Extended Data Fig. 1: RNA immunoprecipitation (RIP) experiments to explore co-translational interactions in TFIID.
From: Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID
a, Volcano plot of endogenous TAF10 RIP-microarray results. TAF1, TAF8 and TAF10 hits are highlighted. p-values are obtained using the fold change rank ordering statistics method using the fcros R package24. b, RT-qPCR results of the systematic GFP-RIP assay summarized in Fig. 1e. Each GFP-tagged TFIID subunit was used as bait in a GFP-RIP assay from polysome extracts and enrichment for TFIID subunits mRNAs was assessed by RT-qPCR. Data are expressed as mRNA fold enrichment over mock IP. When necessary, the left panel is the zoomed version of the indicated grey-shaded area of the full-range plot (right panels). Data points correspond to biological replicas (N=2). The red dashed line threshold corresponds to 4-fold the enrichment level of the negative control target (PPIB). c, The interaction interface between TAF2/TAF8 as mapped in the TFIID Cryo-EM structure (PDB: 7EGH). The rest of TFIID subunits are not shown for clarity. d, Same as in (c) but for TAF5/TAF6. TAF6 completes the β-propeller blade of TAF5 WD40 domain. e, Western blot analysis validating the enrichment of the targeted subunit in RIP experiments against endogenous TAF6 and TAF7 from HeLa cells polysome extracts (related to Fig. 1f, g).
