Cytogenetic and Genome Research最新文献

{"title":"Genetic and Epigenetic Insights into Werner Syndrome.","authors":"Elena Paccosi, Diletta Guzzon, Luca Proietti-De-Santis","doi":"10.1159/000544118","DOIUrl":"10.1159/000544118","url":null,"abstract":"<p><strong>Background: </strong>Werner syndrome is an autosomal recessive disorder characterized by premature aging and cancer predisposition, caused by loss of function mutations in WRN gene. To date, more than 70 different pathogenic variants have been identified across the WRN locus, with an increasing number of newly reported mutations. Even if the clinical phenotypes of WS seem to be indistinguishable among the different WRN mutation types, a certain genotype/phenotype correlation has been identified, especially regarding the predisposition to certain type of malignant disease. Along this line, the knowledge of the genetic aspects related to WRN is a fascinating land still object of intensive studies. Summary and Key Messages: In this review, we discuss both the genetic and epigenetic regulations of the WRN gene, with a special focus on the pathogenic variants that have been identified in the WRN locus across different populations. Indeed, we think that investigating these aspects is the basis starting from which is it possible to depict WRN role in aging and cancer development processes, with the final goal of opening new perspectives for future therapeutic strategies directed to the treatment not only of this syndrome, for which, to date, there is no cure, but also of many types of malignant diseases and all those disturbs related to the physiological aging.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-15"},"PeriodicalIF":1.7,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oxana L. Kolomiets: 42 Years at the Forefront of Meiotic Chromosome Study.","authors":"Sergey N Matveevsky, Tatiana M Grishaeva, Victor E Spangenberg, Igor S Mazheika, Yuri F Bogdanov","doi":"10.1159/000544096","DOIUrl":"10.1159/000544096","url":null,"abstract":"","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-7"},"PeriodicalIF":1.7,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study on DNA Damage Gene in Spermatogonial Stem Cells from Idiopathic Nonobstructive Azoospermia: A Bioinformatics Investigation Based on scRNA-seq Data.","authors":"Yi Wang, Yiming Weng, Yanqiu Wang, Jun Xiang, Wei Le","doi":"10.1159/000545275","DOIUrl":"10.1159/000545275","url":null,"abstract":"<p><strong>Introduction: </strong>DNA damage may affect homeostasis on spermatogonial stem cells (SSCs), while the detailed relationship with male infertility still remains unclear. Therefore, it is important for further research into the mechanisms related to DNA damage and genomic stability in SSCs.</p><p><strong>Methods: </strong>scRNA-seq datasets from idiopathic nonobstructive azoospermia (NOA) and normal testes were collected and testicular cells were further annotated via UMAP. Based on annotation of the sequencing data, WGCNA analysis on the differentially expressed genes was conducted; LASSO regression and the MNC calculation algorithm in Cytoscape were carried out to find genes associated with DNA damage repair.</p><p><strong>Results: </strong>It was found that SSCs were mainly concentrated in normal samples, and the differences in subcluster pathways reflected the heterogeneity of NOA. While the characteristics of the interaction between Leydig cells and other cells were clarified, the importance of the PTN signaling pathway in SSCs development was discovered, which participates in SSCs development through SDC2. Combining the marker genes of SSCs and DNA damage-related genes in single-cell analysis, a PPI network was constructed. Through LASSO regression and the MNC calculation algorithm in Cytoscape, ATRX, DOT1L, and RUVBL2 were finally identified as key diagnostic genes.</p><p><strong>Conclusion: </strong>Our results revealed predictable mechanisms of testicular micro-environment and DNA damage in the regulation of human SSCs and propose potential therapeutic targets for male infertility. Subsequently, further research to confirm the predicted potential mechanisms, pathways, and therapeutic targets should be conducted.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"9-22"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Karyotype and Repetitive DNA Analysis in Turcichondrostoma fahirae (Cypriniformes, Leuciscidae): A Step toward the Use of Molecular Cytogenetics in Taxonomy of Freshwater Fishes in Türkiye.","authors":"Güldane Gözen Tavşan, Atilla Arslan, Büşra Özçay Ekşi, Zafer Alpaslan, Emine Arslan, Alexandr Sember","doi":"10.1159/000544909","DOIUrl":"10.1159/000544909","url":null,"abstract":"<p><strong>Introduction: </strong>Türkiye houses rich freshwater ichthyofauna with many endemic species. This diversity, however, poses taxonomic challenges and leads to ongoing re-evaluations of various fish genera and species. Here, we sought to analyze the karyotype and other chromosomal characteristics of the newly erected monotypic genus Turcichondrostoma to produce and validate cytogenetic markers potentially informative for future comparative studies.</p><p><strong>Methods: </strong>We examined an endemic species Turcichondrostoma fahirae (Tefenni nase) using conventional karyotyping and chromosome banding procedures (C-, fluorescent, and silver-nitrate banding/staining), as well as chromosomal mapping of 5S/18S ribosomal DNA (rDNA), U1/U2 small nuclear DNA (snDNA), and telomeric repeats.</p><p><strong>Results: </strong>A diploid chromosome number (2n) of T. fahirae was 50, consistent with conservative leuciscid pattern. The karyotype was composed of 12 metacentric, 22 submetacentric, 10 subtelocentric, and 6 acrocentric chromosomes. Low amount of constitutive heterochromatin was distributed almost exclusively across the pericentromeric regions of all chromosomes, with the most prominent C-bands being placed on a single chromosome pair carrying nucleolar organizer region (NOR). NORs (visualized consistently by silver-nitrate staining, chromomycin A3, and fluorescence in situ hybridization) exhibited marked size heteromorphism and were adjacent to a more centromere-proximal 5S rDNA site on the long arm. Additional 5S rDNA clusters occupied short arms of four acrocentric chromosomes, and another single subtelocentric pair carried a single co-localized U1/U2 snDNA site. No interstitial telomeric sequences were detected.</p><p><strong>Conclusion: </strong>We performed a pioneer molecular cytogenetic study in Turkish freshwater fish species and our data suggest that molecular cytogenetic markers will aid in future taxonomic comparisons. Our findings further corroborate conserved karyotype structure of leuciscid fishes in general.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"39-50"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Familial Case of 1q31.2q32.2 Deletion with No Phenotypic Presentation.","authors":"Rebecca Littlefield, Jennifer Weiss, Anna Zakas","doi":"10.1159/000543937","DOIUrl":"10.1159/000543937","url":null,"abstract":"<p><strong>Introduction: </strong>Deletions of the interstitial region of chromosome 1q are rare and associated with clinical features including growth restriction, developmental delays, and dysmorphic features. Here, we describe an asymptomatic family with an interstitial 1q31 deletion found incidentally.</p><p><strong>Case presentation: </strong>A 42-year-old male presented with concerns for colonic polyps and underwent multigene panel analysis for hereditary tumor predisposition syndromes which identified a full-gene deletion of CDC73.</p><p><strong>Conclusion: </strong>Microarray analysis of peripheral blood DNA showed a 6.9-Mb heterozygous deletion of 1q31.2q32.2 encompassing 33 genes in both proband and daughter. The absence of symptoms, including any autosomal dominant conditions associated with variants in this region, has been identified in only 1 case report while most other cases of 1q31 deletions report a range of clinical presentations. Further description of 1q31 deletions is essential to the development of genotype-phenotype interpretation and to decrease the uncertainty of care recommendations for patients and their families.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"23-30"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complex Congenital Cardiac Defect Associated with the Combination of 5p Deletion and 4q Duplication in a Newborn: A Case Report.","authors":"Ülkü Nur Kırman, Ferid Aliyev, Merve Soğukpınar, Pelin Özlem Şimşek Kiper, Hayrettin Hakan Aykan, Hasan Tolga Çelik","doi":"10.1159/000543591","DOIUrl":"10.1159/000543591","url":null,"abstract":"<p><strong>Introduction: </strong>Congenital cardiac defects are defined in cases with the deletion of the short arm of chromosome 5 and the duplication of the long arm of chromosome 4. Septal defects and patent ductus arteriosus are among the most common defects reported in the literature.</p><p><strong>Case presentation: </strong>We reported on a case with a complex congenital cardiac defect, dysmorphic facial features, cat-like cry, hypotonia, hyporeflexia, weak swallowing and sucking, limb anomalies, and bilateral undescended testicles. A chromosomal microarray (CMA) revealed a duplication of chromosome 4q26q35.2 and a deletion of chromosome 5p15.33p14.3, originating from the balanced maternal translocation 46,XX,t(4;5)(q27;pter). Our patient showed clinical characteristics compatible with both deletion of 5p and duplication of 4q.</p><p><strong>Conclusion: </strong>We reported a case with a rare chromosomal rearrangement. Similarities and differences between the cases in the literature are discussed. CMA is important to detect multiple copy number variations and genes may be involved. Studies are needed to investigate the genetic and/or epigenetic causes resulting in the clinical findings seen in the combination of deletion of chromosome 5p and duplication of chromosome 4q.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"31-38"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ISCN 2024: Summary of Revisions and New Nomenclature.","authors":"Nicole L Chia, Sarah Moore, Ros J Hastings","doi":"10.1159/000544969","DOIUrl":"10.1159/000544969","url":null,"abstract":"<p><p>The International Standing Committee on Human Cytogenomic Nomenclature (ISCN SC) considered feedback from the cytogenomics community to provide a more user friendly and organized presentation of general rules, improved example descriptions, more representative examples, and additional abbreviations. The ISCN 2024 edition represents one of the most significant reviews. Nomenclature for describing the findings of genomic mapping has been included for the first time. A key achievement of the Committee in preparing the ISCN 2024 is the provision of standardized nomenclature to ensure consistency in the ISCN description of findings irrespective of the cytogenomic technology used. This report highlights the main changes in the ISCN 2024 compared to previous editions and is a guide to assist in the transition to its implementation as the current nomenclature for describing cytogenomic findings.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-8"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revealing the satellite DNA content in Ancistrus sp. (Siluriformes: Loricariidae) by genomic and bioinformatic analysis.","authors":"Gabriel Esbrisse Dos Santos, C. Crepaldi, M. J. da Silva, P. P. Parise-Maltempi","doi":"10.1159/000538926","DOIUrl":"https://doi.org/10.1159/000538926","url":null,"abstract":"Introduction Eukaryotic genomes consist of both single and repetitive sequences, including Satellite DNAs (satDNA), which are non-coding sequences arranged in tandem arrays. These sequences play a crucial role in genomic functions and innovations, influencing processes such as nuclear material maintenance, heterochromatin formation, and sex chromosome differentiation. In this genomic era, advancements in next-generation sequencing and bioinformatic tools have facilitated the comprehensive cataloging of repetitive elements in genomes, particularly in non-model species. This study focuses on the satellitome of Ancistrus sp., a diverse fish species within the Loricariidae family. The genus Ancistrus displays significant karyotypic evolution, with deviations from the ancestral diploid number. Methods Using bioinformatic approaches, we identified 40 satellite DNA families in Ancistrus sp., constituting 5.19% of the genome. The abundance and divergence landscape analysis revealed diverse profiles, indicating recent amplification and homogenization of these satDNA sequences. Results The most abundant satellite, AnSat1-142, constitutes 2.1% of the genome, while the least abundant, AnSat40-52, represents 0.0034%. The monomer repeat length ranges from 16 to 142 base pairs, with an average length of 61 bp. These findings contribute to understanding the genomic dynamics and evolution of satDNAs in Ancistrus sp. Conclusion The study underscores the variability in satDNAs among fish species and provides valuable insights into the chromosomal organization and evolution of repetitive elements in non-model organisms.","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" 37","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140692272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico Characterization of Satellitomes and Cross-Amplification of Putative satDNAs in Two Species of the Hypostomus ancistroides Complex (Siluriformes, Loricariidae).","authors":"Dinaíza Abadia Rocha-Reis, Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegídio, John Seymour Pat Heslop-Harrison, Trude Schwarzacher, Karine Frehner Kavalco","doi":"10.1159/000539429","DOIUrl":"10.1159/000539429","url":null,"abstract":"<p><strong>Introduction: </strong>The mapping of the satellite DNA on chromosomes is vital to understanding the distribution and evolution of repetitions in the genome since these chromosomal studies have shown the origin, evolutionary mode, and function of repetitive sequences. This study aimed to prospect the satellitome and determine its location in the genome of two cryptic species of Hypostomus, H. aff. ancistroides and H. ancistroides, with and without XX/XY sexual chromosome system.</p><p><strong>Methods: </strong>Mitotic chromosomes and DNA extraction were obtained according to protocols. After the whole genome sequencing, the satDNAs were retrieved, amplified, and hybridized in chromosome preparations for male and female individuals.</p><p><strong>Results: </strong>We found 30 satellite families (47 variants, two superfamilies) in H. ancistroides and 38 satellite families (45 variants, four superfamilies) in H. aff. ancistroides. The sequences varied from 14 bp to 2,662 bp in H. ancistroides and from 14 bp to 2,918 bp in H. aff. ancistroides. We did not observe any tandem repeats that were exclusive to each of the libraries; however, many sequences showed very different abundances and copy numbers between the libraries. Four satDNAs did not hybridize on the chromosomes of either species. Conversely, one satDNA hybridized in both species, HxySat1-80. However, the phenotypes found varied among species, populations, and in the same individual. There was no sign of HanSat3-464 and HanSat11-335 in any individuals of H. aff. ancistroides, but markings were in the chromosomes of H. ancistroides. HxySat12-1127 and HxySat8-52, on the other hand, were only hybridized in H. aff. ancistroides, while H. ancistroides had a negative sign. No hybridization of satDNAs was found in the X and Y sex chromosomes as they were mostly composed of euchromatin.</p><p><strong>Conclusion: </strong>We distinguish H. aff. ancistroides as genetically different from H. ancistroides, recognizing that such characteristics go far beyond morphological, karyotypic, and molecular data. Our data support the differential abundance and location of satellite DNAs and confirm that many organisms, including fish, have repetitive sequences that validate the library hypothesis. All found and validated satDNAs and the characterization of the satellitomes of the two species represent important contributions to cytogenomic studies of the genus Hypostomus.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"121-132"},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Delineating the W Sex Chromosome in the Clam Shrimp, Eulimnadia texana.","authors":"Chathumadavi Ediriweera, Stephen C Weeks","doi":"10.1159/000542284","DOIUrl":"10.1159/000542284","url":null,"abstract":"<p><strong>Introduction: </strong>Sex chromosomes have evolved independently across various lineages, often showing convergent degradation of the sex-limited chromosome. While extensively studied in model organisms with ancient sex chromosomal systems, the evolution of early-stage sex chromosomes remains poorly understood. Eulimnadia texana, a freshwater crustacean with a unique androdioecious breeding system (ZZ, ZW, and viable WW genotypes), provides a rare opportunity to study early sex chromosome evolution. This study examines E. texana's W chromosome for evidence of a small localized non-recombining region, characterized by a transposable element (TE) \"hotspot,\" low gene density, and low GC content.</p><p><strong>Methods: </strong>Sex-linked markers were mapped onto the W chromosome (scaffold 1). TEs in the WW genome were identified using RepeatModeler and RepeatMasker. Statistical analyses compared TE distribution between the genome and scaffold 1, which was then divided into 20 equal-sized \"bins\" for finer-scale statistical analyses. Gene density and GC content were analyzed across these bins.</p><p><strong>Results: </strong>While no significant TE accumulation was found across the entire W chromosome compared to the remaining genome, a specific region (6.6-8.8 Mb, fourth bin) showed significantly higher TE accumulation. This region also exhibited low gene density and low GC content, indicative of reduced recombination.</p><p><strong>Conclusion: </strong>Our findings suggest that E. texana's W chromosome contains a smaller region of crossover suppression, supporting the hypothesis that it is a proto-sex chromosome in early evolutionary development. This study provides valuable insights into early sex chromosome evolution and establishes E. texana as an ideal model for further investigation of evolutionary processes driving proto-sex chromosome differentiation.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"257-266"},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}