a substantial body of evidence now shows that the adult thymus retains some thymopoietic function and continues to produce naive T-cells for export to the periphery

on of Taf6 AS1, but not Bcl-x AS into Saos-2 cells effectively increased endogenous TAF6d TAF6d Controls Death Sans p53 The induction of endogenous TAF6d in wild-type Clemizole hydrochloride HCT-116 cells resulted in significant changes in the levels of 321 mRNAs out of a total of 27,868 independent genes measured by microarray analysis. The induction of endogenous TAF6d in HCT116 lacking p53 expression resulted in significant changes in the levels of 444 mRNAs. In both cells 17640949 the majority of mRNAs are increased in response to TAF6d. These data establish that TAF6d acts primarily as a positive regulator of gene expression and rule out the possibility that TAF6d-induced cell death is a result of a global reduction in mRNA transcription. TAF6a physically interacts with p53, yet TAF6d induces apoptosis in cells lacking p53. We therefore analyzed the microarray data to determine whether TAF6d can control gene expression independently of p53. The p53-dependent genes were identified by filtering for genes that are significantly changed in the wild-type HCT-116 versus HCT-116 p53 2/2 in both the presence of the TAF6 SSO or a scrambled control oligonucleotide. As expected, well-established p53 target genes, including FAS, FDXR, SESN1 and p21/CDKN1A were found in the p53-dependent gene set, confirming the sensitivity and accuracy of the microarray methodology. We focused on the identification of genes regulated in both wild-type HCT-116 and HCT-116 p53 2/2 because these mRNAs represent candidates for genes that function to induce p53-independent apoptosis. The different gene sets significantly regulated by TAF6d in wild-type and p53 negative TAF6d Controls Death Sans p53 HCT-116 cells, as well as the p53-dependent genes, are shown by Venn diagrams in Fig. 6C. The absolute numbers of TAF6ddependent genes is underestimated when compared to p53dependent genes because the two gene sets are derived from very technically different approaches. p53-dependence is defined here through the use of an isogenic cell line in which p53 expression is eliminated completely in 100% of cells by genetic ablation through homologous recombination. In contrast TAF6d-dependency is defined by the induction of endogenous TAF6d via transient transfection with splice switching oligonucleotides, that occurs only partially and in fraction of the cells. Nonetheless, the analysis revealed 21 TAF6d-dependent, p53-independent genes. To independently validate the TAF6d-dependent genes we selected 4 genes for real-time quantitative RT-PCR analysis. One gene is within our P-value cut-of, another is TAF6d Controls Death Sans p53 slightly outside the P-value cut-off, and a third substantially outside our cutoff. ACRC, HES1 and HOM-TES-103 were induced by TAF6d in wild-type p53 HCT116 cells as well as HCT-116 p53 2/2 cells. We also verified the expression of ATF3, since it represents the distinct class of genes that are regulated by TAF6d only in the presence of p53. ATF3 induction was documented in HCT-116 cells expressing p53 but not in p53-null HCT-116 cells, as validated by real-time RT-PCR. To reinforce the specificity of all of these effects, we employed two distinct TAF6d-inducing SSOs, both of which caused comparable changes in expression of the four genes tested. These results confirm that TAF6d can induce gene expression independently of the tumor suppressor p53. 9 TAF6d Controls Death Sans p53 TAF6d Controls Death Sans p53 Discussion Here we have combined splice-switching oligonucleotides 15647369 with high-