in the Gene Expression Omnibus database under accession number: GSE10795. The supplementary data files can also be accessed from the Benecke group webpage: http://seg.ihes.fr/. Real time PCR 
Real Time PCR was performed on cDNA prepared as for microarray experiments using ABI TaqManH assays. The genes and their respective assay numbers were ATF3, ACRC, FNBP4 HES1, and HOM-TES-103. Real-time PCR was performed on 10 ng of cDNA with 1.25 ml of 206 TaqManH probes and 12.5 ml 26 TaqManH Universal Master Mix in a final 25 ml reaction. Real-time PCR relative quantification assay was running for 2 min at 50uC, 10 min at 95uC, followed by 40 cycles of 15 sec at 95uC and 1 min at 60uC on an ABI 7500 system. Relative quantity of target genes was calculated using the comparative CT method using FNBP4 as the internal control. with synthetic 29-O-methyl-modified oligoribonucleoside phosphorothioate that hybridizes to the central 20 nucleotides of alternative exon IIa. The ratio of the alternative TAF6d mRNA level with respect to TAF6a mRNA level was analyzed by RT-PCR of RNA samples from transfected HeLa cells. The transfection of the antisense oligonucleotide Taf6 AS1 resulted in a marked increase in the level of the TAF6d mRNA and a concurrent decrease in the level of the major TAF6a mRNA. In contrast, transfection of an oligonucleotide of scrambled sequence had no effect on the TAF6d/TAF6a mRNA ratio. To further demonstrate the specificity of the SSOs, we transfected antisense RNA oligonucleotides shown to enforce the expression of the Bcl-xS splice variant. The TAF6d/TAF6a+d mRNA ratio was increased,3-fold by treatment with the Taf6 AS1 oligonucleotide, but unchanged by the Bcl-x AS oligonucleotide. Conversely the ratio 22803826 of BclxS/Bcl-xL+xS mRNA was increased,10-fold by Bcl-x AS 18421270 but unaffected by Taf6 AS1. Control RT-PCR reactions showed that ratio of TAF6d with respect to total TAF6 mRNA is increased by Taf6 SSO but none of the ratios of any other known TAF6 alternative splice variants was affected. The SSOs used therefore impact specifically on TAF6d alternative splicing without influencing overall expression patterns of TAF6 mRNA. These results demonstrate that TAF6-directed SSOs are an efficient and selective method to enforce the expression of the endogenous TAF6d mRNA in HeLa cells. To further characterize the cellular response to TAF6 splice site switching antisense oligonucleotides we performed a time course analysis. The level of TAF6d mRNA is detectably increased after 4 hours and increases until 24 hours. These results are consistent with a previous study targeting the Bcl-x gene, and establish a kinetic framework to follow the early outcomes of TAF6d mRNA expression in transfected cells. We next investigated the concentration dependence for the Taf6 response to treatment with the AS1 oligonucleotide. The IC261 site induction of TAF6d mRNA was observed with transfection of as little as 50 nM Taf6 AS1 and sharply increased until treatment with 200 nM Taf6 AS1, after which a plateau was reached. Based on these results, we have employed 200 nM oligonucleotide concentrations herein, unless otherwise stated, for robust and specific induction of endogenous TAF6d mRNA in living cells. Results Selective induction of endogenous TAF6d mRNA expression by splice-switching oligonucleotides To date four splice variants of TAF6 have been identified and termed a, b, c, and d. Here we focus on the TAF6d splice variant due to its potentially important role in progra
