RNA-seq expression profiling of cerebral cortices from Taf8 deleted and Taf8 intact mouse embryos

Mutations in genes encoding general transcription factors cause neurological disorders. Despite clinical prominence, the consequences of defects in the basal transcription machinery during brain development are unclear. We found that loss of the TATA-box binding protein associated factor TAF8, a component of the general transcription factor TFIID, in the developing central nervous system affected the expression of many, but notably not all genes. Taf8 deletion caused apoptosis, unexpectedly restricted to forebrain regions. Nuclear levels of the transcription factor p53 were elevated in the absence of TAF8, as were the mRNAs of the pro-apoptotic p53 target genes Noxa, Puma and Bax. The cell death in Taf8–/– forebrain regions was completely rescued by additional loss of p53, but Taf8–/–p53–/– brains failed to initiate a neuronal expression program. Taf8 deletion caused aberrant transcription of promoter regions and splicing anomalies. We propose that TAF8 supports the directionality of transcription and co-transcriptional splicing, and that failure of these processes causes p53- induced apoptosis of neuronal cells in the developing mouse embryo. Taf8 was deleted in the developing mouse central nervous system (CNS) using our Taf8 conditional allele. In the absence of global effects of loss of TAF8 on RNA levels, we determined effects on individual gene loci by RNA sequencing of cortices from Taf8 deleted (E14.5 Taf8lox/–NesCreT/+p53–/–) and control (E14.5 Taf8+/+NesCreT/+p53–/–) cortices. The p53-deficient background was used to avoid complications due to apoptosis, but prevented us from examining changes in p53-induced gene transcription. Four Taf8 deleted and four control corticle samples were prepared, each from a separate mouse. Stranded and unstranded RNA-seq libraries were prepared from each RNA sample.