Search Results (1,476)

Growth rate is a key trait influencing productivity in aquaculture species, and its regulation often differs between males and females. In this study, Nanopore full-length RNA sequencing was used to investigate sex-specific growth regulation in the liver and brain of Pelteobagrus ussuriensis. Male and female groups each included three fast-growing and three slow-growing individuals. In liver tissue, 332 differentially expressed genes were identified in males and 266 in females. Male-biased genes were mainly involved in lipid and cholesterol metabolism, including the peroxisome proliferator-activated receptor signaling pathway, whereas females showed broader metabolic regulation involving carbohydrate, amino acid, and lipid metabolism, as well as growth-related genes such as IGFBP1, ESR1, and PGR. In brain tissue, fewer growth-associated differences were observed, with 26 differentially expressed genes in males and 45 in females. Alternative splicing analysis revealed strong tissue specificity, with approximately 2903 events in liver and 7412 in brain, dominated by exon skipping in liver and alternative first exon usage in brain. Isoform-level analysis further identified transcript differences not detected at the gene level, highlighting the importance of transcript diversity in growth regulation. Full article

Background/Objectives: The RNA-binding protein CELF1 is crucial for cardiac development, but its role in cardiomyocyte hypertrophy is unclear. This study investigates the effects of acute CELF1 knockdown on alternative splicing and hypertrophic growth in cardiomyocytes. Methods: Neonatal rat cardiomyocytes (NRCMs) were transfected with two siRNAs targeting CELF1. Hypertrophy was assessed by cell size and expression of hypertrophic markers via qPCR and Western blot. RNA sequencing was performed in NRCMs to identify alternative splicing events. Tead1 function was tested by knockdown in NRCMs. Selected mechanistic assays were performed primarily in HeLa cells. Results: CELF1 knockdown in NRCMs increased cardiomyocyte size and upregulated hypertrophic markers, while its overexpression restored the phenotype. RNA-seq revealed that CELF1 knockdown alters the alternative splicing pattern. Specifically, the splicing of the transcription factor Tead1 shifted from the full-length long Tead1 isoform (Tead1-L) to the exon 4-skipped short isoform (Tead1-S). In HeLa cells, CELF1 interacted with hnRNPC, an m⁶A reader and splicing factor, and CELF1 perturbation correlated with changes in global m⁶A abundance. Conclusions: These findings suggest that CELF1 regulates hypertrophic phenotypes in cardiomyocytes and is associated with alternative splicing of Tead1. Full article

Background/Objectives: Nusinersen is a synthetic antisense RNA oligonucleotide employed in the management of spinal muscular atrophy, a rare neuromuscular disorder, by modulating the alternative splicing of the survival motor neuron 2 (SMN2) gene. GNR-100 represents the first generic version of the reference listed drug (RLD), containing nusinersen sodium as the active pharmaceutical ingredient. We performed comprehensive evaluations in accordance with FDA guidelines, including side-by-side comparative analyses of critical quality attributes, to thoroughly characterize the structural and functional properties of both nusinersen products. Results/Methods: GNR-100 was comprehensively demonstrated to be highly similar to RLD in terms of oligonucleotide structure, physicochemical properties, impurity profile, and in vitro cell-based assays for SMN-gene splice-switching and SMN-protein activity. Structural analyses confirmed that the oligonucleotide primary sequences and chemical structures were identical. The diastereomeric composition and higher-order structures were also similar between the proposed generic and the reference product. Comparable resistance to phosphodiesterase degradation and nearly identical melting temperatures of the oligonucleotide duplexes with their complementary strand further substantiated the structural sameness of the nusinersen products. The impurity profile of the proposed therapeutic oligonucleotide was consistent with that of RLD, and the collectively reduced levels of impurities, as assessed by orthogonal analytical methods, indicated no meaningful impact on the safety profile. Moreover, both products exhibited comparable biological activity in enhancing the production of full-length SMN2 mRNA transcripts and functional SMN protein in fibroblasts derived from SMA patients. Conclusions: These quality studies demonstrate that GNR-100 exhibits no significant differences from the licensed drug across structural, physicochemical, biophysical, and biological attributes, establishing its potential as a cost-effective therapeutic alternative for patients with spinal muscular atrophy. Full article

Tau proteins are microtubule-associated proteins that regulate axonal structure, dynamics, and transport, and their dysregulation underlies several neurodegenerative diseases. The MAPT gene produces multiple tau isoforms through alternative splicing, including the high-molecular-weight isoform known as Big tau, which contains an insert of the large 4a exon of approximately 250 amino acids. Big tau is predominantly expressed in neurons of the peripheral nervous system (PNS), cranial motor nuclei, and select neurons of the central nervous system (CNS) such as the cerebellum and brainstem. Developmental expression studies indicate a switch from low-molecular-weight isoforms of tau to Big tau during axonal maturation, suggesting that Big tau optimizes cytoskeletal dynamics to accommodate long axonal projections. Comparative sequence and biophysical analyses show that the exon-4a insert is highly acidic, intrinsically disordered, and evolutionarily conserved in its length but not its primary sequence, implying a structural role. Emerging modeling and in vitro assays suggest that the extended projection domain provided by the exon-4a insert spatially and electrostatically shields the aggregation-prone PHF6 and PHF6* motifs in tau’s microtubule-binding domain, thereby reducing β-sheet driven aggregation. This mechanism may explain why tauopathies that involve aggregation of tau have little effect on the PNS and specific regions of the CNS such as the cerebellum, where Big tau predominates. Transcriptomic and proteomic data further suggest that alternative Big tau variants, including 4a-L, are expressed in certain cancerous tissues, indicating broader roles in cytoskeletal remodeling beyond neurons. Despite its putative anti-aggregation properties, the physiological regulation, interaction partners, and in vivo mechanisms of Big tau remain poorly defined. This review summarizes what is known about Big tau and what is missing toward a better understanding of how expansion via inclusion of exon 4a modifies tau’s structural and functional properties. Our purpose is to inspire future studies that could lead to novel therapeutic strategies to mitigate tau aggregation in neurodegenerative diseases. Full article

Sexual size dimorphism (SSD) refers to the phenomenon where males and females of the same species exhibit differences in overall or partial body size, and it is widespread among mammals, birds, reptiles, and fish. Notably, this dimorphism is significantly influenced by the sexually dimorphic secretion of growth hormone (gh), a key pituitary-derived growth regulator. Commonly, the secretion of gh is positively regulated by glucagon family members such as growth hormone-releasing hormone (ghrh) and adenylate cyclase-activating polypeptide 1 (adcyap1). To explore the stimulators for pituitary hormones (especially gh) in the teleost, we performed genome-wide identification and functional characterization of the glucagon family on Chinese tongue sole (Cynoglossus semilaevis) that exhibits typical female-biased sexual size dimorphism. Four members of adcyap1/vasoactive intestinal polypeptide(vip)/ghrh family and ten members of their receptor family were identified. Expression pattern analysis revealed high expression of adenylate cyclase-activating polypeptide 1b (adcyap1b) and its receptors in the brain. Moreover, two alternative splice variants for the adcyap1b gene were discovered, resulting from the skipping of exon 4. Following the acquisition of the two eukaryotic recombinant protein splice variants (ADCYAP1b_tv1 and ADCYAP_tv2) from HEK 293T cells, incubation experiments were conducted using C. semilaevis pituitary cell line. The results demonstrated that both variants promoted the expression of gh, pro-opiomelanocortin (pomc), and corticoliberin (crh), but ADCYAP1b_tv1 had a significantly stronger effect and uniquely stimulated prolactin (prl) and somatolactin (sl). This study demonstrates a functional divergence between the two ADCYAP1b splice variants in teleosts, with ADCYAP1b_tv1 acting as a more potent and versatile pituitary hormone stimulator. Further research on their receptor-binding affinity and downstream signaling pathways would be valuable for exploring the mechanism underlying sexual size dimorphism. Full article

Background/Objectives: Long-term exposure to polychlorinated biphenyls (PCBs), including the mixture of PCBs in Aroclor1260 (Ar1260), results in metabolic dysfunction-associated steatotic liver disease (MASLD) in mice and humans. While the effects of PCBs on gene expression are well-documented using short-read RNA sequencing, the regulatory roles of alternative splicing (AS) and differential transcript usage (DTU) are uncharacterized. AS has been implicated in MASLD. Previously, we reported that chronic (34 wks.) exposure of normal, low-fat-diet (LFD)-fed male mice to Ar1260 resulted in 12 hepatic RNA modifications. Proteomic analysis of these same liver samples identified Ar1260 exposure-associated changes in selenoproteins: GPX4 and SELENBP2 were increased and SELENOS and SELENOF were reduced. Methods: Here we used long-read isoform sequencing (IsoSeq) to identify DTU in four genes in the Ar1260-exposed livers: Adpgk, Blvra, Mup2, and Ndufaf6. Results: Network analysis of the corresponding proteins revealed a strong association with pathways relevant to MASLD including lipid metabolism, glycolysis, and oxidative stress. Conclusions: These findings suggest that PCB exposure alters the transcript isoform landscape of key metabolic genes involved in MASLD. Full article

Alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism in eukaryotes. Plants can cope with complex environmental changes through AS. In this paper, we found that AS plays an important role in plant responses to biotic and abiotic stresses. First, we note that under biotic stress (e.g., disease, insects), AS regulates the expression of immune-related genes and produces splice variants with different functions to regulate plant disease resistance. Second, under abiotic stress (e.g., drought, cold, heat, salt), plants generate functional splice variants via different AS events and change the original function of the gene. At the same time, we also found that splicing factors and regulatory elements, such as serine/arginine-rich proteins associated with AS, are also involved in the regulation of the expression of related resistance genes to improve plant stress resistance. Therefore, this review summarizes the recent progress on the main types of AS events, the functions of related splicing factors, and the action routes and regulatory mechanisms of splice variants. We hope to provide a reference for further understanding of the stress response mechanism of plant AS and provide a theoretical basis for the breeding of resistant varieties. Full article

Genome-wide studies have identified significant allelic associations between genetic variants in or near the IKZF1 gene and multiple autoimmune disorders. IKZF1, encoding the transcription factor IKAROS, produces at least 10 distinct transcripts. To explore the impact of alternative splicing of IKZF1 on the function of mature T cells and the risk of autoimmunity, we generated a panel of human T-cell clones with truncating mutations in IKZF1 exons 4, 6, or both. Differences in gene expression, chromatin accessibility, and protein abundance among clones were assessed by RNA-seq, ATAC-seq, and immunoblotting. Clones with single targeting events clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation of IKZF1 splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKAROS family members. Our results suggest that even modest alterations of IKZF1 splicing can have significant effects on gene expression and function in mature T cells, potentially contributing to autoimmunity in susceptible individuals. Full article

Epithelial–mesenchymal plasticity encompasses a spectrum of epithelial and mesenchymal identity states that enable cells to adapt to changing biological contexts. While CD44 isoform usage and epithelial splicing regulators ESRP1/2 are well-characterized in cancer-associated epithelial–mesenchymal transition (EMT), their regulation across physiological, non-transformed identity states remains less well defined. Here, we employed a non-malignant human cellular system comprising primary dermal fibroblasts, induced pluripotent stem (iPS) cells, and iPS-derived mesenchymal stem cells (iPS-MSCs) to define discrete epithelial, intermediate epithelial/mesenchymal, and mesenchymal identity states positioned along an epithelial–mesenchymal identity axis. Morphological assessment, lineage marker profiling, and RT-qPCR analyses revealed reproducible population-level stratification of these states. CD44 expression and alternative splicing followed this hierarchy, with CD44s predominating in fibroblasts, broad variant exon inclusion in iPS cells, and intermediate patterns in iPS-MSCs. ESRP1 expression mirrored CD44 splicing architecture, and ESRP1 silencing in iPS cells induced a shift toward CD44s, confirming its functional contribution to epithelial-associated CD44 splicing. In contrast, Notch-related transcriptional readouts displayed distinct, context-dependent profiles across the examined identity states. Together, this study establishes a tractable non-transformed human model that captures selected molecular features associated with epithelial–mesenchymal plasticity beyond malignant contexts. Full article

The neurofibromin 1 (NF1) splice-site mutation c.61-2A>G (rs1131691100) is a rare, pathogenic, autosomal dominant variant that disrupts NF1 tumor-suppressor function, causing neurofibromatosis type 1 (NF1). Its pathogenic mechanism is poorly understood, and the potential for personalized therapeutic genome editing remains unknown due to the absence of a standard framework for investigating splicing disorders. Here, we performed a comprehensive multi-omics analysis of a de novo c.61-2A>G case from South Korea, integrating short- and long-read whole genome sequencing, whole transcriptome sequencing, and methylation profiling. We confirm that c.61-2A>G abolishes the canonical splice acceptor site, activating a cryptic splice acceptor 16 nucleotides downstream in exon 2. This splicing shift generates a 16-nucleotide deletion, causing a frameshift and premature stop codon that truncates the protein’s N-terminal region. Long-read sequencing further reveals that the mutation creates a novel CpG dinucleotide, which is methylated in the majority of reads. Finally, we assessed therapeutic correction strategies, revealing that CRISPR-Cas9 prime editing is the only viable approach for in vivo correction. This study provides the first comprehensive multi-omics characterization of the NF1 c.61-2A>G mutation and establishes a minimal framework for precision therapeutic development in silico in monogenic splicing disorders. Full article

The development of cancer immunotherapies has transformed cancer treatment paradigms, yet durable and tumour-specific responses remain elusive for many patients. Neoantigens, immunogenic peptides arising from tumour-specific genomic alterations, have emerged as promising cancer vaccine targets. Early-phase clinical trials using different vaccine platforms, including mRNA, peptide, DNA, and viral vector-based personalised cancer vaccines, have demonstrated the feasibility of targeting neoantigens, with early signals of prolonged survival in some patients. Most current vaccine strategies focus on canonical neoantigens, typically derived from exonic single-nucleotide variants (SNVs) and small insertions/deletions (INDELs), yet this represents only a fraction of the potential neoantigen repertoire. Evidence now shows that non-canonical neoantigens, arising mostly from alternative splicing, intron retention, translation of non-coding RNAs, gene fusions, and retroelement activation, broaden the antigenic landscape, with the potential for increasing tumour specificity and immunogenicity. In this review, we explore the biology of non-canonical neoantigens, the technological advances that now enable their systematic detection, and their potential to inform next-generation personalised cancer vaccines. Full article

Pigs are a major source of animal protein for humans and serve as valuable biomedical models. Compared to Western commercial pig breeds, Jinhua pigs are characterized by superior meat quality due to dynamic muscle development and fat deposition. However, studies investigating dynamic transcriptional regulation of swine meat quality traits across developmental stages remain limited. In this work, we collected longissimus dorsi muscle tissue from three Jinhua and three Landrace × Yorkshire pigs at 1, 90, and 180 days of age, respectively. We have uncovered differentially expressed genes and transcripts, alternative splicing events, and gene fusion events across development stages utilizing RNA sequencing data. CKM exhibited consistent breed-specific alternative splicing and gene fusion events across all three stages, representing a stable regulator of muscle development in Jinhua pigs. On the other hand, our findings highlight day 90 as a critical “window phase” for muscle development and meat quality differences between Jinhua and Landrace × Yorkshire pigs at this stage, exhibiting the greatest number of inter-breed differences in transcriptomic genetic regulation. Additionally, time series analysis revealed that genes with peak expression at day 90 were significantly enriched in pathways associated with muscle development and function. Finally, we identified PFKM, PRKAG3, and CKM as candidate genes with age-specific expression and post-transcriptional regulation that likely influence muscle development. This study advances understanding of transcriptional regulation in pig muscle with implications for meat quality improvement. Full article

The MATα_HMGbox and HMG-box_ROX1-like domains of the MAT1-1-1 and MAT1-2-1 proteins, respectively, play essential roles in DNA binding and the subsequent regulation of gene transcription, controlling Ophiocordyceps sinensis sexual reproduction. Alternative splicing, differential occurrence and transcription of the MAT1-1-1 and MAT1-2-1 genes have been demonstrated in Hirsutella sinensis (GC-biased Genotype #1 of the 17 O. sinensis genotypes), suggesting self-sterility under heterothallic or hybrid outcrossing. In this study, the MATα_HMGbox domains of MAT1-1-1 proteins in wild-type Cordyceps sinensis isolates were shown to cluster into 5 clades in the Bayesian clustering tree and belong to diverse stereostructure morphs under 19 AlphaFold codes. The HMG-box_ROX1-like domains of MAT1-2-1 proteins, on the other hand, were shown to cluster into 2 branched Bayesian clades and belong to stereostructure morphs under 25 AlphaFold codes. Correlation analysis revealed that 1–3 amino acid substitutions in the DNA-binding domains of the mating proteins resulted in altered hydrophobicity and secondary and tertiary structures of the DNA-binding domains of the proteins, especially altered stereostructures of the hydrophobic cores formed by 3 critical α- helices within the functional domains of the proteins. Fungal origin analysis revealed possible heterospecific fungal sources of mating proteins with stereostructure variations in wild-type C. sinensis isolates, suggesting that alterations in DNA binding function and the subsequent regulation of mating-related gene transcription are involved in ensuring the accuracy and genetic diversity of heterothallic and hybrid reproduction of O. sinensis during the lifecycle of the C. sinensis insect–fungal complex. Full article

Gastrointestinal nematode (GIN) infections are the most prevalent parasitic diseases in grazing sheep worldwide, causing significant productivity losses, high mortality and, as a result, economic losses and emerging animal welfare concerns. Conventional control strategies, primarily relying on anthelmintic treatments, face limitations due to rising drug resistance and environmental concerns, underscoring the need for sustainable alternatives. Selective breeding for host genetic resistance has emerged as a promising strategy, while recent advances in transcriptomics and integrative omics research are providing deeper insights into the immune pathways and molecular and genetic mechanisms that underpin host–parasite interactions. This review summarizes current evidence on transcriptomic signatures associated with resistance and susceptibility to H. contortus and T. circumcincta GIN infections, highlighting candidate genes, functional genetic markers, key immune pathways, and regulatory networks. Furthermore, we discuss how other omics approaches, including genomics, proteomics, metabolomics, microbiome, and multi-omics integrations, provide perspectives that enhance the understanding of the complexity of the GIN resistance trait. Transcriptomic studies, particularly using RNA-Sequencing technology, have revealed differential gene expression, functional genetic variants, such as SNPs and INDELs, in expressed regions and splice junctions, and regulatory long non-coding RNAs that distinguish resistance from susceptible sheep, highlighting pathways related to Th2 immunity, antigen presentation, tissue repair, and stress signaling. Genomic analyses have identified SNPs, QTL, and candidate genes linked to immune regulation and parasite resistance. Proteomic and metabolomic profiling further elucidates breed- and tissue-specific alterations in protein abundance and metabolic pathways, while microbiome studies demonstrate distinct microbial signatures in resistant sheep, suggesting a role in modulating host immunity. In conclusion, emerging multi-omics approaches and their integration strategies provide a comprehensive framework for understanding the complex host–parasite interactions that govern GIN resistance, offering potential candidate biomarkers for genomic selection and breeding programs aimed at developing sustainable, parasite-resistant sheep populations. Full article