The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis [CUT&TAG]

RNA polymerase II (Pol II) transcription initiation requires assembly of a preinitiation complex (PIC) comprising the general transcription factors amongst which the multiprotein complex TFIID. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). Recent cryo-electron microscopy studies reported topological reorganization of TFIID upon promoter binding with the TAF11-TAF13 heterodimer as the last TFIID subunits directly contacting TBP prior to deposition on promoter DNA upstream of the transcription start site. To challenge the role of the TAF11-TAF13 heterodimer, we inactivated the gene encoding Taf13 both in mice and embryonic stem cells (ESCs). Taf13 inactivation in mice is embryonic lethal with null embryos implanting but surviving only until E6.5. Taf13-null ESCs are viable, but show slower proliferation and fail to form embryoid bodies and differentiate. Biochemical analyses from these ESCs show that Taf13 loss had minimal effect on TFIID integrity, and genomic profiling shows only a mild reduction of promoter recruitment of TBP and Taf4 while that of Taf1 is increased. Moreover, while TFIIH recruitment is unaffected indicating normal PIC formation, that of Pol II is globally diminished. These data indicate that the Taf11-Taf13 heterodimer is not essential for TBP/TFIID recruitment and PIC formation, but is specifically required for normal Pol II recruitment. Overall design: Cut and Tag experiment was performed on ESCs expressing or lacking 3XHATaf13 using anti TBP, Taf4 and Xpb antibodies