Table 2A.
Cont.
| Motif Discovery | Correlation with Regulated Expression | PolII Occupancy or Histone Modifications | Reference |
|---|---|---|---|
| n/a | n/a | 50% of PolII occupred promoters bound by HNF4α | |
| n/a | 10% of 133 HNF4α-dependent genes showed binding (23 ) | 50% of PolII occupied promoters bound by HNF4α | 22 |
| ERE; half-sites | 6/12 of genes regulated by E2 | n/a | 25 |
| n/a | n/a | n/a | 28 |
| n/a | 43% of the genes with proximal binding are regulated by E2 | PolII recruited to all tested ERα-bound regions (enhanced) upon E2 treatment | |
| ERE (11%) | n/a | n/a | 30 |
| n/a | n/a | n/a | 31 |
| ERE (70%) | n/a | PolII recruited to all tested ERα-bound regions (enhanced upon E2 treatment) | 32 |
| ERE (49%); forkhead | 11/12 E2-regulated genes on chr.21–22 were bound by ERα at promoter | PolII recruited to all tested ERα-bound regions | 2 |
| ERE; AP-1; OCT1; C/EBP; forkhead | E2-up-regulated and late -down-regulated genes associated with ERα binding within 50 kb of TSS (33%) | ERα-bound regions dispersed throughout genome, whereas polII binding correlates with TSS | |
| ERE (71%) | E2-upregulated genes associated with ERα binding within 50 kb of TSS | n/a | 35 |
| ERE (44%) | 9% of ERα-bound promoters associated with E2 - responsive genes | PolII recruited to 43% of all promoters along with AcH3K9 and Me2H3K4 modifications | 36 |
| ERE and AP-1 | ERα-bound promoters correlate with E2- responsiveness | 47% ERα-bound promoters showed E2-dependent PolII recruitment, which correlated with AcH3K9 | 3 |
| n/a | n/a | 40/92 showed AcH3K9; 28/92 showed H3K9Me2; PolII recruitment correlates with ERα recruitment | 38 |
| ERE; ETS; forkhead | 22/209 E2-responsive genes bound by ERα at promoter | n/a | 39 |
| GRE | 8/11 GR-bound promoters correlate with glucocorticoid-regulated genes | n/a | 43 |
| GRE (68%) | 88% of GR-bound regions associated with glucocorticoid responsiveness | n/a | 44 |
| ARE (10%); noncanonical ARE (68%); forkhead; GATA; Oct | 38% of AR-bound regions located within 500 kb of androgen-regulated genes | n/a | 45 |
| ARE (69%) | 84% of the androgen-responsive genes represented on array are bound by AR | n/a | 46 |
| ARE (27%); ETS | 6% of AR-bound promoters showed altered expression upon androgen treatment | n/a | 47 |
| ERRE, NRF-1, CREB, STAT3 | n/a | n/a | 48 49 |
| n/a | High correlation for mitochondrial respiration pathway | n/a | 50 |
| VDRE | Binding correlates with VDR or RNAKL expression | PolII recruitment correlates with histone acetylation | 52 53 |
1, ChIP-cloning; 2, ChIP-on-chip on promoter array (1 kb PCR-generated fragments); 3, ChIP-on-chip on chromosome 21–22 tilled array; 4, ChIP-on-chip on whole-genome tilled array; 5, ChIP-PET; 6, ChIP-DSL (40-oligomer promoter array); 7, ChIP-on-chip on array consisting of ∼900 regions (1 kb PCR-generated fragments): ∼600 E2-responsive promoters, ∼250 control promoters, and ∼50 nonpromoter regions; 8, ChIP-on-chip on CpG islands; 9, ChIP scanning of 11 glucocorticoid-responsive gene promoters; 10, ChIP-on-chip on oligonucleotide tilled array covering large regions around TSS of 548 glucocorticoid-responsive genes; 11, ChIP-on-chip on oligonucleotide tilled array covering large regions around TSS of 205 androgen-responsive genes; 12, ChIP-on-chip on oligonucleotide tiled array covering large regions around the TSS of VDR and RANKL genes. n/a, nonapplicable; ERRE, ERR response element; GRE, glucocorticoid response element; VDRE, vitamin D response element.