Table 2.
Indicators of Enhancer Activation Are Specifically Enriched at NRFEs in Response to Hormone
| Figure/Table ID | Technology | Comparing | Motif | Peak Selection Criteria | Datasets |
|---|---|---|---|---|---|
| Hormone-regulated eRNA transcription | |||||
| Fig. 4(a); Supplemental Table 3:1 | Gro-Seq | Veh vs E2 | ERE | B4 | 74 |
| Fig. 4(b); Supplemental Table 3:3 | Gro-Seq | Veh vs DHT or Dex | HRE | B4 | 10 |
| Supplemental Table 3:2 | Gro-Seq | Veh vs E2 | ERE | B4–B20 | 74 |
| Supplemental Table 3:4 | Gro-Seq | Veh vs DHT or Dex | HRE | B4–B20 | 10 |
| Hormone-regulated RNAPII occupancy | |||||
| Fig. 4(c); Supplemental Table 3:5 | RNAPII ChIP-Seq | Veh vs E2 | ERE | D1000 | 8 |
| Fig. 4(d); Supplemental Table 3:12 | RNAPII ChIP-Seq | Veh vs Cort, Dex, or Pred | HRE | D1000 | 3 |
| Supplemental Table 3:6 | RNAPII ChIP-Seq | Veh vs E2 | ERE | D1000–D20000 | 8 |
| Supplemental Table 3:7 | RNAPII ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 8 |
| Supplemental Table 3:8 | RNAPII ChIP-Seq: ERα-WT and ERα-KIKO | Veh vs E2 | ERE | L4–L20 | 2 |
| Supplemental Table 3:9 | RNAPII ChIP-Seq: ERα-WT and ERα-KIKO | Veh vs E2 | HRE | L4–L20 | 2 |
| Supplemental Table 3:10 | RNAPII ChIP-Seq | Veh vs E2, Tam, or Fulv | ERE | L4–L10 | 3 |
| Supplemental Table 3:13 | RNAPII ChIP-Seq | Veh vs Cort, Dex, or Pred | HRE | D1000–D20000 | 3 |
| Hormone-regulated recruitment of coregulators and chromatin remodeling proteins | |||||
| Fig. 4(e); Supplemental Table 3:14 | p300 ChIP-Seq | Veh vs E2 | ERE | L4 | 2 |
| Fig. 4(f); Supplemental Table 3:16 | p300 ChIP-Seq | Veh vs Dex, T, P4, or R5020 | HRE | L4 | 32 |
| Supplemental Table 3:15 | p300 ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 2 |
| Supplemental Table 3:17 | p300 ChIP-Seq | Veh vs Dex, T, P4, or R5020 | HRE | L4–L20 | 32 |
| Fig. 4(g); Supplemental Table 3:18 | FoxA1 ChIP-Seq | Veh vs E2 | ERE | L4 | 20 |
| Fig. 4(h); Supplemental Table 3:20 | FoxA1 ChIP-Seq | Veh vs Dex, T, or R1881 | HRE | L4 | 10 |
| Supplemental Table 3:19 | FoxA1 ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 20 |
| Supplemental Table 3:21 | FoxA1 ChIP-Seq | Veh vs Dex, T, or R1881 | HRE | L4–L20 | 10 |
| Supplemental Table 3:22 | FoxA1 ChIP-Seq | AR-C562S vs AR-WT | HRE | L4–L20 | 1 |
| Supplemental Table 3:23 | FoxA1 ChIP-Seq | AR-WT vs AR-Q640X | HRE | L4–L20 | 1 |
| Fig. 4(i); Supplemental Table 3:24 | DNase HSS ChIP-Seq | Veh vs E2 | ERE | L4 | 12 |
| Fig. 4(j); Supplemental Table 3:26 | DNase HSS ChIP-Seq | Veh vs Cort, Dex, or T | HRE | L4 | 20 |
| Supplemental Table 3:25 | DNase HSS ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 12 |
| Supplemental Table 3:27 | DNase HSS ChIP-Seq | Veh vs Cort, Dex, or T | HRE | L4–L20 | 20 |
| Supplemental Table 3:28 | Cohesin ChIP-Seq: STAG1 and RAD21 | Veh vs E2 | ERE | L4–L20 | 2 |
| Supplemental Table 3:29 | Cohesin ChIP-Seq: STAG1 and RAD21 | CTCF-knockdown vs CTL | ERE | L4–L20 | 2 |
| Supplemental Table 3:30 | PIAS1 ChIP-Seq | Veh vs R1881 | HRE | L4–L20 | 2 |
| Supplemental Table 3:31 | AR ChIP-Seq | siPIAS1 vs CTL | HRE | L4–L20 | 2 |
| Supplemental Table 3:32 | FoxA1 ChIP-Seq | siPIAS1 vs CTL | HRE | L4–L20 | 2 |
| Supplemental Table 3:33 | Sumo2/3 ChIP-Seq | Veh vs R1881 | HRE | L4–L20 | 2 |
| Supplemental Table 3:34 | Sumo2/3 ChIP-Seq | GR-K721R vs GR-WT | HRE | L4–L20 | 2 |
| Supplemental Table 3:35 | GR ChIP-Seq | GR-K721R vs GR-WT | HRE | L4–L20 | 2 |
| Supplemental Table 3:36 | GR ChIP-Seq | siHic5 vs CTL | HRE | L4–L20 | 2 |
| Supplemental Table 3:37 | HDAC 2 and 3 ChIP-Seq | Veh vs DHT | HRE | L4–L15 | 2 |
| Supplemental Table 3:38 | EZH2 ChIP-Seq | Veh vs DHT | HRE | L4–L20 | 1 |
| Supplemental Table 3:39 | TOP1 ChIP-Seq | Veh vs DHT | HRE | L4–L10 | 1 |
| Supplemental Table 3:40 | MRE11 ChIP-Seq | Veh vs DHT | HRE | L4–L15 | 1 |
| Supplemental Table 3:41 | Gro-Seq: Veh and DHT | siTOP1 or siMRE11 vs CTL | HRE | B4–B20 | 8 |
| Hormone-regulated transcription factor recruitment | |||||
| Supplemental Table 3:42 | GATA3 ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 5 |
| Supplemental Table 3:43 | GATA3 ChIP-Seq: Trans | GATA3-WT vs GATA3-C318R or GATA3-N320K | ERE | L4–L20 | 2 |
| Supplemental Table 3:44 | ERα ChIP-Seq | siGATA3 vs CTL | ERE | L4–L20 | 1 |
| Supplemental Table 3:45 | AR ChIP-Seq | siGATA2 vs CTL | HRE | L4–L20 | 2 |
| Supplemental Table 3:46 | RARα/γ ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 2 |
| Supplemental Table 3:47 | RARα/γ ChIP-Seq: Trans | RARα/γ-WT vs RARα/γ-pBox or RARα/γ-ZF | ERE | L4–L20 | 4 |
| Supplemental Table 3:48 | Gro-Seq: Veh and E2 | shRARs vs CTL | ERE | B4–B20 | 4 |
| Supplemental Table 3:49 | p300 ChIP-Seq | shRARs vs CTL | ERE | L4–L20 | 1 |
| Supplemental Table 3:50 | ERα ChIP-Seq | shRARs vs CTL | ERE | L4–L20 | 1 |
| Supplemental Table 3:51 | pERα-S118 ChIP-Seq | shRARs vs CTL | ERE | L4–L20 | 1 |
| Supplemental Table 3:52 | Med1 ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 2 |
| Supplemental Table 3:53 | Med1 ChIP-Seq: shCTL and shRARs | Veh vs E2 | ERE | L4–L20 | 2 |
| Supplemental Table 3:54 | Gro-Seq | siSMC3 vs CTL | ERE | B4–B20 | 2 |
| Supplemental Table 3:55 | AP2γ ChIP-Seq | Veh vs E2 | ERE | L4–L20 | 1 |
| Supplemental Table 3:56 | Gro-Seq: Veh and E2 | shAP2γ vs CTL | ERE | B4–B20 | 4 |
| Supplemental Table 3:57 | Stat3 ChIP-Seq | Veh vs Dex | HRE | L4–L20 | 3 |
| Supplemental Table 3:58 | ERG ChIP-Seq | Veh vs DHT | HRE | L4–L20 | 1 |
| Supplemental Table 3:59 | CEBP-β ChIP-Seq and ChIP-Exo | Veh vs Dex or Pred | HRE | L4–L20 | 4 |
| Supplemental Table 3:60 | CREB1 ChIP-Seq | Veh vs Dex | HRE | L4–L20 | 2 |
| Supplemental Table 3:61 | DNase HSS ChIP-Seq | dn-CEBP-β vs CTL | HRE | L4–L20 | 2 |
| Supplemental Table 3:62 | AP1 ChIP-Seq | Veh vs Dex | HRE | L4–L10 | 1 |
| Supplemental Table 3:63 | AP1 ChIP-Seq | Veh vs Compound A | HRE | L4–L15 | 1 |
| Supplemental Table 3:64 | Gro-Seq | Veh vs Dex or Compound A | HRE | B4–B15 | 2 |
Summary of genomic features analyzed. See also Supplemental Tables 3:1–64.
Abbreviations: Cort, corticosterone; CTL, control; Dex, dexamethasone; DHT, 5α-dihydrotestosterone; dnCEBP-β, dominant negative-CEBP-β; Fulv, fulvestrant; HSS, hypersensitivity site; Pred, prednisolone; R1881, methyltrienolone; R5020, promegestone; shAP2γ, knockdown of AP2γ; shRAR, knockdown of RARα/γ; siGATA2, knockdown of GATA2; siGATA3, knockdown of GATA3; siHic5, knockdown of Hic5; siMRE11, knockdown of MRE11; siPIAS1, knockdown of PIAS1; siSMC3, knockdown of cohesin subunit SMC3; siTOP1, knockdown of TOP1; T, testosterone; Tam, tamoxifen; Veh, vehicle.