How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms

Endo-bind-n-seq: identifying RNA motifs of RNA binding proteins isolated from endogenous sources

RNA binding proteins (RBPs) are crucial regulators of gene expression and critically depend on the specific recognition of their target RNAs. Accordingly, a selection of methods to analyze RBP specificities has been developed, including protein-RNA crosslinking and sequencing (CLIP) and in vitro selection methods such as SELEX, RNA compete or RNA bind-n-seq. However, limitations like the availability for purified recombinant proteins and custom microarray platforms (RNAcompete) or extensive sequencing depth and sophisticated bioinformatic data processing (CLIP) may limit a broader implementation of these methods. Here, we present an RNA bind-n-seq method that uses short random RNA pools and enables multiple rounds of selection. This results in strong motif enrichment with low positional variance thus reducing sequencing depth requirements. Furthermore, we have coupled our protocol to immunoprecipitation of tagged or endogenous RBPs from cultured cells or tissue samples, eliminating the need for recombinant proteins. Our method also allows for the identification of indirect RNA motifs of proteins that are integral parts of multiprotein RNPs and result in physically more relevant RNA motifs.

Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates

Coronaviruses evade detection by the host immune system with the help of the endoribonuclease Nsp15, which regulates levels of viral double stranded RNA by cleaving 3' of uridine (U). While prior structural data shows that to cleave double stranded RNA, Nsp15's target U must be flipped out of the helix, it is not yet understood whether Nsp15 initiates flipping or captures spontaneously flipped bases. We address this gap by designing fluorinated double stranded RNA substrates that allow us to directly relate a U's sequence context to both its tendency to spontaneously flip and its susceptibility to cleavage by Nsp15. Through a combination of nuclease assays, 19F NMR spectroscopy, mass spectrometry, and single particle cryo-EM, we determine that Nsp15 acts most efficiently on unpaired Us, particularly those that are already flipped. Across sequence contexts, we find Nsp15's cleavage efficiency to be directly related to that U's tendency to spontaneously flip. Overall, our findings unify previous characterizations of Nsp15's cleavage preferences, and suggest that activity of Nsp15 during infection is partially driven by bulged or otherwise relatively accessible Us that appear at strategic positions in the viral RNA.

Using the Tether Function Assay to Identify Potential Regulators of mRNA Translation and mRNA Decay

RNA binding proteins (RBPs) and their associated partners are key factors of posttranscriptional control of gene expression. To study and manipulate the functional consequences of binding of these regulators to their targets, several tethering assays have been developed, in which a protein of interest is brought to a reporter mRNA through heterologous RNA-protein interaction motifs. The effect of such constrained binding is then monitored by measuring the accumulation of the reporter protein and mRNA. This chapter describes a protocol for the λN-BoxB tether system in transiently transfected mammalian cells. Combining the luciferase reporter technology to quantify protein amounts by light measurement and RNA amounts by RT-qPCR, this assay provides a simple and robust way to analyze the consequences of any protein binding in a controlled and defined manner.

Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning

The interactions between long noncoding RNA (lncRNA) and protein play crucial roles in various biological processes. Computational methods are essential for predicting lncRNA-protein interactions and deciphering their mechanisms. In this chapter, we aim to introduce the fundamental framework for predicting lncRNA-protein interactions based on three-dimensional structure information. With the increasing availability of lncRNA and protein molecular tertiary structures, the feasibility of using deep learning methods for automatic representation and learning has become evident. This chapter outlines the key steps in predicting lncRNA-protein interactions using deep learning, including three common non-Euclidean data representations for lncRNA and proteins, as well as neural networks tailored to these specific data characteristics. We also highlight the advantages and challenges of structure-based prediction of lncRNA-protein interactions with geometric deep learning methods.

RBM47 as a potential therapeutic target for thyroid-associated ophthalmopathy

RNA-binding motif 47 (RBM47) is a recently identified RNA-binding protein involved in early vertebrate development, immune homeostasis, and cancer development. This study examined the biological functions of RBM47 in thyroid-associated ophthalmopathy (TAO). Orbital fibroblasts (OFs) were obtained from the control (n = 6) and TAO groups (n = 6). Protein and gene expression in the obtained samples were investigated using immunohistochemistry, western blotting (WB), and RT-PCR. OFs with RBM47 knockdown were established using small interfering RNA. Subsequently, Oil Red O staining, WB, and RT-PCR were performed to assess adipogenesis in the OFs. The IL-1β-induced expression of proinflammatory molecules and hyaluronan (HA) was determined using enzyme-linked immunosorbent assay and RT-PCR. Moreover, TGF-β-induced fibrosis was evaluated using scratch assays, RT-PCR, and WB. RBM47 expression was markedly increased in orbital tissues and OFs obtained from individuals with TAO. RBM47 knockdown decreased adipogenesis and fibrosis in OFs, and downregulated the levels of insulin-like growth factor 1 receptor (IGF-1R), proinflammatory molecules, and HA. Furthermore, low RBM47 expression downregulated IGF-1R, which subsequently inhibited adipocyte differentiation by decreasing extracellular signal-regulated kinase signalling. These findings indicate that RBM47 may be involved in the regulation of adipogenesis, inflammation, HA production, and fibrosis, highlighting its potential of RBM47 as a therapeutic target for TAO.

RNA-binding protein HNRNPD promotes chondrocyte senescence and osteoarthritis progression through upregulating FOXM1

Osteoarthritis (OA) is a common age-related disease that is correlated with a high number of senescent chondrocytes in joint tissues. Heterogeneous nuclear ribonucleoprotein D (HNRNPD) is an RNA-binding protein whose expression imbalance is associated with cell senescence, but the role of HNRNPD in the occurrence and development of OA has not been reported. In this study, HNRNPD was found to be associated with the chondrocyte senescence process. We determined the factors at the posttranscriptional level that regulated the expression of the genes that induce OA and found that HNRNPD was specifically highly expressed in OA-induced rat cartilage and in human OA cartilage. Recombinant adeno-associated virus (rAAV)-mediated HNRNPD gene overexpression alone did not significantly regulate the occurrence and development of OA in the physiological state of the joint. However, rAAV-HNRNPD significantly exacerbated experimental OA in rats subjected to destabilization of the medial meniscus. Overexpression of HNRNPD promoted mitochondrial dysfunction and the expression of FOXM1, which acts as a direct target. Furthermore, downregulation of FOXM1 in chondrocytes weakened the HNRNPD-mediated promotion of chondrocyte senescence and mitochondrial dysfunction. Our results suggest that the RNA-binding protein HNRNPD promotes chondrocyte senescence in the pathology of OA by upregulating FOXM1.

Harnessing RNA-Protein Interactions for Therapeutic Interventions

Interactions between RNAs and proteins play a crucial role in various diseases, including viral infections and cancer. Hence, understanding and inhibiting these interactions are important for the development of novel therapeutics. However, the identification of drugs targeting RNA-protein interactions with high specificity and affinity is challenged by our limited molecular understanding of these interactions. Recent focus on structural and biochemical characterization, coupled with high-throughput screening technologies and computational modeling, have accelerated the identification of new RBPs and optimization of potential inhibitors. This review discusses key examples of inhibitors developed over the past decade that effectively disrupt pathogenic RNA-protein interactions. We focus on small molecule and peptide-based inhibitors that have shown promise in disrupting crucial RNA-protein interactions in eukaryotes, prokaryotes, and viruses. We also present the challenges and future directions in this field, emphasizing the need to achieve improved specificity and reduce the off-target effects of the inhibitors. This review aims to contribute to ongoing efforts towards the development of novel therapeutic agents targeting RNA-protein interactions by providing an in-depth analysis of significant developments and emerging trends in this rapidly growing field.

Interrogation of RNA-bound proteome with XRNAX illuminates molecular alterations in the mouse brain affected with dysmyelination

RNA-protein interactions orchestrate hundreds of pathways in homeostatic and stressed cells. We applied an RNA-protein interactome capture method called protein cross-linked RNA extraction (XRNAX) to shed light on the RNA-bound proteome in dysmyelination. We found sets of canonical RNA-binding proteins (RBPs) regulating alternative splicing and engaged in the cytoplasmic granules to be perturbed at the level of their RNA interactome. We validated these observations for PCBP1 and MBNL1. We show that the number of PCBP1 bodies is markedly increased in the mossy cells of the hippocampus and that the pattern of MBNL1-regulated alternatively spliced exons differs between the myelin-deficient and the wild-type brain, which is likely associated with Mbnl1 splicing perturbation and circular RNA generation from this locus. In the broader perspective, our results demonstrate that, with the application of the RNA-protein interactome approach, we can uncover alterations in RBP functioning in the disease context that are not always directly visible from their mRNA or protein levels.

Insights into the regulation of mRNA translation by scaffolding proteins

Regionalisation of molecular mechanisms allows cells to fine-tune their responses to dynamic environments. In this context, scaffolds are well-known mediators of localised protein activity. These phenomenal proteins act as docking sites where pathway components are brought together to ensure efficient and reliable flow of information within the cell. Although scaffolds are mostly understood as hubs for signalling communication, some have also been studied as regulators of mRNA translation. Here, we provide a brief overview of the work unravelling how scaffolding proteins facilitate the cross-talk between the two processes. Firstly, we examine the activity of AKAP1 and AKAP12, two signalling proteins that not only have the capacity to anchor mRNAs to membranes but can also regulate protein synthesis. Next, we review the studies that uncovered how the ribosome-associated protein RACK1 orchestrates translation initiation. We also discuss the evidence pointing to the scaffolds Ezrin and LASP1 as regulators of early translation stages. In the end, we conclude with some open questions and propose future directions that will bring new insights into the regulation of mRNA translation by scaffolding proteins.

R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning

RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA-protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates in Nostoc sp. PCC 7120. We validated in vivo the RNA-binding capacity of six RBP candidates. Some participate in essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst differentiation (PrpA, PatU3), but their association with RNA was unknown. Validated RBPs Asl3888 and Alr1700 were not previously characterized. Alr1700 is an RBP with two oligonucleotide/oligosaccharide-binding (OB)-fold-like domains that is differentially expressed in heterocysts and interacts with non-coding regulatory RNAs. Deletion of alr1700 led to complete deregulation of the cell differentiation process, a striking increase in the number of heterocyst-like cells, and was ultimately lethal in the absence of combined nitrogen. These observations characterize this RBP as a master regulator of the heterocyst patterning and differentiation process, leading us to rename Alr1700 to PatR.

Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis

RNA-binding proteins (RBPs) play critical cellular roles by mediating various stages of RNA life cycles. Ssd1, an RBP with pleiotropic effects, has been implicated in aneuploidy tolerance in Saccharomyces cerevisiae but its mechanistic role remains unclear. Here, we used a network-based approach to inform on Ssd1's role in aneuploidy tolerance, by identifying and experimentally perturbing a network of RBPs that share mRNA targets with Ssd1. We identified RBPs whose bound mRNA targets significantly overlap with Ssd1 targets. For 14 identified RBPs, we then used a genetic approach to generate all combinations of genotypes for euploid and aneuploid yeast with an extra copy of chromosome XII, with and without SSD1 and/or the RBP of interest. Deletion of 10 RBPs either exacerbated or alleviated the sensitivity of wild-type and/or ssd1Δ cells to chromosome XII duplication, in several cases indicating genetic interactions with SSD1 in the context of aneuploidy. We integrated these findings with results from a global overexpression screen that identified genes whose duplication complements ssd1Δ aneuploid sensitivity. The resulting network points to a subgroup of proteins with shared roles in translational repression and P-body formation, implicating these functions in aneuploidy tolerance. Our results reveal a role for new RBPs in aneuploidy tolerance and support a model in which Ssd1 mitigates translation-related stresses in aneuploid cells.

New therapeutic approaches for fibrosis: harnessing translational regulation

Idiopathic pulmonary fibrosis (IPF) is a progressive and debilitating lung disease characterized by excessive extracellular matrix deposition and tissue scarring. The median survival of patients with IPF is only 4.5 years following diagnosis, and effective treatment options are scarce. Recent studies found aberrant translation of specific mRNAs in various fibrosing diseases, highlighting the role of key translational regulators, including RNA binding proteins (RBPs), microRNAs, long noncoding RNAs, and transcript modifications. Notably, when inhibited, 10 profibrotic RBPs cause a significant attenuation of fibrosis, illuminating potential therapeutic targets. In this review, we describe translational regulation in fibrosis and highlight a model where a conserved evolutionary mechanism may explain this regulation.

Beyond the Bubble: A Debate on microRNA Sorting Into Extracellular Vesicles

Over the past decade, a scientific field has been developed demonstrating microRNAs (miRNAs) to be actively sorted into extracellular vesicles via specific nucleotide motifs that interact with discrete RNA-binding proteins. These miRNAs are proposed to be transported into recipient cells in which they can regulate specific cellular pathways. This mechanism could have enormous potential in explaining how cells signal and regulate other cells nearby or at a distance. Tens of studies have built this theme of a regulated transport of miRNAs. However, some concerns exist about this field. Taken together, there are concerns of a lack of a consistent motif, RNA-binding protein, or preferential miRNA involved in this process. In this study, we provide an expert and extensive analysis of the field that makes the cases for and against an active sorting mechanism. We provide potential explanations on why there is a lack of agreement. Most importantly, we provide ideas on how to move this field forward with more rigor and reproducibility. It is hoped that by engaging in a scientific debate of the pros and cons of this field, more rigorous experiments can be performed to conclusively demonstrate this biological activity.

Water-mediated ribonucleotide-amino acid pairs and higher-order structures at the RNA-protein interface: analysis of the crystal structure database and a topological classification

Water is essential for the formation, stability and function of RNA-protein complexes. To delineate the structural role of water molecules in shaping the interactions between RNA and proteins, we comprehensively analyzed a dataset of 329 crystal structures of these complexes to identify water-mediated hydrogen-bonded contacts at RNA-protein interface. Our survey identified a total of 4963 water bridges. We then employed a graph theory-based approach to present a robust classification scheme, encompassing triplets, quartets and quintet bridging topologies, each further delineated into sub-topologies. The frequency of water bridges within each topology decreases with the increasing degree of water node, with simple triplet water bridges outnumbering the higher-order topologies. Overall, this analysis demonstrates the variety of water-mediated interactions and highlights the importance of water as not only the medium but also the organizing principle underlying biomolecular interactions. Further, our study emphasizes the functional significance of water-mediated interactions in RNA-protein complexes, and paving the way for exploring how these interactions operate in complex biological environments. Altogether, this understanding not only enhances insights into biomolecular dynamics but also informs the rational design of RNA-protein complexes, providing a framework for potential applications in biotechnology and therapeutics. All the scripts, and data are available at https://github.com/PSCPU/waterbridges.

From genes to traits: Trends in RNA-binding proteins and their role in plant trait development: A review

RNA-binding proteins (RBPs) are essential for cellular functions by attaching to RNAs, creating dynamic ribonucleoprotein complexes (RNPs) essential for managing RNA throughout its life cycle. These proteins are critical to all post-transcriptional processes, impacting vital cellular functions during development and adaptation to environmental changes. Notably, in plants, RBPs are critical for adjusting to inconsistent environmental conditions, with recent studies revealing that plants possess, more prominent, and both novel and conserved RBP families compared to other eukaryotes. This comprehensive review delves into the varied RBPs covering their structural attributes, domain base function, and their interactions with RNA in metabolism, spotlighting their role in regulating post-transcription and splicing and their reaction to internal and external stimuli. It highlights the complex regulatory roles of RBPs, focusing on plant trait regulation and the unique functions they facilitate, establishing a foundation for appreciating RBPs' significance in plant growth and environmental response strategies.

AI-integrated network for RNA complex structure and dynamic prediction

RNA complexes are essential components in many cellular processes. The functions of these complexes are linked to their tertiary structures, which are shaped by detailed interface information, such as binding sites, interface contact, and dynamic conformational changes. Network-based approaches have been widely used to analyze RNA complex structures. With their roots in the graph theory, these methods have a long history of providing insight into the static and dynamic properties of RNA molecules. These approaches have been effective in identifying functional binding sites and analyzing the dynamic behavior of RNA complexes. Recently, the advent of artificial intelligence (AI) has brought transformative changes to the field. These technologies have been increasingly applied to studying RNA complex structures, providing new avenues for understanding the complex interactions within RNA complexes. By integrating AI with traditional network analysis methods, researchers can build more accurate models of RNA complex structures, predict their dynamic behaviors, and even design RNA-based inhibitors. In this review, we introduce the integration of network-based methodologies with AI techniques to enhance the understanding of RNA complex structures. We examine how these advanced computational tools can be used to model and analyze the detailed interface information and dynamic behaviors of RNA molecules. Additionally, we explore the potential future directions of how AI-integrated networks can aid in the modeling and analyzing RNA complex structures.

Conformational penalties: New insights into nucleic acid recognition

The energy cost accompanying changes in the structures of nucleic acids when they bind partner molecules is a significant but underappreciated thermodynamic contribution to binding affinity and specificity. This review highlights recent advances in measuring conformational penalties and determining their contribution to the recognition, folding, and regulatory activities of nucleic acids. Notable progress includes methods for measuring and structurally characterizing lowly populated conformational states, obtaining ensemble information in high throughput, for large macromolecular assemblies, and in complex cellular environments. Additionally, quantitative and predictive thermodynamic models have been developed that relate conformational penalties to nucleic acid-protein association and cellular activity. These studies underscore the crucial role of conformational penalties in nucleic acid recognition.

RNA binding motif 4 inhibits the replication of ebolavirus by directly targeting 3'-leader region of genomic RNA

Ebola virus (EBOV) belongs to Filoviridae family possessing single-stranded negative-sense RNA genome, which is a serious threat to human health. Nowadays, no therapeutics have been proven to be successful in efficiently decreasing the mortality rate. RNA binding proteins (RBPs) are reported to participate in maintaining cell integrity and regulation of viral replication. However, little is known about whether and how RBPs participate in regulating the life cycle of EBOV. In our study, we found that RNA binding motif protein 4 (RBM4) inhibited the replication of EBOV in HEK293T and Huh-7 cells by suppressing viral mRNA production. Such inhibition resulted from the direct interaction between the RRM1 domain of RBM4 and the "CU" enrichment elements located in the PE1 and TSS of the 3'-leader region within the viral genome. Simultaneously, RBM4 could upregulate the expression of some cytokines involved in the host innate immune responses to synergistically exert its antiviral function. The findings therefore suggest that RBM4 might serve as a novel target of anti-EBOV strategy.

Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts

Protein-RNA interactions play a critical role in many cellular processes and pathologies. However, experimental determination of protein-RNA structures is still challenging, therefore computational tools are needed for the prediction of protein-RNA interfaces. Although evolutionary pressures can be exploited for structural prediction of protein-protein interfaces, and recent deep learning methods using protein multiple sequence alignments have radically improved the performance of protein-protein interface structural prediction, protein-RNA structural prediction is lagging behind, due to the scarcity of structural data and the flexibility involved in these complexes. To study the evolution of protein-RNA interface structures, we first identified a large and diverse dataset of 2,022 pairs of structurally homologous interfaces (termed structural interologs). We leveraged this unique dataset to analyze the conservation of interface contacts among structural interologs based on the properties of involved amino acids and nucleotides. We uncovered that 73% of distance-based contacts and 68% of apolar contacts are conserved on average, and the strong conservation of these contacts occurs even in distant homologs with sequence identity below 20%. Distance-based contacts are also much more conserved compared to what we had found in a previous study of homologous protein-protein interfaces. In contrast, hydrogen bonds, salt bridges, and π-stacking interactions are very versatile in pairs of protein-RNA interologs, even for close homologs with high interface sequence identity. We found that almost half of the non-conserved distance-based contacts are linked to a small proportion of interface residues that no longer make interface contacts in the interolog, a phenomenon we term "interface switching out". We also examined possible recovery mechanisms for non-conserved hydrogen bonds and salt bridges, uncovering diverse scenarios of switching out, change in amino acid chemical nature, intermolecular and intramolecular compensations. Our findings provide insights for integrating evolutionary signals into predictive protein-RNA structural modeling methods.

Identification of RNA-binding protein genes associated with renal rejection and graft survival

Rejection is one of the major factors affecting the long-term prognosis of kidney transplantation, and timely recognition and aggressive treatment of rejection is essential to prevent disease progression. RBPs are proteins that bind to RNA to form ribonucleoprotein complexes, thereby affecting RNA stability, processing, splicing, localization, transport, and translation, which play a key role in post-transcriptional gene regulation. However, their role in renal transplant rejection and long-term graft survival is unclear. The aim of this study was to comprehensively analyze the expression of RPBs in renal rejection and use it to construct a robust prediction strategy for long-term graft survival. The microarray expression profiles used in this study were obtained from GEO database. In this study, a total of eight hub RBPs were identified, all of which were upregulated in renal rejection samples. Based on these RBPs, the renal rejection samples could be categorized into two different clusters (cluster A and cluster B). Inflammatory activation in cluster B and functional enrichment analysis showed a strong association with rejection-related pathways. The diagnostic prediction model had a high diagnostic accuracy for T cell mediated rejection (TCMR) in renal grafts (area under the curve = 0.86). The prognostic prediction model effectively predicts the prognosis and survival of renal grafts (p < .001) and applies to both rejection and non-rejection situations. Finally, we validated the expression of hub genes, and patient prognosis in clinical samples, respectively, and the results were consistent with the above analysis.

Bridging the gap: RNAylation conjugates RNAs to proteins

In nature, the majority of known RNA-protein interactions are transient. Our recent study has depicted a novel mechanism known as RNAylation, which covalently links proteins and RNAs. This novel modification bridges the realms of RNA and protein modifications. This review specifically explores RNAylation catalyzed by bacteriophage T4 ADP-ribosyltransferase ModB, with a focus on its protein targets and RNA substrates in the context of Escherichia coli-bacteriophage T4 interaction. Additionally, we discuss the biological significance of RNAylation and present perspectives on RNAylation as a versatile bioconjugation strategy for RNAs and proteins.

RNA-protein interaction prediction without high-throughput data: An overview and benchmark of in silico tools

RNA-protein interactions (RPIs) are crucial for accurately operating various processes in and between organisms across kingdoms of life. Mutual detection of RPI partner molecules depends on distinct sequential, structural, or thermodynamic features, which can be determined via experimental and bioinformatic methods. Still, the underlying molecular mechanisms of many RPIs are poorly understood. It is further hypothesized that many RPIs are not even described yet. Computational RPI prediction is continuously challenged by the lack of data and detailed research of very specific examples. With the discovery of novel RPI complexes in all kingdoms of life, adaptations of existing RPI prediction methods are necessary. Continuously improving computational RPI prediction is key in advancing the understanding of RPIs in detail and supplementing experimental RPI determination. The growing amount of data covering more species and detailed mechanisms support the accuracy of prediction tools, which in turn support specific experimental research on RPIs. Here, we give an overview of RPI prediction tools that do not use high-throughput data as the user's input. We review the tools according to their input, usability, and output. We then apply the tools to known RPI examples across different kingdoms of life. Our comparison shows that the investigated prediction tools do not favor a certain species and equip the user with results varying in degree of information, from an overall RPI score to detailed interacting residues. Furthermore, we provide a guide tree to assist users which RPI prediction tool is appropriate for their available input data and desired output.

RNA binding protein RBM22 suppresses non-small cell lung cancer tumorigenesis by stabilizing LATS1 mRNA

Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related mortality worldwide. Despite advancements in diagnostics and therapeutics, the prognosis for NSCLC remains poor, highlighting the urgent need for novel treatment options. RNA binding proteins, particularly RBM22, have emerged as significant contributors to cancer progression by influencing RNA splicing and gene expression. This study investigates the role of RBM22 in NSCLC and its potential as a therapeutic target. We focus on the effects of RBM22 on cell proliferation, invasion, stemness, and its interaction with LATS1 mRNA. RBM22 expression was assessed in samples and cell lines of NSCLC through techniques such as real-time PCR and western blot analysis. To modify RBM22 levels, overexpression and knockdown methods were employed utilizing vectors and siRNAs. We conducted assays for cell proliferation, invasion, and stemness to evaluate the effects of altering RBM22. The interaction between RBM22 and LATS1 mRNA was investigated using RNA immunoprecipitation. In addition, in vivo studies involving subdermal tumor and lung metastasis models in athymic mice were carried out to evaluate how changes in RBM22 influence the tumorigenic and metastatic characteristics of NSCLC. Our analysis revealed a significant underexpression of RBM22 in NSCLC tissues compared to adjacent healthy tissues. Increasing RBM22 expression in NSCLC cell lines led to a marked decrease in cellular proliferation, invasiveness, and stemness, while silencing RBM22 produced opposing effects. Further investigations confirmed that RBM22 directly interacts with LATS1 mRNA, thereby stabilizing and enhancing its expression. In vivo studies validated that elevated RBM22 expression substantially reduced tumor formation and pulmonary metastases, as evidenced by decreased tumor size, mass, and Ki-67 proliferation marker expression, along with a significant reduction in the number of metastatic nodules in the lungs. Our study demonstrates that RBM22 suppresses NSCLC by stabilizing LATS1 mRNA, which in turn reduces tumor growth and metastasis. Consequently, RBM22 emerges as a valuable therapeutic target for NSCLC, offering new strategies for addressing this challenging condition.

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis

An RNA's catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and dictate the formation of functional conformations. These co-transcriptional states remain unknown. Here, we develop CoSTseq, which detects nascent RNA base pairing within and upon exit from RNA polymerases (Pols) transcriptome-wide in living yeast cells. By monitoring each nucleotide's base pairing activity during transcription, we identify distinct classes of behaviors. While 47% of rRNA nucleotides remain unpaired, rapid and delayed base pairing - with rates of 48.5 and 13.2 kb -1 of transcribed rDNA, respectively - typically completes when Pol I is only 25 bp downstream. We show that helicases act immediately to remodel structures across the rDNA locus and facilitate ribosome biogenesis. In contrast, nascent pre-mRNAs attain local structures indistinguishable from mature mRNAs, suggesting that refolding behind elongating ribosomes resembles co-transcriptional folding behind Pol II.

Role of RNA-binding Proteins in Regulating Cell Adhesion and Progression of the Atherosclerotic Plaque and Plaque Erosion

PURPOSE OF REVIEW

RNA-binding proteins (RBPs) have emerged as crucial regulators of post-transcriptional processes, influencing the fate of RNA. This review delves into the biological functions of RBPs and their role in alternative splicing concerning atherosclerosis (AS), highlighting their participation in essential cellular processes. Our goal is to offer new insights for cardiovascular disease research and treatment.

RECENT FINDING

Dysregulation of RBPs is associated with various human diseases, including autoimmune and neurological disorders. The role of RBPs in the pathogenesis of AS is progressively being elucidated, as they influence plaque formation and disease progression by regulating cell function and gene expression. RBPs play intricate biological roles in regulating pre-mRNA, including editing, splicing, stability and translation. Alternative splicing has been demonstrated to enhance biological complexity and diversity. Our findings indicate that alternative splicing is extensively involved in the pathogenesis of AS. The dysregulated expression of specific RBPs in AS is linked to the production of adhesion molecules and vascular endothelium damage. Further research on RBPs could pave the way for the development of novel therapeutic targets.

Beyond RNA-binding domains: determinants of protein-RNA binding

RNA-binding proteins (RBPs) are composed of RNA-binding domains (RBDs) often linked via intrinsically disordered regions (IDRs). Structural and biochemical analyses have shown that disordered linkers contribute to RNA binding by orienting the adjacent RBDs and also characterized certain disordered repeats that directly contact the RNA. However, the relative contribution of IDRs and predicted RBDs to the in vivo binding pattern is poorly explored. Here, we upscaled the RNA-tagging method to map the transcriptome-wide binding of 16 RBPs in budding yeast. We then performed extensive sequence mutations to distinguish binding determinants within predicted RBDs and the surrounding IDRs in eight of these. The majority of the predicted RBDs tested were not individually essential for mRNA binding. However, multiple IDRs that lacked predicted RNA-binding potential appeared essential for binding affinity or specificity. Our results provide new insights into the function of poorly studied RBPs and emphasize the complex and distributed encoding of RBP-RNA interaction in vivo.

DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A reader YTHDF1

RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. Here, we investigate the RNA structurome alteration induced by DHX36 depletion. Our findings reveal that DHX36 binding induces structural remodeling not only at the localized binding sites but also on the entire mRNA transcript most pronounced in 3'UTR regions. DHX36 binding increases structural accessibility at 3'UTRs which is correlated with decreased post-transcriptional mRNA abundance. Further analyses and experiments uncover that DHX36 binding sites are enriched for N6-methyladenosine (m6A) modification and YTHDF1 binding; and DHX36 induced structural changes may facilitate YTHDF1 binding to m6A sites leading to RNA degradation. Altogether, our findings uncover the structural remodeling effect of DHX36 binding and its impact on RNA abundance through regulating m6A dependent YTHDF1 binding.

Decoding the enigma of RNA-protein recognition: quantum chemical insights into arginine fork motifs

Arginine (Arg) forks are noncovalent recognition motifs wherein an Arg interacts with the phosphates and guanine nucleobases of RNA, providing extraordinary specific RNA:protein recognition. In this work, we carried out an in-depth DFT based quantum mechanical investigation on all known classes of Arg forks to estimate their intrinsic structural stabilities and interaction energies. The optimized structures closely mimic the structural characteristics of Arg forks and this close match between experimental and optimized geometries suggests that Arg forks are intrinsically stable and do not require additional support from other RNA or protein components. Both hydrogen-bonding and cation-π interactions are important for the intrinsic stability of Arg forks, providing an average interaction energy of -36.7 kcal mol-1. Furthermore, we found a direct correlation between Arg forks' interaction energies and the number of phosphates involved, which is more delicately modulated by other factors, like the types of hydrogen bonds and cation-π interactions that constitute the Arg fork. Additionally, we observed a positive correlation between the average interaction energies of Arg forks and the frequency of their occurrence in available crystal structures. At the broader level, this work establishes the groundwork for more precise modeling and understanding of RNA-protein interfaces, which could have potential implications in advancing the knowledge of biomolecular recognition patterns.

Phylogenomic instructed target analysis reveals ELAV complex binding to multiple optimally spaced U-rich motifs

ELAV/Hu RNA-binding proteins are gene-specific regulators of alternative pre-mRNA processing. ELAV/Hu family proteins bind to short AU-rich motifs which are abundant in pre-mRNA, making it unclear how they achieve gene specificity. ELAV/Hu proteins multimerize, but how multimerization contributes to decode degenerate sequence environments remains uncertain. Here, we show that ELAV forms a saturable complex on extended RNA. Through phylogenomic instructed target analysis we identify the core binding motif U5N2U3, which is repeated in an extended binding site. Optimally spaced short U5N2U3 binding motifs are key for high-affinity binding in this minimal binding element. Binding strength correlates with ELAV-regulated alternative poly(A) site choice, which is physiologically relevant through regulation of the major ELAV target ewg in determining synapse numbers. We further identify a stem-loop secondary structure in the ewg binding site unwound upon ELAV binding at three distal U motifs. Base-pairing of U motifs prevents ELAV binding, but N6-methyladenosine (m6A) has little effect. Further, stem-loops are enriched in ELAV-regulated poly(A) sites. Additionally, ELAV can nucleate preferentially from 3' to 5'. Hence, we identify a decisive mechanism for ELAV complex formation, addressing a fundamental gap in understanding how ELAV/Hu family proteins decode degenerate sequence spaces for gene-specific mRNA processing.

Down-regulation of PCBP2 suppresses the invasion and migration of trophoblasts via the WNT5A/ROR2 pathway in preeclampsia†

Impaired extravillous trophoblast (EVT) invasion and resulted poor placentation play a vital role in the development of preeclampsia (PE). However, the underlying mechanisms of dysregulated EVTs remain unclear. This study aimed to explore the role of poly (C)-binding protein 2 (PCBP2), a multifunctional RNA-binding protein, in the pathogenesis of PE and to investigate the detailed signaling pathway. Using qRT-PCR, western blot, and immunohistochemistry, we confirmed that the expression of PCBP2 significantly decreased in placentas from 18 early-onset PE and 30 late-onset PE in comparison to those from 30 normotensive pregnancies. Besides, more significant suppression of PCBP2 was observed in the early-onset type. After transfection of HTR-8/SVneo with small-interfering RNA specific to PCBP2, the cellular biological behaviors including vitality, immigration, invasiveness, and apoptosis were evaluated by CCK-8 assay, wound-healing assay, transwell assay, and flow cytometry respectively. RNA-seq was applied to screen differentially expressed genes in HTR-8/SVneo upon PCBP2 silencing. GO and KEGG analysis indicated that WNT signaling pathway and the related processes such as extracellular matrix remodeling and cell adhesion were among the most enriched pathways or processes. Meanwhile, the alternative splicing of WNT5A regulated by PCBP2 was also identified by RIP-seq. Based on HTR-8/SVneo and villous explant, the regulatory roles of PCBP2 on trophoblast were confirmed to be mediated by WNT5A. Besides, it revealed that ROR2/JNK/MMP2/9 pathway was a vital pathway downstream WNT5A in trophoblast cells. In conclusion, this study suggests that down-regulated PCBP2 impaired the functions of EVTs via suppression of WNT5A-mediating ROR2/JNK/MMPs pathway, which may eventually contribute to the development of PE.

Molecular Impact of Sublethal Spinetoram Exposure on Honeybee (Apis mellifera) Larval and Adult Transcriptomes

Pesticide toxicity is a global concern for honeybee populations, and understanding these effects at the molecular level is critical. This study analyzed the transcriptome of honeybees at larval and adult stages after chronic exposure to a sublethal dose (0.0017 µg a.i./larva) of spinetoram (SPI) during the larval phase. Four groups were used: acetone-treated honeybee larvae (ATL), acetone-treated honeybee adults (ATAs), SPI-treated honeybee larvae (STL), and SPI-treated honeybee adults (STAs). In total, 5719 differentially expressed genes (DEGs) were identified for ATL vs. ATAs, 5754 for STL vs. STAs, 273 for ATL vs. STL, and 203 for ATAs vs. STAs (FC ≤ 1.5, p < 0.05). In response to SPI, 29 unique DEGs were identified in larvae and 42 in adults, with 23 overlapping between comparisons, suggesting genes linked to SPI toxicity. Gene ontology analysis showed that SPI affected metabolism-related genes in larvae and lipid-transport-associated genes in adults. KEGG pathway analysis revealed an enrichment of pathways predominantly associated with metabolism, hormone biosynthesis, and motor proteins in STL. The transcriptomic data were validated by qPCR. These findings demonstrated that SPI disrupts essential molecular processes, potentially harming honeybee development and behavior, underscoring the need for safer agricultural practices.

Unravelling stress granules in the deep cold: Characterisation of TIA-1 gene sequence in Antarctic fish species

Stress granules (SGs) are cytoplasmic foci lacking membranes, comprising non-translating messenger ribonucleoproteins, translational initiation factors, and additional proteins. Their formation is crucial for rapidly modulating gene expression in response to adverse environmental conditions, such as pollution and infections. Limited research has focused on investigating the molecular components of SGs in fish, with minimal exploration in Antarctic fish. This study characterises for the first time the transcript sequences of one key protein component of SGs, TIA-1 (T-cell intracellular antigen 1), in two Antarctic endemic fish species, i.e. Trematomus bernacchii and Chionodraco hamatus. The mRNA-binding protein TIA-1 acts as a post-transcriptional regulator of gene expression and its aggregation leads to the formation of SGs in response to cellular damage. The in vitro and bioinformatic analyses of the TIA-1 gene sequences of these two species highlighted interesting peculiarities, which include the transcription of alternatively spliced isoforms unique to the notothenioid lineage, potentially unlocking further insights into their unique adaptations to extreme environmental conditions. This is the first study to analyze tia-1 expression levels in different tissues of Antarctic fish species. Our key findings indicate that the TIA-1 gene is expressed at particularly high levels in the liver and spleen of C. hamatus, as well as in the heart and skeletal muscle of T. bernacchii. This suggests that those tissues play a significant role in the stress response mechanisms of the studied species. This study provides novel insights into the molecular adaptations of Antarctic fish, highlighting the potential importance of TIA-1 in their response to environmental stressors. The unique features of TIA-1 identified in these species may offer broader implications for understanding how Antarctic fish regulate gene transcriptions in their extreme environments.

A primer for junior trainees: Recognition of RNA modifications by RNA-binding proteins

The complexity of RNA cannot be fully expressed with the canonical A, C, G, and U alphabet. To date, over 170 distinct chemical modifications to RNA have been discovered in living systems. RNA modifications can profoundly impact the cellular outcomes of messenger RNAs (mRNAs), transfer and ribosomal RNAs, and noncoding RNAs. Additionally, aberrant RNA modifications are associated with human disease. RNA modifications are a rising topic within the fields of biochemistry and molecular biology. The role of RNA modifications in gene regulation, disease pathogenesis, and therapeutic applications increasingly captures the attention of the scientific community. This review aims to provide undergraduates, junior trainees, and educators with an appreciation for the significance of RNA modifications in eukaryotic organisms, alongside the skills required to identify and analyze fundamental RNA-protein interactions. The pumilio RNA-binding protein and YT521-B homology (YTH) family of modified RNA-binding proteins serve as examples to highlight the fundamental biochemical interactions that underlie the specific recognition of both unmodified and modified ribonucleotides, respectively. By instilling these foundational, textbook concepts through practical examples, this review contributes an analytical toolkit that facilitates engagement with RNA modifications research at large.

Exploring the roles and molecular mechanisms of RNA binding proteins in the sorting of noncoding RNAs into exosomes during tumor progression

BACKGROUND

RNA binding proteins (RBPs) play a role in sorting non-coding RNAs (ncRNAs) into exosomes. These ncRNAs, carried by exosomes, are involved in regulating various aspects of tumor progression, including metastasis, angiogenesis, control of the tumor microenvironment, and drug resistance. Recent studies have emphasized the importance of the RBP-ncRNA-exosome mechanism in tumor regulation.

AIM OF REVIEW

This comprehensive review aims to explore the RBP-ncRNA-exosome mechanism and its influence on tumor development. By understanding this intricate mechanism provides novel insights into tumor regulation and may lead to innovative treatment strategies in the future.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review discusses the formation of exosomes and the complex relationships among RBPs, ncRNAs, and exosomes. The RBP-ncRNA-exosome mechanism is shown to affect various aspects of tumor biology, including metastasis, multidrug resistance, angiogenesis, the immunosuppressive microenvironment, and tumor progression. Tumor development relies on the transmission of information between cells, with RBPs selectively mediating sorting of ncRNAs into exosomes through various mechanisms, which in turn carry ncRNAs to regulate RBPs. The review also provides an overview of potential therapeutic strategies, such as targeted drug discovery and genetic engineering for modifying therapeutic exosomes, which hold great promise for improving cancer treatment.

The role of structure in regulatory RNA elements

Regulatory RNA elements fulfill functions such as translational regulation, control of transcript levels, and regulation of viral genome replication. Trans-acting factors (i.e., RNA-binding proteins) bind the so-called cis elements and confer functionality to the complex. The specificity during protein-RNA complex (RNP) formation often exploits the structural plasticity of RNA. Functional integrity of cis-trans pairs depends on the availability of properly folded RNA elements, and RNA conformational transitions can cause diseases. Knowledge of RNA structure and the conformational space is needed for understanding complex formation and deducing functional effects. However, structure determination of RNAs under in vivo conditions remains challenging. This review provides an overview of structured eukaryotic and viral RNA cis elements and discusses the effect of RNA structural equilibria on RNP formation. We showcase implications of RNA structural changes for diseases, outline strategies for RNA structure-based drug targeting, and summarize the methodological toolbox for deciphering RNA structures.

Filamin B knockdown impairs differentiation and function in mouse pre-osteoblasts via aberrant transcription and alternative splicing

Objective

Filamin B (FLNB) encodes an actin-binding protein that is known to function as a novel RNA-binding protein involved in cell movement and signal transduction and plays a pivotal role in bone growth. This study aimed to investigate possible FLNB function in the skeletal system by characterizing the effecs of FLNB knockdown in mouse preosteoblast cells.

Methods

Stable FLNB MC3T3-E1 knockdown cells were constructed for RNA-seq and alternative splicing event (ASE) analysis of genes involved in osteoblast differentiation and function that may be regulated by FLNB. Standard transwell, MTT, ALP, qPCR, Western blot, and alizarin red staining assays were used to assess functional changes of FLNB-knockdown MC3T3-E1 cells.

Results

Analysis of differentially expressed genes (DEGs) in FLNB knockdown cells revealed enrichment for genes related to osteoblast proliferation, differentiation and migration, such as ITGA10, Cebpβ, Grem1, etc. Alternative splicing (AS) analysis showed changes in the predominant mRNA isoforms of skeletal development-related genes, especially Tpx2 and Evc. Functional asslysis indicated that proliferation, migration, and differentiation were all inhibited upon FLNB knockdown in MC3T3-E1 cells compared to that in vector control cells.

Conclusions

FLNB participates in regulating the transcription and AS of genes required for osteoblast development and function, consequently affecting growth and development in MC3T3-E1 cells.

RBFOX2 as a regulatory linchpin in cancer: insights from a comprehensive review of its roles in tumorigenesis

RNA-binding proteins (RBPs) are essential regulators of RNA expression during both transcriptional and post-transcriptional processes. Recent evidence indicates that dysregulation of RBPs is associated with cancer initiation and progression. Among these, RBFOX2 has been identified as exhibiting variable expression patterns across different cancers and is implicated in various malignant processes, including tumor growth, metastasis, ferroptosis, stemness, and chemoresistance. Despite these findings, the precise mechanisms by which RBFOX2 contributes to carcinogenesis remain largely unexplored. In this comprehensive review, we systematically examine the multifaceted functions of RBFOX2 in tumorigenesis, with a particular focus on its roles in alternative splicing, mRNA stability, and microRNA processing. Upon elucidating the specific roles of RBFOX2 in various cancers, targeted drugs can be devised to inhibit cancer development. Furthermore, we evaluate the specific roles of RBFOX2 in various cancer types, including pancreatic ductal adenocarcinoma, myeloid leukemia, and nasopharyngeal carcinoma. By providing an in-depth analysis, we aim to establish RBFOX2 as a potential diagnostic and therapeutic target in cancer biology and treatment, thereby offering new insights for future research.

The landscape of RNA binding proteins in mammalian spermatogenesis

Despite continuous expansion of the RNA binding protein (RBP) world, there is a lack of systematic understanding of RBPs in the mammalian testis, which harbors one of the most complex tissue transcriptomes. We adapted RNA interactome capture to mouse male germ cells, building an RBP atlas characterized by multiple layers of dynamics along spermatogenesis. Trapping of RNA-cross-linked peptides showed that the glutamic acid-arginine (ER) patch, a residue-coevolved polyampholytic element present in coiled coils, enhances RNA binding of its host RBPs. Deletion of this element in NONO (non-POU domain-containing octamer-binding protein) led to a defective mitosis-to-meiosis transition due to compromised NONO-RNA interactions. Whole-exome sequencing of over 1000 infertile men revealed a prominent role of RBPs in the human genetic architecture of male infertility and identified risk ER patch variants.

The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA

Like all canonical PUF proteins, C. elegans FBF-2 binds to specific RNAs via tripartite recognition motifs (TRMs). Here we report that an FBF-2 mutant protein that cannot bind to RNA, is nonetheless biologically active and maintains stem cells. This unexpected result challenges the conventional wisdom that RBPs must bind to RNAs to achieve biological activity. Also unexpectedly, FBF-2 interactions with partner proteins can compensate for loss of RNA-binding. FBF-2 only loses biological activity when its RNA-binding and partner interactions are both defective. These findings highlight the complementary contributions of RNA-binding and protein partner interactions to activity of an RNA-binding protein.

Codon optimality influences homeostatic gene expression in zebrafish

The ribosome plays a crucial role in translating mRNA into protein; however, the genetic code extends beyond merely specifying amino acids. Upon translation, codons, the three-nucleotide sequences interpreted by ribosomes, have regulatory properties affecting mRNA stability, a phenomenon known as codon optimality. Codon optimality has been previously observed in vertebrates during embryogenesis, where specific codons can influence the stability and degradation rates of mRNA transcripts. In our previous work, we demonstrated that codon optimality impacts mRNA stability in human cell lines. However, the extent to which codon content influences vertebrate gene expression in vivo remained unclear. In this study, we expand on our previous findings by demonstrating that codon optimality has a robust effect on homeostatic mRNA and protein levels in whole zebrafish during normal physiological conditions. Using reporters with nearly identical nucleotide sequences but different codon compositions, all expressed from the same genomic locus, we show that codon composition can significantly influence gene expression. This study provides new insights into the regulatory roles of codon usage in vertebrate gene expression and underscores the importance of considering codon optimality in genetic and translational research. These findings have broad implications for understanding the complexities of gene regulation and could inform the design of synthetic genes and therapeutic strategies targeting mRNA stability.

Insights into the Mode and Mechanism of Interactions Between RNA and RNA-Binding Proteins

Both RNA and protein play important roles in the process of gene expression and regulation, and it has been widely discussed that the interactions between RNA and protein affect gene transcription, translation efficiency, and post-translational modification. As an important class of proteins, RNA-binding proteins bind to RNA and affect gene expression in various ways. Here, we review the structural and functional properties of RNA-binding proteins and illustrate the specific modes of interactions between RNA and RNA-binding proteins and describe the involvement of some representative RNA-binding protein families in this network of action. Furthermore, we also explore the association that exists between RNA-binding proteins and the onset of diseases, as well as their potential in terms of serving as a therapeutic tool for the treatment of diseases. The in-depth exploration of the interactions between RNA and RNA-binding proteins reveals the dynamic process of gene expression and regulation, as well as offering valuable insights to advance the progress in the dissection of disease mechanisms and research and discovery of drugs, which promote the development of molecular biology.

RNA-binding protein IGF2BP1 is required for spermatogenesis in an age-dependent manner

Post-transcriptional regulation mediated by RNA binding proteins is crucial for male germline development. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), an RNA binding protein, is specifically expressed in human and mouse male gonads and is involved in manifold biological processes and tumorigenesis. However, the function of IGF2BP1 in mammalian spermatogenesis remains poorly understood. Herein, we generated an Igf2bp1 conditional knockout mouse model using Nanos3-Cre. Germ cell deficiency of Igf2bp1 in mice caused spermatogenic defects in an age-dependent manner, resulting in decreased numbers of undifferentiated spermatogonia and increased germ cell apoptosis. Immunoprecipitation-mass spectrometry analysis revealed that ELAV-like RNA binding protein 1, a well-recognized mRNA stabilizer, interacted with IGF2BP1. Single cell RNA-sequencing showed distinct mRNA profiles in spermatogonia from conditional knockout versus wide type mice. Further research showed that IGF2BP1 plays a vital role in the modulation of spermatogenesis by regulating Lin28a mRNA, which is essential for clonal expansion of undifferentiated spermatogonia. Thus, our results highlight the crucial effects of IGF2BP1 on spermatogonia for the long-term maintenance of spermatogenesis.

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. Serpine1 mRNA-binding protein 1 (SERBP1) is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. We defined SERBP1's interactome, uncovered novel roles in splicing, cell division and ribosomal biogenesis, and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.

C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes

Cys2-His2 zinc-finger proteins (C2H2-ZNFs) constitute the largest class of DNA-binding transcription factors (TFs) yet remain largely uncharacterized. Although certain family members, e.g., GTF3A, have been shown to bind both DNA and RNA, the extent to which C2H2-ZNFs interact with-and regulate-RNA-associated processes is not known. Using UV crosslinking and immunoprecipitation (CLIP), we observe that 148 of 150 analyzed C2H2-ZNFs bind directly to RNA in human cells. By integrating CLIP sequencing (CLIP-seq) RNA-binding maps for 50 of these C2H2-ZNFs with data from chromatin immunoprecipitation sequencing (ChIP-seq), protein-protein interaction assays, and transcriptome profiling experiments, we observe that the RNA-binding profiles of C2H2-ZNFs are generally distinct from their DNA-binding preferences and that they regulate a variety of post-transcriptional processes, including pre-mRNA splicing, cleavage and polyadenylation, and m6A modification of mRNA. Our results thus define a substantially expanded repertoire of C2H2-ZNFs that bind RNA and provide an important resource for elucidating post-transcriptional regulatory programs.

PAIP1 binds to pre-mRNA and regulates alternative splicing of cancer pathway genes including VEGFA

BACKGROUND

Poly (A) binding protein interacting protein 1 (PAIP1) has been shown to causally contribute to the development and progression of cancer. However, the mechanisms of the PAIP1 regulation in tumor cells remain poorly understood.

RESULTS

Here, we used a recently developed UV cross-linking and RNA immunoprecipitation method (iRIP-seq) to map the direct and indirect interaction sites between PAIP1 and RNA on a transcriptome-wide level in HeLa cells. We found that PAIP1 not only binds to 3'UTRs, but also to pre-mRNAs/mRNAs with a strong bias towards the coding region and intron. PAIP1 binding sites are enriched in splicing enhancer consensus GA-rich motifs. RNA-seq analysis revealed that PAIP1 selectively modulates the alternative splicing of genes in some cancer hallmarks including cell migration, the mTOR signaling pathway and the HIF-1 signaling pathway. PAIP1-regulated alternative splicing events were strongly associated with PAIP1 binding, demonstrating that the binding may promote selection of the nearby splice sites. Deletion of a PAIP1 binding site containing seven repeats of GA motif reduced the PAIP1-mediated suppression of the exon 6 inclusion in a VEGFA mRNA isoform. Proteomic analysis of the PAIP1-interacted proteins revealed the enrichment of the spliceosome components and splicing factors.

CONCLUSIONS

These findings suggest that PAIP1 is both a polyadenylation and alternative splicing regulator, that may play a large role in RNA processing via its role in alternative splicing regulation.

Fluorogenic RNA-based biomaterials for imaging and tracking the cargo of extracellular vesicles

Extracellular vesicles (EVs), or exosomes, play important roles in physiological and pathological cellular communication and have gained substantial traction as biological drug carriers. EVs contain both short and long non-coding RNAs that regulate gene expression and epigenetic processes. To fully capitalize on the potential of EVs as drug carriers, it is important to study and understand the intricacies of EV function and EV RNA-based communication. Here we developed a genetically encodable RNA-based biomaterial, termed EXO-Probe, for tracking EV RNAs. The EXO-Probe comprises an EV-loading RNA sequence (EXO-Code), fused to a fluorogenic RNA Mango aptamer for RNA imaging. This fusion construct allowed the visualization and tracking of EV RNA and colocalization with markers of multivesicular bodies; imaging RNA within EVs, and non-destructive quantification of EVs. Overall, the new RNA-based biomaterial provides a useful and versatile means to interrogate the role of EVs in cellular communication via RNA trafficking to EVs and to study cellular sorting decisions. The system will also help lay the foundation to further improve the therapeutic efficacy of EVs as drug carriers.

Unveiling the veil of RNA binding protein phase separation in cancer biology and therapy

RNA-binding protein (RBP) phase separation in oncology reveals a complex interplay crucial for understanding tumor biology and developing novel therapeutic strategies. Aberrant phase separation of RBPs significantly influences gene regulation, signal transduction, and metabolic reprogramming, contributing to tumorigenesis and drug resistance. Our review highlights the integral roles of RBP phase separation in stress granule dynamics, mRNA stabilization, and the modulation of transcriptional and translational processes. Furthermore, interactions between RBPs and non-coding RNAs add a layer of complexity, providing new insights into their collaborative roles in cancer progression. The intricate relationship between RBPs and phase separation poses significant challenges but also opens up novel opportunities for targeted therapeutic interventions. Advancing our understanding of the molecular mechanisms and regulatory networks governing RBP phase separation could lead to breakthroughs in cancer treatment strategies.

RNA-Binding Protein-Mediated Alternative Splicing Regulates Abiotic Stress Responses in Plants

The alternative splicing of pre-mRNA generates distinct mRNA variants from a pre-mRNA, thereby modulating a gene's function. The splicing of pre-mRNA depends on splice sites and regulatory elements in pre-mRNA, as well as the snRNA and proteins that recognize these sequences. Among these, RNA-binding proteins (RBPs) are the primary regulators of pre-mRNA splicing and play a critical role in the regulation of alternative splicing by recognizing the elements in pre-mRNA. However, little is known about the function of RBPs in stress response in plants. Here, we summarized the RBPs involved in the alternative splicing of pre-mRNA and their recognizing elements in pre-mRNA, and the recent advance in the role of RBP-mediated alternative splicing in response to abiotic stresses in plants. This review proposes that the regulation of pre-mRNA alternative splicing by RBPs is an important way for plants to adapt to abiotic stresses, and the regulation of alternative splicing by RBPs is a promising direction for crop breeding.

RNAelem: an algorithm for discovering sequence-structure motifs in RNA bound by RNA-binding proteins

Motivation

RNA-binding proteins (RBPs) play a crucial role in the post-transcriptional regulation of RNA. Given their importance, analyzing the specific RNA patterns recognized by RBPs has become a significant research focus in bioinformatics. Deep Neural Networks have enhanced the accuracy of prediction for RBP-binding sites, yet understanding the structural basis of RBP-binding specificity from these models is challenging due to their limited interpretability. To address this, we developed RNAelem, which combines profile context-free grammar and the Turner energy model for RNA secondary structure to predict sequence-structure motifs in RBP-binding regions.

Results

RNAelem exhibited superior detection accuracy compared to existing tools for RNA sequences with structural motifs. Upon applying RNAelem to the eCLIP database, we were not only able to reproduce many known primary sequence motifs in the absence of secondary structures, but also discovered many secondary structural motifs that contained sequence-nonspecific insertion regions. Furthermore, the high interpretability of RNAelem yielded insightful findings such as long-range base-pairing interactions in the binding region of the U2AF protein.

Availability and implementation

The code is available at https://github.com/iyak/RNAelem.