Search Results (104)

Intron retention (IR) is one of the cellular mechanisms to perform alternative splicing and thus control gene expression in several mammalian cellular pathways. IR in PI-PLC γ1 mRNA was observed in some primary synoviocyte samples from osteoarthritis (OA) patients, likely due to inter-patient variability. The aim of the present manuscript was to explore the PI-PLC γ1 IR molecular mechanism as a consequence of nutraceutical treatment of synoviocytes and the molecular basis of individual response. To evaluate the gene expression modulation of molecules involved in mRNA splicing, an RNA-seq analysis was performed, and the transcription modulation of six differentially expressed genes was validated by RT-PCR. Moreover, through a silencing experiment, the relationship between PI-PLC γ1 IR and the six modulated genes was explored. Finally, two of them, the RNA-binding proteins CELF1 and PTBP3, whose mRNA levels were elevated in samples exhibiting IR, were analyzed in detail. CELF1 and PTBP3 were overexpressed in synoviocytes lacking PI-PLC γ1 IR, and we found that CELF1 was responsible for IR, whereas PTBP3 did not seem to be involved. In conclusion, in our experimental model, the role of CELF1 protein in PI-PLC γ1 IR was explored, opening new scenarios for understanding the molecular mechanisms underlying the IR phenomenon present in several kinds of diseases. Full article

For 40 years, Intron Retention (IR) was dismissed as splicing noise and is now recognized as a dynamic and evolutionarily conserved mechanism of post-transcriptional gene regulation. Unlike canonical splicing, which excises all introns from pre-mRNAs, IR selectively retains intronic sequences, albeit at seemingly random places; however, current research now reveals that this process is strategic in its retention. IR influences mRNA stability, localization, and translational potential. Retained introns can lead to nonsense-mediated decay, promote nuclear retention, or give rise to novel protein isoforms that contribute to expanding proteomic and transcriptomic profiles. IR is finely regulated by splice site strength, splicing regulatory elements, chromatin structure, methylation patterns, RNA polymerase II elongation rates, and the availability of co-transcriptional splicing factors. IR plays critical roles in cell-type and tissue-specific gene expression with observed patterns, particularly during neuronal, cardiac, hematopoietic, and immune development. It also functions as a molecular switch during cellular responses to environmental and physiological stressors such as hypoxia, heat shock, and infection. Dysregulated IR is increasingly associated with cancer, neurodegeneration, aging, and immune dysfunction, where it may alter protein function, suppress tumor suppressor genes, or generate immunogenic neoepitopes. Experimental and computational tools like RNA-seq, RT-PCR, IRFinder, and IntEREst have enabled transcriptome-wide detection and validation of IR events, uncovering their widespread functional roles. This review will examine current knowledge on the function, regulation, and detection of IR, and also summarize recent advances in understanding its role in both normal and pathophysiological settings. Full article

Ginseng rusty root symptoms (GRSs) compromise the yield and quality of Panax ginseng. While transcriptomic analyses have demonstrated extensive remodeling of stress signaling networks, the post-transcriptional defense circuitry remains obscure. We profiled alternative splicing (AS) in three phloem tissues, the healthy phloem (AG), the non-reddened phloem neighboring lesions (BG), and the reddened lesion core (CG), to delineate AS reprogramming during GRS progression. The frequency of AS was sharply elevated in CG, with intron retention predominating. Extensive gains and losses of splice events indicate large-scale rewiring of the splice network. Overlapping differentially alternative spliced genes (DAGs) identified in both CG vs AG and CG vs BG contrasts were significantly enriched for RNA–spliceosome assembly and stress–response pathways, revealing a conserved post-transcriptional response associated with lesion formation. Integrative analysis of differentially expressed genes uncovered 671 loci under dual regulation; functional classification categorized these genes in receptor-like kinase signaling and chromatin-remodeling modules, underscoring the synergy between AS and transcriptional control. Moreover, the B subgenome disproportionately contributed stress-responsive transcripts in diseased tissue, suggesting an adaptive, subgenome-biased strategy. These findings demonstrate that dynamic AS remodeling and subgenome expression bias jointly orchestrate ginseng defense against GRS and provide a framework for breeding disease-resilient crops. Full article

Determining the genetic variations of candidate genes in affected subjects will help identify early pathological biomarkers of Alzheimer’s disease (AD) and develop effective treatments. It has recently been found that some genes that are linked share an increase in intron retention (IR). In this review, we discuss a few instances of mRNA-IR in various genes linked to AD, including APOE, MAPT-Tau, Psen2, Farp1, Gpx4, Clu, HDAC4, Slc16a3, and App genes. These genes are vulnerable to IR, encompassing additional crucial proteins for brain functionality, but they are frequently involved in pathways linked to the control of mRNA and protein homeostasis. Despite the advancements in human in vivo RNA therapy, as far as we know, there are no reports of data generated regarding artificial in vivo splicing in either animal models or humans. To prevent genetic variations and improve or repair errors in expression of desired genes, humans have adopted new gene editing techniques like CRISPR-Cas9 and RNAi modalities. Ultimately, IR could be utilized as a therapeutic potential biomarker for disorders related to intronic expansion. Full article

While the U1 small nuclear ribonucleoprotein (snRNP) plays a crucial role in early spliceosome assembly, the mechanisms by which it coordinates with other splicing factors for efficient assembly remain elusive. This study aimed to examine the role of the Swt21 protein in regulating U1 snRNP in Saccharomyces cerevisiae. Swt21p was required for efficient pre-mRNA splicing both in vivo and in vitro. Deletion of SWT21 altered the splicing patterns of two-intron SUS1 RNA, causing intron retention and exon skipping. Spliceosome assembly analysis revealed that in the pre-B complex, the levels of U1 protein components, as well as U1 RNA, were decreased following SWT21 deletion, highlighting the compromised stability of U1 snRNP during this stage. Consistently, in the absence of Swt21p, free isoform of U1 component Nam8p was observed, and its proper nuclear localization was disrupted, demonstrating the functional importance of Swp21p for the stable association of Nam8p with U1 snRNP. Moreover, Swt21p remained primarily in a free state under physiological conditions and did not associate with the pre-B complex. Additionally, TAP analysis revealed that Swt21p-associated proteins are involved in cellular processes beyond splicing. These findings collectively indicate that Swt21p functions as a spliceosome regulator rather than a core component and support a model wherein Swt21p contributes to U1 snRNP stability during early spliceosome assembly. Full article

Severe physiological fruit abscission significantly limits yield potential in macadamia. Polygalacturonase (PG), a key hydrolytic enzyme in pectin degradation, plays a critical role in fruit abscission. However, in the macadamia genome, the PG gene family and the members involved in fruit abscission remain poorly understood. In this study, 56 PG gene family members, which were unevenly distributed across 13 of the 14 chromosomes, were identified in the macadamia genome. Phylogenetic analysis clustered these genes into seven clades, with most members found in clades D and E. The MiPGs contained 3–11 exons and 2–10 introns, and except for those in clades E and G, most contained conserved domains I–IV and were predicted to be localized exclusively to the cell membrane. MiPG promoter analysis revealed numerous light-, phytohormone-, and stress-responsive cis-elements. Expression profiling during fruit development showed that twelve MiPGs were either undetectable or expressed at low levels in the fruit abscission zone, whereas eight were highly expressed. MiPG9, MiPG37, and MiPG53 were significantly upregulated during abscission induced by a combination of girdling with defoliation and ethephon treatments. Moreover, transient MiPG37 overexpression in lily petals promoted premature abscission, suggesting that this gene plays a pivotal role in macadamia fruit abscission. These findings advance the functional characterization of macadamia PG genes and highlight a subset of candidate genes for further genetic manipulation to improve fruit retention. Full article

Alzheimer’s disease (AD) is the most common form of dementia, characterized by β-amyloid (Aβ) plaques and neurofibrillary tangles, leading to neuronal loss and cognitive impairments. Recent studies have reported the dysregulation of RNA splicing in AD pathogenesis. Our previous transcriptomic study demonstrated the neuroprotective effect of the phytocannabinoid cannabinerol (CBNR) against the cell viability loss induced by Aβ in differentiated SH-SY5Y cells. This study also highlighted the deregulation of genes involved in mRNA splicing after Aβ exposure or CBNR pre-treatment. Here, we investigated whether CBNR could restore the splicing defects induced by Aβ in an AD in vitro model. Using the rMATS computational tool for detecting differential alternative splicing events (DASEs) from RNA-Seq data, we obtained 96 DASEs regulated in both conditions and, remarkably, they were all restored by CBNR pre-treatment. The pathway analysis indicated an over-representation of the “Alzheimer’s disease–amyloid secretase pathway”. Additionally, we observed that Aβ exposure increased the frequency of retained introns (RIs) among the shared DASEs, and that this frequency returned to normality by CBNR pre-treatment. Interestingly, most of these RIs contain a premature in-frame stop codon within the RNA sequence. Finally, analyzing the DASE regions for miRNA hybridization, we found 33 potential DASE/miRNA interactions that were relevant in AD pathogenesis. These findings revealed a novel trans-gene regulation by CBNR, potentially explaining part of its neuroprotective role. This is the first study demonstrating the involvement of a cannabinoid in the regulation of mRNA splicing in an AD model. Full article

Background/Objectives: Missplicing caused by toxic DMPK-mRNA is described as a hallmark of myotonic dystrophy type 1 (DM1). Yet, there is an expressional misregulation of additional splicing factors described in DM1, and missplicing has been observed in other myopathies. Here, we compare the expressional misregulation of splicing factors and the resulting splicing profiles between three different hereditary myopathies. Methods: We used publicly available RNA-sequencing datasets for the three muscular dystrophies—DM1, facioscapulohumeral muscular dystrophy (FSHD) and Emery–Dreifuss muscular dystrophy (EDMD)—to compare the splicing factor expression and missplicing genome-wide using DESeq2 and MAJIQ. Results: Upregulation of alternative splicing factors and downregulation of constitutive splicing factors were detected for all three myopathies, but to different degrees. Correspondingly, the missplicing events were mostly alternative exon usage and skipping events. In DM1, most events were alternative exon usage and intron retention, while exon skipping was prevalent in FSHD, with EDMD being in between the two other myopathies in terms of splice factor regulation as well as missplicing. Accordingly, the missplicing events were only partially shared between these three myopathies, sometimes with the same locus being spliced differently. Conclusions: This indicates a combination of primary (toxic RNA) and more downstream effects (splicing factor expression) resulting in the DM1 missplicing phenotype. Furthermore, this analysis allows the distinction between disease-specific missplicing and general myopathic splicing alteration to be used as biomarkers. Full article

G-quadruplexes (G4s) are unique nucleic acid structures composed of guanine-rich (G-rich) sequences that can form diverse topologies based on the arrangement of their four strands. G4s have attracted attention for their potential roles in various biological processes and human diseases. In this review, we focus on the G4 structures formed by human telomeric sequences, (GGGTTA)_n, and the hexanucleotide repeat expansion, (GGGGCC)_n, in the first intron region of the chromosome 9 open reading frame 72 (C9orf72) gene, highlighting their structural diversity and biological significance. Human telomeric G4s play crucial roles in telomere retention and gene regulation. In particular, we provide an in-depth summary of known telomeric G4s and focus on our recently discovered chair-type conformation, which exhibits distinct folding patterns. The chair-type G4s represent a novel folding pattern with unique characteristics, expanding our knowledge of telomeric G4 structural diversity and potential biological functions. Specifically, we emphasize the G4s formed by the (GGGGCC)_n sequence of the C9orf72 gene, which represents the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The thorough structural analysis in this review advances our comprehension of the disease mechanism and provides valuable insights into developing targeted therapeutic strategies in ALS/FTD. Full article

Background/Objectives: Dermatophytosis, a prevalent fungal infection of keratinized tissues, is primarily caused by the filamentous fungus Trichophyton rubrum. Sertraline (SRT), an antidepressant with antifungal activity, has already demonstrated therapeutic potential against this fungus. Elucidating the effects of SRT may provide insights into its mechanism of action and fungal adaptation to this drug. Differential gene expression and alternative splicing (AS) facilitate fungal adaptations to various environmental conditions. This study aimed to provide a comprehensive overview of AS events and their implications in T. rubrum cultivated under sub-inhibitory concentrations of SRT. Method: The transcriptome of T. rubrum challenged with SRT was analyzed to detect AS events. Results: RNA-seq analysis revealed that SRT affected transcriptional and post-transcriptional events in numerous T. rubrum genes, including those encoding transcription factors, kinases, and efflux pumps. Among the AS events, intron retention was predominant. After 12 h of SRT exposure, intron-3 retention levels in the serine/arginine protein kinase mRNA transcripts were significantly increased compared with those in the control. This new isoform would produce a putative protein that partially lost its phosphotransferase domain. Conclusions: These findings highlight the potential mechanisms of action of SRT and suggest how T. rubrum adapts itself to this drug. Full article

Rice (Oryza sativa L.) is a staple crop for nearly half of the global population and one of China’s most extensively cultivated cereals. Heading date, a critical agronomic trait, determines the regional and seasonal adaptability of rice varieties. In this study, a series of mutants (elh5 to elh12) exhibiting extremely late heading under both long-day (LD) and short-day (SD) conditions were identified from an ethyl methanesulfonate (EMS) mutant library. Using MutMap and map-based cloning, the causative gene was identified as a novel allele of Ehd2/OsID1/RID1/Ghd10. Functional validation through CRISPR/Cas9 knockout and complementation assays confirmed its role in regulating heading. The elh6 mutation was found to cause intron retention due to alternative splicing. Ehd2 encodes a Cys-2/His-2-type zinc finger transcription factor with an IDD domain and transcriptional activity in yeast. Its expression peaks in developing leaves before heading and spikes during reproductive conversion. In elh6 mutants, delayed heading resulted from downregulating the Ehd1-Hd3a pathway genes. Salinity stress significantly hampers rice growth and productivity. Transcriptomic analysis of elh10 and ZH8015 seedlings exposed to salt stress for 24 h identified 5150 differentially expressed genes (DEGs) at the seedling stage, predominantly linked to stress response pathways. Ehd2 was revealed as a modulator of salt tolerance, likely through the regulation of ion transport, enzyme activity, and antioxidant systems. This study establishes Ehd2 as a pivotal factor in promoting heading while negatively regulating salt tolerance in rice. Full article

Circular RNAs (circRNAs) are a class of unique transcripts characterized by a covalently closed loop structure, which differentiates them from conventional linear RNAs. The formation of circRNAs occurs co-transcriptionally and post-transcriptionally through a distinct type of splicing known as back-splicing, which involves the formation of a head-to-tail splice junction between a 5′ splice donor and an upstream 3′ splice acceptor. This process, along with exon skipping, intron retention, cryptic splice site utilization, and lariat-driven intron processing, results in the generation of three main types of circRNAs (exonic, intronic, and exonic–intronic) and their isoforms. The intricate biogenesis of circRNAs is regulated by the interplay of cis-regulatory elements and trans-acting factors, with intronic Alu repeats and RNA-binding proteins playing pivotal roles, at least in the formation of exonic circRNAs. Various hypotheses regarding pathways of circRNA turnover are forwarded, including endonucleolytic cleavage and exonuclease-mediated degradation; however, similarly to the inconclusive nature of circRNA biogenesis, the process of their degradation and the factors involved remain largely unclear. There is a knowledge gap regarding whether these processes are guided by universal pathways or whether each category of circRNAs requires special tools and particular mechanisms for their life cycles. Understanding these factors is pivotal for fully comprehending the biological significance of circRNAs. This review provides an overview of the various pathways involved in the biogenesis and degradation of different types of circRNAs and explores key factors that have beneficial or adverse effects on the formation and stability of these unique transcripts in higher eukaryotes. Full article

Sertraline, a selective serotonin reuptake inhibitor (SSRI), is commonly used to treat various psychiatric disorders such as depression and anxiety due to its ability to increase serotonin availability in the brain. Recent findings suggest that sertraline may also influence the expression of genes related to synaptic plasticity and neuronal signaling pathways. Alternative splicing, a process that allows a single gene to produce multiple protein isoforms, plays a crucial role in the regulation of neuronal functions and plasticity. Dysregulation of alternative splicing events has been linked to various neurodevelopmental and neurodegenerative diseases. This study aims to explore the effects of sertraline on alternative splicing events, including exon inclusion, exon exclusion, and mutually exclusive splicing events, in genes associated with neuronal function in Drosophila melanogaster and to use this model to investigate the molecular impacts of SSRIs on gene regulation in the nervous system. RNA sequencing (RNA-seq) was performed on central nervous system samples from Drosophila melanogaster adults exposed to sertraline for 24 h when they were third instar larvae. Alternative splicing events were analyzed to identify changes in exon inclusion and exclusion, as well as intron retention. Sertraline treatment significantly altered alternative splicing patterns in key genes related to neuronal stability and function. Specifically, sertraline promoted the inclusion of long Ank2 isoforms, suggesting enhanced axonal stability, and favored long ATPalpha isoforms, which support Na⁺/K⁺ ATPase activity essential for ionic balance and neuronal excitability. Intron retention in the yuri gene suggests that cytoskeletal reorganization could impact neuronal morphology. Additionally, splicing alterations in sxc and Atg18a indicate a potential influence of sertraline on epigenetic regulation and autophagy processes, fundamental aspects for neuronal plasticity and cellular homeostasis. These findings suggest that sertraline influences alternative splicing in the central nervous system of Drosophila melanogaster, potentially contributing to its therapeutic effects by modulating neuronal stability and adaptability. Full article

Alternative splicing (AS) is a prevalent post-transcriptional regulatory mechanism in eukaryotes and plays a crucial role in plant disease resistance. Here, we used the Illumina Novaseq sequencing platform to conduct transcriptome sequencing on canola (Brassica napus) leaves infected with the blackleg pathogen (Leptosphaeria biglobosa strain nm⁻¹) at 0 h, 72 h, 120 h, and 168 h post-inoculation to investigate the mechanism of AS coordination with transcriptional regulation in canola’s response to blackleg disease. The rMATS software (4.1.0) was employed to analyze different AS events in samples taken at 72 h, 120 h, and 168 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to elucidate the biological functions of differentially spliced genes at various time points, while Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify key modules and hub genes. As a result, our analysis reveals 16908 AS events across three time points, with 221 being differently spliced. Intron retention (RI) was the most common AS event, accounting for approximately 55% of all events, while alternative 5′ splice site events were least common, comprising only 2%. Furthermore, a total of 213 significantly differentially spliced genes were identified, which were enriched in functions related to protein kinase activity, transferase activity, and pathways such as MAPK signaling pathway—plant and plant hormone signal transduction. WGCNA identified three key modules and ten hub genes, including calcium-binding transcription activator 1, LRR class receptor serine/threonine protein kinase FEI 2, PLATZ transcription factor family proteins, serine/threonine protein kinase PRP4, and E3 ubiquitin ligase SUD1, all of which are associated with canola resistance to L. biglobosa. Thus, this study provides a theoretical basis for identifying disease-resistance genes involved in AS and for exploring the functions of AS gene isoforms in canola. Full article

Vairimorpha (Nosema) ceranae is a single-cellular fungus that obligately infects the midgut epithelial cells of adult honeybees, causing bee microsporidiosis and jeopardizing bee health and production. This work aims to construct the full-length transcriptome of V. ceranae and conduct a relevant investigation using PacBio single-molecule real-time (SMRT) sequencing technology. Following PacBio SMRT sequencing, 41,950 circular consensus (CCS) were generated, and 25,068 full-length non-chimeric (FLNC) reads were then detected. After polishing, 4387 high-quality, full-length transcripts were gained. There are 778, 2083, 1202, 1559, 1457, 1232, 1702, and 3896 full-length transcripts that could be annotated to COG, GO, KEGG, KOG, Pfam, Swiss-Prot, eggNOG, and Nr databases, respectively. Additionally, 11 alternative splicing (AS) events occurred in 6 genes were identified, including 1 alternative 5′ splice-site and 10 intron retention. The structures of 225 annotated genes in the V. ceranae reference genome were optimized, of which 29 genes were extended at both 5′ UTR and 3′ UTR, while 90 and 106 genes were, respectively, extended at the 5′ UTR as well as 3′ UTR. Furthermore, a total of 29 high-confidence lncRNAs were obtained, including 12 sense-lncRNAs, 10 lincRNAs, and 7 antisense-lncRNAs. Taken together, the high-quality, full-length transcriptome of V. ceranae was constructed and annotated, the structures of annotated genes in the V. ceranae reference genome were improved, and abundant new genes, transcripts, and lncRNAs were discovered. Findings from this current work offer a valuable resource and a crucial foundation for molecular and omics research on V. ceranae. Full article