Biology subjects

Fox, A. H.

Publications and source records attributed to Fox, A. H..

4 recordsLinked to original sources

bioRxiv2024

Spatial proteomic mapping of human nuclear bodies reveals new functional insights into RNA regulation

Nuclear bodies are diverse membraneless suborganelles with emerging links to development and disease. Explaining their structure, function, regulation, and implications in human health will require understanding their protein composition; however, isolating nuclear bodies for proteomic analysis remains challenging. We present the first comprehensive proximity proteomics-based map of nuclear bodies, featuring 140 bait proteins (encoded by 119 genes) and 1,816 unique prey proteins. We identified 641 potential nuclear body components, including 131 paraspeckle proteins and 147 nuclear speckle proteins. After validating 31 novel paraspeckle and nuclear speckle components, we discovered regulatory functions for the poorly characterised nuclear speckle- and RNA export-associated proteins PAXBP1, PPIL4, and C19ORF47, and revealed that QKI regulates paraspeckle size. This work provides a systematic framework of nuclear body composition in live cells that will accelerate future research into their organisation and roles in human health and disease.

cell biology↗

bioRxiv2022

Different low-complexity regions of SFPQ play distinct roles in the formation of biomolecular condensates

Demixing of proteins and nucleic acids into condensed liquid phases is rapidly emerging as a ubiquitous mechanism governing the organisation of molecules within the cell. Long disordered low complexity regions (LCRs) are a common feature of proteins that form biomolecular condensates. RNA-binding proteins with prion-like composition have been highlighted as drivers of liquid demixing to form condensates such as nucleoli, paraspeckles and stress granules. Splicing factor proline- and glutamine-rich (SFPQ) is an RNA- and DNA-binding protein essential for DNA repair and paraspeckle formation. Here, we show that the shorter C-terminal LCR of SFPQ is the main region responsible for the condensation of SFPQ in vitro and in the cell. In contrast, we find that, unexpectedly, the longer N-terminal prion-like LCR of SFPQ attenuates condensation, suggesting a more regulatory role in preventing aberrant condensate formation in the cell. Our data add nuance to the emerging understanding of biomolecular condensate formation, by providing the first example of a common multifunctional nucleic acid-binding protein with an extensive prion-like region that serves to regulate rather than drive condensate formation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/518278v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@ed464dorg.highwire.dtl.DTLVardef@1a26fdcorg.highwire.dtl.DTLVardef@15debecorg.highwire.dtl.DTLVardef@12bd4ae_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

RNA binding is essential for NONO condensates to modulate pre-mRNA processing in neuroblastoma

High-risk neuroblastoma patients have poor survival rates and require better therapeutic options. High expression of a multifunctional DNA and RNA binding protein, NONO, in neuroblastoma is associated with poor patient outcome, however there is little understanding of the mechanism of NONO-dependent oncogenic gene regulatory activity in neuroblastoma. Here, we used cell imaging, biophysical and molecular analysis to reveal complex NONO-dependent regulation of gene expression, finding that NONO forms RNA- and DNA-tethered phase-separated condensates throughout the nucleus. CLIP analyses show that NONO mainly binds to the 5 end of pre-mRNAs and modulates pre-mRNA processing, dependent on its RNA binding activity. NONO preferentially regulates super enhancer-associated genes, including HAND2 and GATA2. In the absence of functional NONO-RNA condensates, inefficient pre-mRNA processing at these loci leads to decreased expression of HAND2 and GATA2. Thus, future development of agents that target RNA binding activity of NONO may have therapeutic potential in this cancer context.

cell biology↗

bioRxiv2018

Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing

Oligonucleotides and nucleic acid analogues that alter gene expression are showing therapeutic promise for selected human diseases. The modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, however, such modifications may also confer unexpected physicochemical and biological properties. Here we report backbone-specific effects of modified oligonucleotides on subnuclear organelles, altered distribution of nuclear proteins, the appearance of novel structured nuclear inclusions, and modification of RNA processing in cultured cells transfected with antisense oligonucleotides on a phosphorothioate backbone. Phosphodiester and phosphorodiamidate morpholino oligomers elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of fibroblasts exhibiting such disruption. These data suggest that the toxic effects and adverse events reported after clinical evaluation of phosphorothioate nucleic acid drugs may be mediated, at least in part, by non-specific interaction of nuclear components with the phosphorothioate backbone.

molecular biology↗