Search Results (3,063)

Tail docking, serving as an important management intervention in animal husbandry, plays a significant role in regulating tail fat deposition and improving production performance and health status in fat-tailed sheep. This study systematically revealed the reprogramming effects of tail docking on the epigenetic landscape and transcriptome of fat-tailed sheep by integrating whole-genome bisulfite sequencing (WGBS) and RNA m6A methylated immunoprecipitation sequencing (MeRIP-seq). At the DNA level, the tail-docked group exhibited a pronounced trend of hypomethylation across multiple functional genomic regions, including promoters, exons, and introns. Differentially methylated regions (DMRs) were significantly enriched in pathways related to tissue development and stress response, such as the Hippo signaling pathway and adherens junctions. Pyrosequencing validation of the promoter region of the key gene DGAT1 further confirmed the reliability of the WGBS data. At the RNA level, RNA m6A modifications showed an overall up-regulated pattern: the tail-docked group displayed higher numbers of m6A peaks, greater total peak length, and increased genomic coverage compared to the control group, along with better overall prediction of modification sites. Genes associated with differential m6A peaks were closely related to processes such as stem cell pluripotency and cytoskeleton regulation. qPCR validation of several methylation-related enzyme genes (e.g., METTL3, FTO, YTHDF1) yielded results consistent with the sequencing trends. Through integrated analysis of DNA methylation and RNA methylation, we identified 143 genes with concurrent changes in methylation and mRNA expression, among which 41 genes were regulated by both DNA and RNA methylation. These genes were primarily enriched in the adherens junction pathway. Notably, two core genes CITED4 and ZNF644 showed significant changes across all three levels: DNA methylation, RNA methylation, and mRNA expression. This study systematically elucidates the epigenetic mechanism by which tail docking stress induces coordinated DNA hypo-methylation and RNA m6A hyper-methylation to regulate transcriptomic reprogramming in response to environmental intervention. The findings provide novel insights into the molecular basis of trait formation in livestock. Full article

Polyglutamine expansion in Ataxin-2 (ATXN2) is responsible for rare, dominantly inherited Spinocerebellar Ataxia type 2 (SCA2). Together with its paralog Ataxin-2-like (ATXN2L), both proteins have received much interest, since the deletion of their yeast and fly orthologs alleviates TDP-43-triggered neurotoxicity in Amyotrophic Lateral Sclerosis models. Their typical structure across evolution combines LSm with LSm-Associated Domains and a PAM2 motif. To understand the physiological regulation and functions of Ataxin-2 homologs, the phylogenesis of sequences was analyzed. Human ATXN2 harbors multiple alternative start codons, e.g., from an intrinsically disordered sequence (IDR) present since armadillo, or from the polyQ sequence that arose since amphibians, or from the LSm domain since primitive eukaryotes. Multiple smaller isoforms also exist across the C-terminus. Therapeutic knockdown of polyQ expansions in human ATXN2 should selectively target exon 1B. PolyQ repeats developed repeatedly, usually framed and often interrupted by (poly)Pro, originally near PAM2. The LSmAD sequence appeared in algae as the characteristic Ataxin-2 feature with strong conservation. Frequently, Ataxin-2 has added domains, likely due to transcriptional readthrough of neighbor genes during cell stress. These chimerisms show enrichment of rRNA processing; nutrient store mobilization; membrane strengthening via lipid, protein, and glycosylated components; and cell protrusions. Thus, any mutation of Ataxin-2 has complex effects, also affecting membrane resilience. Full article

Background/Objectives: Circular RNAs (circRNAs) are emerging players in human diseases, with functions as part of competing endogenous networks. Given the importance of messenger RNA (mRNA) regulation in human diseases and the potential of circRNAs in this regulation, we studied the circRNA–mRNA couple in blood within a cohort of 712 patients suspected of having hereditary colorectal cancer (CRC) and 249 matched controls. Methods: The circRNA–mRNA couple was studied by SEALigHTS (Splice and Expression Analyses by exon Ligation and High-Throughput Sequencing) with a panel of 23 genes involved in CRC predisposition, comprising 788 probes designed at exon ends, enabling the exploration of all exon–exon junctions. Following reverse transcription and probe hybridization on cDNA, nearby probes were ligated, and the number of ligations was quantified using unique molecular identifiers and sequencing. Results: We identified 220 circular junctions, including 47 novel ones. The circRNA/mRNA ratio was 2.42-fold higher in patients compared to controls (p < 10⁻¹⁶), irrespective of age at cancer onset. This increase was mainly driven by POLD1 (fold change 3.84) and a single circPOLD1(3,2) with oncogenic potential Conclusions: This study supports the existence of a physiological balance between circRNA and mRNA that can be disrupted under pathological conditions. It rules out a competitive mechanism between circular and linear transcripts in CRC predisposition and raises questions about the role of specific circRNAs in the development of CRC, either as a cause or a consequence. Full article

A genome-wide identification and expression analysis was performed to examine the response of the amino acid permease (AAP) gene family to drought stress in tomato (Solanum lycopersicum L.). Ten AAP genes were identified across seven of the twelve chromosomes and classified into four subfamilies (I–IV) based on phylogenetic relationships. Expansion of the SlAAP family appears to have been driven mainly by segmental and tandem duplication events. Members within the same subfamily displayed high similarity in exon–intron organization and conserved motif architecture. Promoter analysis revealed the presence of multiple cis-acting elements associated with stress and defence regulation. Under drought stress, all putative genes exhibited significant transcriptional induction, with SlAAP8, SlAAP9 and SlAAP10 showing the strongest upregulation, suggesting their potential involvement in drought adaptation. Drought treatment also led to a marked decline in nitrate (NO₃⁻) and total nitrogen (N) contents, while simultaneously increasing the accumulation of total amino acids, ammonium (NH₄⁺), and proline in both leaf and root tissues of tomato. The expression profiles of the ten putative SlAAP genes showed strong positive correlations with total amino acid levels in both organs, suggesting their involvement in amino acid redistribution under stress. Collectively, these results underscore the functional complexity of the SlAAP gene family and provide a robust foundation for future investigations into their molecular roles and potential applications in enhancing drought tolerance in tomato and other crop species. Full article

Synthetic RNA has become an essential modality in therapeutic development. Linear mRNA is already clinically validated, which demonstrated that in vitro-transcribed (IVT) RNA can achieve robust protein expression in humans and can be manufactured at a large scale. Circular RNA (circRNA) represents a more recent format characterized by a covalently closed backbone that confers enhanced resistance to exonucleases and supports sustained translation when paired with appropriate regulatory elements. Although both formats are produced through cell-free synthesis, their manufacturing pathways are distinct. Linear mRNA synthesis requires transcription, capping, polyadenylation, and stringent removal of double-stranded RNA contaminants. circRNA production generally proceeds through transcription of a linear precursor followed by enzymatic or ribozyme-mediated circularization, with emerging strategies such as permuted intron-exon designs improving efficiency and reducing extraneous sequence content. This review summarizes the principal methods used to generate linear and circRNA and identifies the technical barriers that must be overcome during the manufacturing process. Full article

As one of the five major indigenous yellow cattle breeds in China, Qinchuan cattle are characterized by stable genetic performance and desirable meat quality. However, compared with imported commercial breeds, Qinchuan cattle have a relatively slow growth rate. Therefore, improving the growth rate of Qinchuan cattle has become a top priority in Qinchuan cattle breeding. The CDC10 (Septin 7) gene, an important member of the Septin family, participates in various cellular physiological processes including intracellular substance transport, cell division, cell cycle regulation, and apoptosis. Studies have repeatedly mapped the CDC10 gene to quantitative trait loci influencing growth-related traits, such as body weight and carcass weight in many beef cattle breeds. Previous study has also demonstrated the high expression of CDC10 in JB cattle with high performance for carcass weight, however, the association between CDC10 and growth-related traits in Qinchuan cattle remain unclear. Therefore, in this study, we selected five individuals each from Chinese Simmental, Mongolian cattle, Luxi cattle, and Qinchuan cattle for direct sequencing, aiming to identify mutations within the CDC10 gene of native Chinese yellow cattle. Subsequently, we performed genotyping of 367 Qinchuan cattle using the MassARRAY technology, followed by genetic diversity analysis of the identified mutations and association analysis between these sites and growth-related traits of Qinchuan cattle. This study demonstrated high expression of the CDC10 gene in Qinchuan cattle with high performance for carcass weight. Furthermore, we identified the g.61303052G>C and c.225A>G SNPs in the promoter and exon regions, respectively, as being significantly associated with multiple growth-related traits in Qinchuan cattle. The c.225A>G SNP was also found to alter the secondary structure of the CDC10 protein. These findings provide reliable molecular markers for enhancing the growth rate of Qinchuan cattle and establish a solid theoretical foundation for the development of the beef cattle industry. Full article

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

Rye (Secale cereale L.) is a small-grain cereal traditionally cultivated under low-input conditions, where locally adapted populations have contributed substantially to the maintenance of genetic diversity. Despite this importance, Greek rye germplasm has received limited attention at the molecular level. In the present study, 33 rye accessions, including gene bank landraces, locally cultivated populations and one commercial variety, were analyzed using inter-simple sequence repeat (ISSR), start codon-targeted (SCoT), and exon-based amplified polymorphism (EBAP) markers. All three marker systems generated high proportions of polymorphic loci and comparable estimates of expected heterozygosity, indicating considerable genetic variability within the studied material. Multivariate analyses revealed moderate population structuring and consistently identified a small number of genetically divergent accessions, most notably T-492, K-163, and K-166. No clear clustering according to geographical origin was detected, as in most cases of landraces or local populations. Taken together, the results provide a detailed molecular overview of Greek rye germplasm—which has never been performed before for Greek rye genetic material—and offer a useful basis for conservation priorities and future pre-breeding efforts. Full article

β-thalassemia patients often experience ocular abnormalities such as angioid streaks (ASs), retinal pigmented epithelium degradation, visual field defects, and in rare instances choroidal neovascularization (CNV). Although ASs are common in individuals with hemoglobinopathies, the occurrence of choroidal neovascularization without preceding ASs is exceptionally rare. In this report, we describe a β-thalassemia patient who had developed CNV at the age of 27 years and also had experience of renal stones at the age of 19 years. He had undergone splenectomy and was under conservative therapy of iron supplementation. We conducted whole-exome sequencing (WES) in search of CNV-associated variants. Through variant filtering and Phenolyzer analysis, we have identified a rare heterozygous missense variant in the ABCC6 gene, ABCC6:NM_001171:exon25:c.3524T>C (rs376062004). In silico analysis revealed that this variant is present in the highly conserved region and is likely to decrease the stability of the protein. Mutation in the ABCC6 gene leads to pseudoxanthoma elasticum (PXE). Previously, it was believed that ASs and subsequent CNV-like ocular complication may develop due to the pathophysiological condition of thalassemia. However, our study provides compelling evidence that rare mutations in the ABCC6 gene, in combination with oxygen insufficiency, may contribute to the development of CNV in β-thalassemia patients. This finding highlights the potential genetic basis of PXE-mediated CNV development in β-thalassemia. 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: Spondylocostal dysostosis (SCDO) is a rare disorder characterized by congenital malformations of the spine and ribs. SCDO affects 1 in 40,000 human births, with rare cases also reported in dogs. Mutations in DLL3, encoding a critical Notch signaling pathway ligand, account for a majority of human SCDO cases. The remaining cases have variants in HES7, LFNG, MESP2, RIPPLY2, TBX6, and DLL1, which code for proteins in the Notch pathway. A mixed-breed litter of three dogs presented with varying degrees of spinal malformations and underwent comprehensive phenotyping including radiographic and neurologic examination. Two littermates demonstrated classic SCDO features including shortened torsos, vertebral malformations, and rib abnormalities, while a third showed only caudal vertebral truncation. Methods: Short-read whole-genome sequencing was performed on all three animals, followed by variant filtering and analysis using the two severely affected dogs as cases and 173 control dogs of various breeds. Variants were prioritized based on segregation patterns, population frequency, and predicted functional impact using established bioinformatics tools. Results: Variant analysis identified a novel splice acceptor variant in DLL3 (c.650-2A>C). This mutation, located at the splice acceptor site preceding exon 5, is predicted to disrupt critical EGF-like domains and O-fucosylation sites essential for DLL3 protein function. Conclusions: This study identifies a DLL3 splice variant causing SCDO in dogs, demonstrating phenotypic conservation with humans. These findings refine our understanding of genotype–phenotype correlations and demonstrate the value of comparative genomics for rare developmental disorders. Full article

Based on the discrete element method (DEM), a sand particle contact force model and a motion model for the 3D sand printing (3DSP) process were developed. By accounting for the viscous support force and contact force between sand particles, and gravity acting on each individual sand particle, the displacement of sand particles was calculated, enabling the simulation of the 3DSP process using sand particle ensembles. Furthermore, the effects of the ratio of silica sand to ceramsite sand and the recoating speed on sand-recoating performances and mechanical properties were investigated. Irregularly shaped sand particles (primarily silica sand) were constructed via the multi-sphere filling method. The simulation was performed on a virtual sand-recoating device (180 mm in length, 100 mm in width, 70 mm in height) with reference to the EXONE S-MAX printer. Meanwhile, the EXONE S-MAX was utilized to print the bending samples for experimental validation. Simulation and experimental results indicate that as the ratio increases, the porosity first decreases and then increases, whereas mechanical properties exhibit an initial increase followed by a decrease. At a ratio of 3:7, the porosity reaches a minimum of 21.3%; correspondingly, the shear force of bonding bridges peaks at 908 mN, and the bending strength of specimens attains a maximum of 2.87 MPa. With the increasing recoating speed, the porosity rises consistently, while the shear force of bonding bridges and the bending strength of specimens first increase and then decrease, which is primarily attributed to the penetration behavior of the binder under capillary force. At a recoating speed of 160 mm·s⁻¹, the shear force of bonding bridges reaches its maximum, and the specimens achieve a maximum bending strength of 2.89 MPa. The simulation results are well-validated by the experiments. The DEM-based simulation method proposed in this study offers a practical and convenient tool for parameter optimization in 3DSP process. 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