cell Type | Criteria for linking NR binding sites to target genes | % Activ. | % Repr |
| ERα16 | MCF-7 (h) | ERα site within 50kb of genes showing E2-dependent RNAPII enrichment | 89% | 47% |
| ERα14 | MCF-7 (h) | ERα site within 50kb of E2-responsive genes (multiple time points) | 18-33% | 17-24% |
| ERα52 | MCF-7 (h) | ERα site within 10kb of E2-responsive TSS in GRO-seq (multiple time points) | 33%-50% | 8% |
| ERα23 | MDA-MB-231 (h) | ERα site within 50kb of E2-responsive gene | 53% | 27% |
| ERα69 | MCF-7 (h) | ERα+Cohesin site within 20kb of E2-responsive gene | ~30% | ~40% |
| GR48 | A549 (h) | GR site within 10kb of dex-responsive gene | 47% | 8% |
| VDR59 | THP-1 (h) | VDR site within 400kb of ligand-responsive gene | 72% | 43% |
| PPARγ18 | 3T3-L1 (m) | PPARγ site assigned to nearest gene within 50kb | ~60% | ~20% |
| PPARγ60 | Macrophages (m) | PPARγ site assigned to nearest gene within 100kb | 39% | 15% |
| LXR24 | Liver (m) | LXR:RXR sites assigned to nearest TSS | 63% | 70% |
| RARα/γ66 | MEF (m) | RAR bound to ChIP-chip probe associated with regulated gene | 12% | 5% |