Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them

Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling

Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields of science and industry. Genomic data for Agaricomycetes are accumulating rapidly; however, this is not paralleled by improvements of gene annotations, which leave gene function notoriously poorly understood. We set out to improve our functional understanding of the model mushroom Coprinopsis cinerea by integrating a new, chromosome-level assembly, high-quality gene predictions, and functional information derived from broad gene-expression profiling data. The new annotation includes 5' and 3' untranslated regions (UTRs), polyadenylation sites (PASs), upstream open reading frames (uORFs), splicing isoforms, and microexons, as well as core gene sets corresponding to carbon starvation, light response, and hyphal differentiation. As a result, the genome of C. cinerea has now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.

Genome-Wide Analysis of Stable RNA Secondary Structures across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics

Small molecules targeting specific RNA-binding sites, including stable and transient RNA structures, are emerging as effective pharmacological approaches for modulating gene expression. However, little is understood about how stable RNA secondary structures are shared across organisms, which is an important factor in controlling drug selectivity. In this study, I provide an analytical pipeline named RNA secondary structure finder (R2S-Finder) to discover short, stable RNA structural motifs in humans, Escherichia coli (E. coli), SARS-CoV-2, and Zika virus by leveraging existing in vivo and in vitro genome-wide chemical RNA-probing datasets. I found several common features across the organisms. For example, apart from the well-documented tetraloops, AU-rich tetraloops are widely present in different organisms. I also validated that the 5' untranslated region (UTR) contains a higher proportion of stable structures than the coding sequences in humans and Zika virus. In general, stable structures predicted from in vitro (protein-free) and in vivo datasets are consistent across different organisms, indicating that stable structure formation is mostly driven by RNA folding, while a larger variation was found between in vitro and in vivo data for certain RNA types, such as human long intergenic noncoding RNAs (lincRNAs). Finally, I predicted stable three- and four-way RNA junctions that exist under both in vivo and in vitro conditions and can potentially serve as drug targets. All results of stable structures, stem-loops, internal loops, bulges, and n-way junctions have been collated in the R2S-Finder database (https://github.com/JingxinWangLab/R2S-Finder), which is coded in hyperlinked HTML pages and tabulated in CSV files.

IFIT3 RNA-binding activity promotes influenza A virus infection and translation efficiency

Host cells produce a vast network of antiviral factors in response to viral infection. The interferon-induced proteins with tetratricopeptide repeats (IFITs) are important effectors of a broad-spectrum antiviral response. In contrast to their canonical roles, we previously identified IFIT2 and IFIT3 as pro-viral host factors during influenza A virus (IAV) infection. During IAV infection, IFIT2 binds and enhances translation of AU-rich cellular mRNAs, including many IFN-simulated gene products, establishing a model for its broad antiviral activity. But, IFIT2 also bound viral mRNAs and enhanced their translation resulting in increased viral replication. The ability of IFIT3 to bind RNA and whether this is important for its function was not known. Here we validate direct interactions between IFIT3 and RNA using electromobility shift assays (EMSAs). RNA-binding site identification (RBS-ID) experiments then identified an RNA-binding surface composed of residues conserved in IFIT3 orthologs and IFIT2 paralogs. Mutation of the RNA-binding site reduced the ability IFIT3 to promote IAV gene expression and translation efficiency when compared to wild type IFIT3. The functional units of IFIT2 and IFIT3 are homo- and heterodimers, however the RNA-binding surfaces are located near the dimerization interface. Using co-immunoprecipitation, we showed that mutations to these sites do not affect dimerization. Together, these data establish the link between IFIT3 RNA-binding and its ability to modulate translation of host and viral mRNAs during IAV infection.

Analysis of RNA translation with a deep learning architecture provides new insight into translation control

Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human transcripts, our model learned hidden rules of translation control and achieved a near perfect prediction of canonical translation sites across entire human transcriptome. Surprisingly, this model revealed a new role of codon usage in regulating translation termination, which was experimentally validated. We also identified thousands of new open reading frames in mRNAs or lncRNAs, some of which were confirmed experimentally. The model trained with human mRNAs achieved high prediction accuracy of canonical translation sites in all eukaryotes and good prediction in polycistronic transcripts from prokaryotes or RNA viruses, suggesting a high degree of conservation in translation control. Collectively, we present TranslationAI (https://www.biosino.org/TranslationAI/), a general and efficient deep learning model for RNA translation that generates new insights into the complexity of translation regulation.

Non-Viral RNA Therapies for Non-Small Cell Lung Cancer and Their Corresponding Clinical Trials

Ribonucleic acid (RNA)-based therapies represent a promising class of drugs for the treatment of non-small cell lung cancer (NSCLC) due to their ability to modulate gene expression. Therapies leveraging small interfering RNA (siRNA), messenger RNA (mRNA), microRNA (miRNA), and antisense oligonucleotides (ASOs) offer various advantages over conventional treatments, including the ability to target specific genetic mutations and the potential for personalized medicine approaches. However, the clinical translation of these therapeutics for the treatment of NSCLC faces challenges in delivery due to their immunogenicity, negative charge, and large size, which can be mitigated with delivery platforms. In this review, we provide a description of the pathophysiology of NSCLC and an overview of RNA-based therapeutics, specifically highlighting their potential application in the treatment of NSCLC. We discuss relevant classes of RNA and their therapeutic potential for NSCLC. We then discuss challenges in delivery and non-viral delivery strategies such as lipid- and polymer-based nanoparticles that have been developed to address these issues in preclinical models. Furthermore, we provide a summary table of clinical trials that leverage RNA therapies for NSCLC [which includes their National Clinical Trial (NCT) numbers] to highlight the current progress in NSCLC. We also discuss how these NSCLC therapies can be integrated with existing treatment modalities to enhance their efficacy and improve patient outcomes. Overall, we aim to highlight non-viral strategies that tackle RNA delivery challenges while showcasing RNA's potential as a next-generation therapy for NSCLC treatment.

Exploring the Cytoplasmic Retention of CRISPR-Cas9 in Eukaryotic Cells: The Role of Nuclear Localization Signals and Ribosomal Interactions

Cas9 must be localized to the nucleus to access the genome of mammalian cells. For most proteins, adding a single nuclear localization signal (NLS) is sufficient to promote nuclear entry. However, Cas9 nuclear entry appears to be inefficient as multiple NLSs are typically added to Cas9. Here, we found that three different Cas9 variants interact with the ribosome in HEK293T cells, and that this interaction is RNA mediated. Following immunoprecipitation-mass spectrometry of cytoplasmic-localized Cas9-0NLS and nuclear-localized Cas9-4NLS constructs, we identified novel Cas9 interactors in postmitotic neurons, including KEAP1 and additional ribosomal subunits, the latter were enriched in Cas9-0NLS samples. Collectively, our results suggest that Cas9 is sequestered in the cytoplasm of mammalian cells, in part, via interaction with the ribosome. Increasing the number of NLSs on Cas9 and/or increasing the amount of cytoplasmic guide RNA has the potential to outcompete ribosomal RNA binding and promote efficient nuclear localization of CRISPR-Cas9 variants.

The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution

The nonstructural protein 1 (NSP1) of SARS-CoV-2 blocks the messenger RNA (mRNA) entry channel of the 40S ribosomal subunit, causing inhibition of translation initiation and subsequent degradation of host mRNAs. However, target mRNA specificity and how viral mRNAs escape NSP1-mediated degradation have not been clarified to date. Here we found that NSP1 acts as a translational switch capable of blocking or enhancing translation depending on how preinitiation complex, 43S-PIC, is recruited to the mRNA, whereas NSP1-mediated mRNA degradation mostly depends on codon usage bias. Thus, fast-translating mRNAs with optimal codon usage for human cells that preferentially recruit 43S-PIC by threading showed a dramatic sensitivity to NSP1. Translation of SARS-CoV-2 mRNAs escapes NSP1-mediated inhibition by a proper combination of suboptimal codon usage and slotting-prone 5' UTR. Thus, the prevalence of nonoptimal codons found in SARS-CoV-2 and other coronavirus genomes is favored by the distinctive effect that NSP1 plays on translation and mRNA stability.

Stress-induced changes in endogenous TP53 mRNA 5' regulatory region

Tumor suppressor protein p53 is regulated in a number of ways, including during initiation of TP53 mRNA translation. The 5' end of TP53 mRNA contains regulatory structures that enable noncanonical initiation using mechanisms that remain poorly described. Here we analyze per-nucleotide reactivity changes in the 5' end secondary structure of TP53 mRNA under in-cell conditions using A549 human lung carcinoma cells. We first construct a cell-free secondary structure model using SHAPE reagent 5-nitroisatoic anhydride on gently extracted and deproteinated RNA. We observe previously described regulatory features of the TP53 mRNA 5' end including two motifs which we refer to as long stem-loop (LSL) and short stem-loop (SSL), respectively. We observe a domain-forming helix that groups LSL and SSL, forming a three-helix junction. Applying in-cell selective 2' hydroxyl acylation analyzed by primer extension and mutational profiling, we assess reactivity profiles with unstressed cells and with chemically induced stress conditions expected to stimulate TP53 cap-independent translation. We analyze the effects of etoposide-induced DNA damage, CoCl2-induced hypoxia, and 5' cap inhibition with 4EGI-1 treatment. Identifying stress-associated changes in the TP53 5' end may help elucidate the role of regulatory RNA structure in cap-independent translation. Using ΔSHAPE, we identify in-cell protection sites that correspond with previously described RNA-protein binding sites on the apical loops of LSL and SSL. Furthermore, we identify several other potential interaction sites, some associated with specific types of stress. Some noteworthy changes include ΔSHAPE sites proximal to the start codons, at the three-helix junction and on the domain-forming helix. We summarize potential interactions on the cell-free secondary structure model.

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic data of individuals with European ancestry, introducing potential biases that remain uncharacterized. Here, we generate over 800 million full-length reads with long-read RNA-seq in 43 lymphoblastoid cell line samples from eight genetically-diverse human populations and build a cross-ancestry gene annotation. We show that transcripts from non-European samples are underrepresented in reference gene annotations, leading to systematic biases in allele-specific transcript usage analyses. Furthermore, we show that personal genome assemblies enhance transcript discovery compared to the generic GRCh38 reference assembly, even though genomic regions unique to each individual are heavily depleted of genes. These findings underscore the urgent need for a more inclusive gene annotation framework that accurately represents global transcriptome diversity.

Exploiting the SunTag system to study the developmental regulation of mRNA translation

The ability to quantitatively study mRNA translation using SunTag imaging is transforming our understanding of the translation process. Here, we expand the SunTag method to study new aspects of translation regulation in Drosophila. Repression of the maternal hunchback (hb) mRNA in the posterior of the Drosophila embryo is a textbook example of translational control. Using SunTag imaging to quantify translation of maternal SunTag-hb mRNAs, we show that repression in the posterior is leaky, as ∼5% of SunTag-hb mRNAs are translated. In the anterior of the embryo, the maternal and zygotic SunTag-hb mRNAs show similar translation efficiency despite having different untranslated regions (UTRs). We demonstrate that the SunTag-hb mRNA can be used as a reporter to study ribosome pausing at single-mRNA resolution, by exploiting the conserved xbp1 mRNA and A60 pausing sequences. Finally, we adapt the detector component of the SunTag system to visualise and quantify translation of the short gastrulation (sog) mRNA, encoding an essential secreted extracellular BMP regulator, at the endoplasmic reticulum in fixed and live embryos. Together, these tools will facilitate the future dissection of translation regulatory mechanisms during development.

A versatile toolbox for determining IRES activity in cells and embryonic tissues

Widespread control of gene expression through translation has emerged as a key level of spatiotemporal regulation of protein expression. A prominent mechanism by which ribosomes can confer gene regulation is via internal ribosomal entry sites (IRESes), whose functions have however, remained difficult to rigorously characterize. Here we present a set of technologies in embryos and cells, including IRES-mediated translation of circular RNA (circRNA) reporters, single-molecule messenger (m)RNA isoform imaging, PacBio long-read sequencing, and isoform-sensitive mRNA quantification along polysome profiles as a new toolbox for understanding IRES regulation. Using these techniques, we investigate a broad range of cellular IRES RNA elements including Hox IRESes. We show IRES-dependent translation in circRNAs, as well as the relative expression, localization, and translation of an IRES-containing mRNA isoform in specific embryonic tissues. We thereby provide a new resource of technologies to elucidate the roles of versatile IRES elements in gene regulation and embryonic development.

Revolutionizing immunization: a comprehensive review of mRNA vaccine technology and applications

Messenger RNA (mRNA) vaccines have emerged as a transformative platform in modern vaccinology. mRNA vaccine is a powerful alternative to traditional vaccines due to their high potency, safety, and efficacy, coupled with the ability for rapid clinical development, scalability and cost-effectiveness in manufacturing. Initially conceptualized in the 1970s, the first study about the effectiveness of a mRNA vaccine against influenza was conducted in 1993. Since then, the development of mRNA vaccines has rapidly gained significance, especially in combating the COVID-19 pandemic. Their unprecedented success during the COVID-19 pandemic, as demonstrated by the Pfizer-BioNTech and Moderna vaccines, highlighted their transformative potential. This review provides a comprehensive analysis of the mRNA vaccine technology, detailing the structure of the mRNA vaccine and its mechanism of action in inducing immunity. Advancements in nanotechnology, particularly lipid nanoparticles (LNPs) as delivery vehicles, have revolutionized the field. The manufacturing processes, including upstream production, downstream purification, and formulation are also reviewed. The clinical progress of mRNA vaccines targeting viruses causing infectious diseases is discussed, emphasizing their versatility and therapeutic potential. Despite their success, the mRNA vaccine platform faces several challenges, including improved stability to reduce dependence on cold chain logistics in transport, enhanced delivery mechanisms to target specific tissues or cells, and addressing the risk of rare adverse events. High costs associated with encapsulation in LNPs and the potential for unequal global access further complicate their widespread adoption. As the world continues to confront emerging viral threats, overcoming these challenges will be essential to fully harness the potential of mRNA vaccines. It is anticipated that mRNA vaccines will play a major role in defining and shaping the future of global health.

Identification and phylogenetic characterization of novel hunnivirus recombinant strains in cattle from Guangxi, China

Introduction

Hunnivirus (HuV), a member of the Picornaviridae family, is a single-stranded RNA virus associated with gastrointestinal issues in animals and poses potential zoonotic risks. While HuV has been detected in various animals, its prevalence and genetic characteristics in cattle remain poorly understood.

Methods

From 2021 to 2023, we collected 1,017 fecal samples from cattle across Guangxi, China, and analyzed them for HuV using RT-PCR. Phylogenetic and sequence analyses were conducted to assess the virus's genetic diversity and potential recombination events. Additionally, five HuV-positive samples were selected for whole-genome amplification and sequencing.

Results

The overall prevalence of HuV was 3.05%, with significantly higher detection rates in diarrheic cattle (9.59%) compared to healthy cattle (2.54%). Regional prevalence varied, with the highest in Liuzhou (5.66%) and the lowest in Nanning (1.51%). Phylogenetic analysis identified a novel recombinant strain with distinct evolutionary patterns in the P3 genomic region. Sequence analysis revealed low homology in the VP1 and P1 regions compared to known genotypes, suggesting the classification of these strains as a new genotype. Additionally, the 5' untranslated region (5'UTR) analysis confirmed the presence of type II Internal Ribosome Entry Sites (IRES), showing up to 91.8% nucleotide similarity with human parechovirus HPeV-3.

Discussion

These findings reveal significant genetic diversity and regional adaptation of HuV in cattle populations. The virus is associated with gastrointestinal symptoms, especially in areas with suboptimal farming conditions, and exhibits a potential for zoonotic transmission. This study provides a foundation for further research into the virus's pathogenicity and zoonotic risk, highlighting the need for continued surveillance to monitor its spread and evolution.

Post-Transcriptional Regulation of Gene Expression and the Intricate Life of Eukaryotic mRNAs

In recent years, there has been a growing appreciation for how regulatory events that occur either co- or post-transcriptionally contribute to the control of gene expression. Messenger RNAs (mRNAs) are extensively regulated throughout their metabolism in a precise spatiotemporal manner that requires sophisticated molecular mechanisms for cell-type-specific gene expression, which dictates cell function. Moreover, dysfunction at any of these steps can result in a variety of human diseases, including cancers, muscular atrophies, and neurological diseases. This review summarizes the steps of the central dogma of molecular biology, focusing on the post-transcriptional regulation of gene expression.

Signals from the niche promote distinct modes of translation initiation to control stem cell differentiation and renewal in the Drosophila testis

Stem cells have the unique ability among adult cells to give rise to cells of different identities. To do so, they must change gene expression in response to environmental signals. Much work has focused on how transcription is regulated to achieve these changes; however, in many cell types, transcripts and proteins correlate poorly, indicating that post-transcriptional regulation is important. To assess how translational control can influence stem cell fate, we use the Drosophila testis as a model. The testis niche secretes a ligand to activate the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway in two stem cell populations, germline stem cells (GSCs) and somatic cyst stem cells (CySCs). We find that global translation rates are high in CySCs and decrease during differentiation, and that JAK/STAT signaling regulates translation. To determine how translation was regulated, we knocked down translation initiation factors and found that the cap binding complex, eIF4F, is dispensable in differentiating cells, but is specifically required in CySCs for self-renewal, acting downstream of JAK/STAT activity. Moreover, we identify eIF3d1 as a key regulator of CySC fate, and show that two eIF3d1 residues subject to regulation by phosphorylation are critical to maintain CySC self-renewal. We further show that Casein Kinase II (CkII), which controls eIF3d1 phosphorylation, influences the binding of eIF3d and eIF4F in mammalian cells, and that CkII expression is sufficient to restore CySC function in the absence of JAK/STAT. We propose a model in which niche signals regulate a specific translation programme in which only some mRNAs are translated. The mechanism we identify allows stem cells to switch between modes of translation, adding a layer of regulation on top of transcription and providing cells with the ability to rapidly change gene expression upon receiving external stimuli.

Engineering Lipid Nanoparticles for mRNA Immunotherapy

Over the last decades, messenger RNA (mRNA) has emerged as a promising therapeutic modality, enabling the delivery of genetic instructions to cells for producing therapeutic proteins or antigens. As such, mRNA-based therapies can be developed for a wide range of conditions, including infections, cancer, metabolic disorders, and genetic diseases. Nevertheless, using mRNA therapeutically requires chemical modifications to reduce immunostimulatory effects and nanotechnology to prevent degradation and ensure intracellular delivery. Lipid nanoparticles (LNPs) have become the most effective delivery platform for mRNA therapeutics, which are primarily employed for vaccine purposes following local administration and hepatic applications following systemic administration. Here, we review the state-of-the-art LNP-mRNA technology and discuss its potential for immunotherapy. We first outline the requirements for mRNA to be used therapeutically, including the role of LNP-mediated delivery. Next, we highlight LNP-mRNA immunotherapy approaches for vaccination, immuno-oncology, and autoimmune disorders. In addition, we discuss challenges that are limiting LNP-mRNA's widespread use, including tunable biodistribution and immunostimulatory effects. Finally, we provide an outlook on how implementing approaches such as library screening and machine learning will guide the development of next-generation mRNA therapeutics.

Ornithine decarboxylase and its role in cancer

Cancer is among the leading causes of death worldwide. The effectiveness of conventional chemotherapy has some drawbacks, therefore, there is an urgency to develop novel strategies to fight this disease. Ornithine decarboxylase (ODC) is the most finely tuned enzyme of the polyamine (PA) biosynthesis pathway as it is regulated at different levels: transcriptional, translational, post-translational, and by feedback inhibition. In cancer, this enzyme is overexpressed due to its regulation by the protooncogene c-Myc, thus it has been proposed as a drug target against this disease. This review describes information regarding the biochemistry and regulation of the ODC at different levels and its role in cancer. Moreover, we discuss the molecules aiming on the inhibition of the ODC activity that have been tested as therapeutic options. ODC remains as a therapeutic opportunity that needs to be more explored.

Current innovations in mRNA vaccines for targeting multidrug-resistant ESKAPE pathogens

The prevalence of multidrug-resistant (MDR) ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, represents a critical global public health challenge. In response, mRNA vaccines offer an adaptable and scalable platform for immunotherapy against ESKAPE pathogens by encoding specific antigens that stimulate B-cell-driven antibody production and CD8+ T-cell-mediated cytotoxicity, effectively neutralizing these pathogens and combating resistance. This review examines recent advancements and ongoing challenges in the development of mRNA vaccines targeting MDR ESKAPE pathogens. We explore antigen selection, the nuances of mRNA vaccine technology, and the complex interactions between bacterial infections and antibiotic resistance. By assessing the potential efficacy of mRNA vaccines and addressing key barriers to their paraclinical implementation, this review highlights the promising function of mRNA-based immunization in combating MDR ESKAPE pathogens.

Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks

RNA inverse design is an essential part of many RNA therapeutic strategies. To date, there have been great advances in computationally driven RNA design. The current machine learning approaches can predict the sequence of an RNA given its 3D structure with acceptable accuracy and at tremendous speed. The design and engineering of RNA regulators such as riboswitches, however, is often more difficult, partly due to their inherent conformational switching abilities. Although recent state-of-the-art models do incorporate information about the multiple structures that a sequence can fold into, there is great room for improvement in modeling structural switching. In this work, a relational geometric graph neural network is proposed that explicitly incorporates alternative structures to predict an RNA sequence. Converting the RNA structure into a geometric graph, the proposed model uses edge types to distinguish between the primary structure, secondary structure, and spatial positioning of the nucleotides in representing structures. The results show higher native sequence recovery rates over those of gRNAde across different test sets (eg. 72% vs. 66%) and a benchmark from the literature (60% vs. 57%). Secondary-structure edge types had a more significant impact on the sequence recovery than the spatial edge types as defined in this work. Overall, these results suggest the need for more complex and case-specific characterization of RNA for successful inverse design.

Structural Features of 5' Untranslated Region in Translational Control of Eukaryotes

Gene expression is a complex process regulated at multiple levels in eukaryotic cells. Translation frequently represents a pivotal step in the control of gene expression. Among the stages of translation, initiation is particularly important, as it governs ribosome recruitment and the efficiency of protein synthesis. The 5' untranslated region (5' UTR) of mRNA plays a key role in this process, often exhibiting a complicated and structured landscape. Numerous eukaryotic mRNAs possess long 5' UTRs that contain diverse regulatory elements, including RNA secondary structures, specific nucleotide motifs, and chemical modifications. These structural features can independently modulate translation through their intrinsic properties or by serving as platforms for trans-acting factors such as RNA-binding proteins. The dynamic nature of 5' UTR elements allows cells to fine-tune translation in response to environmental and cellular signals. Understanding these mechanisms is not only fundamental to molecular biology but also holds significant biomedical potential. Insights into 5' UTR-mediated regulation could drive advancements in synthetic biology and mRNA-based targeted therapies. This review outlines the current knowledge of the structural elements of the 5' UTR, the interplay between them, and their combined functional impact on translation.

Optimizing Human Cell-Free System for Efficient Protein Production

We present a highly efficient human HEK293-based cell-free protein synthesis (CFPS) system capable of producing up to 300 μg/ml reporter protein. One of the limitations of the CFPS systems with respect to protein yield has been the decline of the protein-synthesizing activity of the system upon prolonged incubation. Though factors contributing to this decline in activity have been investigated in yeast, little is known about the factors in mammalian systems. We find that a rapid depletion of the components of the energy-regeneration system is a major factor behind the decreasing protein-synthesis activity in the HEK293-derived system. In addition, we demonstrate that a functional CFPS system can be prepared from other mammalian cell lines as evidenced by our use of a human neuroblastoma SH-SY5Y-derived CFPS system. We also find that exogenous creatine kinase (CK) is dispensable for the functionality of the energy-regeneration system in HEK293 due to the presence of a sufficiently high endogenous CK activity in an HEK293 cell-free extract.

OCT4 translationally promotes AKT signaling as an RNA-binding protein in stressed pluripotent stem cells

BACKGROUND

Despite numerous studies addressing the molecular mechanisms by which pluripotent stem cells (PSCs) maintain self-renewal and pluripotency under normal culture conditions, the fundamental question of how PSCs manage to survive stressful conditions remains largely unresolved. Post-transcriptional/translational regulation emerges to be vital for PSCs, but how PSCs coordinate and balance their survival and differentiation at translational level under extrinsic and intrinsic stress conditions is unclear.

METHODS

The high-throughput sequencing of cross-linking immunoprecipitation cDNA library (HITS-CLIP) was employed to decipher the genome-wide OCT4-RNA interactome in human PSCs, a combined RNC-seq/RNA-seq analysis to assess the role of OCT4 in translational regulation of hypoxic PSCs, and an OCT4-protein interactome to search for OCT4 binding partners that regulate cap-independent translation initiation. By taking the Heterozygous Knocking In N-terminal Tags (HKINT) approach that specifically disrupts the 5'-UTR secondary structure and tagging its protein product of the mRNA from one allele while leaving that from the other allele intact, we examined the effect of disrupting the OCT4/5'-UTR interaction on translation of AKT1 mRNA.

RESULTS

We revealed OCT4 as a bona fide RNA-binding protein (RBP) in human PSCs that bound to the 5'-UTR, 3'-UTR and CDS regions of mRNAs. Multiple known proteins participating in IRES-mediated translation initiation were detected in the OCT4-protein interactome, and a combined RNC-seq/RNA-seq analysis further confirmed a crucial role of OCT4 in translational regulation of PSCs in response to hypoxic stress. Remarkably, OCT4 bound to the GC-rich elements in the 5'-UTR of AKT1 and multiple PI3K/AKT-pathway-gene mRNAs, and promoted their translation initiation via IRES-mediated pathways under stress conditions. Specifically disrupting the AKT1 mRNA 5'-UTR structure and the OCT4/5'-UTR interaction by the HKINT approach significantly reduced the translation level of AKT1 that led to a higher susceptibility of PSCs to oxidative stress-induced apoptotic death and prioritized differentiation toward ectoderm and endoderm.

CONCLUSIONS

Our results reveal OCT4 as an anti-stress RBP for translational regulation that critically coordinates the survival and differentiation of PSCs in response to various stressors.

A capless hairpin-protected mRNA vaccine encoding the full-length Influenza A hemagglutinin protects mice against a lethal Influenza A infection

The success of mRNA vaccines in controlling the COVID 19 pandemic has confirmed the efficacy of synthetically synthesized mRNA in humans and has also provided a blueprint on how to design them in terms of molecular structure and cost. We describe a mRNA vector that, unlike linear mRNAs used in current vaccines/therapeutics, does not require a 5' cap to function. The described mRNA vector initiates translation from an internal ribosomal entry site (IRES) and contains specially designed self-folding secondary structures (hairpins) to protect the 5' end against degradation, dramatically improving its stability. The produced mRNA did not require any additional modifications for functionality. The 5' hairpins completely inhibited cap-dependent translation, and all vectors containing them required an IRES to express protein. When this capless mRNA vector was constructed to express the full-length Influenza A membrane protein hemagglutinin (HA), complexed with pre-formed lipid-based nanoparticles, and then injected into mice as a vaccine, it generated high titers of anti-HA antibodies and protected mice against a lethal dose of Influenza A.

Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed

Most genetic variants associated with complex traits and diseases occur in non-coding genomic regions and are hypothesized to regulate gene expression. To understand the genetics underlying gene expression variability, we characterize 14,324 ancestrally diverse RNA-sequencing samples from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and integrate whole genome sequencing data to perform cis and trans expression and splicing quantitative trait locus (cis-/trans-e/sQTL) analyses in six tissues and cell types, most notably whole blood (N=6,454) and lung (N=1,291). We show this dataset enables greater detection of secondary cis-e/sQTL signals than was achieved in previous studies, and that secondary cis-eQTL and primary trans-eQTL signal discovery is not saturated even though eGene discovery is. Most TOPMed trans-eQTL signals colocalize with cis-e/sQTL signals, suggesting many trans signals are mediated by cis signals. We fine-map European UK BioBank GWAS signals from 164 traits and colocalize the resulting 34,107 fine-mapped GWAS signals with TOPMed e/sQTL signals, finding that of 10,611 GWAS signals with a colocalization, 7,096 GWAS signals colocalize with at least one secondary e/sQTL signal. These results demonstrate that larger e/sQTL analyses will continue to uncover secondary e/sQTL signals, and that these new signals will benefit GWAS interpretation.

Internal cap-initiated translation for efficient protein production from circular mRNA

Circular mRNA faces challenges in enhancing its translation potential as an RNA therapeutic. Here we introduce two molecular designs that bolster circular mRNA translation through an internal cap-initiated mechanism. The first consists of a circular mRNA with a covalently attached N7-methylguanosine (m7G) cap through a branching structure (cap-circ mRNA). This modification allows circular mRNA to recruit translation machinery and produce proteins more efficiently than internal ribosome entry site (IRES)-containing circular mRNAs. Combining with an N1-methylpseudouridine (m1Ψ) modification, cap-circ mRNA exhibits a lower acute immunostimulatory effect, maintaining high translation in mice. The second design features the non-covalent attachment of an m7G cap to a circular mRNA through hybridization with an m7G cap-containing oligonucleotide, enhancing translation by more than 50-fold. This setup allows circular mRNAs to synthesize reporter proteins upon hybridizing with capped mRNAs or long non-coding RNAs and to undergo rolling circle-type translation. These advancements broaden the therapeutic applications of circular mRNAs by minimizing their molecular size, elevating translation efficiency and facilitating cell-type-selective translation.

The RNA-Binding Properties of Annexins

Annexins are a family of calcium-dependent phospholipid-binding proteins involved in crucial cellular processes such as cell division, calcium signaling, vesicle trafficking, membrane repair, and apoptosis. In addition to these properties, Annexins have also been shown to bind RNA, although this function is not universally recognized. In the attempt to clarify this important issue, we employed an integrated combination of experimental and computational approaches. Using the catRAPID algorithm, we accurately predicted known RNA-binding partners of Annexins, supported by experimental validation. We then constructed a virtual library of potential mRNA partners for Annexin A2, identifying regions within its structure directly involved in RNA binding. Beyond RNA interaction, some Annexins, notably AnxA7 and AnxA11, exhibit strong phase separation tendencies driven by their N-termini. These biophysical properties likely play roles in RNA trafficking and localization particularly in neurons, where they may influence processes such as synaptic plasticity, learning, and memory. Our predictions contribute to a deeper understanding of the Annexin function, emphasizing their potential impact on RNA regulation and cellular compartmentalization through phase separation and propose a powerful computational tool for the prediction of RNA-binding properties.

Mutations in the 5' untranslated region fine-tune translational control of heterologously expressed genes

Strict control of the expression levels of heterologously introduced protein-coding genes is important for the functional analysis of the protein of interest and its effective use in new situations. For this purpose, various promoters with different expression strengths, codon optimization, and expression stimulation by low-molecular-weight compounds are commonly used. However, methods to control protein expression levels by combining regulation of translation efficiency have not been studied in detail. We previously observed relatively high basal expression of Cre when it was heterologously expressed in fission yeast. Here, we used a fission yeast strain that is susceptible to centromere disruption, and thus highly sensitive to Cre levels, and report successful fine-tuning of heterologous Cre expression by modulating the Cre translation efficiency. To inhibit Cre translation initiation, we generated two mutations in the 5' untranslated region of the Cre mRNAs, both of which interfered with the scanning process of start codon recognition, mediated by specialized ribosomal subunits. These mutations successfully reduced the levels of exogenously expressed Cre to different degrees in fission yeast. Combining them with promoters of different strengths allowed us to conduct centromere disruption experiments in fission yeast. Our data indicate that modification of translational control is an additional tool in heterologous gene expression.

LMX1B haploinsufficiency due to variants in the 5'UTR as a cause of Nail-Patella syndrome

Nail-Patella syndrome (NPS) is a rare autosomal dominant condition due to haploinsufficiency of LMX1B, caused by loss-of-function variants affecting the coding sequence, or partial/whole deletions of the gene. In here, we describe two familial cases of NPS, carrying novel variants of the LMX1B 5'UTR region (-174C>T and -226G>A). To verify their pathogenic role, we carried out a functional characterization, both by reporter gene assays in heterologous systems and in patient's derived cells. We demonstrated that both variants impair LMX1B expression at post-transcriptional level. They introduce two upstream open reading frames (uORFs), out-of-frame with the main LMX1B coding sequence, generating transcripts detected by the non-sense mediated decay (NMD). We also demonstrated that the escape of the altered mRNA from NMD, if any, may lead to the synthesis of an aberrant LMX1B protein.

Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex

Recognition of "non-self" nucleic acids, including cytoplasmic dsDNA, dsRNA, or mRNAs lacking proper 5' cap structures, is critical for the innate immune response to viruses. Here, we demonstrate that short 5' untranslated regions (UTRs), a characteristic of many viral mRNAs, can also serve as a molecular pattern for innate immune recognition via the interferon-induced proteins IFIT2 and IFIT3. The IFIT2-IFIT3 heterodimer, formed through an intricate domain swap structure resolved by cryo-EM, mediates viral mRNA 5' end recognition, translation inhibition, and ultimately antiviral activity. Critically, 5' UTR lengths <50 nucleotides are necessary and sufficient to sensitize an mRNA to translation inhibition by the IFIT2-IFIT3 complex. Accordingly, diverse viruses whose mRNAs contain short 5' UTRs, such as vesicular stomatitis virus and parainfluenza virus 3, are sensitive to IFIT2-IFIT3-mediated antiviral activity. Our work thus reveals a pattern of antiviral nucleic acid immune recognition that takes advantage of the inherent constraints on viral genome size.

Full-length mRNA sequencing resolves novel variation in 5' UTR length for genes expressed during human CD4 T-cell activation

Isoform sequencing (Iso-Seq) uses long-read technology to produce highly accurate full-length reads of mRNA transcripts. Visualization of individual mRNA molecules can reveal new details of transcript variation within understudied portions of mRNA, such as the 5' untranslated region (UTR). Differential 5' UTRs may contain motifs, upstream open reading frames (uORFs), and secondary structures that can serve to regulate translation or further indicate changes in promoter usage, where transcriptional control may impact protein expression levels. To begin to explore isoform variation during T-cell activation, we generated the first Iso-Seq reference transcriptome of activated human CD4 T cells. Within this dataset, we discovered many novel splice- and end-variant transcripts. Remarkably, one in every eight genes expressed in our dataset was found to have a notable proportion of transcripts with 5' UTR lengthened by over 100 bp compared to the longest corresponding UTR within the Gencode dataset. Among these end-variant transcripts, two novel isoforms were identified for CXCR5, a chemokine receptor associated with T follicular helper cell (Tfh) function and differentiation. When investigated in a model cell system, these lengthened UTR conferred reduced transcript stability and, for one of these isoforms, short uORFs introduced by the added length altered protein expression kinetics. This study highlights instances in which current reference databases are incomplete relative to the information obtained by long-read sequencing of intact mRNA. Iso-Seq is thus a promising approach to better understanding the plasticity of promoter usage, alternative splicing, and UTR sequences that influence RNA stability and translation efficiency.

UTR-Insight: integrating deep learning for efficient 5' UTR discovery and design

The 5' UTR is critical for mRNA stability and translation efficiency in therapeutics. We developed UTR-Insight, a model integrating a pretrained language model with a CNN-Transformer architecture, explaining 89.1% of the mean ribosome load (MRL) variation in random 5' UTRs and 82.8% in endogenous 5' UTRs, surpassing existing models. Using UTR-Insight, we performed high-throughput in silico screening of hundreds of thousands of endogenous 5' UTRs from primates, mice, and viruses. The screened sequences increased protein expression by up to 319% compared to the human α-globin 5' UTR, and UTR-Insight-designed sequences achieved even greater expression levels than high-performing endogenous 5' UTRs.

Developing mRNA lipid nanoparticle vaccine effective for cryptococcosis in a murine model

Cryptococcus neoformans is considered a critical fungal pathogen by the World Health Organization and developing a vaccine for cryptococcosis is a top priority. Here, we employed mRNAs encoding an antigen(s) packaged in lipid nanoparticles (LNPs) to develop vaccines for cryptococcosis. Remarkably, when coupled with capsule adjuvant, vaccination with CDA1-LNPs protected the vast majority of mice from the otherwise lethal cryptococcosis. These results support the promise of mRNA-LNP vaccines against fungal diseases.

Finding functional microproteins

Genome-wide translational profiling has uncovered the synthesis in human cells of thousands of microproteins, a class of proteins traditionally overlooked in functional studies. Although an increasing number of these microproteins have been found to play critical roles in cellular processes, the functional relevance of the majority remains poorly understood. Studying these low-abundance, often unstable proteins is further complicated by the challenge of disentangling their functions from the noncoding roles of the associated DNA, RNA, and the act of translation. This review highlights recent advances in functional genomics that have led to the discovery of >1000 human microproteins required for optimal cell proliferation. Ongoing technological innovations will continue to clarify the roles and mechanisms of microproteins in both normal physiology and disease, potentially opening new avenues for therapeutic exploration.

5'-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges

RNA G-quadruplexes (rG4s) in 5'-UTRs represent complex regulatory elements capable of both inhibiting and activating mRNA translation through diverse mechanisms in eukaryotes. This review analyzes the evolution of our understanding of 5'-UTR rG4-mediated translation regulation, from early discoveries of simple translation inhibitors to the current recognition of their multifaceted regulatory roles. We discuss canonical and non-canonical rG4 structures, their interactions with regulatory proteins, including helicases and FMRP, and their function in both cap-dependent and IRES-mediated translation. Special attention is given to the synergistic effects between rG4s and upstream open reading frames (uORFs), stress-responsive translation regulation, and their role in repeat-associated non-AUG (RAN) translation linked to neurodegenerative diseases. We critically evaluate methodological challenges in the field, including limitations of current detection methods, reporter system artifacts, and the necessity to verify rG4 presence in endogenous transcripts. Recent technological advances, including genome editing and high-throughput sequencing approaches, have revealed that rG4 effects are more complex and context-dependent than initially thought. This review highlights the importance of developing more robust methodologies for studying rG4s at endogenous levels and carefully reevaluating previously identified targets, while emphasizing their potential as therapeutic targets in various diseases.

Micropeptides derived from long non-coding RNAs: Computational analysis and functional roles in breast cancer and other diseases

Long non-coding RNAs (lncRNAs), once thought to be mere transcriptional noise, are now revealing a hidden code. Recent advancements like ribosome sequencing have unveiled that many lncRNAs harbor small open reading frames and can potentially encode functional micropeptides. Emerging research suggests these micropeptides, not the lncRNAs themselves, play crucial roles in regulating homeostasis, inflammation, metabolism, and especially in breast cancer progression. This review delves into the rapidly evolving computational tools used to predict and validate lncRNA-encoded micropeptides. We then explore the diverse functions and mechanisms of action of these micropeptides in breast cancer pathogenesis, with a focus on their roles in various species. Ultimately, this review aims to illuminate the functional landscape of lncRNA-encoded micropeptides and their potential as therapeutic targets in cancer.

The antifungal peptide AnAFP from Aspergillus niger promotes nutrient mobilization through autophagic recycling during asexual development

Antifungal peptides are promising drug candidates to fight fungal infections in the clinics and agriculture. However, recent data suggest that antifungal peptides might also play a role within their own producing organism to survive nutrient limiting conditions. We have therefore studied the function of the antifungal AnAFP in Aspergillus niger in more detail. To achieve this, we established a Tet-on controlled anafp expression system, which allowed us to study a null and an overexpression phenotype in the same isolate. We observed that increased intracellular AnAFP expression reduces growth of A. niger and prematurely activates autophagy. Comparative transcriptome analyses of glucose-starving mycelium demonstrated that increased anafp expression strongly impacts expression of genes important for cell wall integrity and remodeling, as well as genes with a predicted function in metabolism and transport of carbohydrates, proteins, and lipids. Notably, genes encoding regulators of conidiophore development such as flbC and flbD became induced upon anafp overexpression. Fluorescent analyses of a Tet-on driven AnAFP::eGFP fusion protein congruently unraveled that AnAFP localizes to cell walls and septa of A. niger. Moreover, AnAFP::eGFP expression is spatially restricted to selected compartments only and affected cells displayed a sudden reduction in hyphal diameter. From these data we conclude that AnAFP is important to drive vegetative growth and sporulation in A. niger during nutrient limitation through autophagic recycling. We predict that AnAFP drives nutrient mobilization through selective cell lysis to ensure the survival of the whole colony during phases of starvation.

mRNA-LM: full-length integrated SLM for mRNA analysis

The success of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) messenger RNA (mRNA) vaccine has led to increased interest in the design and use of mRNA for vaccines and therapeutics. Still, selecting the most appropriate mRNA sequence for a protein remains a challenge. Several recent studies have shown that the specific mRNA sequence can have a significant impact on the translation efficiency, half-life, degradation rates, and other issues that play a major role in determining vaccine efficiency. To enable the selection of the most appropriate sequence, we developed mRNA-LM, an integrated small language model for modeling the entire mRNA sequence. mRNA-LM uses the contrastive language-image pretraining integration technology to combine three separate language models for the different mRNA segments. We trained mRNA-LM on millions of diverse mRNA sequences from several different species. The unsupervised model was able to learn meaningful biology related to evolution and host-pathogen interactions. Fine-tuning of mRNA-LM allowed us to use it in several mRNA property prediction tasks. As we show, using the full-length integrated model led to accurate predictions, improving on prior methods proposed for this task.

Hybrid exons evolved by coupling transcription initiation and splicing at the nucleotide level

Exons within transcripts are traditionally classified as first, internal or last exons, each governed by different regulatory mechanisms. We recently described the widespread usage of 'hybrid' exons that serve as terminal or internal exons in different transcripts. Here, we employ an interpretable deep learning pipeline to dissect the sequence features governing the co-regulation of transcription initiation and splicing in hybrid exons. Using ENCODE data from human tissues, we identified 80 000 hybrid first-internal exons. These exons often possess a relaxed chromatin state, allowing transcription initiation within the gene body. Interestingly, transcription start sites of hybrid exons are typically centered at the 3' splice site, suggesting tight coupling between splicing and transcription initiation. We identified two subcategories of hybrid exons: the majority resemble internal exons, maintaining strong 3' splice sites, while a minority show enrichment in promoter elements, resembling first exons. Diving into the evolution of their sequences, we found that human hybrid exons with orthologous first exons in other species usually gained 3' splice sites or whole exons upstream, while those with orthologous internal exons often gained promoter elements. Overall, our findings unveil the intricate regulatory landscape of hybrid exons and reveal stronger connections between transcription initiation and RNA splicing than previously acknowledged.

Protein binding in an mRNA 5'-UTR sterically hinders translation

Structures in the 5' untranslated regions (UTRs) of mRNAs can physically modulate translation efficiency by impeding the scanning ribosome or by sequestering the translational start site. We assessed the impact of stable protein binding in 5'- and 3'-UTRs on translation efficiency by targeting the MS2 coat protein to a reporter RNA via its hairpin recognition site. Translation was assessed from the reporter RNA when coexpressed with MS2 coat proteins of varying affinities for the RNA, and at different expression levels. Binding of high-affinity proteins in the 5'-UTR hindered translation, whereas no effect was observed when the coat protein was targeted to the 3'-UTR. Inhibition of translation increased with coat protein concentration and affinity, reaching a maximum of 50%-70%. MS2 proteins engineered to bind two reporter mRNA sites had a stronger effect than those binding a single site. Our findings demonstrate that protein binding in an mRNA 5'-UTR physically impedes translation, with the effect governed by affinity, concentration, and sterics.

The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis

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.

40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion

During eukaryotic translation initiation, the small (40S) ribosomal subunit is recruited to the 5' cap and subsequently scans the 5' untranslated region (5' UTR) of mRNA in search of the start codon. The molecular mechanism of mRNA scanning remains unclear. Here, using GFP reporters in Saccharomyces cerevisiae cells, we show that order-of-magnitude variations in the lengths of unstructured 5' UTRs have a modest effect on protein synthesis. These observations indicate that mRNA scanning is not rate limiting in yeast cells. Conversely, the presence of secondary structures in the 5' UTR strongly inhibits translation. Loss-of-function mutations in translational RNA helicases eIF4A and Ded1, as well as mutations in other initiation factors implicated in mRNA scanning, namely eIF4G, eIF4B, eIF3g and eIF3i, produced a similar decrease in translation of GFP reporters with short and long unstructured 5' UTRs. As expected, mutations in Ded1, eIF4B and eIF3i severely diminished translation of the reporters with structured 5' UTRs. Evidently, while RNA helicases eIF4A and Ded1 facilitate 40S recruitment and secondary structure unwinding, they are not rate-limiting for the 40S movement along the 5' UTR. Hence, our data indicate that, instead of helicase-driven translocation, one-dimensional diffusion predominately drives mRNA scanning by the 40S subunits in yeast cells.

Influence of 5'-UTR nucleotide composition on translation efficiency in Escherichiacoli

Translation initiation for 5'-UTR contributes primarily to the efficient protein expression in Escherichia coli. Many studies have focused on constructing random 5'-UTR libraries to investigate the impact of mRNA features on protein translation efficiency. However, the study on the effect of the absence of specific types of nucleotides in the entire 5'-UTR region on translation efficiency has not yet been reported. Here, we constructed four reporter plasmid libraries encoding the sfGFP fluorescent protein, each preceded by 5'-UTRs that lack one specific nucleotide (25B, 25D, 25H, 25V). Each library was transformed into E. coli cells, and the fluorescence distribution among the different libraries was analyzed by flow cytometer. Additionally, we quantified the activity of 256 unique 5'-UTR sequences and analyzed the impact of the corresponding mRNA sequence features on translation efficiency. We found that the 25D library, which lacks the C nucleotide, exhibited the highest overall translation efficiency compared to the other three libraries. Moreover, the minimum free energy and 16S rRNA hybridization energy of the 5'-UTR sequence could work coordinately to influence translation efficiency. The 5'-UTR sequences lacking the C nucleotide also achieve efficient protein translation. These findings may provide several guiding principles for precisely tuning protein expression.

Therapeutic applications of cell engineering using mRNA technology

Engineering and reprogramming cells has significant therapeutic potential to treat a wide range of diseases, by replacing missing or defective proteins, to provide transcription factors (TFs) to reprogram cell phenotypes, or to provide enzymes such as RNA-guided Cas9 derivatives for CRISPR-based cell engineering. While viral vector-mediated gene transfer has played an important role in this field, the use of mRNA avoids safety concerns associated with the integration of DNA into the host cell genome, making mRNA particularly attractive for in vivo applications. Widespread application of mRNA for cell engineering is limited by its instability in the biological environment and challenges involved in the delivery of mRNA to its target site. In this review, we examine challenges that must be overcome to develop effective therapeutics.

Small molecule-based regulation of gene expression in human astrocytes switching on and off the G-quadruplex control systems

A great deal of attention is being paid to strategies seeking to uncover the biology of the four-stranded nucleic acid structure G-quadruplex (G4) via their stabilization in cells with G4-specific ligands. The conventional definition of chemical biology implies that a complete assessment of G4 biology can only be achieved by implementing a complementary approach involving the destabilization of cellular G4s by ad hoc molecular effectors. We report here on an unprecedented comparison of the cellular consequences of G4 chemical stabilization by pyridostatin (PDS) and destabilization by phenylpyrrolocytosine (PhpC) at both transcriptome- and proteome-wide scales in patient-derived primary human astrocytes. Our results show that the stabilization of G4s by PDS triggers the dysregulation of many cellular circuitries, the most drastic effects originating in the downregulation of 354 transcripts and 158 proteins primarily involved in RNA transactions. In contrast, destabilization of G4s by PhpC modulates the G4 landscapes in a far more focused manner with upregulation of 295 proteins, mostly involved in RNA transactions as well, thus mirroring the effects of PDS. Our study is the first of its kind to report the extent of G4-associated cellular circuitries in human cells by systematically pitting the effect of G4 stabilization against destabilization in a direct and unbiased manner.

mRNA vaccine sequence and structure design and optimization: Advances and challenges

Messenger RNA (mRNA) vaccines have emerged as a powerful tool against communicable diseases and cancers, as demonstrated by their huge success during the coronavirus disease 2019 (COVID-19) pandemic. Despite the outstanding achievements, mRNA vaccines still face challenges such as stringent storage requirements, insufficient antigen expression, and unexpected immune responses. Since the intrinsic properties of mRNA molecules significantly impact vaccine performance, optimizing mRNA design is crucial in preclinical development. In this review, we outline four key principles for optimal mRNA sequence design: enhancing ribosome loading and translation efficiency through untranslated region (UTR) optimization, improving translation efficiency via codon optimization, increasing structural stability by refining global RNA sequence and extending in-cell lifetime and expression fidelity by adjusting local RNA structures. We also explore recent advancements in computational models for designing and optimizing mRNA vaccine sequences following these principles. By integrating current mRNA knowledge, addressing challenges, and examining advanced computational methods, this review aims to promote the application of computational approaches in mRNA vaccine development and inspire novel solutions to existing obstacles.

Spectrum and genotyping strategies of "dark" genetic matter in germline susceptibility genes of tumor syndromes

PURPOSE

Despite the widespread use of high-throughput genotyping strategies, certain mutation types remain understudied. We provide an overview of these often overlooked mutation types, with representative examples from common hereditary cancer syndromes.

METHODS

We conducted a comprehensive review of the literature and locus-specific variant databases to summarize the germline pathogenic variants discovered through non-routine genotyping methods. We evaluated appropriate detection and analysis methods tailored for these specific genetic aberrations. Additionally, we performed in silico splice predictions on deep intronic variants registered in the ClinVar database.

RESULTS

Our study suggests that, aside from founder mutations, most cases are sporadic. However, we anticipate a relatively high likelihood of splice effects for deep intronic variants. The findings underscore the significant clinical utility of genome sequencing techniques and the importance of applying relevant analysis methods.

Bacterial 5' UTR: A treasure-trove for post-transcriptional regulation

In bacteria, where gene transcription and translation occur concurrently, post-transcriptional regulation is acknowledged to be effective and precise. The 5' untranslated regions (5' UTRs) typically harbor diverse post-transcriptional regulatory elements, like riboswitches, RNA thermometers, small RNAs, and upstream open reading frames, that serve to modulate transcription termination, translation initiation, and mRNA stability. Consequently, exploring 5' UTR-derived regulatory elements is vital for synthetic biology and metabolic engineering. Over the past few years, the investigation of successive mechanisms has facilitated the development of various genetic tools from bacterial 5' UTRs. This review consolidates current understanding of 5' UTR regulatory functions, presents recent progress in 5' UTR-element design and screening, updates the tools and regulatory strategies developed, and highlights the challenges and necessity of establishing reliable bioinformatic analysis methods and non-model bacterial chassis in the future.

NaP-TRAP reveals the regulatory grammar in 5'UTR-mediated translation regulation during zebrafish development

The cis-regulatory elements encoded in an mRNA determine its stability and translational output. While there has been a considerable effort to understand the factors driving mRNA stability, the regulatory frameworks governing translational control remain more elusive. We have developed a novel massively parallel reporter assay (MPRA) to measure mRNA translation, named Nascent Peptide Translating Ribosome Affinity Purification (NaP-TRAP). NaP-TRAP measures translation in a frame-specific manner through the immunocapture of epitope tagged nascent peptides of reporter mRNAs. We benchmark NaP-TRAP to polysome profiling and use it to quantify Kozak strength and the regulatory landscapes of 5' UTRs in the developing zebrafish embryo and in human cells. Through this approach we identified general and developmentally dynamic cis-regulatory elements, as well as potential trans-acting proteins. We find that U-rich motifs are general enhancers, and upstream ORFs and GC-rich motifs are global repressors of translation. We also observe a translational switch during the maternal-to-zygotic transition, where C-rich motifs shift from repressors to prominent activators of translation. Conversely, we show that microRNA sites in the 5' UTR repress translation following the zygotic expression of miR-430. Together these results demonstrate that NaP-TRAP is a versatile, accessible, and powerful method to decode the regulatory functions of UTRs across different systems.

Identification of a minimal strong translation enhancer within the 5'-untranslated region of OsMac3 mRNA

The long 5' untranslated region (5'UTR) exhibits enhancer activity in translation of rice OsMac3 mRNA. In this report, we describe elements of OsMac3 5'UTR that may be responsible for its enhancer activity, including a long uORF and several secondary structure elements. OsMac3 5'UTR can be dissected into three stem-loop structures SL1, small SL and SL2, where the uORF starts within SL1 and ends within SL2. As expected, uORF inhibits translation of downstream ORF since deletion of the uORF AUG or the SL1 stem-loop increases translation by approximately two-fold. Thus, the 158 nt 3' region of the 5'UTR lacking SL1 together with the AUG uORF, which has significant enhancer activity, was named dMac3. We investigated two critical regions within dMac3 mRNA that influence its translation: SL2, which destabilization potentially decreases translation activity, and another 13 nt located downstream of SL2. We further confirmed that dMac3 promotes mRNA translation initiation in an in vitro translation system and during transient expression in either cultured cells or Nicotiana benthamiana leaves. Thus, the dMac3 5'UTR is a useful tool for efficient protein production in various in vitro and in vivo translation systems.

PPARγ-dependent remodeling of translational machinery in adipose progenitors is impaired in obesity

Adipose tissue regulates energy homeostasis and metabolic function, but its adaptability is impaired in obesity. In this study, we investigate the impact of acute PPARγ agonist treatment in obese mice and find significant transcriptional remodeling of cells in the stromal vascular fraction (SVF). Using single-cell RNA sequencing, we profile the SVF of inguinal and epididymal adipose tissue of obese mice following rosiglitazone treatment and find an induction of ribosomal factors in both progenitor and preadipocyte populations, while expression of ribosomal factors is reduced with obesity. Notably, the expression of a subset of ribosomal factors is directly regulated by PPARγ. Polysome profiling of the epididymal SVF shows that rosiglitazone promotes translational selectivity of mRNAs that encode pathways involved in adipogenesis and lipid metabolism. Inhibition of translation using a eukaryotic translation initiation factor 4A (eIF4A) inhibitor is sufficient in blocking adipogenesis. Our findings shed light on how PPARγ agonists promote adipose tissue plasticity in obesity.