TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells

Abstract

PSF (a.k.a. SFPQ) is a ubiquitously expressed, essential nuclear protein with important roles in DNA damage repair and RNA biogenesis. In stimulated T cells, PSF binds to and suppresses the inclusion of CD45 exon 4 in the final mRNA; however, in resting cells, TRAP150 binds PSF and prevents access to the CD45 RNA, though the mechanism for this inhibition has remained unclear. Here, we show that TRAP150 binds a region encompassing the RNA recognition motifs (RRMs) of PSF using a previously uncharacterized, 70 residue region we have termed the PSF-interacting domain (PID). TRAP150's PID directly inhibits the interaction of PSF RRMs with RNA, which is mediated through RRM2. However, interaction of PSF with TRAP150 does not appear to inhibit the dimerization of PSF with other Drosophila Behavior, Human Splicing (DBHS) proteins, which is also dependent on RRM2. Finally, we use RASL-Seq to identify ∼40 T cell splicing events sensitive to PSF knockdown, and show that for the majority of these, PSF's effect is antagonized by TRAP150. Together these data suggest a model in which TRAP150 interacts with dimeric PSF to block access of RNA to RRM2, thereby regulating the activity of PSF toward a broad set of splicing events in T cells.

Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq

“…1d ). All three proteins contain two RNA recognition motif (RRM) domains that confer binding specificity to RNA 17 and a coiled-coil domain that mediates protein aggregation 18 . Sfpq and NonO are multifunctional RNA-binding proteins that can regulate different steps of the mRNA life cycle, including splicing, nuclear localization, and degradation 19 , 20 .…”

“…Because Sfpq aggregates to form polymers on nucleic acids 17 , 18 to facilitate miRNA targeting (Fig. 4f, g ), we hypothesized that the two Sfpq-binding motifs would serve as substrates to promote Sfpq aggregation on target 3′UTRs.…”

The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold

“…A similar scenario is apparent for AR mediated transcription ( 18 , 54 ). A more recent study showed SFPQ displays inhibited RNA binding when in a complex with TRAP150, resulting in altered post-transcriptional processing ( 162 ). From a structural perspective, it is not yet clear how multiple, sometimes simultaneous, protein–protein interactions are mediated by DBHS proteins.…”

Splicing in immune cells—mechanistic insights and emerging topics

“…Paraspeckles contain PSP1 (paraspeckle protein 1), p54/nrb (Nono), the splicing factor SFPQ (PSF) and probably also TDP-43, which associate around the long non-coding RNA (lncRNA) NEAT1 ( 31 , 34 , 35 ), for all of which an association with immune cell function has been described. SFPQ binds to exon 4 of CD45 in stimulated T cells and suppresses its inclusion, which is prevented by the binding of TRAP150 to SFPQ in resting cells ( 36 ). Moreover, ~40 T-cell AS events that were sensitive to SFPQ knockdown could be identified ( 36 ).…”

“…SFPQ binds to exon 4 of CD45 in stimulated T cells and suppresses its inclusion, which is prevented by the binding of TRAP150 to SFPQ in resting cells ( 36 ). Moreover, ~40 T-cell AS events that were sensitive to SFPQ knockdown could be identified ( 36 ). These included splicing of the transcription factor LEF1, LRR1 or the splicing factor PRPF3, which in turn might influence splicing in a re-stimulation-dependent manner ( 36 ).…”