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International Journal of Molecular... Jun 2024The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the gene, which interacts with the promoter region of...
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the gene, which interacts with the promoter region of the contiguous gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional activity of , directly affecting eye color pigmentation. Recent advancements in technology have elucidated the precise spatial organization of the genome within the cell nucleus, with chromatin architecture playing a pivotal role in regulating various genome functions. In this study, we investigated the organization of the chromatin close to the locus in human lymphocyte nuclei using fluorescence in situ hybridization (FISH) and high-throughput chromosome conformation capture (Hi-C) data. The 3 Mb of genomic DNA that belonged to the chromosomal region 15q12-q13.1 revealed the presence of three contiguous chromatin loops, which exhibited a different level of compaction depending on the presence of the A or G allele in the SNP rs12913832. Moreover, the analysis of the genomic organization of the genes has demonstrated that this chromosomal region is evolutionarily highly conserved, as evidenced by the analysis of syntenic regions in species from other Vertebrate classes. Thus, the role of rs12913832 variant is relevant not only in determining the transcriptional activation of the gene but also in the chromatin compaction of a larger region, underscoring the critical role of chromatin organization in the proper regulation of the involved genes. It is crucial to consider the broader implications of this finding, especially regarding the potential regulatory role of similar polymorphisms located within intronic regions, which do not influence the same gene by modulating the splicing process, but they regulate the expression of adjacent genes. Therefore, caution should be exercised when utilizing whole-exome sequencing for diagnostic purposes, as intron sequences may provide valuable gene regulation information on the region where they reside. Thus, future research efforts should also be directed towards gaining a deeper understanding of the precise mechanisms underlying the role and mode of action of intronic SNPs in chromatin loop organization and transcriptional regulation.
Topics: Polymorphism, Single Nucleotide; Humans; Chromatin; Guanine Nucleotide Exchange Factors; Animals; Evolution, Molecular; Membrane Transport Proteins; In Situ Hybridization, Fluorescence; Vertebrates; Pigmentation; Ubiquitin-Protein Ligases
PubMed: 38928306
DOI: 10.3390/ijms25126602 -
Genes Jun 2024Peroxisome proliferator-activated receptor γ (PPARG) has various splicing variants and plays essential roles in the regulation of adipocyte differentiation and...
Peroxisome proliferator-activated receptor γ (PPARG) has various splicing variants and plays essential roles in the regulation of adipocyte differentiation and lipogenesis. However, little is known about the expression pattern and effect of the PPARG on milk fat synthesis in the buffalo mammary gland. In this study, we found that only and of the splicing variant were expressed in the buffalo mammary gland. Amino acid sequence characterization showed that the proteins encoded by and are endonuclear non-secreted hydrophilic proteins. Protein domain prediction found that only the -encoded protein had PPAR ligand-binding domains (NR_LBD_PPAR), which may lead to functional differences between the two splices. RNA interference (RNAi) and the overexpression of and in buffalo mammary epithelial cells (BMECs) were performed. Results showed that the expression of fatty acid synthesis-related genes (, , , , , ) was significantly modified ( < 0.05) by the RNAi and overexpression of and . All kinds of FAs detected in this study were significantly decreased ( < 0.05) after RNAi of or . Overexpression of or significantly decreased ( < 0.05) the SFA content, while significantly increased ( < 0.05) the UFA, especially the MUFA in the BMECs. In conclusion, there are two splicing variants expressed in the BMECs that can regulate FA synthesis by altering the expression of diverse fatty acid synthesis-related genes. This study revealed the expression characteristics and functions of the gene in buffalo mammary glands and provided a reference for further understanding of fat synthesis in buffalo milk.
Topics: Animals; Buffaloes; PPAR gamma; Mammary Glands, Animal; Female; Epithelial Cells; Alternative Splicing; Fatty Acids; Protein Isoforms; Milk
PubMed: 38927715
DOI: 10.3390/genes15060779 -
Genes May 2024X-linked hypophosphatemia (XLH) is a rare inherited disorder of renal phosphate wasting with a highly variable phenotype caused by loss-of-function variants in the...
X-linked hypophosphatemia (XLH) is a rare inherited disorder of renal phosphate wasting with a highly variable phenotype caused by loss-of-function variants in the gene. The diagnosis of individuals with mild phenotypes can be challenging and often delayed. Here, we describe a three-generation family with a very mild clinical presentation of XLH. The diagnosis was unexpectedly found in a 39-year-old woman who was referred for genetic testing due to an unclear childhood diagnosis of a tubulopathy. Genetic testing performed by next-generation sequencing using a kidney disease gene panel identified a novel non-canonical splice site variant in the gene. Segregation analysis detected that the consultand's father, who presented with hypophosphatemia and decreased tubular phosphate reabsorption, and the consultand's son also carried this variant. RNA studies demonstrated that the non-canonical splice site variant partially altered the splicing of the gene, as both wild-type and aberrant splicing transcripts were detected in the two male members with only one copy of the gene. In conclusion, this case contributes to the understanding of the relationship between splicing variants and the variable expressivity of XLH disease. The mild phenotype of this family can be explained by the coexistence of transcripts with aberrant and wild-type splicing.
Topics: Humans; PHEX Phosphate Regulating Neutral Endopeptidase; Adult; Female; Familial Hypophosphatemic Rickets; Male; Pedigree; RNA Splice Sites; RNA Splicing; Phenotype; Genetic Diseases, X-Linked; Mutation
PubMed: 38927615
DOI: 10.3390/genes15060679 -
Genes May 2024The current investigation endeavors to identify differentially expressed alternatively spliced (DAS) genes that exhibit concordant expression with splicing factors (SFs)...
The current investigation endeavors to identify differentially expressed alternatively spliced (DAS) genes that exhibit concordant expression with splicing factors (SFs) under diverse multifactorial abiotic stress combinations in Arabidopsis seedlings. SFs serve as the post-transcriptional mechanism governing the spatiotemporal dynamics of gene expression. The different stresses encompass variations in salt concentration, heat, intensive light, and their combinations. Clusters demonstrating consistent expression profiles were surveyed to pinpoint DAS/SF gene pairs exhibiting concordant expression. Through rigorous selection criteria, which incorporate alignment with documented gene functionalities and expression patterns observed in this study, four members of the serine/arginine-rich (SR) gene family were delineated as SFs concordantly expressed with six DAS genes. These regulated SF genes encompass , -like, , and -like. The identified concordantly expressed DAS genes encode diverse proteins such as the 26.5 kDa heat shock protein, chaperone protein DnaJ, potassium channel GORK, calcium-binding EF hand family protein, DEAD-box RNA helicase, and 1-aminocyclopropane-1-carboxylate synthase 6. Among the concordantly expressed DAS/SF gene pairs, /-box RNA helicase, and -like/ emerge as promising candidates, necessitating further examinations to ascertain whether these SFs orchestrate splicing of the respective DAS genes. This study contributes to a deeper comprehension of the varied responses of the splicing machinery to abiotic stresses. Leveraging these DAS/SF associations shows promise for elucidating avenues for augmenting breeding programs aimed at fortifying cultivated plants against heat and intensive light stresses.
Topics: Arabidopsis; Alternative Splicing; Gene Expression Regulation, Plant; Arabidopsis Proteins; Stress, Physiological; Seedlings; RNA Splicing Factors
PubMed: 38927612
DOI: 10.3390/genes15060675 -
Biology May 2024has emerged as a promising model organism for basic studies in Decapod. However, the current transcriptome information on this species is based on next-generation...
has emerged as a promising model organism for basic studies in Decapod. However, the current transcriptome information on this species is based on next-generation sequencing technologies, which are limited by a short read length. Therefore, the present study aimed to generate a full-length transcriptome assembly of utilizing the PacBio Sequel Ⅱ platform. The resulting transcriptome assembly comprised 5831 transcripts with an N50 value of 3697 bp. Remarkably, 90.5% of these transcripts represented novel isoforms of known genes. The transcripts were further searched against the NR, SwissProt, KEGG, KOG, GO, NT, and Pfam databases. A total of 24.8% of the transcripts can be annotated across all seven databases. Additionally, 1236 alternative splicing events, 344 transcription factors, and 124 long non-coding RNAs (LncRNAs) were predicted. Based on the alternative splicing annotation results, a RING finger protein NHL-1 gene from () was identified. There are 15 transcripts in . The longest transcript is 4995 bp in length and encodes a putative protein of 1665 amino acids. A phylogenetic analysis showed its close relationship with NHL-1 from other crustacean species. This report represents the full-length transcriptome of and will facilitate research on functional genomics and environmental adaptation in this species.
PubMed: 38927246
DOI: 10.3390/biology13060366 -
Biomolecules Jun 2024Dilated cardiomyopathy (DCM) is a common cause of heart failure (HF) and heart transplantation (HTx), with genetic factors playing a significant role. In recent years,... (Review)
Review
Dilated cardiomyopathy (DCM) is a common cause of heart failure (HF) and heart transplantation (HTx), with genetic factors playing a significant role. In recent years, the RNA-binding protein motif 20 (), which affects the gene splicing of various proteins with different cellular functions, was identified as the first DCM gene with regulatory properties. Variants of have been associated with severe forms of DCM. The aim of this critical systematic review was to analyse cardiomyopathy clinical features and outcomes. According to PRISMA guidelines, a search was run in the PubMed, Scopus and Web of Science electronic databases using the following keywords: ""; "cardiomyopathy"; "arrhythmias"; "heart failure". A total of 181 records were screened, of which 27 studies were potentially relevant to the topic. Through the application of inclusion and exclusion criteria, eight papers reporting 398 patients with pathogenic variants were analysed. The mean age at presentation was 41 years. Familiarity with cardiomyopathy was available in 59% of cases, with 55% of probands reporting a positive family history. Imaging data indicated a mild reduction of left ventricular ejection fraction (mean LVEF 40%), while tissue characterization was reported in 24.3% of cases, showing late gadolinium enhancement in 33% of patients. Composite outcomes of sustained monomorphic ventricular tachycardia or ventricular fibrillation occurred in 19.4% of patients, with 12% undergoing HTx. There were no gender differences in arrhythmic outcomes, while 96.4% of patients who underwent HTx were male. In conclusion, cardiomyopathy exhibits a severe phenotypic expression, both in terms of arrhythmic burden and HF progression.
Topics: Humans; RNA-Binding Proteins; Cardiomyopathy, Dilated; Male; Female; Adult
PubMed: 38927106
DOI: 10.3390/biom14060702 -
Scientific Reports Jun 2024Breast cancer has become the most common type of cancers worldwide. Its high prevalence and malignant features are associated with various environmental factors and...
Breast cancer has become the most common type of cancers worldwide. Its high prevalence and malignant features are associated with various environmental factors and molecules. The KH-type splicing regulatory protein (KHSRP) participates in the development of breast cancer, while the underlying mechanisms are largely unknown. In this study, we silenced KHSRP expression in MDA-MB-231 cells by small interfering RNA (siKHSRP), and then assessed its effects on cellular features. Finally, we performed whole transcriptome sequencing (RNA-seq) experiments to explore the downstream targets of KHSRP, and validated their changed pattern using quantitative polymerase chain reaction. We found KHSRP showed higher expression level and was associated with worse prognosis in breast cancer patients. In siKHSRP samples, the proliferation, invasion, and migration abilities were significantly repressed compared with negative control (NC) samples, while the apoptosis level was increased. By investigating the RNA-seq data, we found KHSRP globally regulates the expression and alternative splicing profiles of MDA-MB-231 cells by identifying 1632 differentially expressed genes (DEGs) and 1630 HKSRP-regulated AS events (RASEs). Functional enriched analysis of DEGs demonstrated that cilium assembly and movement and extracellular matrix organization pathways were specifically enriched in up DEGs, consistent with the repressed migration and invasion abilities in siKHSRP cells. Interestingly, the cell cycle and DNA damage and repair associated pathways were enriched in both down DEGs and RASE genes, suggesting that KHSRP may modulate cell proliferation by regulating genes in these pathways. Finally, we validated the changed expression and AS patterns of genes in cell cycle and DNA damage/repair pathways. Expression levels of BIRC5, CCNA2, CDK1, FEN1, FOXM1, PTTG1, and UHRF1 were downregulated in siKHSRP samples. The AS patterns of PARK7, ERCC1, CENPX, and UBE2A were also dysregulated in siKHSRP samples and confirmed PCR experiments. In summary, our study comprehensively explored the downstream targets and their functions of KHSRP in breast cancer cells, highlighting the molecular mechanisms of KHSRP on the oncogenic features of breast cancer. The identified molecular targets could be served as potential therapeutic targets for breast cancer in future.
Topics: Humans; Breast Neoplasms; Alternative Splicing; DNA Repair; Cell Line, Tumor; Gene Expression Regulation, Neoplastic; Female; Cell Proliferation; Cell Movement; RNA-Binding Proteins; Apoptosis; Carcinogenesis; MDA-MB-231 Cells
PubMed: 38926398
DOI: 10.1038/s41598-024-64687-0 -
Discovery Medicine Jun 2024Genetic mutations play a crucial role in the development and progression of myelodysplastic syndromes (MDS), impacting the immune microenvironment and influencing the...
BACKGROUND
Genetic mutations play a crucial role in the development and progression of myelodysplastic syndromes (MDS), impacting the immune microenvironment and influencing the choice of treatment regimen, as well as the efficacy and prognosis of patients. The objective of this study was to examine variations in hematological and immunological characteristics associated with common gene mutations in MDS patients and establish a foundation for the precise treatment of MDS.
METHODS
The hematological, immunological, and other clinical features of 71 recently diagnosed MDS patients from January 1, 2019, to July 31, 2023, were retrospectively analyzed. These patients were categorized based on their gene mutations, and the variances in hematological and immunological characteristics among distinct groups were compared.
RESULTS
Hematological variances were observed among different gene mutation groups. Specifically, platelet counts in the splicing factor 3B subunit 1 () mutation group were notably higher compared to the wild-type group ( = 0.009). Conversely, in the additional sex combs like 1 () mutation groups, monocyte ratios were significantly elevated in comparison to the wild-type group ( = 0.046), and in the ten-eleven translocation 2 () mutation group, lymphocyte ratios were significantly lower ( = 0.022). Additionally, the leukocyte ( = 0.005), neutrophil ratio ( = 0.002), and lymphocyte ratio ( = 0.001) were significantly higher in the Runt-related transcription factor 1 () mutation group. Regarding immunological distinctions, the Natural Killer (NK) cell ratio demonstrated a significant increase in the mutation group ( = 0.005). Moreover, the mutation group exhibited a significantly higher Interleukin-8 (IL-8) level ( = 0.017). In contrast, the U2 small nuclear RNA auxiliary factor 1 () group displayed significantly lower levels of IL-1β ( = 0.033), IL-10 ( = 0.033), and Tumour Necrosis Factor-α (TNF-α) ( = 0.009).
CONCLUSION
Distinct variations exist in the immune microenvironment of MDS associated with different genetic mutations. Further studies are imperative to delve into the underlying mechanisms that drive these differences.
Topics: Humans; Myelodysplastic Syndromes; Mutation; Female; Male; Middle Aged; Aged; RNA Splicing Factors; Retrospective Studies; Adult; Dioxygenases; Aged, 80 and over; DNA-Binding Proteins; Phosphoproteins; Killer Cells, Natural; Core Binding Factor Alpha 2 Subunit; Platelet Count; Repressor Proteins
PubMed: 38926115
DOI: 10.24976/Discov.Med.202436185.119 -
American Journal of Human Genetics Jun 2024Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations...
Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with genome-wide association studies to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-sequencing datasets, BrainGVEX and CommonMind, revealing 137 and 88 trait-associated exons (in 84 and 67 genes), respectively. Enriched biological functions in the associated gene sets converged on neuronal function and development, immune cell activation, and cellular transport, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein binding sites, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level, identifying 36 genes and 48 exons as putatively causal for SCZ. We highlight VPS45 and APOPT1, where splicing of specific exons was associated with disease risk, eluding detection by conventional gene expression analysis. Collectively, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ, providing a valuable approach for future investigations in this area.
PubMed: 38925119
DOI: 10.1016/j.ajhg.2024.06.001 -
Science Advances Jun 2024A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human accelerated regions (HARs)...
A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human accelerated regions (HARs) are prime candidates for driving gene regulatory modifications in human development. The locus is densely populated with HARs, providing a set of potential regulatory elements that could have changed its expression in the human lineage. Here, we examined the role of -HARs using transgenic zebrafish reporter assays and identified 15 transcriptional enhancers that are active in the developing nervous system, 9 of which displayed differential activity between the human and chimpanzee sequences. The engineered loss of two selected -HARs in knockout mouse models modified expression at specific developmental stages and tissues in the brain, influencing the expression and splicing of a high number of target genes. Our results provided insight into the spatial and temporal changes in gene expression driven by -HARs.
Topics: Humans; Animals; RNA Splicing Factors; Enhancer Elements, Genetic; Zebrafish; Evolution, Molecular; Mice; Gene Expression Regulation, Developmental; Mice, Knockout; Animals, Genetically Modified; Gene Regulatory Networks; Pan troglodytes; Genetic Loci
PubMed: 38924416
DOI: 10.1126/sciadv.adl1049