Table 2.
Induction of Ngn and NeuroD targets in mammalian P19 cells
| UniGene for Xenopus genes | UniGene for mouse orthologs | Gene title | Induction by Ngn2a | Induction by NeuroD1a | Range of Ct values in qRT–PCRb |
|---|---|---|---|---|---|
| Xl.437 | Mm.2474 | Nescient helix loop helix 1 (Nhlh1, HEN1)c | 229.1 | 198.0 | 29–33 |
| Xl.879 | Mm.3280 | Twist gene homolog 1 (Drosophila) | 0.8 | 0.8 | 24–26 |
| Xl.1263 | Mm.10695 | Neurogenic differentiation 4 (NeuroD4, Math3, NeuroM)c | 22.6 | 123.7 | 31–34 |
| Xl.1274/Xl.21449d | Mm.297371 | POU domain, class 3, transcription factor 1 (Pou3f1, Oct6)c | ND | 3.5 | 26–28 |
| Mm.129387 | POU domain, class 3, transcription factor 2 (Pou3f2, Brn2)c | ND | 5.6 | 33–34 | |
| Xl.450 | Mm.136217 | Achaete–scute complex homolog-like 1 (Ascl1) | 1.8 | 1.8 | 34–37 |
| Xl.23642 | Mm.330700 | Zinc finger protein 238 (RP58)c | 1.7 | 1.7 | 24–25 |
| Xl.53293/Xl.76708 | Mm.21145 | Angiomotin-like 2 (Amotl2) | 1.7 | 1.7 | 21–24 |
| Xl.16456/Xl.4960 | Mm.29914 | Core-binding factor, runt domain, alpha subunit 2, translocated to, 2 homolog (Cbfa2t2h, MTGR1)c | 1.3 | 1.5 | 22–25 |
| Xl.34957 | Mm.440140 | BTB (POZ) domain containing 6 (Btbd6) | ND | 1.0 | 28–31 |
| Xl.958 | Mm.440702 | Zinc finger homeobox 1b (Zfhx1b, SIP1)c | ND | 1.0 | 20–21 |
| Xl.24147 | Mm.60590 | Myosin 10 | ND | 1.9 | 24–25 |
| Xl.547/Xl.237 | Mm.319947 | Early B-cell factor 2 (Ebf2) | 84.5 | 84.4 | 28–31 |
| Xl.57163/Xl.31433 | Mm.130005 | Myelin transcription factor 1 (MYT1, NZF-2b)c | 1.7 | 1.8 | 26–28 |
| Xl.5041 | Mm.11186 | Solute carrier family 43, member 2/L-type amino-acid transporter 4 (Slc43a2/LAT4) | ND | 0.7 | 24–25 |
| Xl.4522 | Mm.238044 | Iroquois-related homeobox 3 (Irx3)c | 1.1 | 1.1 | 24–26 |
| Xl.5764 | Mm.142455 | Solute carrier family 7 (cationic amino-acid transporter, y+ system), member 7 (Slc7a7) | ND | 0.9 | 20–22 |
| Xl.15305 | Mm.10026 | Cell death-inducing DFFA-like effector c (CIDE-c, FSP27) | 0.9 | 1.4 | 29–31 |
| Xl.71386 | Mm.274011 | UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3 (B4galt3) | ND | 1.1 | 22–24 |
| Xl.8440 | Mm.137268 | Hairy and enhancer of split 5 (Hes5) | 2.7 | 8.1 | 30–37 |
| Xl.16835 | Mm.259022 | Polo-like kinase 3 (Plx3) mRNA (Plk3)c | ND | 0.8 | 32–34 |
| Xl.54916 | Mm.4875 | Delta-like 1 (Dll1)c | 6.2 | 3.1 | 33–35 |
| Xl.1035 | Mm.347707 | ELAV-like 3 (HuC, Elavl3)c | 5.1 | 9.4 | 29–31 |
| Xl.24275 | Mm.2734 | Spermidine/spermine N1-acetyltransferase 1 (Sat1) | ND | 2.9 | 33–36 |
| Xl.7556 | Mm.150314 | Prickle1c | 1.0 | 1.2 | 22–23 |
| Xl.12125 | Mm.281298 | Growth arrest and DNA-damage-inducible 45 gamma (Gadd45g) | ND | 7.3 | 28–30 |
| Xl.5886 | Mm.29811 | Response gene to complement 32 (Rgc32) | ND | 2.0 | 33–35 |
| Xl.51207 | Mm.130063 | RIKEN cDNA 9330182L06 gene | ND | 3.7 | 25–27 |
| Xl.1717 | Mm.29768 | Pyruvate dehydrogenase kinase, isoenzyme 2 (Pdk2) | ND | 2.0 | 24–25 |
| Xl.632e | Mm.258708 | Early B-cell factor 3 (Ebf3) | 10.2 | 26.1 | 32–34 |
| Average fold change of three independent experiments determined by qRT–PCR, ND indicates not determined | |||||
| qRT–PCR threshold cycle numbers (Ct) represent when target cDNA begins to be exponentially amplified during PCR and inversely correlate with target cDNA abundance. Target genes from the Xenopus microarrays that were not or weakly induced were often already highly expressed in P19 cells and Ngn/NeuroD transfection did not further increase expression | |||||
| These genes were also predicted as Ngn/NeuroD targets in a computational, genome-wide analysis with the PAP program. See text for further details | |||||
| Two mouse genes (Pou3f1/Oct6 and Pou3f2/Brn2) showed highest homology to POU50 (Xl.1274/Xl.21449) depending on the alignment method (Clustal W or Clustal V). Thus, it was unclear which gene was a true ortholog of Xenopus POU50 and we tested both genes | |||||
| Xl.632 Ebf3 was not identified in our microarray experiments (see Supplementary methods) but is a known NeuroD target and we confirmed its induction by NeuroD by qRT–PCR in Xenopus. Thus, we included Ebf3 in this list | |||||