The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (ChIP-Seq)

RNA polymerase II transcription initiation requires assembly of a preinitiation complex (PIC). According to the stepwise model of PIC assembly, TFIID is the first GTF to be recruited. TFIID comprises TBP and 13 TBP-associated factors (TAFs). We focused on TAF13, the smallest subunit of TFIID. Taf13 has a histone-like domain that heterodimerizes with its partner Taf11. Recently published structures of TFIID place the Taf13-Taf11 heterodimer in lobe A where it forms a “bridge” between TBP and TFIID. According to this structure, the Taf11-Taf13 heterodimer has been suggested to be critical for TBP deposition at promoters. To better address this question, we generated mouse Embryonic Stem Cells (ESCs) cell lines and genetically modified mice where the gene coding for Taf13 was inactivated. Taf13-null mice died at E6.5-E7.5, whereas ESCs survived up to 15 days after inactivation of Taf13, but showed slower growth as compared to controls. To understand how Taf13 inactivation impacts TFIID and RNA polymerase II (Pol II) recruitment, we performed ChIP seq for the TBP and Taf1 subunits of TFIID along with PolII on ESC lines expressing or not Taf13. ChIP seq for histone marks H3K4Me3 and H3K27ac were also performed. Taf13 inactivation does not impair TBP recruitment at promoters, while that of Pol II was reduced both at the promoter and gene body. Surprisingly, recruitment of Taf1 was increased and while the H3K4Me3 mark was not affected, H3K27ac was notably increased in the absence of Taf13. Taken together, these data showed that loss of the Taf11-Taf13 heterodimer did not strongly impact TBP recruitment to promoters, but led to increased Taf1 and H3K27ac levels, but reduced paused and elongating Pol II. ChIP was performed on MNase digested ESC chromatin for TBP, Taf1 and Taf13 (ChIP against HA) and sonicated chromatin for PolII, H3K4Me3 and H3K27ac. Each ChIP was done on chromatin from Taf13-/- ESCs ectopically expressing or not ectopic 3XHATaf13.