The ELAV/Hu family represents a crucial group of RNA-binding proteins predominantly expressed in neurons, playing significant roles in mRNA transcription and translation. These proteins bind to AU-rich elements in transcripts to regulate the expression of cytokines, growth factors, and the development and maintenance of neurons. Elav-like RNA-binding proteins exhibit remarkable molecular weight conservation across different species, highlighting their evolutionary conservation. Although these proteins are widely expressed in the nervous system and other cell types, variations in the DNA sequences of the four Elav proteins contribute to their distinct roles in neurological disorders, cancer, and other Diseases . Elavl1, a ubiquitously expressed family member, is integral to processes such as cell growth, ageing, tumorigenesis, and inflammatory diseases. Elavl2, primarily expressed in the nervous and reproductive systems, is critical for central nervous system and retinal development; its dysregulation has been implicated in neurodevelopmental disorders such as autism. Both Elavl3 and Elavl4 are restricted to the nervous system and are involved in neuronal differentiation and excitability. Elavl3 is essential for cerebellar function and has been associated with epilepsy, while Elavl4 is linked to neurodegenerative diseases, including Parkinson's and Alzheimer's diseases. This paper provides a comprehensive review of the ELAV/Hu family's role in nervous system development, neurological disorders, cancer, and other diseases.

The FXR1 protein regulates the stability and translation of a number of RNA molecules and plays an important role in the regulation of cellular processes under normal conditions and stress. In particular, this protein is known to be a negative regulator of the key proinflammatory cytokine TNF alpha. We had previously shown that FXR1 functioned in the amyloid form in neurons of the brain of jawed vertebrates. Under stress conditions, FXR1 is incorporated into stress granules in some cell lines, but such studies have not been conducted for neuronal cells. Here, we showed the ability of the FXR1 protein to form cytoplasmic granules in a neuroblastoma cell line under various types of stress. This protein colocalizes with core proteins of neuronal stress granules upon heat shock and sodium arsenite treatment. We also showed that FXR1 colocalizes with anti-amyloid antibodies OC under both normal and stress conditions. Given that stress granules are dynamic structures, we propose that amyloid FXR1-containing RNP particles interact with other stress granule proteins through weak intermolecular hydrogen bonds. Using a yeast model system, we found that FXR1 colocalizes and physically interacts with stress granule proteins such as TIA-1, FMRP, FXR2, and SFPQ. Overall, our results provide new insights into the role of the RNA-binding protein FXR1 in neuronal stress response. We believe that FXR1 inactivation in neuronal stress granules can contribute to an increase in the level of the proinflammatory cytokine TNF alpha in neurodegenerative diseases.

RNA-binding proteins (RBPs) have emerged as critical regulators of cancer progression, influencing virtually all hallmarks of cancer. Their ability to modulate gene expression patterns that promote or inhibit tumorigenesis has positioned RBPs as promising targets for novel anti-cancer therapies. This mini-review summarizes the current state of RBP-targeted cancer treatments, focusing on five examples, eIF4F, FTO, SF3B1, RBM39 and nucleolin. We highlight the diversity of current targeting approaches and discuss ongoing challenges including the complexity of RBP regulatory networks, potential off-target effects and the need for more specific targeting methods. By assessing the future potential of novel therapeutic avenues, we provide insights into the evolving landscape of cancer treatment and the critical role RBPs may play in next-generation therapeutics.

RNA-binding proteins (RBPs) act as crucial regulators of gene expression within cells, exerting precise control over processes such as RNA splicing, transport, localization, stability, and translation through their specific binding to RNA molecules. The diversity and complexity of RBPs are particularly significant in cancer biology, as they directly impact a multitude of RNA metabolic events closely associated with tumor initiation and progression. The fragile X mental retardation protein (FMRP), as a member of the RBP family, is central to the neurodevelopmental disorder fragile X syndrome and increasingly recognized in the modulation of cancer biology through its influence on RNA metabolism. The protein's versatility, stemming from its diverse RNA-binding domains, enables it to govern a wide array of transcript processing events. Modifications in FMRP's expression or localization have been associated with the regulation of mRNAs linked to various processes pertinent to cancer, including tumor proliferation, metastasis, epithelial-mesenchymal transition, cellular senescence, chemotherapy/radiotherapy resistance, and immunotherapy evasion. In this review, we emphasize recent findings and analyses that suggest contrasting functions of this protein family in tumorigenesis. Our knowledge of the proteins that are regulated by FMRP is rapidly growing, and this has led to the identification of multiple targets for therapeutic intervention of cancer, some of which have already moved into clinical trials or clinical practice.

A significant proportion of neurodevelopmental disorders (NDDs) are caused by gain-of-function (GOF) or loss-of-function (LOF) of specific genes. Strategies to normalize disease gene expression offer therapeutic potential for these disorders. The success and approval of RNA-based therapeutics for various disorders have led to a surge in RNA-based therapeutic research for NDDs with antisense oligonucleotides leading the field. This review discusses recent advances in therapeutic strategies that target pre-mRNA or mRNA for GOF and LOF NDDs that have promising preclinical evidence. These developments highlight important considerations and exciting future avenues for the development of therapies for NDDs.

The structural plasticity of proteins at the molecular level is largely dictated by backbone torsion angles, which play a critical role in ligand recognition and binding. To establish the anion-induced cooperative arrangement of the main-chain (mc) torsion, herein, we analyzed a set of naturally occurring CαNN motifs as "static models" for their anion-binding competence through docking and molecular dynamics simulations and decoded its torsion angle influenced mc-driven anion recognition potential. By comparing a pool of 20 distinct sets of CαNN motif with identical sequences in their "anion bound/present, aP" and "anion free/absent, aA" versions, we could discern that there exists a positive correlation between the "difference of anion residence time (ΔRT)" and "difference among the main-chain torsion angle" of the aP and aA population. Notably, the anion interaction with CαNNs is locally energetically favorable even in a context-free non-proteinaceous environment and if the difference of the mc-torsion angles involving the Cα-1, N0, N1 residues for a population is higher between the aP and aA state, the difference among the ligand RT is also greater. At the atomistic level, the accommodation of anion is highly synergistic and cooperatively sways the interacting mc-atom torsions. By comparing the clustering of H-bonding patterns, the free energy of binding, and RT in both states, we provide evidence that to establish favorable thermodynamics and kinetics of ligand accommodation in these short structural motifs, proper reorientation of local-mc governed by torsions is a prerequisite. Our findings position the CαNN motif as a promising scaffold for peptidomimetic design and emphasize the critical role of loop region dynamics in protein structure-function relationships.

As important types of noncoding RNAs, long noncoding RNAs (lncRNAs) have been found to be involved in the progression of various cancers. Accumulating evidence indicates that LINC02154 plays a critical role in cancer progression, but the underlying mechanisms regulating esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we found that LINC02154 is significantly upregulated in ESCC cell lines and ESCC tissues. LINC02154 knockdown significantly inhibited the proliferation and migration of ESCC cells in vitro and suppressed the progression of ESCC in vivo. Mechanistically, LINC02154 can bind to IGF2BP2 and activate the PI3K-AKT-mTOR signaling pathway. High expression of LINC02154 is positively correlated with poor prognosis in ESCC patients. In conclusion, LINC02154 functions as an oncogenic factor to facilitate ESCC progression through the IG2BP2-PI3K-AKT-mTOR pathway and has the potential to be a promising diagnostic marker and therapeutic target for ESCC patients.

RNA-binding proteins (RBPs) are important regulators in RNA metabolism and gene expression in eukaryotes. Emerging studies support that RBPs play important roles in human development, metabolism and various diseases. However, the function of fungal RBPs is less identified and understood. The present study identifies an RBP FgNam8 which is U1 auxiliary component nuclear accommodation of mitochondria 8 (Nam8). The FgNam8 contains three RNA recognition motifs (RRM) and localizes to the cytoplasm and nucleus in F. graminearum. The ΔFgNam8 is reduced in vegetative growth and production of conidia. RNA-seq analyses show multiple RNA-associated biological processes and secondary metabolite biosynthesis pathways are altered in the ΔFgNam8. Furthermore, ΔFgNam8 is significantly reduced in deoxynivalenol (DON) production and virulence. More importantly, we verify the NDR (nuclear Dbf2-related) protein kinase FgCot1 interacts with FgNam8. Taken together, our results indicate that FgNam8 is important for the vegetative development, conidia production, DON production and virulence of F. graminearum, which may help to provide a candidate target for the treatment of Fusarium disease.

Ovarian cancer has the highest mortality rate among gynecologic tumors worldwide, with unclear underlying mechanisms of pathogenesis. RNA-binding proteins (RBPs) primarily direct post-transcriptional regulation through modulating RNA metabolism. Recent evidence demonstrates that RBPs are also implicated in transcriptional control. However, the role and mechanism of RBP-mediated transcriptional regulation in tumorigenesis remain largely unexplored. Here, we show that the RBP heterogeneous ribonucleoprotein L (hnRNPL) interacts with chromatin and regulates gene transcription by forming phase-separated condensates in ovarian cancer. hnRNPL phase separation activates PIK3CB transcription and glycolysis, thus promoting ovarian cancer progression. Notably, we observe that the PIK3CB promoter is transcribed to produce a non-coding RNA which interacts with hnRNPL and promotes hnRNPL condensation. Furthermore, hnRNPL is significantly amplified in ovarian cancer, and its high expression predicts poor prognosis for ovarian cancer patients. By using cell-derived xenograft and patient-derived organoid models, we show that hnRNPL knockdown suppresses ovarian tumorigenesis. Together, our study reveals that phase separation of the chromatin-associated RBP hnRNPL promotes PIK3CB transcription and glycolysis to facilitate tumorigenesis in ovarian cancer. The formed hnRNPL-PIK3CB-AKT axis depending on phase separation can serve as a potential therapeutic target for ovarian cancer.

Emerging evidence suggests that dysregulated RNA-binding proteins (RBPs) are associated with a wide variety of cancers. However, the exact roles and pathways of RBPs in the tumorigenesis of hepatocellular carcinoma (HCC), the most common subtype of liver cancer, remain largely unknown. Here, we systematically searched for altered RBP candidates in HCC through multi-omics data integrative analyses and identified that GPATCH4 gene is amplified in >70% HCC patients and its high expression predicts poor prognosis. We mapped the in vivo RNA binding sites of GPATCH4 by iCLIP-seq and characterized that GPATCH4 primarily bound ribosomal RNA (rRNAs). GPATCH4 promoted HCC cell proliferation and transformation both in vitro and in vivo through increasing rRNA transcription and global protein synthesis. GPATCH4 is mainly localized in the nucleolus and helps to unwind RNA loops formed at the rDNA through interacting with DDX21 via its C-terminal intrinsically disordered region. Removal of accumulated R-loops induced by GPATCH4 depletion rescued decreased rRNA transcription and cell proliferation. Taken together, we characterized the understudied GPATCH4 as an RBP with oncogenic function in HCC and revealed a new mechanism by which GPATCH4 functions as a regulator of nucleolar R-loops to control rRNA transcription through interacting with DDX21.

The coronavirus disease 2019 (COVID-19) pandemic has been linked to long-term neurological effects with multifaceted complications of neurodegenerative diseases. Several studies have found that pathological changes in transactive response DNA-binding protein of 43 kDa (TDP-43) are involved in these cases. This review explores the causal interactions between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and TDP-43 from multiple perspectives. Some viral proteins of SARS-CoV-2 have been shown to induce pathological changes in TDP-43 through its cleavage, aggregation, and mislocalization. SARS-CoV-2 infection can cause liquid-liquid phase separation and stress granule formation, which accelerate the condensation of TDP-43, resulting in host RNA metabolism disruption. TDP-43 has been proposed to interact with SARS-CoV-2 RNA, though its role in viral replication remains to be fully elucidated. This interaction potentially facilitates viral replication, while viral-induced oxidative stress and protease activity accelerate TDP-43 pathology. Evidence from both clinical and experimental studies indicates that SARS-CoV-2 infection may contribute to long-term neurological sequelae, including amyotrophic lateral sclerosis-like and frontotemporal dementia-like features, as well as increased phosphorylated TDP-43 deposition in the central nervous system. Biomarker studies further support the link between TDP-43 dysregulation and neurological complications of long-term effects of COVID-19 (long COVID). In this review, we presented a novel integrative framework of TDP-43 pathology, bridging a gap between SARS-CoV-2 infection and mechanisms of neurodegeneration. These findings underscore the need for further research to clarify the TDP-43-related neurodegeneration underlying SARS-CoV-2 infection and to develop therapeutic strategies aimed at mitigating long-term neurological effects in patients with long COVID.

The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR suffices to confer temporal dynamics to translation initiation and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, Danio Optimus 5-Prime (DaniO5P), identified a combined role for 5' UTR length, translation initiation site context, upstream AUGs, and sequence motifs on ribosome recruitment. DaniO5P predicts the activities of maternal and zygotic 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in development and lays the foundation for identifying the underlying molecular effectors.

Temozolomide (TMZ) is used in the treatment of glioblastoma (GBM). However, the primary obstacle remains the emergence of TMZ chemotherapy resistance. Non-POU domain-containing octamer-binding protein (NONO) and splicing factor proline/glutamine rich (SFPQ) are multifunctional nuclear proteins involved in genome stability and gene regulation. However, the specific role of NONO and SFPQ in TMZ resistance of GBM remains to be explored.

RNA-binding protein immunoprecipitation-microarray and RNA microarray of TMZ-resistant and parental cells were performed for the gain of HSD52. The effects of HSD52 on TMZ resistance were investigated through in vitro assays, intracranial xenograft, and GBM organoid models. The underlying mechanisms were explored by DNA methylation chip, RNA immunoprecipitation, RNA pull-down assays, among others. GBM clinical samples were rolled in to investigate the clinical significance of HSD52.

We identified a novel noncoding RNA, HSD52, that was highly expressed in TMZ-resistant GBM and facilitated the interaction between NONO and SFPQ. H3 ubiquitination attenuation and reduced DNA methyltransferase 1 (DNMT1) recruitment increased HSD52 transcription via DNA hypo-methylation. HSD52 formed an RNA duplex with UFM1 specific ligase 1 (UFL1) mRNA, thereby promoting NONO/SFPQ complex binding to UFL1 mRNA and enhancing its stability, and then contributed to TMZ resistance through activating the ataxia telangiectasia mutated signaling pathway. In vivo xenograft and GBM organoid models showed significant repression in tumor growth after HSD52 knockout with TMZ treatment. In GBM clinical samples, HSD52 was responsible for the malignant progression and TMZ resistance.

Our results revealed that HSD52 could serve as a promising therapeutic target to overcome TMZ resistance, improving the clinical efficacy of TMZ chemotherapy in GBM.

The oral periodontal pathogen Porphyromonas gingivalis must adapt to an ever-changing environment to survive and cause disease. So far, most of the efforts concerning the regulatory mechanisms employed by the bacterium centered on DNA-binding regulators. Although global regulatory mechanisms employing RNA-binding proteins (RBP) are reported in most forms of life so far, such mechanism of regulation remains unknown in the oral Bacteroidetes group. Examination of the genome of P. gingivalis led to the discovery of a putative RBP with the RNA recognition motif 1 (RRM-1) designated here RbpPg1 (RNA-binding protein Porphyromonas gingivalis 1). The recombinant form of the protein-bound RNA and RNA-pull down identified a zinc exporter transcript as the most enriched one in agreement with the higher levels of zinc in the absence of the protein. Deletion of RbpPg1 reduced the ability of the bacterium to grow with 0.5 mM zinc. The RgpB protein level and the Arg-X protease activity was reduced in both iron replete and iron deplete conditions in the mutant strain when compared to the wild type. Lys-X protease activity was reduced, although Kgp protein levels were not altered by deletion of RbpPg1. The mutant grew better in hemin-deplete conditions when compared to the wild type. Finally, RbpPg1 was indispensable for the bacterium to survive with host cells. We have determined that both the transcriptome and proteome are affected by the deletion of RbpPg1 and found that the major group of proteins with elevated expression were the ones associated with response to environmental stress changes, while proteins mediating metabolic processes were downregulated. Overall, the first RBP characterized in P. gingivalis plays a significant role in the biology of the bacterium and differs from RBPs in other Gram-negative bacteria. Data are available via ProteomeXchange with identifier PXD034144 and via the NCBI Gene Expression Omnibus (GEO) and under accession number GSE168570.

In a human cell, DNA is packed with histones, RNA, and chromatin-associated proteins, forming a cohesive gel. At any given moment, only a subset of the proteome has physical access to the DNA and organizes its structure, transcription, replication, repair, and other essential molecular functions. We have developed a "zero-distance" photo-crosslinking approach to quantify proteins in direct contact with DNA in living cells. Collecting DNA interactomes from human breast cancer cells, we present an atlas of over one thousand proteins with physical access to DNA and hundreds of peptide-nucleotide crosslinks pinpointing protein-DNA interfaces with single-amino-acid resolution. Quantitative comparisons of DNA interactomes from differentially treated cells recapitulate the recruitment of key transcription factors as well as DNA repair proteins and uncover fast-acting restrictors of chromatin accessibility on a timescale of minutes. This opens a direct way to explore genomic regulation in a hypothesis-free manner, applicable to many organisms and systems.

Iron responsive element (IREs) mRNA and iron regulatory proteins (IRPs) regulate iron homeostasis. 5'-untranslated region motifs of APP IREs fold into RNA stem loops bind to IRP to control translation. Through the 5'-UTR APP IREs, iron overload accelerated the translation of the Alzheimer's amyloid precursor protein (APP). The protein synthesis activator eIF4F and the protein synthesis repressor IRP1 are the two types of proteins that IREs bind. Iron regulates the competitive binding of eIF4F and IRP1 to IRE. Iron causes the IRE and eIF4F to associate with one other, causing the dissociation of IRPs and altered translation. In order to control IRE-modulated expression of APP, messenger RNAs are becoming attractive targets for the development of small molecule therapeutics. Many mRNA interference strategies target the 2-D RNA structure, but messenger RNAs like rRNAs and tRNAs can fold into complicated, three-dimensional structures that add another level of complexity. IREs family is one of the few known 3-D mRNA regulatory elements. In this review, I present IREs structural and functional characteristics. For iron metabolism, the mRNAs encoding the proteins are controlled by this family of similar base sequences. Iron has a similar way of controlling the expression of Alzheimer's APP as ferritin IRE RNA in their 5ÚTR. Further, iron mis regulation by IRPs can be investigated and contrasted using measurements of expression levels of APP, amyloid-β and tau formation. Accordingly, IRE-modulated APP expression in Alzheimer's disease has great therapeutic potential through targeting mRNA structures.

Dephosphorylation of spliceosome components is an essential regulatory step for intron removal from pre-mRNA, thereby controlling gene expression. However, the specific phosphatase responsible for this dephosphorylation step has not been identified. Here, we show that Arabidopsis thaliana (Arabidopsis) PROTEIN PHOSPHATASE 2A B'η (PP2A B'η), a B subunit of PP2A, interacts with the splicing factors PRP18a, PRP16, and RH2 and facilitates their dephosphorylation by recognizing substrates through a conserved binding motif. This dephosphorylation is crucial for proper splicing of retained introns in heat stress-responsive genes, which is mediated by the PP2A interactor PRE-MRNA PROCESSING FACTOR 18a. Genetic inactivation of PP2A B'η abolished thermotolerance during seed germination and resulted in widespread intron retention in heat stress-responsive genes. Conversely, overexpression of PP2A B'η conferred enhanced thermotolerance, accompanied by the efficient removal of retained introns under heat stress. We demonstrate that a B regulatory subunit of PP2A plays a central role in dephosphorylating spliceosome components, regulating alternative splicing, facilitating acclimation to heat stress, and targeting specific spliceosome subunits that activate pre-mRNA splicing.

Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer and is responsible for about 467,000 cancer deaths annually. An oftentimes asymptomatic early phase of this disease results in a delayed diagnosis, and patients often present with advanced disease. Current treatment options have limited survival benefits, and only a minor patient population carries actionable genomic alterations. Hence, innovative personalized treatment strategies that consider molecular, cellular and functional analyses are urgently needed for pancreatic cancer patients. However, the majority of the genetic alterations found in PDAC are currently undruggable, or patients' response is not as expected. Therefore, non-genomic biomarkers and alternative molecular targets should be considered in order to advance the clinical management of PDAC patients. In line with this, recent gene expression and single-cell transcriptome analyses have identified molecular subtypes and transcriptional cell states that affect disease progression and drug efficiency. In this review, we will introduce long non-coding RNAs (lncRNAs) as well as RNA-binding proteins (RBPs) that are able to modulate the transcriptome of a cell through diverse mechanisms, thereby contributing to disease progression. We will provide a brief overview about the general functions of lncRNAs and RBPs, respectively. Subsequently, we will highlight selected lncRNAs and RBPs that have been shown to play a role in PDAC development, progression and drug response. Finally, we will present strategies aiming to interfere with the expression and function of lncRNAs and RBPs.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects nearly 3% of children and has a strong genetic component. While hundreds of ASD risk genes have been identified through sequencing studies, the genetic heterogeneity of ASD makes identifying additional risk genes using these methods challenging. To predict candidate ASD risk genes, we developed a simple machine learning model, ASiDentify (ASiD), using human genomic, RNA- and protein-based features. ASiD identified over 1,300 candidate ASD risk genes, over 300 of which have not been previously predicted. ASiD made accurate predictions of ASD risk genes using 6 features predictive of ASD risk gene status, including mutational constraint, synapse localization and gene expression in neurons, astrocytes and non-brain tissues. Particular functional groups of proteins found to be strongly implicated in ASD include RNA-binding proteins (RBPs) and chromatin regulators. We constructed additional logistic regression models to make predictions and assess informative features specific to RBPs, including mutational constraint, or chromatin regulators, for which both expression level in excitatory neurons and mutational constraint were informative. The fact that RBPs and chromatin regulators had informative features distinct from all protein-coding genes suggests that specific biological pathways connect risk genes with different molecular functions to ASD.

Metastasis is the leading cause of recurrence and mortality in triple-negative breast cancer (TNBC), an aggressive subtype that predominantly spreads to the lungs, brain, bones, and liver, with lung metastasis being particularly prevalent. Despite the clinical significance of TNBC metastasis, the molecular mechanisms that drive lung-specific metastasis remain poorly understood. RNA-binding proteins (RBPs) are crucial regulators of post-transcriptional gene expression and are frequently dysregulated in cancers. This study identifies SORBS2 as a critical RBP implicated in TNBC lung metastasis. Using RNA sequencing (RNA-seq) and LACE-seq, we demonstrate that SORBS2 regulates a specific set of genes through direct binding to coding sequences (CDS), introns, and 3' untranslated regions (UTRs), and its binding targets are linked to various pathways, including a possible association with Wnt/β-catenin signaling, among others. Functional assays confirm that SORBS2 knockdown inhibits proliferation, migration, and invasion in TNBC cells. These findings highlight SORBS2 as a key regulator of TNBC lung metastasis, with a context-dependent role that promotes metastatic behavior in highly metastatic TNBC cells, providing potential avenues for novel therapeutic strategies.

Long interspersed nuclear element-1 (LINE-1) is an autonomous retrotransposon that makes up a substantial portion of the human genome, contributing to genetic diversity and genome evolution. LINE-1 encodes two proteins, ORF1p and ORF2p, both essential for successful retrotransposition. ORF2p has endonuclease and reverse transcription activity, while ORF1p binds RNA. Many copies of ORF1p assemble onto the LINE-1 RNA to form a ribonucleoprotein (RNP) condensate. However, the function of these condensates in the LINE-1 life cycle remains unclear. Using reconstitution assays on DNA curtains, we show that L1 RNP condensates gain DNA binding activity only when RNA is super-saturated with ORF1p. In cells, L1 RNP condensates bind to chromosomes during mitosis. Mutational analysis reveals that DNA binding is crucial for nuclear entry and LINE-1 retrotransposition activity. Thus, a key function of ORF1p is to form an RNP condensate that gains access to the genome through DNA binding upon nuclear envelope breakdown.

RNA-binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport and translation1-3. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease1,4,5; however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. Here, to address this, non-isotopic ligation-based ultraviolet-light-induced cross-linking and immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, revealing patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodelling in response to epidermal growth factor (EGF), revealing that EGF-induced recruitment of UPF1 adjacent to HNRNPC promotes splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships observed in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.

To explore the role of long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A) in posterior capsule opacification (PCO) and their underlying mechanisms.

The localization of lncRNAs and proteins was analyzed using fluorescence in situ hybridization and immunofluorescence staining. RNA m6A quantification, RNA immunoprecipitation, co-immunoprecipitation, MeRIP-seq, MeRIP-qPCR, western blotting, wound healing, and Transwell assays were applied to elucidate the underlying mechanisms.

The levels of lncRNA HOX transcript antisense intergenic RNA (HOTAIR) and m6A methylation increased significantly during epithelial-mesenchymal transition (EMT) in lens epithelial cells (LECs). HOTAIR promoted EMT and m6A methyltransferase activity but had no effect on methyltransferase activity and was not modified by m6A. Nevertheless, HOTAIR interacted with WT1-associated protein (WTAP), a key m6A writer protein, facilitating WTAP-mediated recruitment of METTL3-METTL14 heterodimers and enhancing m6A modification. The HOTAIR/WTAP complex elevated m6A levels, thrombospondin 1 (THBS1) expression, and EMT in LECs.

LncRNA HOTAIR enhances the assembly of the WTAP/METTL3/METTL14 complex and promotes EMT in LECs by upregulating m6A modification and THBS1 expression. Targeting the HOTAIR/WTAP/THBS1 pathway may prevent or treat PCO.

Much of our understanding of RNA-protein interactions, and how these interactions shape gene expression and cell state, have come from studies looking at these interactions in vitro or inside the cell. However, recent data demonstrates the presence of extracellular and cell surface-associated RNA such as glycosylated RNA (glycoRNA), suggesting an entirely new environment and cellular topology in which to study RNA-RNA binding protein (RBP) interactions. Here, we explore emerging ideas regarding the landscape of cell surface RNA and RBPs. We also discuss open questions concerning the trafficking and anchoring of RBPs to the cell surface, whether cell surface RBPs (csRBPs) directly interact with cell surface RNA, and how changes in the presentation of csRBPs may drive autoimmune responses.

RNA-binding proteins (RBPs) are a diverse class of proteins that interact with their target RNA molecules to regulate gene expression at the transcriptional and post-transcriptional levels. RBPs contribute to almost all aspects of RNA processing with sequence-specific, structure-specific, and nonspecific binding modes. Advances in our understanding of the mechanisms of RBP-mediated regulatory networks consisting of DNAs, RNAs, and protein complexes and the association between these networks and human diseases have been made very recently. Here, we discuss the "unconventional" functions of RBPs in transcriptional regulation by focusing on the cutting-edge investigations of chromatin-associated RBPs (ChRBPs). We briefly introduce examples of how ChRBPs influence the genomic features and molecular structures at the level of transcription. In addition, we focus on the post-transcriptional functions of various RBPs that regulate the biogenesis, transportation, stability control, and translation ability of circular RNA molecules (circRNAs). Lastly, we raise several questions about the clinical significance and potential therapeutic utility of disease-relevant RBPs.

Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) is an oncofetal protein, is strongly associated with tumor initiation and progression due to its upregulation. However, the regulatory mechanisms driving IGF2BP3 upregulation and its contribution to the development and progression in hepatocellular carcinoma (HCC) remain unclear. In this study, we demonstrated that IGF2BP3 is re-expressed in HCC mouse models, with elevated levels correlating with a poor prognosis in patients with HCC. Our data revealed that histone acetylation at the IGF2BP3 promoter region drives transcription activation of IGF2BP3 in primary hepatocytes. Notably, histone acetylation and transcriptional reactivation of IGF2BP3 were observed in human HCC tissues as well. Mechanistically, IGF2BP3 knockdown modulated the cell cycle and cell proliferation by limiting G1/S phase transition, which is dependent on cyclin D1. We further showed that IGF2BP3 maintains CCND1 mRNA stability by directly interacting with its 3'UTR. Importantly, IGF2BP3 recruits the RNA stabilizer PABPC1 to potentiate CCND1 mRNA stability. These two proteins synergistically protect CCND1 mRNA from degradation. Furthermore, IGF2BP3-depleted HCC cells were unable to form tumors in the xenograft model. High IGF2BP3 and CCND1 levels predicted poor outcomes in patients. Collectively, our findings highlight the pivotal role of the IGF2BP3/cyclin D1 axis and reveal a new regulatory mechanism for IGF2BP3 re-expression via transcriptional activation during hepatocarcinogenesis. These results indicate that the IGF2BP3/CCND1 axis is a promising prognostic biomarker and potential therapeutic target for HCC.

RNA-binding proteins (RBPs) have emerged as key players in posttranscriptional gene regulation, yet their full scale role in fruit ripening remains to be fully elucidated. However, due to the complex structure and composition of fruit tissue, exploring RBPs in fruits still faces many challenges. Here, we optimized the plant phase extraction method and successfully applied it to tomato fruits for the unbiased excavation of RBPs in fruits, this method were named as "plant phase extraction in tomato fruit" (termed tfPPE). We yielded a comprehensive candidate RNA-binding proteome (RBPome) composed of 230 proteins and disclosed that approximately 66% of them were unconventional RBPs. Validation of the RNA-binding activities of six candidate RBPs unveiled that metabolic enzymes function as moonlighting RBPs. Furthermore, combined with transcriptome analysis, we identified 41 candidate RBPs associated with fruit ripening. Remarkably, we proposed that SlER21 and SlFER1 play significant roles in fruit coloring and ripening process. Taken together, these results demonstrate that tfPPE was an impactful approach for unbiased excavation RBPs in fruits and pave the way for investigating RBP functions in fruit-ripening regulatory network.

Despite the prevalence of non-small cell lung cancer (NSCLC) is high, the limited early detection and management of these tumors are restricted since there is an absence of reliable and precise diagnostic biomarkers and therapeutic targets. Exosomes transport functional molecules for facilitating intercellular communication, especially in the tumor microenvironment, indicating their potential as cancer biomarkers and therapeutic targets. Circular RNA (circRNA), a type of non-coding RNA possessing a covalently closed loop structure, substantial abundance, and tissue-specific expression patterns, is stably enriched in exosomes. In recent years, significant breakthroughs have been made in research on exosomal circRNA in NSCLC. This review briefly introduces the biogenesis, characterizations, and functions of circRNAs and exosomes, and systematically describes the biological functions and mechanisms of exosomal circRNAs in NSCLC. In addition, this study summarizes their role in the progression of NSCLC and discusses their clinical significance as biomarkers and therapeutic targets for NSCLC.

Intrinsically disordered regions within proteins drive specific molecular functions despite lacking a defined structure1,2. Although disordered regions are integral to controlling mRNA stability and translation, the mechanisms underlying these regulatory effects remain unclear3. Here we reveal the molecular determinants of this activity using high-throughput functional profiling. Systematic mutagenesis across hundreds of regulatory disordered elements, combined with machine learning, reveals a complex pattern of molecular features important for their activity. The presence and arrangement of aromatic residues strongly predicts the ability of seemingly diverse protein sequences to influence mRNA stability and translation. We further show how many of these regulatory elements exert their effects by engaging core mRNA decay machinery. Our results define molecular features and biochemical pathways that explain how disordered regions control mRNA expression and shed light on broader principles within functional, unstructured proteins.

RNA-binding proteins (RBPs) are essential regulators of cellular RNA processes, including RNA stability, translation, and post-translational regulation. During viral infections, RBPs are key regulators of the viral cycle due to their interaction with both host and viral RNAs. Herein, we initially explore the roles of specific RBP families, namely heterogeneous nuclear ribonucleoproteins (hnRNPs), DEAD-box helicases, human antigen R (HuR), and the eukaryotic initiation factors of the eIF4F complex, in viral RNA replication, translation, and assembly. Next, we examine the potential of these RBPs as host-targeting antivirals against pandemic-prone RNA viruses that have been gaining momentum in recent years. Targeting RBPs could disrupt cellular homeostasis, leading to unintended effects on host cells; however, RBPs have been successfully targeted mainly in anticancer therapies, showcasing that their modulation can be safely achieved by drug repurposing. By disrupting key viral-RBP interactions or modulating RBP functions, such therapeutic interventions aim to inhibit viral propagation and restore normal host processes. Thus, conceivable benefits of targeting RBPs as alternative antiviral strategies include their broad-spectrum activity and potential for combination therapies with conventional antivirals, reduced or delayed resistance development, and concomitant enhancement of host immune responses. Our discussion also highlights the broader implications of leveraging host-directed therapies in an attempt to overcome viral resistance. Finally, we emphasise the need for continued innovation to refine these strategies for broad-spectrum antiviral applications.

Thyroid cancer, a prevalent endocrine malignancy, has an age-standardized incidence rate of 9.1 per 100,000 people and a mortality rate of 0.44 per 100,000 as of 2024. Despite significant advances in precision oncology driven by large-scale international consortia, gaps persist in understanding the genomic landscape of thyroid cancer and its impact on therapeutic efficacy across diverse populations.

To address this gap, we performed comprehensive data mining and in silico analyses to identify pathogenic variants in thyroid cancer driver genes, calculate allele frequencies, and assess deleteriousness scores across global populations, including African, Amish, Ashkenazi Jewish, East and South Asian, Finnish and non-Finnish European, Latino, and Middle Eastern groups. Additionally, pharmacogenomic profiling, in silico drug prescription, and clinical trial data were analyzed to prioritize targeted therapeutic strategies.

Our analysis examined 56,622 variants in 40 thyroid cancer-driver genes across 76,156 human genomes, identifying 5,001 known and predicted oncogenic variants. Enrichment analysis revealed critical pathways such as MAPK, PI3K-AKT-mTOR, and p53 signaling, underscoring their roles in thyroid cancer pathogenesis. High-throughput validation strategies confirmed actionable genomic alterations in RET, BRAF, NRAS, KRAS, and EPHA7. Ligandability assessments identified these proteins as promising therapeutic targets. Furthermore, our findings highlight the clinical potential of targeted drug inhibitors, including vandetanib, dabrafenib, and selumetinib, for improving treatment outcomes.

This study underscores the significance of integrating genomic insights with pharmacogenomic strategies to address disparities in thyroid cancer treatment. The identification of population-specific oncogenic variants and actionable therapeutic targets provides a foundation for advancing precision oncology. Future efforts should focus on including underrepresented populations, developing population-specific prevention strategies, and fostering global collaboration to ensure equitable access to pharmacogenomic testing and innovative therapies. These initiatives have the potential to transform thyroid cancer care and align with the broader goals of personalized medicine.

Osteosarcoma (OS) is a rapidly progressive primary malignant bone tumor that occurs in children and adolescents aged between 15 and 19 years and adults aged over 60 years. As alternative splicing (AS) changes caused by abnormal splicing factors contribute to tumor progression, gene expression and AS analyses were performed on 44 osteosarcoma patients to create a genome-wide co-expression network of RNA-binding proteins (RBPs), AS events, and AS genes. A gain- or loss-of-function osteosarcoma cell model was established, and an interactive network analysis and enrichment analysis were performed. Karyopherin Subunit Alpha 2 (KPNA2) negatively correlated with patient survival. KPNA2 transports splicing factor Y-box Binding Protein 1 (YBX1) into the nucleus and YBX1 accelerates the degradation of the ATP-dependent RNA helicase DDX3X (DDX3X) through the nonsense-mediated decay (NMD) pathway to promote intron retention of the DDX3X gene, thus reducing DDX3X protein levels. KPNA2/YBX1 axis regulates the stability of DDX3X mRNA and cell cycle progression. KPNA2/YBX1/DDX3X axis might be potential targets for inhibiting disease progression and improving OS patient survival. It integrates AS control of DDX3X into the progression of OS and represents a potential prognostic biomarker and therapeutic target for OS therapy.

Clearance of circulating plasma LDL (low-density lipoprotein) cholesterol by the liver requires hepatic LDLR (low-density lipoprotein receptor). Complete absence of functional LDLR manifests in severe hypercholesterolemia and premature atherosclerotic cardiovascular disease. Since the discovery of the LDLR 50 years ago by Brown and Goldstein, all approved lipid-lowering medications have been aimed at increasing the abundance and availability of LDLR on the surface of hepatocytes to promote the removal of LDL particles from the circulation. As such a critical regulator of circulating and cellular cholesterol, it is not surprising that LDLR activity is tightly regulated. Despite over half a century's worth of study, there are still many facets of LDLR biology that remain unexplored. This review will focus on pathways that regulate the LDLR and emerging concepts of LDLR biology.

RNA-binding proteins (RBPs) play a crucial role in RNA metabolism, influencing processes like transcription, splicing, transport, and stability, as well as cell proliferation and immune responses. Their links to diseases, such as cancer and neurological disorders, make them prime candidates for therapeutic targeting. Among these, heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) is notable for its regulation of gene expression and involvement in telomere maintenance and DNA repair. Its activity in various cancers and neurodegenerative diseases positions it as a promising target for drug development. The quartz crystal microbalance (QCM) method offers an efficient alternative to traditional binding affinity assessments such as spectroscopy, allowing experiments with minimal reagents and without extensive modifications. A key to effective QCM analysis is immobilization of the target protein to prevent denaturation. This study outlines a strategy for immobilizing hnRNPA2B1 onto a gold electrode using a polyethylenimine (PEI) layer. Adsorption processes and stability were monitored via frequency shift (Δf/n) and dissipation change (ΔD/n) measurements. The results showed that hnRNPA2B1's adsorption on branched PEI resulted in weak binding interactions, while adsorption on a linear PEI layer led to a negative frequency shift of -21 Hz. Increasing the ionic strength to 0.1 mM significantly enhanced protein adsorption (Δf/n = -69 Hz). These findings emphasize the role of the PEI layer structure in optimizing protein immobilization, paving the way for further exploration of RBPs and their ligands.

Perturbation of mRNA splicing is commonly observed in human cancers and plays a role in various aspects of cancer hallmarks. Understanding the mechanisms and functions of alternative splicing (AS) not only enables us to explore the complex regulatory network involved in tumour initiation and progression but also reveals potential for RNA-based cancer treatment strategies. This review provides a comprehensive summary of the significance of AS in liver cancer, covering the regulatory mechanisms, cancer-related AS events, abnormal splicing regulators, as well as the interplay between AS and post-transcriptional and post-translational regulations. We present the current bioinformatic approaches and databases to detect and analyse AS in cancer, and discuss the implications and perspectives of AS in the treatment of liver cancer.

Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying separation-of-function mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein for its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein-RNA interactions.

The human heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is a prototypical RNA-binding protein essential for regulating a wide range of post-transcriptional events in cells. As a multifunctional protein with a key role in RNA metabolism, deregulation of its functions has been linked to neurodegenerative diseases, tumor aggressiveness, and chemoresistance, which has fuelled efforts to develop novel therapeutics that modulate its RNA-binding activities. Here, using a combination of molecular dynamics simulations and graph neural network pocket predictions, we showed that hnRNPA1 N-terminal RNA-binding domain (unwinding protein 1 [UP1]) contains several cryptic pockets capable of binding small molecules. To identify chemical entities for the development of potent drug candidates and experimentally validate identified druggable hotspots, we carried out a large fragment screening on UP1 protein crystals. Our screen identified 36 hits that extensively sample UP1 functional regions involved in RNA recognition and binding as well as map hotspots onto novel protein interaction surfaces. We observed a wide range of ligand-induced conformational variation by stabilization of dynamic protein regions. Our high-resolution structures, the first of an hnRNP in complex with a fragment or small molecule, provide rapid routes for the rational development of a range of different inhibitors and chemical tools for studying molecular mechanisms of hnRNPA1-mediated splicing regulation.

Chronic kidney disease (CKD) affects more than 10% of people worldwide and is a leading cause of death. However, the pathogenesis of CKD remains elusive. The oxidative stress and mitochondrial membrane potential were detected using Enzyme-linked immunosorbent assay and JC-1 assay. Co-immunoprecipitation, dual-luciferase assay, chromatin IP, RNA IP and RNA pull-down were used to validate the interactions among genes. Exploiting a H2O2-induced fibrosis model in vitro, PUM2 expression was upregulated in Human kidney 2 cell (HK-2) cells, along with reduced cell viability, enhanced oxidative stress, impaired mitochondrial potential, and upregulated expressions of fibrosis-associated proteins. While PUM2 knockdown reversed the H2O2-induced injury in HK-2 cells. Mechanically, Wnt/β-catenin pathway activated PUM2 transcription via TCF4. It was further identified that Wnt/β-catenin pathway inhibited YME1L expression through PUM2-mediated destabilizing of its mRNA. PUM2 aggravated H2O2-induced oxidative stress, mitochondrial dysfunction, and renal fibrosis in HK-2 cell via suppressing YME1L expression. Our study revealed that Wnt/β-catenin aggravated renal fibrosis by activating PUM2 transcription to repress YME1L-mediated mitochondrial homeostasis, providing novel insights and potential therapeutic targets for the treatment of kidney fibrosis.

Erythropoiesis is a process that requires tight control of gene transcription, mRNA stability, and protein synthesis and degradation. These regulatory layers adapt dynamically to developmental needs and physiological stresses, ensuring precise control of erythroid production. Ribosomopathies, such as Diamond-Blackfan anemia (DBA), are characterized by defects in ribosome function. Zooming in on erythroid precursors, ribosomopathies lead to dysregulated translation of mRNAs encoding specific and essential erythropoietic genes, including master transcription factors such as GATA1. This causes defective maturation and increased apoptosis of erythroid progenitors, and consequently, anemia. Beyond ribosomal proteins, RNA-binding proteins have been put forward as an additional and targeted checkpoint regulating cellular proteostasis. CAPRIN2, which is present in neurons and erythroid cells, is one such RNA-binding protein, involved in RNA translation regulation and its levels rise during terminal erythroid differentiation. Overexpression of CAPRIN2 in Chinese hamster ovary (CHO) cells causes reduced growth, cell cycle arrest, and apoptosis. Here, we demonstrate that GATA1 potentially regulates Caprin2 transcription, and that Caprin2 loss boosts erythroid production and maturation during gestation and adulthood, a phenomenon that is enhanced in situations of stress erythropoiesis. Our results provide new insight into the role of CAPRIN2 in erythropoiesis. We hypothesize that it regulates the translation of key mRNAs during erythropoiesis. We propose that CAPRIN2 is involved in the balance of erythroid production and that its manipulation may control erythroid production, offering a potential and promising approach to manage altered erythropoiesis.