What Are 3' UTRs Doing?

Genetic landscape of phospholamban cardiomyopathies

Phospholamban (PLN) is a key regulator of cardiac muscle contractility and has become a central focus in the study of cardiac disease. Variants in the PLN gene have been identified in patients with a wide range of phenotypes, including hypertrophic, dilated, and arrhythmogenic cardiomyopathies. The growing number of identified variants highlights the previously underappreciated role of PLN in cardiac pathophysiology. This review offers a comprehensive examination of the genetic landscape of PLN and evaluates the mechanistic effects of specific variants on cardiac function, aiming to uncover potential genotype-phenotype correlations. The rapidly expanding body of knowledge in this area is driving the development of advanced diagnostic and prognostic tools, as well as highly targeted therapeutic strategies. These advances underscore the importance of recognizing PLN's role in cardiac disease and the value of genetic testing for accurate diagnosis, prognosis, effective management, and early risk prediction for family members.

RNA epigenetic modifications as dynamic biomarkers in cancer: from mechanisms to clinical translation

RNA modifications are crucial for post-transcriptional gene regulation. Research on RNA modifications has become a novel frontier of epitranscriptomics. Up to now, over 170 kinds of modifications have been identified on mRNA and diverse non-coding RNA. Three classes of proteins (writers, erasers, and readers) regulate the addition, removal, and identification of epigenetic marks, thus affecting RNA biological functions. Increasing evidence identifies the dysregulation of RNA modifications in different cancer types and the therapeutic potential of targeting RNA-modifying enzymes. The ability of RNA modifications to improve mRNA stability and translation efficacy and decrease immunogenicity has been exploited for the clinical use of mRNA cancer vaccines. This review aims to shed light on several vital cap, tail, and internal modifications of RNA with a focus on the connection between RNA epigenetic pathways and cancer pathogenesis. We further explore the clinical potential of RNA modifications as dynamic biomarkers for cancer diagnosis, prognosis, and therapeutic response prediction, addressing both technological challenges and translational opportunities. Finally, we analyze the limitations of current studies and discuss the research focus in the future.

High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes

Concentrations of RNAs and proteins provide important determinants of cell fate. Robust gene circuit design requires an understanding of how the combined actions of individual genetic components influence both messenger RNA (mRNA) and protein levels. Here, we simultaneously measure mRNA and protein levels in single cells using hybridization chain reaction Flow-FISH (HCR Flow-FISH) for a set of commonly used synthetic promoters. We find that promoters generate differences in both the mRNA abundance and the effective translation rate of these transcripts. Stronger promoters not only transcribe more RNA but also show higher effective translation rates. While the strength of the promoter is largely preserved upon genome integration with identical elements, the choice of polyadenylation signal and coding sequence can generate large differences in the profiles of the mRNAs and proteins. We used long-read direct RNA sequencing to define the transcription start and splice sites of common synthetic promoters and independently vary the defined promoter and 5' UTR sequences in HCR Flow-FISH. Together, our high-resolution profiling of transgenic mRNAs and proteins offers insight into the impact of common synthetic genetic components on transcriptional and translational mechanisms. By developing a novel framework for quantifying expression profiles of transgenes, we have established a system for building more robust transgenic systems.

Transcriptome-wide RNA accessibility mapping reveals structured RNA elements and pervasive conformational rearrangements under stress

RNA structure plays a central role in post-transcriptional gene regulation, modulating RNA stability, translation, and interactions with RNA-binding proteins (RBPs). However, capturing RNA conformations at scale remains challenging. Here, we introduce DMS-TRAM-seq (Dimethyl Sulfate-Transcriptome-wide RNA Accessibility Mapping by sequencing), which probes RNA structure across nearly the entire transcriptome. Using DMS-TRAM-seq, we generated secondary structure predictions for over 9,000 human transcripts, including hundreds of non-coding RNAs, and identified more than 700 previously unannotated, high-confidence structured elements. Importantly, the enhanced coverage provided by DMS-TRAM-seq enabled comparative analyses, revealing RNAs that undergo structural rearrangements in response to cellular perturbations. Integration with RBP motifs and ribosome profiling uncovered altered RNA-RBP interactions during oxidative stress and showed that translation inhibition broadly drives RNAs toward their thermodynamically favored conformations. DMS-TRAM-seq enables interrogation of the RNA structurome and its plasticity at an unprecedented scale, opening new directions for elucidating the structural basis of RNA regulation.

LSM12 promotes the lung squamous cell carcinoma progression through mediating alternative splicing of ARRB1

Like-Smith protein 12 (LSM12), an RNA-binding protein, is highly expressed in tumor tissues of patients with lung squamous cell carcinoma (LUSC). However, the role of LSM12 in LUSC is unclear. In this study, overexpression of LSM12 promotes the proliferation, migration, and invasion and prevents the apoptosis of LUSC cells. In vivo, LSM12 accelerates the tumor growth and metastasis of LUSC cells using male BALB/c nude mice. Furthermore, we find that the Sterile alpha motif domain containing 4A (SAMD4A) is directly bound to the mRNA of LSM12 and accelerates the mRNA degradation. High-throughput omics analysis is performed to identify the potential target genes of LSM12 in LUSC cells. LSM12 regulates alternative splicing events and increases exon 13 skipped splicing of ARRB1 and mRNA expression. Our findings may provide fundamental research for the investigation of the development of LUSC and the potential role of LSM12 in LUSC cells.

Novel Fluorescent and Photoconvertible Fusions Reveal Dorsal Activator Dynamics

Over the last two decades, new in vivo and in cellulo imaging technologies have uncovered the inherently dynamic nature of transcriptional regulation in embryonic development and, in particular, in the fruit fly D. melanogaster. These technologies have made it possible to characterize the subnuclear and single-molecule dynamics of transcription factors. However, a lack of appropriate fluorescent protein fusions has, until now, limited these studies to only a few of the dozens of important transcription factors in the fruit fly gene regulatory network dictating early development. Here, we report the creation of four new fluorescent protein fusions to Dorsal, a member of the NF-κB/Rel family that initiates dorsal-ventral patterning. We generated and characterized two bright fluorescent protein fusions for Dorsal, meGFP and mNeonGreen, and two photoconvertible fluorescent protein fusions, mEos4a and Dendra2. We show that removal of the DsRed2 cassette commonly used to mark the CRISPR integration restores endogenous Dorsal mRNA and protein levels and enables the fusion allele to rescue a dorsal null allele, meeting the gold standard for endogenous function of a tagged protein in a fruit fly. We then demonstrate that our bright fluorescent protein fusions can be used to dissect the spatiotemporal dynamics of stable Dorsal clusters that traverse the nucleoplasm and uncovered that these clusters preferentially interact with active sites of Dorsal-modulated transcription. We further demonstrate that our photoconvertible fluorescent protein fusions make it possible to detect individual molecules of Dorsal in the nuclei of developing embryos. These new fluorescent protein fusions constitute a valuable resource for the community to elucidate the role of Dorsal activator dynamics in dictating fruit fly early embryonic development.

Recent strategies for enhanced delivery of mRNA to the lungs

mRNA-based therapies have emerged as a transformative tool in modern medicine, gaining significant attention following their successful use in COVID-19 vaccines. Delivery to the lungs offers several compelling advantages for mRNA delivery. The lungs are one of the most vascularized organs in the body, which provides an extensive surface area that can facilitate efficient drug transport. Local delivery to the lungs bypasses gastrointestinal degradation, potentially enhancing therapeutic efficacy. In addition, the extensive capillary network of the lungs provides an ideal target for systemic delivery. However, developing effective mRNA therapies for the lungs presents significant challenges. The complex anatomy of the lungs and the body's immune response to foreign particles create barriers to delivery. This review discusses key approaches for overcoming these challenges and improving mRNA delivery to the lungs. It examines both local and systemic delivery strategies aimed at improving lung delivery while mitigating off-target effects. Although substantial progress has been made in lung-targeted mRNA therapies, challenges remain in optimizing cellular uptake and achieving therapeutic efficacy within pulmonary tissues. The continued refinement of delivery strategies that enhance lung-specific targeting while minimizing degradation is critical for the clinical success of mRNA-based pulmonary therapies.

Genome-wide identification of the Medicago sativa L. MYB family and its transcriptional dynamics during pollen development

BACKGROUND

The myeloblastosis (MYB) gene family plays crucial roles in the development of anthers and the establishment of pollen morphology during plant growth. However, little is known about the role of MYB transcription factors in pollen development in alfalfa (Medicago sativa L.).

RESULTS

In this study, we identified 161 MsMYBs in the alfalfa genome, including 34 1R-MYBs, 123 R2R3-MYBs, 3 3R-MYBs, and 1 4R-MYBs (categorized by the number of repeats). These were classified into six subfamilies based on the phylogenetic analysis, conserved structural domains, and gene structures. All MsMYBs were predicted to be hydrophilic and localized in the cell nucleus. The promoter regions contained three classes of cis-regulatory elements related to pollen development, as well as a variable set of functionally diverse elements, including hormone responsiveness, growth and development, and stress responsiveness elements. A transcriptome and qRT-PCR analysis revealed 12 MsMYBs with anther-specific expression and exhibited distinct expression patterns. Some MsMYBs showed a close phylogenetic relationship with Arabidopsis MYBs related to pollen development, such as MsMYB49 and MsMYB100, were found to be localized in the nucleus upon subcellular localization analysis. This genetic proximity suggests a potential role for these MsMYBs in the developmental processes of pollen.

CONCLUSIONS

This study provides a comprehensive understanding of MsMYBs in alfalfa and elucidates their potential roles and expression patterns in pollen development.

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.

Transcriptome-wide association study of alternative polyadenylation identifies susceptibility genes in non-small cell lung cancer

Alternative polyadenylation (APA) plays a crucial role in cancer development and prognosis. However, the molecular characteristics of APA related to non-small cell lung cancer (NSCLC) susceptibility remain understudied, especially in East Asian populations. In this study, we constructed an atlas of APA-regulated 3' untranslated region (3'UTR) and profiled its genetic regulation in 747 lung tissue samples (including tumors and paired normal tissues) from 417 NSCLC Chinese patients. We verified a significant global shortening of 3'UTRs in tumor samples compared to normal samples and underscored the value of APA-regulation as a prognostic marker. The 3'UTR APA quantitative trait loci (3'aQTL) was identified by regressing the percentage of distal poly(A) site usage index (PDUI) value on genetic variants. We found that a significant proportion 3'aQTLs are independent of genetic regulation of expression and are specific in Chinese. We also conducted a 3'UTR APA transcriptome-wide association study (3'aTWAS) by integrating the APA regulation atlas with a genome-wide association study (GWAS) for NSCLC involving 7035 cases and 185,413 cancer-free controls. We identified NSCLC-associated genes, highlighting TUBB, TEAD3, and PPP1R10. Combining the consistent results from colocalization analysis, differential APA analysis, and survival analysis, we provide novel evidence for the role TUBB APA regulation in NSCLC and identified potential upstream regulators. Overall, our study profiled the APA regulation and highlighted the substantial role of APA in NSCLC carcinogenesis and prognosis in East Asian populations.

The Bright Future of mRNA as a Therapeutic Molecule

The rapid success of messenger (m) RNA vaccines against COVID-19 has pushed the mRNA to the forefront of drug research. The promise of mRNA-based therapeutics and vaccines in other areas is not new but is now emerging stronger. We review basic concepts, key historical aspects, and recent research on mRNA as a therapeutic molecule to fight infectious diseases and cancer. We also show a current patent perspective of this field. Altogether, we describe that the technology of mRNA as a therapeutic molecule is a rapidly moving field aiming for a bright future.

Optimizing mRNA translation efficiency through rational 5'UTR and 3'UTR combinatorial design

Advances in molecular medicine and biotechnology have demonstrated messenger RNA (mRNA)-based therapies to be a promising therapeutic modality for infectious diseases, genetic disorders, and cancers. However, key challenges persist, including low translation efficiency and short half-life of exogenous mRNA. The untranslated regions (UTRs) influence important parameters like mRNA stability and translation efficiency. This study adopted a combinatorial screening strategy to enhance exogenous mRNA translation efficiency by de novo designing 5'UTRs and combining them with multiple potential 3'UTRs. We designed a novel 5'UTR, 5UTR05, which exhibited comparable protein expression levels to the reference mRNA-1273 5'UTR that has been found to exhibit high expression in the COVID-19 vaccine development. Furthermore, the screening experiments found that combining 5UTR05 with both the 3'UTR of immunoglobulin heavy constant gamma 2 (IGHG2) and the 3'UTR of mitochondrially encoded 12S ribosomal RNA (mtRNR1) significantly improved mRNA translation efficiency, compared to individual 3'UTRs. Collectively, these findings provide valuable insights for UTR optimization strategies aimed at augmenting exogenous mRNA therapeutic translation. Continuing exploration of synergistic UTR combinations offers promise to advance customized mRNA constructs with optimized expression profiles tailored for diverse applications.

Long read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases

With ongoing improvements in the detection of complex genomic and epigenomic variations, long-read sequencing (LRS) technologies could serve as a unified platform for clinical genetic testing, particularly in rare disease settings, where nearly half of patients remain undiagnosed using existing technologies. Here, we report a simplified funnel-down filtration strategy aimed at enhancing the identification of small and large deleterious variants as well as abnormal episignature disease profiles from whole-genome LRS data. This approach detected all pathogenic single nucleotide, structural, and methylation variants in a positive control set (N = 76) including an independent sample set with known methylation profiles (N = 57). When applied to patients who previously had negative short-read testing (N = 51), additional diagnoses were uncovered in 10% of cases, including a methylation profile at the spinal muscular atrophy locus utilized for diagnosing this life-threatening, yet treatable, condition. Our study illustrates the utility of LRS in clinical genetic testing and the discovery of novel disease variation.

Technological breakthroughs and advancements in the application of mRNA vaccines: a comprehensive exploration and future prospects

mRNA vaccines utilize single-stranded linear DNA as a template for in vitro transcription. The mRNA is introduced into the cytoplasm via the corresponding delivery system to express the target protein, which then performs its relevant biological function. mRNA vaccines are beneficial in various fields, including cancer vaccines, infectious disease vaccines, protein replacement therapy, and treatment of rare diseases. They offer advantages such as a simple manufacturing process, a quick development cycle, and ease of industrialization. Additionally, mRNA vaccines afford flexibility in adjusting antigen designs and combining sequences of multiple variants, thereby addressing the issue of frequent mutations in pathogenic microorganisms. This paper aims to provide an extensive review of the global development and current research status of mRNA vaccines, with a focus on immunogenicity, classification, design, delivery vector development, stability, and biomedical application. Moreover, the study highlights current challenges and offers insights into future directions for development.

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.

A review of RNA nanoparticles for drug/gene/protein delivery in advanced therapies: Current state and future prospects

Nanotechnology involves the utilization of materials with exceptional properties at the nanoscale. Over the past few years, nanotechnologies have demonstrated significant potential in improving human health, particularly in medical treatments. The self-assembly characteristic of RNA is a highly effective method for designing and constructing nanostructures using a combination of biological, chemical, and physical techniques from different fields. There is great potential for the application of RNA nanotechnology in therapeutics. This review explores various nano-based drug delivery systems and their unique features through the impressive progress of the RNA field and their significant therapeutic promises due to their unique performance in the COVID-19 pandemic. However, a significant hurdle in fully harnessing the power of RNA drugs lies in effectively delivering RNA to precise organs and tissues, a critical factor for achieving therapeutic effectiveness, minimizing side effects, and optimizing treatment outcomes. There have been many efforts to pursue targeting, but the clinical translation of RNA drugs has been hindered by the lack of clear guidelines and shared understanding. A comprehensive understanding of various principles is essential to develop vaccines using nucleic acids and nanomedicine successfully. These include mechanisms of immune responses, functions of nucleic acids, nanotechnology, and vaccinations. Regarding this matter, the aim of this review is to revisit the fundamental principles of the immune system's function, vaccination, nanotechnology, and drug delivery in relation to the creation and manufacturing of vaccines utilizing nanotechnology and nucleic acids. RNA drugs have demonstrated significant potential in treating a wide range of diseases in both clinical and preclinical research. One of the reasons is their capacity to regulate gene expression and manage protein production efficiently. Different methods, like modifying chemicals, connecting ligands, and utilizing nanotechnology, have been essential in enabling the effective use of RNA-based treatments in medical environments. The article reviews stimuli-responsive nanotechnologies for RNA delivery and their potential in RNA medicines. It emphasizes the notable benefits of these technologies in improving the effectiveness of RNA and targeting specific cells and organs. This review offers a comprehensive analysis of different RNA drugs and how they work to produce therapeutic benefits. Recent progress in using RNA-based drugs, especially mRNA treatments, has shown that targeted delivery methods work well in medical treatments.

Arid4a Suppresses Breast Tumor Metastasis by Enhancing MTSS1 Expression via mRNA Stability

BACKGROUND

Tumor metastasis is one of the main causes of death in cancer patients; however, the mechanism controlling metastasis is unclear. The posttranscriptional regulation of metastasis-related genes mediated by AT-rich interactive domain-containing protein 4A (Arid4a), an RNA-binding protein (RBP), has not been elucidated.

METHODS

Bioinformatic analysis, qRT-PCR, immunohistochemistry, and immunoblotting were employed to determine the expression of Arid4a in breast tumor tissues and its association with the survival of cancer patients. In vitro and in vivo cellular experiments were used to assess the function of Arid4a in breast tumor metastasis. PCR array, RNA immunoprecipitation (RIP), luciferase, mRNA stability, RIP-ChIP, and EMSA were conducted to elucidate the potential mechanism of Arid4a.

RESULTS

Reduced expression of Arid4a in breast tumor samples was detected via bioinformatic analyses and experimental methods. Low Arid4a expression was significantly correlated with poor prognosis in breast cancer patients. Gain-of-function and silencing experiments confirmed the inhibitory effect of Arid4a on tumor metastasis in vitro and in vivo. Mechanistically, Arid4a preferentially stabilizes metastasis-suppressing transcripts, including metastasis suppressor 1 (MTSS1), tissue inhibitor of metalloproteinase 2 (TIMP2), retinoblastoma 1 (Rb1), and phosphatase and tensin homolog (PTEN), through binding to a conserved structural RNA element localized in the 3' untranslated region (3'UTR). The Arid domain of Arid4a is required for its mRNA stabilization and metastasis inhibition. Notably, the expression of Arid4a and metastasis-suppressing genes was positively correlated in human breast tumor tissues.

CONCLUSIONS

Arid4a was confirmed to suppress breast tumor metastasis progression by stabilizing the transcripts of tumor metastasis-suppressing genes, suggesting that Arid4a might be a potential therapeutic target for breast cancer treatment.

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.

METTL14-mediated m6A modification of ZFP14 inhibits clear cell renal cell carcinoma progression via promoting STAT3 ubiquitination

Therapeutic options for advanced clear cell renal cell carcinoma (ccRCC) are currently inadequate. Earlier research has shown that the enzyme methyltransferase-like 14 (METTL14) can suppress ccRCC development through the modification of N6-methyladenosine (m6A). This study further explored its complex biological functions and underlying molecular mechanisms. Here, we identified zinc finger protein 14 (ZFP14) as a novel target of METTL14-mediated m6A, and its under-expression was associated with ccRCC tumourigenesis and progression. Detailed investigations revealed that METTL14 interacted directly with the 3' untranslated region of ZFP14 mRNA, promoting m6A modification at two specific sites. These modifications were recognised by the protein insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), which stabilised and enhanced the expression of ZFP14 mRNA. Functionally, the METTL14/ZFP14 axis suppressed in vitro growth, migration and invasiveness and in vivo proliferation and metastasis of ccRCC cells. ZFP14 potentially regulated numbers of transcripts, among which matrix metalloproteinase 1/3 (MMP1/3) were validated to be under-expressed by ZFP14. Crucially, ZFP14 interacted with the signal transducer and activator of transcription 3 (STAT3), augmenting its K48-linked ubiquitination and destabilising it via the proteasome pathway. Moreover, ZFP14 repressed ccRCC cell in vivo growth and metastasis as well as decreasing MMP1/3 levels by under-expressing STAT3. These observations confirmed that ZFP14 served as both a novel target for METTL14-mediated m6A modification and a significant tumour suppressor in ccRCC, shedding light on the cellular and molecular operations in ccRCC and opening up possibilities for novel therapeutic strategies. KEY POINTS: ZFP14 under-expression is associated with ccRCC tumourigenesis and progression. METTL14-mediated m6A enhances ZFP14 mRNA stability and expression with IGF2BP2 as the reader in ccRCC. ZFP14 promotes the degradation of STAT3 by enhancing its K48-linked ubiquitination, inhibiting ccRCC progression.

mRNA stability fine-tunes gene expression in the developing cortex to control neurogenesis

RNA abundance is controlled by rates of synthesis and degradation. Although mis-regulation of RNA turnover is linked to neurodevelopmental disorders, how it contributes to cortical development is largely unknown. Here, we discover the landscape of RNA stability regulation in the cerebral cortex and demonstrate that intact RNA decay machinery is essential for corticogenesis in vivo. We use SLAM-seq to measure RNA half-lives transcriptome-wide across multiple stages of cortical development. Leveraging these data, we discover cis-acting features associated with RNA stability and probe the relationship between RNA half-life and developmental expression changes. Notably, RNAs that are up-regulated across development tend to be more stable, while down-regulated RNAs are less stable. Using compound mouse genetics, we discover CNOT3, a core component of the CCR4-NOT deadenylase complex linked to neurodevelopmental disease, is essential for cortical development. Conditional knockout of Cnot3 in neural progenitors and their progeny in the developing mouse cortex leads to severe microcephaly due to altered cell fate and p53-dependent apoptosis. Finally, we define the molecular targets of CNOT3, revealing it controls expression of poorly expressed, non-optimal mRNAs in the cortex, including cell cycle-related transcripts. Collectively, our findings demonstrate that fine-tuned control of RNA turnover is crucial for brain development.

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.

Blood-Based Whole-Genome Methylation Analysis of Yili Horses Pre- and Post-Racing

This study aims to analyze the whole-genome DNA methylation differences in Yili horses before and after racing, with the goal of identifying differentially methylated genes associated with racing performance and exploring the epigenetic mechanisms underlying exercise in horses. Blood samples were collected from the jugular veins of the top 3 Yili horses in a 5000 m race, which included 25 competitors, both prior to and within 5 min after the race. Genomic DNA was extracted, followed by sequencing using Whole-Genome Bisulfite Sequencing (WGBS) to assess DNA methylation levels, differentially methylated regions (DMRs), and differentially methylated genes (DMGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the identified DMGs to select candidate genes potentially associated with equine exercise. A total of 18,374 differentially methylated CG regions, 254 differentially methylated CHG regions, and 584 differentially methylated CHH regions were identified. A total of 4293 DMGs were anchored in gene bodies and 2187 DMGs in promoter regions. Functional analysis revealed that these DMGs were mainly enriched in terms related to binding and kinase activity, as well as pathways such as PI3K-Akt signaling and Kaposi sarcoma-associated herpesvirus infection. Further analysis indicated that genes such as IFNAR2, FGF4, and DGKH could be potential candidate genes associated with equine athletic performance. The findings of this study contribute to understanding the epigenetic regulatory mechanisms of equine athletic performance, providing a reference for further in-depth research on horse racing.

A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions

RNA-binding proteins (RBPs) are essential modulators in the regulation of mRNA processing. The binding patterns, interactions, and functions of most RBPs are not well-characterized. Previous studies have shown that motif context is an important contributor to RBP binding specificity, but its precise role remains unclear. Despite recent computational advances to predict RBP binding, existing methods are challenging to interpret and largely lack a categorical focus on RBP motif contexts and RBP-RBP interactions. There remains a need for interpretable predictive models to disambiguate the contextual determinants of RBP binding specificity in vivo . Here, we present a novel and comprehensive pipeline to address these knowledge gaps. We devise a Natural Language Processing-based decomposition method to deconstruct sequences into entities consisting of a central target k -mer and its flanking regions, then use this representation to formulate the RBP binding prediction task as a weakly supervised Multiple Instance Learning problem. To interpret our predictions, we introduce a deterministic motif discovery algorithm designed to handle our data structure, recapitulating the established motifs of numerous RBPs as validation. Importantly, we characterize the binding motifs and binding contexts for 71 RBPs, with many of them being novel. Finally, through feature integration, transitive inference, and a new cross-prediction approach, we propose novel cooperative and competitive RBP-RBP interaction partners and hypothesize their potential regulatory functions. In summary, we present a complete computational strategy for investigating the contextual determinants of specific RBP binding, and we demonstrate the significance of our findings in delineating RBP binding patterns, interactions, and functions.

Impact of rare non-coding variants on human diseases through alternative polyadenylation outliers

Although rare non-coding variants (RVs) play crucial roles in complex traits and diseases, understanding their mechanisms and identifying disease-associated RVs continue to be major challenges. Here we constructed a comprehensive atlas of alternative polyadenylation (APA) outliers (aOutliers), including 1334 3' UTR and 200 intronic aOutliers, from 15,201 samples across 49 human tissues. These aOutliers exhibit unique characteristics from transcription or splicing outliers, with a pronounced RV enrichment. Mechanistically, aOutlier-RVs alter poly(A) signals and splicing sites, and perturbation indeed triggers APA events. Furthermore, we developed a Bayesian-based APA RV prediction model, which successfully pinpointed a specific set of 1799 RVs impacting 278 genes with significantly large disease effect sizes. Notably, we observed a convergence effect between rare and common cancer variants, exemplified by regulation in the DDX18 gene. Together, this study introduced an APA-enhanced framework for genome annotation, underscoring APA's role in uncovering functional RVs linked to complex traits and diseases.

Effect of FABP4 Gene Polymorphisms on Fatty Acid Composition, Chemical Composition, and Carcass Traits in Sonid Sheep

Fatty acids (FAs) are a group of organic compounds that are regulated by polygenic and environmental factors and affect the taste, nutritional value, and quality of meat. Lamb meat is rich in FAs required by the human body, which has directed more attention to sheep research and meat production. The fatty acid-binding protein 4 (FABP4) gene is considered a candidate gene that can affect FA composition in livestock. Therefore, the aim of this study was to screen for genetic polymorphisms of FABP4 and confirm the association between these polymorphisms and FAs, chemical composition, and carcass traits in Sonid lambs. The results of the association study showed that g.57764667T>C, g.57764436T>G, g.57764242G>A, and g.57757988A>G were associated with the composition of certain long-chain FAs, and g.57764242G>A, g.57764436T>G, and g.57758026G>A were associated with free amino acid levels. In addition, g.57764667T>C and g.57757988A>G were associated with carcass weight and live weight in Sonid lambs. Therefore, the polymorphisms of the FABP4 gene are expected to be a genetic selection marker for superior traits in Sonid sheep breeding, which also provides new insights into how the ovine FABP4 gene affects traits of lamb quality.

In Silico Prediction of Maize microRNA as a Xanthine Oxidase Inhibitor: A New Approach to Treating Hyperuricemia Patients

INTRODUCTION

Hyperuricemia is characterized by increased uric acid (UA) in the body. The ability to block xanthine oxidase (XO) is a useful way to check how different bioactive molecules affect hyperuricemia. Previous reports showed the significant effect of corn against hyperuricemia disorder with its anti-XO activity. The identification of stable Zea mays miRNA (zma-miR) in humans has opened up a new avenue for speculation about its part in regulating novel human gene targets.

AIMS

The aim of this study was to investigate the prospects of zma-miRs in XO gene regulation, the possible mechanism, and the interaction analysis of the zma-miR-XO mRNA transcript.

METHOD

Significant features of miRNA-mRNA interaction were revealed using two popular miRNA target prediction software-intaRNA (version 3.3.1) and RNA hybrid (version 2.2.1) Results: Only 12 zma-miR-156 variants, out of the 325 zma-miR's sequences reported in the miRNA database, efficiently interact with the 3'UTR of the XO gene. Characteristics of miRNA-mRNA interaction were as follows: the positioning of zma-miR-156 variants shows that they all have the same 11-mer binding sites, guanine (G), and uracil (U) loops at the 13th and 14th positions from the 5' end, and no G: U wobble pairing. These factors are related to the inhibition of functional mRNA expression. Additionally, the zma-miR-156 variants exhibit a single-base variation (SBV), which leads to distinct yet highly effective alterations in their interaction pattern with the XO mRNA transcript and the corresponding free energy values.

CONCLUSION

Therefore, we propose that zma-miR-156 variants may be a promising new bioactive compound against hyperuricemia and related diseases.

SINE retrotransposons import polyadenylation signals to 3'UTRs in dog (Canis familiaris)

BACKGROUND

Messenger RNA 3' untranslated regions (3'UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA (AATAAA in DNA) is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3'UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy numbers. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands of Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may terminate transcript in some dog genes.

RESULTS

Each of the dog's nine Can-SINE consensus sequences carry an average of three AATAAA PASs on their sense strands but zero on their antisense strands. Consistent with the idea that Can-SINEs can terminate transcripts, we find that sense-oriented Can-SINEs are approximately ten times more frequent at 3' ends of 3'UTRs compared to further upstream within 3'UTRs. Furthermore, the count of AATAAA PASs on head-to-tail SINE sequences differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3'UTR ends are likely to carry an AATAAA motif on the mRNA sense strand while those further upstream are not. We identified loci where Can-SINE insertion has truncated or altered a 3'UTR of the dog genome (dog 3'UTR) compared to the human ortholog. Dog 3'UTRs have peaks of AATAAA PAS frequency at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp length for target site duplications (TSDs). All dog Can-SINE types favor integration at TSDs beginning with A(4).

CONCLUSION

Dog Can-SINE retrotransposition has imported AATAAA PASs into gene transcripts and led to alteration of 3'UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3'UTR regions but are retained at the far downstream end of 3'UTRs, which we infer reflects their role as termination sequences for these transcripts.

Polymorphism of the prolactin gene and its association with reproductive traits in F2 local crossed chickens

Background and Aim

Reproductive traits are crucial for genetic improvement in chickens. Prolactin (PRL) is a gene involved in a complex hormonal network that regulates reproduction in chickens. In this study, three local chicken breeds were crossed and had been produce a second filial (F2) generation, referred to as the F2 local crossed chicken. This study aimed to evaluate reproductive traits, identify single-nucleotide polymorphisms (SNPs), and assess genetic variation in the PRL gene of F2 local crossed chickens.

Materials and Methods

Data on reproductive traits, including body weight (BW) at first egg laying, total egg production (EP) at the first 90 days of laying eggs, egg weight (EW), egg length (EL), and egg width (EWd), and blood samples from 60 hens of F2 local crossed chicken (Merawang × Kampung Unggul Balitbangtan [KUB], n= 30; Murung Panggang × KUB [MP × KUB], n= 30) were collected. SNPs within PRL gene were identified using BioEdit version 7.0. Genetic diversity was calculated using Popgen 1.32. Statistical analysis of reproductive traits and its association with genotypes were assessed using Statistical Product and Service Solutions version 20.

Results

Crossing patterns had no significant effect on reproductive traits (p > 0.05), except for EWd (p < 0.05). Five polymorphic SNPs were identified in exon 5 of the PRL gene: 8052T>C, 8113G>C, 8187C>T, 8188G>A, and 8321C>T. Observed and expected heterozygosity range from 0.15-0.52 and 0.14-0.38, respectively. All SNPs were in the Hardy-Weinberg equilibrium based on Chi-square test (χ2 <3.841), except for SNP 8052T>C in F2 crossing of MP × KUB. SNP 8052T>C was significantly associated with BW (p < 0.05), with TT genotype chickens showing higher BW. SNP 8187C>T was associated with EW and EL (p < 0.05), with CT genotype chickens having higher values for both traits.

Conclusion

This study demonstrates the significant role of the PRL gene in influencing reproductive traits in F2 local crossed chickens. While crossing patterns showed limited impact, specific SNPs in exon 5 of the PRL gene were associated with BW, EW, and EL. The findings highlight PRL gene polymorphisms as valuable markers for improving reproductive traits in poultry breeding programs.

Associations Between Preoperative Shortness of Breath and Potassium Channels Gene Variations in Women With Breast Cancer

OBJECTIVES

Shortness of breath is a common symptom in patients with cancer. However, the mechanisms that underlie this troublesome symptom are poorly understood. Therefore, this study aimed to determine the prevalence of and associated risk factors for shortness of breath in women prior to breast cancer surgery and identify associations between shortness of breath and polymorphisms for potassium channel genes.

METHODS

Patients were recruited prior to breast cancer surgery and completed a self-report questionnaire on the occurrence of shortness of breath. Genotyping of single nucleotides polymorphism (SNPs) in potassium channel genes was performed using a custom array. Multiple logistic regression analyses were done to identify associations between the occurrence of shortness of breath and SNPs in ten candidate genes.

RESULTS

Of the 398 patients, 11.1% reported shortness of breath. These patients had a lower annual household income, a higher comorbidity burden, and a lower functional status. After controlling for functional status, comorbidity burden, genomic estimates of ancestry and self-reported race and ethnicity, the genetic associations that remained significant in the multiple regression analyses were for potassium voltage-gated channel subfamily D (KCND2) rs12673992, potassium voltage-gated channel modifier subfamily S (KCNS1) rs4499491, and potassium two pore channel subfamily K (KCNK2) rs4411107.

CONCLUSIONS

While these findings warrant replication, they suggest that alterations in potassium channel function may contribute to the occurrence of shortness of breath in women prior to breast cancer surgery.

Recent progress in mRNA cancer vaccines

The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.

Characterization of Myf6 and association with growth traits in swimming crab (Portunus trituberculatus)

BACKGROUND

Myogenic factor 6 (Myf6) plays an important role in muscle growth and differentiation. In aquatic animals and livestock, Myf6 contributes to improving meat quality and strengthening the accumulation of muscle flavor substances. However, studies on Myf6 gene polymorphisms in crustaceans have not been reported.

RESULTS

In the current study, we characterized the Myf6 gene for Portunus trituberculatus to better understand its biological function. The full-length cDNA of Myf6 was 4,101 bp, with a 915 bp open reading frame encoding 304 amino acids. In addition, Myf6 included a conservative bHLH domain. Homology analysis showed that Myf6 shared the highest identity with Penaeus vannamei. Expression pattern analysis of Myf6 in fast- and slow-growing groups revealed that the expression level of the latter was significantly higher than that of the former (P < 0.05). qPCR studies revealed that Myf6 was expressed in various tissues with the highest level in muscle. Nineteen single nucleotide polymorphisms (SNPs) of Myf6 were identified and five of them were significantly associated with growth-related traits of P. trituberculatus (P < 0.05), including full carapace width, carapace length, body height, and body weight. The AG and GG genotypes of g.1,187,834 A > G exhibited superior growth-related traits than the AA genotype. In the combined genotypes of g.1,187,324 C > T and g.1,187,834 A > G, the average body weight of diplotype D5 (CT-GG) was higher than that of diplotype D1 (CC-AA), D2 (CC-AG), and D3 (CC-GG) in a cultivated population. A haploblock was generated by three significant SNPs (g.1187834 A > G, g.1188616 A > G, and g.1189024 C > A), containing four haplotypes (AAA, AAC, AGC, and GGC), among which GGC haplotype exhibited superior growth traits (full carapace width and body weight) than the AAA haplotype.

CONCLUSIONS

To our knowledge, this is the first report on Myf6 in crustaceans. The results of this study would contribute to elucidating multiple functions of the Myf6 gene in crustaceans and exploring the potential as a candidate gene in selective breeding programs of P. trituberculatus.

Jasmonate induces translation of the Arabidopsis transfer RNA-binding protein YUELAO1, which activates MYC2 in jasmonate signaling

Jasmonate is ubiquitous in the plant kingdom and regulates multiple physiological processes. Although jasmonate signaling has been thoroughly investigated in Arabidopsis thaliana, most studies have focused on the transcriptional mechanisms underlying various jasmonate responses. It remains unclear whether (and how) translation-related pathways help improve transcription efficiency to modulate jasmonate signaling, which may enable plants to respond to stressful conditions effectively. Here, we demonstrate that jasmonate induces translation of the transfer RNA (tRNA)-binding protein YUELAO 1 (YL1) via a specific region in its 3' untranslated region (3' UTR). YL1 and its homolog YL2 redundantly stimulate jasmonate responses such as anthocyanin accumulation and root growth inhibition, with the YL1 3' UTR being critical for YL1-promoted jasmonate responses. Once translated, YL1 acts as an activator of the MYC2 transcription factor through direct interaction, and disrupting YL1 3' UTR impairs the YL1-mediated transcriptional activation of MYC2. YL1 enhances jasmonate responses mainly in a MYC2-dependent manner. Together, these findings reveal a translational mechanism involved in jasmonate signaling and advance our understanding of the transcriptional regulation of jasmonate signaling. The YL1 3' UTR acts as a crucial signal transducer that integrates translational and transcriptional regulation, allowing plants to respond to jasmonate in a timely fashion.

Cellular RNA interacts with MAVS to promote antiviral signaling

Antiviral signaling downstream of RIG-I-like receptors (RLRs) proceeds through a multi-protein complex organized around the adaptor protein mitochondrial antiviral signaling protein (MAVS). Protein complex function can be modulated by RNA molecules that provide allosteric regulation or act as molecular guides or scaffolds. We hypothesized that RNA plays a role in organizing MAVS signaling platforms. We found that MAVS, through its central intrinsically disordered domain, directly interacted with the 3' untranslated regions of cellular messenger RNAs. Elimination of RNA by ribonuclease treatment disrupted the MAVS signalosome, including RNA-modulated MAVS interactors that regulate RLR signaling and viral restriction, and inhibited phosphorylation of transcription factors that induce interferons. This work uncovered a function for cellular RNA in promoting signaling through MAVS and highlights generalizable principles of RNA regulatory control of immune signaling complexes.

SORBS2-Mediated inhibition of malignant behaviors in esophageal squamous cell carcinoma through TIMP3

BACKGROUND

Esophageal squamous cell carcinoma (ESCC) is characterized by high invasiveness and poor prognosis. The role of Sorbin and SH3 domain-containing protein 2 (SORBS2) in ESCC remains largely unexplored.

METHODS

The expression levels of SORBS2 in ESCC were detected using RNA-seq and proteomics data. The biological functions of SORBS2 in ESCC were investigated through in vivo and in vitro experiments. The mechanism of SORBS2 was explored using RIP-seq technology, which identified the key downstream molecule metalloproteinase-3 (TIMP3). The interaction between SORBS2 and TIMP3, including specific binding sites, was validated through RIP-qPCR and RNA pull-down assays. The impact of altered SORBS2 expression in ESCC on HUVECs was assessed using endothelial tube formation assays.

RESULTS

SORBS2 expression was significantly downregulated in ESCC tissues, and its decreased expression was associated with poor prognosis. Overexpression of SORBS2 in ESCC cell lines inhibited cell proliferation, migration, and invasion both in vitro and in vivo. Mechanistically, SORBS2 bound to the 3' UTR of TIMP3 mRNA, enhancing its stability and thereby regulating TIMP3 expression. Rescue experiments demonstrated that increased TIMP3 expression could reverse the promotive effects of SORBS2 knockdown on ESCC, confirming TIMP3 as a critical downstream molecule of SORBS2. Furthermore, downregulation of SORBS2 in ESCC cells was associated with activation of HUVEC functions, whereas upregulation of TIMP3 could reverse this effect. The SORBS2/TIMP3 axis may exert tumor suppressive effects by influencing extracellular matrix degradation.

CONCLUSION

This study confirms that SORBS2 inhibits ESCC tumor progression by regulating extracellular matrix degradation through TIMP3, providing a potential therapeutic target for future treatment interventions.

Therapeutic mRNAs for cancer immunotherapy: From structure to delivery

mRNA carries genetic information and is used for the synthesis of proteins, fragments of proteins, and peptides in the scope of biotechnology and medicine. Once introduced into cells, this mRNA gets translated into a corresponding protein with cellular machinery. All kinds of mRNA encoding any protein, peptide, and fragment of proteins have been designed to be used for various therapeutic goals, including cancerous diseases, immunotherapy, vaccine preparation, tissue engineering, and genetic disorders, among others. These vaccines encode tumor-specific antigens that stimulate the immune system to recognize and attack cancer cells. Additionally, mRNA can be designed to produce proteins that modulate immune checkpoints, thereby enhancing the immune system's ability to target cancer cells. Synthetic mRNA can also engineer immune cells, such as T cells, to improve their cancer-fighting capabilities. For instance, mRNA can be engineered to generate CAR T cells targeting specific antigens that are expressed in the cancer. Designed mRNA can encode functional proteins in patients suffering from genetic disorders characterized by an absence or defect in a particular protein. However, mRNA is intrinsically unstable and may require special mechanisms to protect it from degradation. mRNA delivery to target cells remains a challenge. Engineered nanocarriers containing mRNA can improve the efficiency and enable the delivery to specific sites, that can provide a stimulant or substance for therapeutic purposes. This combination may improve their stability and efficacy in multiple applications of therapies. The following chapter throws light on basic advances in mRNA-based cancer therapy and provides insights into the nanotherapeutics using mRNA in key preclinical developments and the evolving clinical landscape.

Role of the RNA binding protein IGF2BP1 in cancer multidrug resistance

The insulin-like growth factor-2 mRNA-binding protein 1 (IGF2BP1), a member of a conserved family of single-stranded RNA-binding proteins (IGF2BP1-3), is expressed in a broad range of fetal tissues, placenta and more than sixteen cancer types but only in a limited number of normal adult tissues. IGF2BP1is required for the transport from nucleus to cytoplasm of certain mRNAs that play essential roles in embryogenesis, carcinogenesis, and multidrug resistance (MDR), by affecting their stability, translation, or localization. The purpose of this review is to gather and present information on MDR mechanisms in cancer and the significance of IGF2BP1 in this context. Within this review, we will provide an overview of IGF2BP1, including its tissue distribution, expression, molecular targets in the context of tumorigenesis and its inhibitors. Our main focus will be on elucidating the interplay between IGF2BP1 and MDR, particularly with regard to chemoresistance mediated by ABC transporters.

Transcriptome analysis of two isolates of the tomato pathogen Cladosporium fulvum, uncovers genome-wide patterns of alternative splicing during a host infection cycle

Alternative splicing (AS) is a key element of eukaryotic gene expression that increases transcript and proteome diversity in cells, thereby altering their responses to external stimuli and stresses. While AS has been intensively researched in plants and animals, its frequency, conservation, and putative impact on virulence, are relatively still understudied in plant pathogenic fungi. Here, we profiled the AS events occurring in genes of Cladosporium fulvum isolates Race 5 and Race 4, during nearly a complete compatible infection cycle on their tomato host. Our studies revealed extensive heterogeneity in the transcript isoforms assembled from different isolates, infections, and infection timepoints, as over 80% of the transcript isoforms were singletons that were detected in only a single sample. Despite that, nearly 40% of the protein-coding genes in each isolate were predicted to be recurrently AS across the disparate infection timepoints, infections, and the two isolates. Of these, 37.5% were common to both isolates and 59% resulted in multiple protein isoforms, thereby putatively increasing proteome diversity in the pathogen by 31% during infections. An enrichment analysis showed that AS mostly affected genes likely to be involved in the transport of nutrients, regulation of gene expression, and monooxygenase activity, suggesting a role for AS in finetuning adaptation of C. fulvum on its tomato host during infections. Tracing the location of the AS genes on the fungal chromosomes showed that they were mostly located in repeat-rich regions of the core chromosomes, indicating a causal connection between gene location on the genome and propensity to AS. Finally, multiple cases of differential isoform usage in AS genes of C. fulvum were identified, suggesting that modulation of AS at different infection stages may be another way by which pathogens refine infections on their hosts.

Regulating translation in aging: from global to gene-specific mechanisms

Aging is characterized by a decline in various biological functions that is associated with changes in gene expression programs. Recent transcriptome-wide integrative studies in diverse organisms and tissues have revealed a gradual uncoupling between RNA and protein levels with aging, which highlights the importance of post-transcriptional regulatory processes. Here, we provide an overview of multi-omics analyses that show the progressive uncorrelation of transcriptomes and proteomes during the course of healthy aging. We then describe the molecular changes leading to global downregulation of protein synthesis with age and review recent work dissecting the mechanisms involved in gene-specific translational regulation in complementary model organisms. These mechanisms include the recognition of regulated mRNAs by trans-acting factors such as miRNA and RNA-binding proteins, the condensation of mRNAs into repressive cytoplasmic RNP granules, and the pausing of ribosomes at specific residues. Lastly, we mention future challenges of this emerging field, possible buffering functions as well as potential links with disease.

P-stalk ribosomes act as master regulators of cytokine-mediated processes

Inflammatory cytokines are pivotal to immune responses. Upon cytokine exposure, cells enter an "alert state" that enhances their visibility to the immune system. Here, we identified an alert-state subpopulation of ribosomes defined by the presence of the P-stalk. We show that P-stalk ribosomes (PSRs) are formed in response to cytokines linked to tumor immunity, and this is at least partially mediated by P-stalk phosphorylation. PSRs are involved in the preferential translation of mRNAs vital for the cytokine response via the more efficient translation of transmembrane domains of receptor molecules involved in cytokine-mediated processes. Importantly, loss of the PSR inhibits CD8+ T cell recognition and killing, and inhibitory cytokines like transforming growth factor β (TGF-β) hinder PSR formation, suggesting that the PSR is a central regulatory hub upon which multiple signals converge. Thus, the PSR is an essential mediator of the cellular rewiring that occurs following cytokine exposure via the translational regulation of this process.

Progressive polyadenylation and m6A modification of Ighg1 mRNA maintain IgG1 antibody homeostasis in antibody-secreting cells

Antigen-specific antibodies are generated by antibody-secreting cells (ASCs). How RNA post-transcriptional modification affects antibody homeostasis remains unclear. Here, we found that mRNA polyadenylations and N6-methyladenosine (m6A) modifications maintain IgG1 antibody production in ASCs. IgG heavy-chain transcripts (Ighg) possessed a long 3' UTR with m6A sites, targeted by the m6A reader YTHDF1. B cell-specific deficiency of YTHDF1 impaired IgG production upon antigen immunization through reducing Ighg1 mRNA abundance in IgG1+ ASCs. Disrupting either the m6A modification of a nuclear-localized splicing intermediate Ighg1 or the nuclear localization of YTHDF1 reduced Ighg1 transcript stability. Single-cell RNA sequencing identified an ASC subset with excessive YTHDF1 expression in systemic lupus erythematosus patients, which was decreased upon therapy with immunosuppressive drugs. In a lupus mouse model, inhibiting YTHDF1-m6A interactions alleviated symptoms. Thus, we highlight a mechanism in ASCs to sustain the homeostasis of IgG antibody transcripts by integrating Ighg1 mRNA polyadenylation and m6A modification.

Intracellular abundance, localization, and enzymatic activity of a saxitoxin biosynthesis enzyme, SxtG, in two sister subclones of the dinoflagellate Alexandrium catenella with extremely different levels of paralytic shellfish toxins

Paralytic shellfish poisoning is caused by saxitoxin (STX), and its analogues (paralytic shellfish toxins (PSTs)) produced by marine dinoflagellates. SxtA and SxtG are the most essential enzymes in STX biosynthesis. Previous studies investigated the abundance and subcellular localization (i.e., chloroplasts) of SxtA in dinoflagellates using immunostaining. The present study characterized SxtG, and positive signals were detected in sister subclones of Alexandrium catenella (Group I) with extremely different levels of PSTs. Multiplex fluorescence immunostaining detection of a PST-positive subclone revealed co-localization of SxtA and SxtG, suggesting that SxtG localizes to chloroplasts. In vitro amidino-transfer from arginine to Int-A', the first intermediate product in the biosynthesis, was presumed to be catalyzed by SxtG, and the reaction was established using crude extracts of PST-positive and negative A. catenella subclones. These analyses suggested that the PST-negative subclone expresses active SxtG but not SxtA. These findings support our hypothesis that decrease of SxtA leads to the loss of toxicity in the PST-negative subclone of A. catenella. Our results identified a key reaction that could enhance understanding of the biochemistry of STX biosynthesis in dinoflagellates.

Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence

Ostreid herpesvirus 1 (OsHV-1), a member of the family Malacoherpesviridae (order Herpesvirales), is a major pathogen of bivalves. However, the molecular details of the malacoherpesvirus infection cycle and its overall similarity to the replication of mammalian herpesviruses (family Orthoherpesviridae) remain obscure. Here, to gain insights into the OsHV-1 biology, we performed long-read sequencing of infected blood clams, Anadara broughtonii, which yielded over one million OsHV-1 long reads. These data enabled the annotation of the viral genome with 78 gene units and 274 transcripts, of which 67 were polycistronic mRNAs, 35 ncRNAs, and 20 natural antisense transcripts (NATs). Transcriptomics and proteomics data indicate preferential transcription and independent translation of the capsid scaffold protein as an OsHV-1 capsid maturation protease isoform. The conservation of this transcriptional architecture across Herpesvirales likely indicates its functional importance and ancient origin. Moreover, we traced RNA editing events using short-read sequencing and supported the presence of inosine nucleotides in native OsHV-1 RNA, consistent with the activity of adenosine deaminase acting on dsRNA 1 (ADAR1). Our data suggest that, whereas RNA hyper-editing is concentrated in specific regions of the OsHV-1 genome, single-nucleotide editing is more dispersed along the OsHV-1 transcripts. In conclusion, we reveal the existence of conserved pan-Herpesvirales transcriptomic architecture of the capsid maturation module and uncover a transcription-based viral counter defence mechanism, which presumably facilitates the evasion of the host ADAR antiviral system.

Sm-site containing mRNAs can accept Sm-rings and are downregulated in Spinal Muscular Atrophy

Sm-ring assembly is important for the biogenesis, stability, and function of uridine-rich small nuclear RNAs (U snRNAs) involved in pre-mRNA splicing and histone pre-mRNA processing. Sm-ring assembly is cytoplasmic and dependent upon the Sm-site sequence and structural motif, ATP, and Survival motor neuron (SMN) protein complex. While RNAs other than U snRNAs were previously shown to associate with Sm proteins, whether this association follows Sm-ring assembly requirements is unknown. We systematically identified Sm-sites within the human and mouse transcriptomes and assessed whether these sites can accept Sm-rings. In addition to snRNAs, Sm-sites are highly prevalent in the 3' untranslated regions of long messenger RNAs. RNA immunoprecipitation experiments confirm that Sm-site containing mRNAs associate with Sm proteins in the cytoplasm. In modified Sm-ring assembly assays, Sm-site containing RNAs, from either bulk polyadenylated RNAs or those transcribed in vitro , specifically associate with Sm proteins in an Sm-site and ATP-dependent manner. In cell and animal models of Spinal Muscular Atrophy (SMA), mRNAs containing Sm-sites are downregulated, suggesting reduced Sm-ring assembly on these mRNAs may contribute to SMA pathogenesis. Together, this study establishes that Sm-site containing mRNAs can accept Sm-rings and identifies a novel mechanism for Sm proteins in regulation of cytoplasmic mRNAs.

GRAPHICAL ABSTRACT

YTHDF1-regulated ALOX5 in retinal pigment epithelial cells under hypoxia enhances VEGF expression and promotes viability, migration, and angiogenesis of vascular endothelial cells

Upregulation of vascular endothelial growth factor (VEGF) and enhanced angiogenesis have been implicated in the severe progression of age-related macular degeneration (AMD). Abnormal arachidonate 5-lipoxygenase (ALOX5) is associated with AMD pathogenesis. However, no reports have shown the causal role of ALOX5 in angiogenesis during AMD. In the present study, ARPE-19 cells were exposed to hypoxia, an inducer of VEGF expression. Potential proteins implicated in AMD progression were predicted using bioinformatics. RNA affinity antisense purification-mass spectrometry (RAP-MS) was applied to identify the binding proteins of ALOX5 3'UTR. Expression of ALOX5 and YTH N6-methyladenosine RNA-binding protein 1 (YTHDF1) was detected by qRT-PCR and western blotting. VEGF expression and secretion were assessed by immunofluorescence and ELISA, respectively. The chicken embryo chorioallantoic membrane (CAM) was used to analyze the effect of ALOX5 on angiogenesis. RNA stability was assayed using the Actinomycin D assay. The results show that hypoxia promoted cell growth and increased VEGF expression in ARPE-19 cells. ALOX5 was associated with AMD progression, and hypoxia upregulated ALOX5 expression in ARPE-19 cells. ALOX5 silencing reduced VEGF expression induced by hypoxia in ARPE-19 cells. Moreover, the conditioned medium of ALOX5-silenced ARPE-19 cells could suppress the viability and migration of HUVECs and diminish angiogenesis in the CAM. Furthermore, YTHDF1 was validated to bind to ALOX5 3'UTR, and YTHDF1 promoted ALOX5 expression by elevating the stability of ALOX5 mRNA. In conclusion, our findings demonstrate that YTHDF1-regulated ALOX5 increases VEGF expression in hypoxia-exposed ARPE-19 cells and enhances the viability, migration, and angiogenesis of vascular endothelial cells.

Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation

RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc-finger families. We show that multiple ZFPs are previously unknown regulators of RNA splicing, alternative polyadenylation, stability, or translation. The examined ZFPs show widespread sequence-specific RNA binding and preferentially bind proximal to transcription start sites. Additionally, several ZFPs associate with their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DNA/RNA-associated protein that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation.

Advances in the design and delivery of RNA vaccines for infectious diseases

RNA medicines represent a paradigm shift in treatment and prevention of critical diseases of global significance, e.g., infectious diseases. The highly successful messenger RNA (mRNA) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were developed at record speed during the coronavirus disease 2019 pandemic. A consequence of this is exceptionally shortened vaccine development times, which in combination with adaptability makes the RNA vaccine technology highly attractive against infectious diseases and for pandemic preparedness. Here, we review state of the art in the design and delivery of RNA vaccines for infectious diseases based on different RNA modalities, including linear mRNA, self-amplifying RNA, trans-amplifying RNA, and circular RNA. We provide an overview of the clinical pipeline of RNA vaccines for infectious diseases, and present analytical procedures, which are paramount for characterizing quality attributes and guaranteeing their quality, and we discuss future perspectives for using RNA vaccines to combat pathogens beyond SARS-CoV-2.

Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal distinct regulation patterns and disease relevance

Studying the genetic regulation of protein expression (through protein quantitative trait loci (pQTLs)) offers a deeper understanding of regulatory variants uncharacterized by mRNA expression regulation (expression QTLs (eQTLs)) studies. Here we report cis-eQTL and cis-pQTL statistical fine-mapping from 1,405 genotyped samples with blood mRNA and 2,932 plasma samples of protein expression, as part of the Japan COVID-19 Task Force (JCTF). Fine-mapped eQTLs (n = 3,464) were enriched for 932 variants validated with a massively parallel reporter assay. Fine-mapped pQTLs (n = 582) were enriched for missense variations on structured and extracellular domains, although the possibility of epitope-binding artifacts remains. Trans-eQTL and trans-pQTL analysis highlighted associations of class I HLA allele variation with KIR genes. We contrast the multi-tissue origin of plasma protein with blood mRNA, contributing to the limited colocalization level, distinct regulatory mechanisms and trait relevance of eQTLs and pQTLs. We report a negative correlation between ABO mRNA and protein expression because of linkage disequilibrium between distinct nearby eQTLs and pQTLs.

Helicases DDX5 and DDX17 promote heterogeneity in HBV transcription termination in infected human hepatocytes

BACKGROUND & AIMS

Transcription termination fine-tunes gene expression and contributes to the specification of RNA function in eukaryotic cells. Transcription termination of HBV is subject to the recognition of the canonical polyadenylation signal (cPAS) common to all viral transcripts. However, the regulation of this cPAS and its impact on viral gene expression and replication is currently unknown.

METHODS

To unravel the regulation of HBV transcript termination, we implemented a 3' RACE (rapid amplification of cDNA ends)-PCR assay coupled to single molecule sequencing both in in vitro-infected hepatocytes and in chronically infected patients.

RESULTS

The detection of a previously unidentified transcriptional readthrough indicated that the cPAS was not systematically recognized during HBV replication in vitro and in vivo. Gene expression downregulation experiments demonstrated a role for the RNA helicases DDX5 and DDX17 in promoting viral transcriptional readthrough, which was, in turn, associated with HBV RNA destabilization and decreased HBx protein expression. RNA and chromatin immunoprecipitation, together with mutation of the cPAS sequence, suggested a direct role of DDX5 and DDX17 in functionally linking cPAS recognition to transcriptional readthrough, HBV RNA stability and replication.

CONCLUSIONS

Our findings identify DDX5 and DDX17 as crucial determinants of HBV transcriptional fidelity and as host restriction factors for HBV replication.

IMPACT AND IMPLICATIONS

HBV covalently closed circular (ccc)DNA degradation or functional inactivation remains the holy grail for the achievement of HBV cure. Transcriptional fidelity is a cornerstone in the regulation of gene expression. Here, we demonstrate that two helicases, DDX5 and DDX17, inhibit recognition of the HBV polyadenylation signal and thereby transcriptional termination, thus decreasing HBV RNA stability and acting as restriction factors for efficient cccDNA transcription and viral replication. The observation that DDX5 and DDX17 are downregulated in patients chronically infected with HBV suggests a role for these helicases in HBV persistence in vivo. These results open new perspectives for researchers aiming at identifying new targets to neutralise cccDNA transcription.

ADAR1 promotes cisplatin resistance in intrahepatic cholangiocarcinoma by regulating BRCA2 expression through A-to-I editing manner

Aberrant A-to-I RNA editing, mediated by ADAR1 has been found to be associated with increased tumourigenesis and the development of chemotherapy resistance in various types of cancer. Intrahepatic cholangiocarcinoma (iCCA) is a highly aggressive malignancy with a poor prognosis, and overcoming chemotherapy resistance poses a significant clinical challenge. This study aimed to clarify the roles of ADAR1 in tumour resistance to cisplatin in iCCA. We discovered that ADAR1 expression is elevated in iCCA patients, particularly in those resistant to cisplatin, and associated with poor clinical outcomes. Downregulation of ADAR1 can increase the sensitivity of iCCA cells to cisplatin treatment, whereas its overexpression has the inverse effect. By integrating RNA sequencing and Sanger sequencing, we identified BRCA2, a critical DNA damage repair gene, as a downstream target of ADAR1 in iCCA. ADAR1 mediates the A-to-I editing in BRCA2 3'UTR, inhibiting miR-3157-5p binding, consequently increasing BRCA2 mRNA and protein levels. Furthermore, ADAR1 enhances cellular DNA damage repair ability and facilitates cisplatin resistance in iCCA cells. Combining ADAR1 targeting with cisplatin treatment markedly enhances the anticancer efficacy of cisplatin. In conclusion, ADAR1 promotes tumour progression and cisplatin resistance of iCCA. ADAR1 targeting could inform the development of innovative combination therapies for iCCA.

Determination of the Frequency of BCL-2 Polymorphisms (c.-717C>A and c.*2364G>A) and LIF Polymorphism (c.*1414T>G) in Patients with Congenital Anomalies of the Kidney and Urinary Tract

Introduction

Congenital anomalies of the kidney and urinary tract (CAKUT) are characterized by several malformations. Its prevalence is 0.3-0.6% in live births. The B-cell lymphoma (BCL-2) gene regulates apoptosis, and the Leukemia Inhibitory Factor (LIF) gene plays a role in many biological processes, such as blastocyst growth and uterine preparation for implantation. In this study, two single nucleotide polymorphisms (SNPs) of the BCL-2 gene (rs2279115 and rs4987856) and one SNP of the LIF gene (rs929271) were investigated in CAKUT patients for the first time.

Methods

Hundred and twenty-nine CAKUT patients and 105 controls were enrolled in this study. We used polymerase chain reaction-restriction fragment length polymorphism for rs2279115 and rs929271 and SNaPshot for rs4987856. The χ2 test was used to compare discrete variables, and the independent sample t test was used to compare continuous variables.

Results

The allele frequencies for the rs2279115 and rs4987856 polymorphisms of BCL-2 and the rs929271 polymorphism of LIF were not significantly different between the patient and control groups (p = 0.162, p = 0.053, p = 0.635, respectively). However, the co-segregation analysis revealed a significant difference in the distribution of allele frequencies between the patient and control groups for two genetic variations: LIF rs929271 SNP and BCL-2 rs4987856 SNP (p = 0.034). The relative odds ratio was 2.444 (95% Confidence Interval (CI) 1.054-5.671).

Conclusion

This study, which is the first time in the literature, showed that changes in BCL-2 and LIF genes are associated with CAKUT disease.