Prediction of protein-RNA interactions from single-cell transcriptomic data

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(6), P. e31 - e31

Published: Feb. 14, 2024

Abstract Proteins are crucial in regulating every aspect of RNA life, yet understanding their interactions with coding and noncoding RNAs remains limited. Experimental studies typically restricted to a small number cell lines limited set RNA-binding proteins (RBPs). Although computational methods based on physico-chemical principles can predict protein-RNA accurately, they often lack the ability consider cell-type-specific gene expression broader context regulatory networks (GRNs). Here, we assess performance several GRN inference algorithms predicting from single-cell transcriptomic data, propose pipeline, called scRAPID (single-cell transcriptomic-based RnA Protein Interaction Detection), that integrates these catRAPID algorithm, which identify direct physical between RBPs molecules. Our approach demonstrates RBP–RNA be predicted performances comparable or superior those achieved for well-established task inferring transcription factor–target interactions. The incorporation significantly enhances accuracy identifying interactions, particularly long RNAs, enables identification hub RNAs. Additionally, show detected inferred targets. software is freely available at https://github.com/tartaglialabIIT/scRAPID.

Language: Английский

---

Liquid − liquid phase separation of tau: Driving forces, regulation, and biological implications

Neurobiology of Disease, Journal Year: 2023, Volume and Issue: 183, P. 106167 - 106167

Published: May 23, 2023

The past 15 years have witnessed an explosion in the studies of biomolecular condensates that are implicated numerous biological processes and play vital roles human health diseases. Recent findings demonstrate microtubule-associated protein tau forms liquid through liquid–liquid phase separation (LLPS) vitro experiments using purified recombinant proteins cell-based experiments. Although vivo lacking, emerged as important assembly state physiological pathological LLPS can regulate function microtubules, mediate stress granule formation, accelerate amyloid aggregation. In this review, we summarize recent advances LLPS, aiming to unveiling delicate interactions driving LLPS. We further discuss association with physiology disease context sophisticated regulation Deciphering mechanisms underlying liquid-to-solid transition enables rational design molecules inhibit or delay formation solid species, thus providing novel targeted therapeutic strategies for tauopathies.

Language: Английский

---

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

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 3, 2024

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

Language: Английский

---

TIA1‐Mediated Stress Granules Promote the Neuroinflammation and Demyelination in Experimental Autoimmune Encephalomyelitis through Upregulating IL‐31RA Signaling

Advanced Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 13, 2025

Abstract The dysfunction of stress granules (SGs) plays a crucial role in the pathogenesis various neurological disorders, with T cell intracellular antigen 1 (TIA1) being key component SGs. However, and mechanism TIA1‐mediated SGs experimental autoimmune encephalomyelitis (EAE) remain unclear. In this study, upregulation TIA1, its translocation from nucleus to cytoplasm, co‐localization G3BP1 (a marker SGs) are observed spinal cord neurons EAE mice. Deletion TIA1 CNS alleviates neuroinflammation, suppresses demyelination axonal damage, reduces neuronal loss Furthermore, alleviation autophagy reduction chronic persistent Tia1 Nestin ‐CKO Mechanistically, IL‐31RA levels decreased mice, which inhibit downstream PI3K/AKT signaling pathway associated IL‐31RA, thereby enhancing suppressing NF‐κB pathway, further alleviating symptoms. Knockdown primary N2a cells treated sodium arsenite also formation These findings reveal an unrecognized promoting neuroinflammation demyelination, offering novel therapeutic targets for MS.

Language: Английский

---

Regulation of stress granule maturation and dynamics by poly(ADP-ribose) interaction with PARP13

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 13, 2025

Non-covalent interactions of poly(ADP-ribose) (PAR) facilitate condensate formation, yet the impact these on properties remains unclear. Here, we demonstrate that PAR-mediated through PARP13, specifically PARP13.2 isoform, are essential for modulating dynamics stress granules—a class cytoplasmic condensates form upon stress, including types frequently observed in cancers. Single amino acid mutations which reduce its PAR-binding activity, lead to formation smaller more numerous granules than wild-type. This fragmented granule phenotype is also apparent PARP13 variants with cancer-associated single-nucleotide polymorphisms (SNPs) disrupt PAR binding. Notably, this conserved across a variety stresses trigger via diverse pathways. Furthermore, mutant diminishes and impedes fusion. Overall, our study uncovers important role PAR-protein maturation, mediated PARP13. Stress granules, cellular structures response, require as multivalent scaffold. authors show disrupting binding alters size, dynamics, despite lacking ADPribosyltransferase activity.

Language: Английский

---

Chirality engineering-regulated liquid–liquid phase separation of stress granules and its role in chemo-sensitization and side effect mitigation

Journal of Colloid and Interface Science, Journal Year: 2025, Volume and Issue: 685, P. 637 - 647

Published: Jan. 22, 2025

Language: Английский

---

Engineering a Novel NIR RNA-Specific Probe for Tracking Stress Granule Dynamics in Living Cells

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 21, 2025

Real-time monitoring of the dynamics cytosolic RNA-protein condensates, termed stress granules (SGs), is vital for understanding their biological roles in response and related disease treatment but challenging due to lack simple accurate methods. Compared with protein visualization that requires complex transfection procedures, direct RNA labeling offers an ideal alternative tracking SG living cells. Here, we propose a novel molecular design strategy construct near-infrared RNA-specific fluorescent probe (HQBT) SGs The positively charged HQBT was designed target negative groove RNA, its binding affinity significantly improved by adjusting position nitrogen atom molecule. Furthermore, additional hydroxyl group introduced achieve emission enhance RNA-binding capability. can rapidly stain within 5 s cells showed performance superior commercial SYTO RNA-Select dye terms photostability selectivity. Importantly, reversible assembly disassembly are successfully visualized using this RNA-selective imaging probe.

Language: Английский

---

Fragile X mental retardation protein modulates translation of proteins with predicted tendencies for liquid-liquid phase separation

Biosystems, Journal Year: 2025, Volume and Issue: unknown, P. 105405 - 105405

Published: Jan. 1, 2025

Language: Английский

---

Dynamic Proximal Interactomics and Chemical Genetic Screening Reveal CCR4-NOT Sequestration in Stress Granules as a Mechanism for Transcript Stabilization

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

ABSTRACT Living cells adapt to stress by protecting essential resources, such as stabilizing transcripts. Stress granules, which form during through the coalescence of polyadenylated transcripts released from polysomes and RNA-binding proteins, are implicated in post-transcriptional regulation, although their precise roles remain contested. To address this, we generated dynamic proteomic landscapes granules assembly disassembly under oxidative hyperosmotic using multi-bait BioID profiling combined with quantitative mass spectrometry. Our analysis reveals rewiring granule proximal interaction networks, identifying proteins involved translation repression mRNA decay, including CCR4-NOT deadenylase complex, universal molecular signatures condensed granules. Using complex a model, demonstrate function components associated Complementary genome-wide chemical genetic screening identified regulators formation. Reduced activity, lengthens poly(A) tails, enhanced assembly, while shortened tails inhibited it. Furthermore, stress-induced sequestration coincided known global tail lengthening. These findings suggest that condensation promotes transcriptome stabilization regulating localization part an adaptive response. This work underscores power integrating proteomics genetics advance our understanding biomolecular condensates diverse biological processes.

Language: Английский

---

Molecular Underpinnings of Plant Stress Granule Dynamics in Response to High-Temperature Stress

New Crops, Journal Year: 2025, Volume and Issue: unknown, P. 100069 - 100069

Published: Feb. 1, 2025

Language: Английский

---