TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors [RNA-Seq]

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. To investigate gene expression changes and alternative splicing events of GFP-NLS-TAF2deltaIDR and GFP-TAF2 expressing cells, we performed RNA sequencing (RNA-seq). HeLa Flp-In T-Rex cells harboring a transgene under the control of a doxycycline-inducible promoter were used to express GFP-NLS-TAF2deltaIDR and GFP-TAF2 with 1 ug/mL doxycycline for 17.5 h. Control cells without transgene were also induced with 1 ug/mL doxycycline. The experiment was performed as technical triplicate.