Table II. NF-κB dependent genes rescued by IKKα independent of its kinase activity.
Twenty representative genes meeting the criteria of being rescued by both the Wt . IKKα and IKKα(K44M) proteins are shown. Fold Change values of these twenty genes obtained from duplicate microarray comparisons using independent samples of IKKα(−/−) + IKKα(K44M) 2T vs. IKKα(−/−) + EV 2T are indicated in Column 1. Column 2 shows the results obtained for the same genes in duplicate microarray comparisons of IKKα(−/−) + Wt. IKKα 2T vs. IKKα(−/−) + EV 2T. Column 3 displays their relative dependencies on IKKα in the context of wild type MEFs (i.e., Wt. MEF 2T vs. IKKα(−/−) 2T as previously described)(26)(and data not shown). Columns 4–5 shows their NF-κB dependencies by comparing their expressions in Wt. MEF 2T compared to either p50 null MEF 2T (Column 4) or Wt. MEF + IκBαSR(super repressor) 2T (26)(Column 5). The TNFα dependencies for the IKKα rescued expression of each gene are shown in the context of their independent rescues by physiological levels of either IKKα(K44M) (Column 6) or Wt. IKKα (Column 7). The criteria for assigning the TNFα responsiveness of each rescued gene was determined on the basis of duplicate S (2T) vs. US microarray screens [for Wt. IKKα or IKKα(K44M) rescued IKKα(−/−) MEFs as indicated] (see description of criteria in Experimental Procedures). Examples of signal values of three genes are shown in Figure 7 and TaqMan ‘real time’ PCR analyses of selected genes are in Figure 9. Genes induced by TNFα are assigned a (+) sign and genes whose expression was not significantly stimulated by TNFα were given a (−). The IKKα(K44M) mutant in a TNFα responsive manner comparable to that achieved by Wt. IKKα rescued three genes highlighted in gray.
| Accession# | Genes | |||||||
|---|---|---|---|---|---|---|---|---|
| Inflammation/Stress & Immune-like Responses | IKKα( −/−) + IKKα (K44M) vs IKKα( −/−) | IKKα( −/−) + Wt. IKKα vs IKKα( −/−) + EV | Wt. MEF vs IKKα( −/−) | Wt. MEF vs p50(−/−) | Wt. MEF vs Wt. MEF + IκBαSR | TNFα (K44M) | TNFα (Wt. IKKα) | |
| M26071 | Coagulation factor III | 2.2/2.6 | 1.7/1.6 | 4.2 | 2.8 | 4.8 | − | − |
| X56824 | Heme oxygenase 1/Hmox1/HO-1 | 1.8/2.1 | 1.5/1.6 | 4.6 | 6.0 | 9.2 | − | − |
| AA615831 | Heat shock protein 4/Hsp4/Apg-2 | 1.5/1.4 | 1.5/1.5 | 2.0 | 2.6 | 1.6 | − | − |
| NF-κB Regulation | ||||||||
| U19463 | A20/somatostatin receptor 1 | 18.6/6.8 | 5.8/12.6 | 5.7 | 5.7 | 3.3 | + | + |
| U40930 | Sequestosome 1/Sqstm1/p62 | 1.7/1.3 | 2.3/1.8 | 1.4 | 2.3 | 2.4 | − | − |
| D10727 | NPC derived proline rich protein 1/NDPP1/CARD8 | 1.5/1.8 | 1.4/1.7 | 1.1 | 2.9 | 1.5 | − | − |
| Growth & Develoment/Differentiation & Cell Fate | ||||||||
| U19118 | Activating transcription factor 3/ATF3 | 3.8/2.0 | 2.8/2.1 | 1.7 | 3.6 | 1.5 | − | + |
| Growth Arrest & Apoptosis | ||||||||
| X54149 | GADD45β/MyD118 (2hits) | 2.8/1.9 | 2.2/2.8 | 4.3 | 4.5 | 2.2 | − | + |
| AF064088 | TGFβ inducible early growth response/Tieg1/GIF | 2.2/3.9 | 1.6/1.3 | 4.0 | 5.0 | 6.1 | − | − |
| U20735 | Jun-B oncogene | 1.7/2.2 | 1.5/1.5 | 1.5 | 21.7 | 5.6 | − | + |
| Proliferation & Survival | ||||||||
| X16009 | Proliferin 3/PLF3 | 5.0/83.3 | 3.7/4.5 | 5.4 | 264.5 | 3.8 | − | − |
| K03235 | Proliferin 2/PLF2 | 2.6/22.3 | 2.0/2.5 | 5.3 | 397.4 | 3.4 | − | − |
| AA270365 | Cytokine receptor-like factor 1/Crlf1 | 14.1/4.9 | 2.0/1.8 | 3.6 | −1.3 | 2.6 | − | − |
| M21952 | M-CSF1 | 2.2/1.7 | 1.9/2.1 | 2.7 | 6.0 | 3.3 | + | + |
| Adhesion/Extracellular matrix | ||||||||
| AW121179 | Microfibrillar associated protein 5/Mfap5/Magp2 | 5.0/3.8 | 3.6/4.5 | −1.2 | −6.8 | 4.4 | − | − |
| AA980164 | SPARC related modular calcium binding 2/Smoc2 | 3.4/2.5 | 2.3/2.2 | −1.6 | −11.8 | 4.0 | − | − |
| Metabolic Pathways | ||||||||
| AW046181 | Serum/glucocorticoid regulated kinase | 2.4/3.8 | 1.7/2.0 | 3.1 | 4.6 | 2.2 | − | − |
| AW049647 | ADP-ribosylation factor-like 6 interacting protein 5/Arl6ip5/GTRAP 3-18 | 1.5/1.4 | 1.5/1.4 | 1.9 | 2.1 | 1.2 | − | − |
| Miscellaneous | ||||||||
| C85523 | mVL30/Murine retrotransposon | 2.1/2.1 | 2.4/1.4 | 2.9 | 2.7 | 4.6 | + | + |
| AI847054 | EST | 1.9/1.7 | 2.0/2.4 | 22.6 | 19.7 | 32.1 | − | − |