Table 1. Examples of three regulatory classes of genes co-bound by Six2 and β-catenin in nephron progenitors.
Class I and III genes are both up-regulated by canonical Wnt signaling when BIO treated cultures are compared with control DMSO treated cultures at 24 hrs; however, class III genes are expressed at high levels in the CM initially, while class I genes are more weakly expressed at this time and strongly induced on BIO treatment, correlating with induction of RV progenitors. Class II genes are expressed in the CM and repressed by canonical Wnt signaling upon differentiation in response to BIO relative to DMSO treated controls. The enhancers tested in transgenic analyses are indicated in bold.
| Fold change
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|---|---|---|---|---|---|---|---|---|---|
| Genes | RefSeq | Probe ID | BIO/DMSO | BIO/0hr | Peak location | Peak length | Highest score | Relative position | Distance to TSS |
|
Class I (DMSO@24hr < BIO@24hr AND 0hr < BIO@24hr)
| |||||||||
| Cxcr4 | NM_009911 | 1448710_at | 32.35 | 2.82 | chr1:130718705-130718922 | 218 | 51.3 | TSS-upstream | -229938 |
| Wnt4 | NM_009523 | 1441687_at | 10.26 | 4.79 | chr4:136773187-136773353 | 167 | 120.9 | TSS-upstream | -60279 |
| Fgf8 | NM_010205 | 1451882_a_at | 7.75 | 8.19 | chr19:45695446-45695814 | 369 | 55.0 | TES-downstream | 121560 |
| Bmp7 | NM_007557 | 1418910_at | 6.82 | 1.73 | chr2:172667933-172668149 | 217 | 90.4 | TES-downstream | 97752 |
| Aldh1a2 | NM_009022 | 1422789_at | 4.28 | 1.45 | chr9:71065207-71065805 | 599 | 62.3 | Intron | 1911 |
| Lhfpl2 | NM_172589 | 1434129_s_at | 4.52 | 1.30 | chr13:94853201-94853454 | 254 | 116.4 | Intron | 25577 |
|
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|
Class II (DMSO@24 > BIO@24hr AND 0hr > BIO@24hr)
| |||||||||
| Sox4 | NM_009238 | 1419156_at | -5.36 | -5.99 | chr13:28810434-28811092 | 659 | 50.6 | TES-downstream | 234787 |
| Dlc1 | NM_015802 | 1460602_at | -3.66 | -1.79 | chr8:37744738-37744926 | 189 | 51.1 | TSS-upstream | -67905 |
| Gas1 | NM_008086 | 1416855_at | -3.48 | -4.43 | chr13:60201125-60201558 | 434 | 45.0 | TES-downstream | 77554 |
| Mllt3 | NM_027326 | 1429205_at | -3.33 | -2.23 | chr4:87025468-87025844 | 377 | 53.3 | TES-downstream | 426561 |
| Zbtb20 | NM_019778 | 1437598_at | -2.86 | -5.94 | chr16:43361297-43361493 | 197 | 101.1 | Intron | 113999 |
| Six2 | NM_011380 | 1427436_at | -2.84 | -5.07 | chr17:86147429-86147586 | 158 | 114.5 | TSS-upstream | -59914 |
| Meis2 | NM_010825 | 1457632_s_at | -2.10 | -1.77 | chr2:115694660-115695137 | 478 | 40.9 | Intron | 195458 |
| Hmga2 | NM_010441 | 1450780_s_at | -2.02 | -3.06 | chr10:119857810-119858640 | 831 | 56.1 | Intron | 55765 |
|
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|
Class III (DMSO@24hr < BIO@24hr AND 0hr > BIO@24hr)
| |||||||||
| Gdnf | NM_010275 | 1419080_at | 4.12 | -1.74 | chr15:7647936-7648151 | 216 | 40.3 | TSS-upstream | -112967 |
| Itga8 | NM_001001309 | 1454966_at | 3.13 | -1.63 | chr2:11941243-11941615 | 373 | 76.6 | TES-downstream | 282117 |
| Itga8 | NM_001001309 | 1454966_at | 3.13 | -1.63 | chr2:11944818-11945605 | 788 | 59.5 | TES-downstream | 278335 |
| Sall1 | NM_021390 | 1437983_at | 3.17 | -1.15 | chr8:91936032-91936284 | 253 | 111.7 | TSS-upstream | -368098 |
| Sall1 | NM_021390 | 1437983_at | 3.17 | -1.15 | chr8:92130016-92130238 | 223 | 74.6 | TSS-upstream | -562067 |
| Eya1 | NM_010164 | 1457424_at | 1.89 | -1.93 | chr1:14235068-14235289 | 222 | 44.9 | Intron | 65101 |
| Eya1 | NM_010164 | 1457424_at | 1.89 | -1.93 | chr1:14625742-14625927 | 186 | 62.2 | TSS-upstream | -325555 |
| Hoxb4 | NM_010459 | 1460379_at | 1.73 | -1.23 | chr11:96180625-96180790 | 166 | 92.3 | Intron | 655 |