DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer binds DNA (PubMed:25765647). The SFPQ-NONO heteromer may be involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Functions as transcriptional activator (PubMed:25765647). Transcriptional repression is mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional activity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex through histone deacetylation (By similarity). Required for the assembly of nuclear speckles (PubMed:25765647). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). Heterodimer with NONO (PubMed:25765647). Monomer and component of the SFPQ-NONO complex, which is probably a heterotetramer of two 52 kDa (NONO) and two 100 kDa (SFPQ) subunits (PubMed:8439294, PubMed:25765647). The coiled coil domain mediates interaction with NONO, and can also mediate formation of long, linear homooligomers (in vitro) (PubMed:25765647). SFPQ is a component of spliceosome and U5.4/6 snRNP complexes (PubMed:9409622, PubMed:8045264, PubMed:12403470). Interacts with SNRPA/U1A (PubMed:9848648). Component of a snRNP-free complex with SNRPA/U1A (PubMed:9848648). Part of complex consisting of SFPQ, NONO and MATR3 (PubMed:11525732). Interacts with polypyrimidine tract-binding protein 1/PTB (PubMed:10653975). Part of a complex consisting of SFPQ, NONO and NR5A1 (PubMed:11897684). Interacts with RXRA, probably THRA, and SIN3A (PubMed:11259580). Interacts with TOP1 (PubMed:9756848). Part of a complex consisting of SFPQ, NONO and TOP1 (PubMed:9756848). Interacts with SNRNP70 in apoptotic cells (PubMed:11514619). Interacts with PSPC1. Interacts with RNF43 (PubMed:18655028). Interacts with PITX3 and NR4A2/NURR1 (By similarity). Interacts with PTK6 (PubMed:19439179). Interacts with THRAP3; the interaction is dependent on SFPQ phosphorylation at 'Thr-687' and inhibits binding of SFPQ to a ESS1 exonic splicing silencer element-containing RNA (PubMed:20932480). The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. Interacts with PER1 and PER2 (By similarity). Interacts with PQBP1 (PubMed:21933836). Component of a multiprotein complex with NONO and WASL (PubMed:16767080). Interacts with ERCC6 (PubMed:26030138). (Microbial infection) Interacts with M.tuberculosis protein Rv3654c, which probably leads to the cleavage of PSF, diminishes the level of caspase-8 in macrophages and suppresses macrophage apoptosis by blocking the extrinsic pathway. Part of the HDP-RNP complex composed of at least HEXIM1, PRKDC, XRCC5, XRCC6, paraspeckle proteins (SFPQ, NONO, PSPC1, RBM14, and MATR3) and NEAT1 RNA. Predominantly in nuclear matrix. Additional isoforms seem to exist. The coiled coil domain mediates interaction with NONO, and can also mediate formation of long, linear homooligomers (in vitro). The coiled coil domain is required for optimal DNA binding, and optimal transcription activation. The N-terminus is blocked. Phosphorylated on multiple serine and threonine residues during apoptosis. In vitro phosphorylated by PKC. Phosphorylation stimulates binding to DNA and D-loop formation, but inhibits binding to RNA. Phosphorylation of C-terminal tyrosines promotes its cytoplasmic localization, impaired its binding to polypyrimidine RNA and led to cell cycle arrest. In resting T-cells is phosphorylated at Thr-687 by GSK3B which is proposed to promote association with THRAP and to prevent binding to PTPRC/CD45 pre-mRNA; T-cell activation leads to reduced phosphorylation at Thr-687. A chromosomal aberration involving SFPQ may be a cause of papillary renal cell carcinoma (PRCC). Translocation t(X;1)(p11.2;p34) with TFE3. Was originally thought to be myoblast cell surface antigen 24.1D5 and a possible membrane-bound protein ectokinase.