Journal of Applied Genetics最新文献

{"title":"Cannabidiol (CBD) modulates the transcriptional profile of ethanol-exposed human dermal fibroblast cells.","authors":"Artur Gurgul, Jakub Żurowski, Tomasz Szmatoła, Mirosław Kucharski, Sebastian Sawicki, Ewelina Semik-Gurgul, Ewa Ocłoń","doi":"10.1007/s13353-024-00915-7","DOIUrl":"10.1007/s13353-024-00915-7","url":null,"abstract":"<p><p>Cannabidiol (CBD) is abundant in the Cannabis sativa plant and exhibits complex immunomodulatory, anxiolytic, antioxidant, and antiepileptic properties. Several studies suggest that CBD could be used for different purposes in alcohol use disorder (AUD) and alcohol-related injuries to the brain and the liver. In this study, we focused on analyzing transcriptional alterations in human dermal fibroblasts (HDFs) cell line challenged simultaneously with ethanol and CBD as an ethanol-protective agent. We aimed to expose the genes and pathways responsible for at least some of the CBD effects in those cells that can be related to the AUD. Transcriptome analysis was performed using HDFs cell line that expresses both cannabinoid receptors and can metabolize ethanol through alcohol dehydrogenase activity. Fibroblasts are also responsible for the progression of liver fibrosis, a common comorbidity in AUD. With the use of a cellular test, we found that CBD at the lowest applied concentration (0.75 μM) was able to stimulate depressed metabolism and reduce the level of apoptosis of cells treated with different concentrations of ethanol to the level observed in the control cells. Similar observations were made at the transcriptome level, in which cells treated with ethanol and CBD had similar expression profiles to the control cells. CBD also affects several genes connected with extracellular matrix formation (especially its collagen constituent), which can have potential implications for, e.g., fibrosis process.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"773-796"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of genome size, endopolyploidy and SCoT markers in 20 Trigonella (Fabaceae) species.","authors":"Monika Rewers, Agnieszka Lojko, Dorota Olszewska, Aleksandra Niklas, Iwona Jedrzejczyk","doi":"10.1007/s13353-024-00886-9","DOIUrl":"10.1007/s13353-024-00886-9","url":null,"abstract":"<p><p>The Trigonella species possess medicinal, nutraceutical and pharmaceutical properties due to the presence of many bioactive compounds. Its therapeutic effects are mostly valuable in medicine, cosmetics and the functional food industry. Correct genetic characterisation of plant material is needed to increase the potential of Trigonella species by breeding and conservation programs. The aim of this study was to develop a reliable marker system to support the morphological and phytochemical analysis in Trigonella taxonomic research, species identification and characterization as well as determination of the interspecific variation within this genus along with relationships between species. For this purpose, flow cytometry and SCoT molecular markers were combined. Flow cytometric analyses revealed that Trigonella species possess very small and small genomes. The range of genome sizes was from 1.10 to 5.76 pg/2C, with most species possessing very small genomes (< 2.8 pg/2C). In seeds of 14 species endopolyploid nuclei were detected. Flow cytometric analysis of genome size enabled quick identification of four out of 20 species, while combined with endopolyploidy detection in seeds, facilitated distinction of the next seven species. ScoT molecular markers helped to identify closely related species with similar genome size and cell cycle activity. Therefore, flow cytometry was proposed as the first-choice method for quick accession screening, while the more detailed genetic classification was obtained using SCoT molecular markers.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"693-703"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell integrated transcriptomics reveals the role of keratinocytes in head and neck squamous cell carcinoma.","authors":"Shaokun Liu, Meng Lian, Boxuan Han, Jugao Fang, Zhenlin Wang","doi":"10.1007/s13353-024-00842-7","DOIUrl":"10.1007/s13353-024-00842-7","url":null,"abstract":"<p><p>Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignant tumor with significant morbidity and mortality. Understanding the molecular mechanisms of HNSCC and identifying prognostic markers and therapeutic targets are crucial for improving patient outcomes. In this study, we utilized single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data to comprehensively analyze HNSCC at the cellular level. We identified keratinocytes as the predominant cell type in tumor samples, suggesting their potential role in HNSCC development. Through hdWGCNA co-expression network analysis, we identified gene modules associated with HNSCC progression. Furthermore, we constructed a prognostic model based on specific genes and demonstrated its robust predictive performance in multiple datasets. The model exhibited strong correlations with immune cell infiltration patterns and signaling pathways related to tumor progression. Additionally, drug sensitivity analysis revealed potential chemotherapeutic targets for HNSCC treatment. Our findings provide valuable insights into the molecular characteristics and immune microenvironment of HNSCC, offering new perspectives for prognosis prediction and therapeutic interventions in clinical practice. Further research is warranted to validate and expand upon these findings, ultimately improving patient outcomes in HNSCC.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"727-745"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139990149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering early responsive signature genes in rice blast disease: an integrated temporal transcriptomic study.","authors":"Ajitha Antony, Shanthi Veerappapillai, Ramanathan Karuppasamy","doi":"10.1007/s13353-024-00901-z","DOIUrl":"10.1007/s13353-024-00901-z","url":null,"abstract":"<p><p>Rice blast disease, caused by Magnaporthe oryzae, reigns as the top-most cereal killer, jeopardizing global food security. This necessitates the timely scouting of pathogen stress-responsive genes during the early infection stages. Thus, we integrated time-series microarray (GSE95394) and RNA-Seq (GSE131641) datasets to decipher rice transcriptome responses at 12- and 24-h post-infection (Hpi). Our analysis revealed 1580 differentially expressed genes (DEGs) overlapped between datasets. We constructed a protein-protein interaction (PPI) network for these DEGs and identified significant subnetworks using the MCODE plugin. Further analysis with CytoHubba highlighted eight plausible hub genes for pathogenesis: RPL8 (upregulated) and RPL27, OsPRPL3, RPL21, RPL9, RPS5, OsRPS9, and RPL17 (downregulated). We validated the expression levels of these hub genes in response to infection, finding that RPL8 exhibited significantly higher expression compared with other downregulated genes. Remarkably, RPL8 formed a distinct cluster in the co-expression network, whereas other hub genes were interconnected, with RPL9 playing a central role, indicating its pivotal role in coordinating gene expression during infection. Gene Ontology highlighted the enrichment of hub genes in the ribosome and protein translation processes. Prior studies suggested that plant immune defence activation diminishes the energy pool by suppressing ribosomes. Intriguingly, our study aligns with this phenomenon, as the identified ribosomal proteins (RPs) were suppressed, while RPL8 expression was activated. We anticipate that these RPs could be targeted to develop new stress-resistant rice varieties, beyond their housekeeping role. Overall, integrating transcriptomic data revealed more common DEGs, enhancing the reliability of our analysis and providing deeper insights into rice blast disease mechanisms.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"665-681"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach.","authors":"Rishabh Gurung, Mohammad Masood, Prithvi Singh, Prakash Jha, Anuradha Sinha, Swati Ajmeriya, Milin Sharma, Ravins Dohare, Mohammad Mahfuzul Haque","doi":"10.1007/s13353-024-00843-6","DOIUrl":"10.1007/s13353-024-00843-6","url":null,"abstract":"<p><p>Head and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, some associated with carcinomas. Chromobox (CBX) family is known to modulate physiological and oncological processes. In our study, we analyzed AQPs and CBXs having significant expression followed by their prognostic and mutational assessment. Next, we performed enrichment and tumor infiltration analysis followed by HPA validation. Lastly, we established a 3-node miRNA-TF-mRNA regulatory network and performed protein-protein docking of the highest-degree subnetwork motif between TF and mRNA. Significant upregulation of CBX3/2 and downregulation of AQP3/5/7 correlated with poor overall survival (OS) in HNSC patients. The most significant pathway, GO-BP, GO-MF, and GO-CC terms associated with AQP3 and CBX3 were passive transport by aquaporins, response to vitamin, glycerol channel activity, and condensed chromosome, centromeric region. AQP3 negatively correlated with <math> <msup><mrow><mtext>CD</mtext> <mn>4</mn></mrow> <mo>+</mo></msup> </math> T cells, positively with <math> <msup><mrow><mtext>CD</mtext> <mn>8</mn></mrow> <mo>+</mo></msup> </math> T cells and B cells, and negatively with tumor purity, whereas CBX3 positively correlated with <math> <msup><mrow><mtext>CD</mtext> <mn>4</mn></mrow> <mo>+</mo></msup> </math> T cells, negatively with <math> <msup><mrow><mtext>CD</mtext> <mn>8</mn></mrow> <mo>+</mo></msup> </math> T cells and B cells, and positively with tumor purity. Three-node miRNA-TF-mRNA regulatory network revealed a highest-degree subnetwork motif comprising one TF (SMAD3), one miRNA (miR-423-5p), and one mRNA (AQP3). Protein-protein interaction studies suggested a direct interaction between AQP3 and Smad3 proteins. We concluded that AQP3 and CBX3 hold potential as treatment strategies and individual prognostic biomarkers, while further protein-protein interaction studies of AQP3 could offer insights into its interactions with Smad3 proteins.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"839-851"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139735271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of multidisciplinary diagnostic and therapeutic model of care in Lamb-Shaffer syndrome - case report.","authors":"Urszula Sajewicz-Radtke, Ariadna Łada-Maśko, Małgorzata Lipowska, Bartosz M Radtke, Beata S Lipska-Ziętkiewicz, Katarzyna Krempla-Patron","doi":"10.1007/s13353-024-00838-3","DOIUrl":"10.1007/s13353-024-00838-3","url":null,"abstract":"<p><p>This case study illustrates a multidisciplinary diagnostic and therapeutic model of care for a 7-year-old male with Lamb-Shaffer syndrome (LAMSHF). LAMSHF is an ultra-rare genetic neurodevelopmental disorder, caused by heterozygous alterations in the SOX5 gene. An integrative model of therapy of cognitive functions and speech is described. The presented approach allows the development of language competences through stimulation of basic cognitive functions, which allows the learning of the abstract rules of an inflected language. A surprising, unexpected improvement in the cognitive functioning of the child was observed (both in terms of reasoning and speech), as well as an increase in his independence. The clinically important problem of the need for continued stimulation of cognitive development, in spite of the unfavourable prognosis associated with LAMSHF, is highlighted.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"747-755"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11560983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA-Seq transcriptome profiling of Nile rat livers reveals novel insights on the anti-diabetic mechanisms of Water-Soluble Palm Fruit Extract.","authors":"Soon-Sen Leow, Jia-Shiun Khoo, Wei-Kang Lee, Chee-Choong Hoh, Syed Fairus, Ravigadevi Sambanthamurthi, K C Hayes","doi":"10.1007/s13353-024-00880-1","DOIUrl":"10.1007/s13353-024-00880-1","url":null,"abstract":"<p><p>Water-Soluble Palm Fruit Extract (WSPFE) has been shown to confer anti-diabetic effects in the Nile rat (NR) (Arvicanthis niloticus). Liquid and powder WSPFE both deterred diabetes onset in NRs fed a high-carbohydrate (hiCHO) diet, but the liquid form provided better protection. In this study, NRs were fed either a hiCHO diet or the same diet added with liquid or powder WSPFE. Following feeding of the diets for 8 weeks, random blood glucose levels were measured to categorize NRs as either diabetes-resistant or diabetes-susceptible, based on a cut-off value of 75 mg/dL. Livers were then obtained for Illumina HiSeq 4000 paired end RNA-sequencing (RNA-Seq) and the data were mapped to the reference genome. Consistent with physiological and biochemical parameters, the gene expression data obtained indicated that WSPFE was associated with protection against diabetes. Among hepatic genes upregulated by WSPFE versus controls, were genes related to insulin-like growth factor binding protein, leptin receptor, and processes of hepatic metabolism maintenance, while those downregulated were related to antigen binding, immunoglobulin receptor, inflammation- and cancer-related processes. WSPFE supplementation thus helped inhibit diabetes progression in NRs by increasing insulin sensitivity and reducing both the inflammatory effects of a hiCHO diet and the related DNA-damage compensatory mechanisms contributing to liver disease progression. In addition, the genetic permissiveness of susceptible NRs to develop diabetes was potentially associated with dysregulated compensatory mechanisms involving insulin signaling and oxidative stress over time. Further studies on other NR organs associated with diabetes and its complications are warranted.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"867-895"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the genetic diversity, population structure, and stability for yield-related traits of rice genotypes in mid-hills of northeastern India.","authors":"Riya Raj, Amit Kumar, Balakrishnan C, Simardeep Kaur, Veerendra Kumar Verma, Mayank Rai, S P Das, Vinay Kumar Mishra","doi":"10.1007/s13353-024-00925-5","DOIUrl":"https://doi.org/10.1007/s13353-024-00925-5","url":null,"abstract":"<p><p>The cultivation of nearly 10,000 indigenous rice landraces in the North-Eastern Hill (NEH) region by various ethnic groups creates opportunities for the utilization of unique landraces through systematic evaluation of genetic variability. In the present study, a set of 102 rice landraces were assessed based on morphological and SSR markers, and five checks in augmented design vis-à-vis high-yielding rice genotypes with stable performance were identified. The presence of high estimates of heritability, genotypic coefficient of variation, and genetic advance over mean indicated the predominance of additive gene action, which necessitated the effectiveness of selection in augmenting productivity. A total of 83.73% of the total variation was accounted by the first five principal components. A total of 132 alleles were detected, with an average of 3 alleles per locus. The PIC values ranged from 0.01 to 0.70, with an average of 0.40. Based on F_ST value (5.1%), significant differences between the genotypes of Arunachal Pradesh and Sikkim were observed. The percentage of variation among the population, among individuals within the population, and within individuals was 5.14, 75.66, and 19.2%, respectively. Both Nei's genetic distance and model-based clustering have differentiated the genotypes into five distinct clusters. Principal coordinate analysis illustrated that the genotypes of Manipur were scattered in all quadrants, showing that they are highly diverse, while the genotypes of Nagaland, Sikkim, and Meghalaya were found together, which represent the chance of mixing of the population at a certain point in time. Markers, namely RM 474, OSR 13, RM 413, and RM 259, were found to be associated with key traits for increasing yielding ability of plant. In a stability evaluation based on AMMI analysis and multi-trait genotype-ideoptype distance matrix (MGIDI), genotypes, namely Jyotrirmayie, RCPL 1-411, Tsamum firri, Ching Phouren, Rato Bhan Joha, MN-47, and Tara bali, were selected with higher yield potential.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Experimental and in silico analysis of LINC01279 expression in tumor of patients with breast cancer.","authors":"Negar Mokhtari, Najmeh Ahmadi, Sahar Moradi, Shiva Farmani, Elham Kheyrani, Nasrin Fattahi Dolatabadi","doi":"10.1007/s13353-024-00908-6","DOIUrl":"https://doi.org/10.1007/s13353-024-00908-6","url":null,"abstract":"<p><p>Breast cancer (BC) is characterized by the increase of malignant cells in the breast. The malignant cells begin in the lining of the breast milk glands or ducts (ductal epithelium). BC is the most frequent cancer in women, but it may also occur in males. Long non-coding RNAs (lncRNA) have been demonstrated to control the development and incidence of cancer. However, some lncRNAs experience potential changes in BC, but their role has not been well studied. LINC01279 is known as a valuable biomarker in gastric cancer but has not yet been studied in BC. Changes in LINC01279 expression levels in BC samples were investigated by microarray. Q-PCR was also used to evaluate the expression of LINC01279 in the tumor and normal adjacent samples of 30 BC patients. The LINC01279 co-expressed gene module was discovered using weighted gene correlation network analysis (WGCNA) on the relevant dataset. The top ten hub genes were determined using gene ontology (GO) functional enrichments on the co-expressed gene module. The results of the bioinformatics study showed an increase in LINC01279 expression levels (log2FC = 3.228749561, adj.P.Val = 1.69E - 12) in tumor samples compared to normal marginal tissue. Q-PCR results also showed a significant increase in LINC01279 expression (P-value = 0.0005) in tumor samples. WGCNA analysis identified that the black module is the LINC01279 co-expressed module, and functional annotation analysis of black module genes enriched in significant cancer-related pathways and processes, including cell growth and/or maintenance, regulation of immune response, regulation of cell proliferation, and epithelial-to-mesenchymal transition (EMT). Regarding the real-time PCR results, the analysis of expression patterns has illuminated a distinct association between the heightened expression levels of LINC01279, and the stages of cancer progression as well as the metastatic potential of tumors. However, intriguingly, our observations have failed to reveal any statistically significant correlations between the relative expression of LINC01279 and tumor grade classification, or the presence of ER, PR, and HER2 biomarkers. The present study could provide a new perspective on the molecular regulatory. Processes associated with BC pathogenic mechanisms are linked to the LINC01279, although further research is needed on the possible role of this lncRNA in BC.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA methylation dysregulation patterns in the 1p36 region instability.","authors":"Joanna Swierkowska-Janc, Michal Kabza, Malgorzata Rydzanicz, Maciej Giefing, Rafal Ploski, Lisa G Shaffer, Marzena Gajecka","doi":"10.1007/s13353-024-00913-9","DOIUrl":"https://doi.org/10.1007/s13353-024-00913-9","url":null,"abstract":"<p><p>In the monosomy 1p36 deletion syndrome, the role of DNA methylation in the genomic stability of the 1p36 region remains elusive. We hypothesize that changes in the methylation pattern at the 1p36 breakpoint hotspot region influenced the chromosomal breakage leading to terminal deletions. From the monosomy 1p36 material collection, four cases with 4.0 to 5.5 Mb terminal deletions and their parents were investigated. DNA samples were assessed by targeted bisulfite sequencing (NimbleGen SeqCap Epi) to examine DNA methylation status in the 1p36 hotspot region at single-base resolution as compared to the chromosomal hotspot regions, 9p22, 18q21.1, and 22q11.2. Additionally, in in silico assessment, the mean GC content of various classes of repeats in the genome and especially in the breakpoint regions was evaluated. A complex landscape of DNA methylation in the 1p36 breakpoint hotspot region was found. Changes in DNA methylation level in the vicinity of the breakpoint in the child's DNA when compared to parents' and control DNA were observed, with a shift from 15.1 to 70.8% spanning the breakpoint region. In the main classes of evaluated repeats, higher mean GC contents in the 1p36 breakpoint region (47.06%), 22q11.2 (48.47%), and 18q21.1 (44.21%) were found, compared to the rest of the genome (40.78%). The 9p22 region showed a lower GC content (39.42%) compared to the rest of the genome. Both dysregulation of DNA methylation and high GC content were found to be specific for the 1p36 breakpoint hotspot region suggesting that methylation abnormalities could contribute to aberrations at 1p36.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}