TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors [CUT&RUN]

TFIID is an essential basal transcription factor, crucial for RNA polymerase II (pol II) promoter recognition and transcription initiation. The TFIID complex consists of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs) that contain intrinsically disordered regions (IDRs) with currently unknown functions. Here, we show that a conserved IDR drives TAF2 to nuclear speckle condensates independently of other TFIID subunits. Quantitative mass spectrometry analyses reveal TAF2 proximity to RNA splicing factors including specific interactions of the TAF2 IDR with SRRM2 in nuclear speckles. Deleting the IDR from TAF2 does not majorly impact global gene expression but results in changes of alternative splicing events. Further, genome-wide binding analyses suggest that the TAF2 IDR impedes TAF2 promoter association by guiding TAF2 to nuclear speckles. This study demonstrates that an IDR within the large multiprotein complex TFIID controls nuclear compartmentalization and thus links distinct molecular processes, namely transcription initiation and RNA splicing. Cleavage under targets and release using nuclease (CUT&RUN) and greenCUT&RUN followed by DNA sequencing for TFIID subunits TAF1, TAF2, TAF7, TBP and RNA polymerase II subunit RPB1 (CUT&RUN) and for GFP-TAF2, GFP-NLS-TAF2, GFP-NLS-TAF2delta1009-1199 (2 replicates), GFP-NLS-TAF2delta1142-1171 (2 replicates) (greenCUT&RUN). Each CUT&RUN sample has a respective IgG control sample. Each greenCUT&RUN sample has a respective control sample (-Ca2+). All libraries contain spike-in DNA from Drosophila melanogaster. HeLa Flp-In T-Rex cells harboring a transgene under the control of a doxycycline-inducible promoter were used. Protein expression was induced with 1 ug/mL doxycycline where appropriate.