Cytogenetic and Genome Research最新文献

{"title":"Genomic Imprinting: Insights into Diverse Epigenetic Regulatory Mechanisms.","authors":"Gaurav Kumar Pandey, Rajiva Raman","doi":"10.1159/000547555","DOIUrl":"10.1159/000547555","url":null,"abstract":"<p><strong>Background: </strong>Genomic imprinting is a well-known phenomenon in which certain genes are expressed in a sex-of-the-parent-specific manner, resulting in mono-allelic expression.</p><p><strong>Summary: </strong>Over the years, the diversity of mechanisms observed in imprinted gene clusters has provided a valuable model system for exploring the complexities of epigenetics, which can be extended to other cellular and disease models. This review examines these different mechanisms throughout early embryonic development and offers insights into the interactions among key players such as DNA methylation, histone modifications, and non-coding RNAs, as well as their regulatory impact on gene expression.</p><p><strong>Key message: </strong>Genomic imprinting, although being a classical genetic concept, has emerged as a model system for understanding diverse epigenetic regulatory mechanisms. This review offers an overview of such regulatory mechanisms that have been learnt over the years through studies on imprinted clusters.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-18"},"PeriodicalIF":1.3,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144689425","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":"Fork Stalling and Template Switching in a Complex der(6)dn with Duplication of 6q24.3qter and 6p25.3: A Case Report.","authors":"Thania Alejandra Aguayo-Orozco, Ma Guadalupe Domínguez-Quezada, Horacio Rivera, Luis E Figuera, Eduardo Esparza-García, Luis Ángel Núñez-García, Elvira Garza-González, Carlos Córdova-Fletes","doi":"10.1159/000547454","DOIUrl":"10.1159/000547454","url":null,"abstract":"<p><strong>Introduction: </strong>Partial trisomy of the 6q24qter region is a rare chromosomal disorder characterized by variable clinical features and poorly understood mechanistic origins.</p><p><strong>Case presentation: </strong>We describe a de novo complex der(6) chromosome in a patient with features consistent with partial 6q trisomy syndrome, including congenital heart disease, growth restriction, developmental delay, and dysmorphic traits. Molecular Findings: Whole-genome sequencing (WGS) identified duplications of 1.5 Mb on 6p25.3 and 23.3 Mb on 6q24.3-qter. While the 6p duplication appears benign, the phenotype is likely driven by dosage-sensitive 6q genes (ARID1B, TAB2, QKI) and possible additive effects from other duplicated genes. No parental pericentric inversion was detected by classical or molecular cytogenetics, and WGS revealed no inversion-associated breakpoints. Instead, chimeric (q-/q+) and truncated reads at the 6q junction support a replication-based origin, such as reversed template switching. FISH confirmed direct insertion of the 6q segment into 6p25.3, without a del/dup pattern typical of inversion-derived recombinants. Notably, WGS detected no direct 6p-6q junction reads but identified chimeric 6p-15q-6q reads with 2-bp microhomologies, suggesting that chromosome 15 transiently mediated the rearrangement. Interspersed telomeric sequences and flanking Alu elements were also found at both breakpoints.</p><p><strong>Conclusion: </strong>Altogether, these findings support a model in which replication fork stalling and template switching - potentially facilitated by telomere dynamics and repetitive elements - led to the formation of a recombinant-like der(6) chromosome. This case highlights the mechanistic complexity of structural rearrangements and the role of replication-based errors in shaping human genomic variation.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-8"},"PeriodicalIF":1.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658673","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":"Post-Translational Modifications of the Werner Syndrome Protein WRN.","authors":"Amrita Machwe, David K Orren","doi":"10.1159/000547163","DOIUrl":"10.1159/000547163","url":null,"abstract":"<p><strong>Background: </strong>Werner syndrome has been an excellent model for the study of human aging and how chromosomal instability is related to phenotypes of normal aging including cancer. George Martin devoted his life to the study of Werner syndrome and human aging, and this review is dedicated to his memory.</p><p><strong>Summary: </strong>In this review, we highlight the post-translational modifications of WRN, the protein whose function is lacking in individuals with Werner syndrome. WRN is subject to phosphorylation, acetylation, ubiquitination, and SUMOylation.</p><p><strong>Key messages: </strong>These modifications of WRN control its localization and function in the response to replication fork stress and repair of double-strand breaks that are a consequence of this stress.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-7"},"PeriodicalIF":1.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144552594","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":"Clustered Structural Variants Involving PHEX at Xp22 in a Female Patient with X-Linked Hypophosphatemia.","authors":"Erika Uehara, Yasuhiro Naiki, Atsushi Hattori, Maki Fukami, Keiko Matsubara","doi":"10.1159/000547186","DOIUrl":"10.1159/000547186","url":null,"abstract":"<p><strong>Introduction: </strong>X chromosomal structural changes involving PHEX result in X-linked hypophosphatemia (XLH). However, their underlying mechanisms were poorly determined. Moreover, X chromosome inactivation (XCI) statuses in female patients with XLH remain to be studied.</p><p><strong>Case presentation: </strong>We conducted systematic genomic analyses for a woman with XLH and detected a 3.2 Mb tandem duplication at Xp22.33, a 1.9 Mb tandem duplication at Xp22.31, and a 0.8 Mb deletion involving PHEX at Xp22.11 on the paternally derived chromosome. The fusion junctions contained templated insertions and short nucleotide additions indicative of non-homologous end joining (NHEJ) or alternative NHEJ. The patient had random XCI.</p><p><strong>Conclusion: </strong>This study provides evidence that PHEX haploinsufficiency leads to typical XLH in women with random XCI and that a 5.9 Mb rearrangement on Xp22 permits random XCI. Our results, together with previous findings, imply that clustered structural changes due to NHEJ/alternative NHEJ are a unique type of human genomic rearrangements.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-6"},"PeriodicalIF":1.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144552593","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":"Erratum.","authors":"","doi":"10.1159/000546684","DOIUrl":"https://doi.org/10.1159/000546684","url":null,"abstract":"","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"72"},"PeriodicalIF":1.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144539509","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":"Establishment of Cell Cultures from the Cavefish Astyanax mexicanus: A Resource for in vitro Studies of Supernumerary B Chromosome Biology.","authors":"João Pedro Silva Climaco, Cesar Martins, Adauto Lima Cardoso","doi":"10.1159/000546231","DOIUrl":"10.1159/000546231","url":null,"abstract":"<p><strong>Introduction: </strong>Supernumerary B chromosomes have been extensively investigated using diverse in vivo approaches, revealing insights into their origin, nature, evolutionary dynamics, maintenance mechanisms, and effects on their carriers. Despite its broad applicability across various biological research fields, in vitro cell culture remains underexplored as a tool for studying B chromosome biology, with studies limited to using cell cultures only as a source of chromosome preparations.</p><p><strong>Methods: </strong>In the present study, cell cultures of the fish Astyanax mexicanus were established, with (AMEcfB) and without (AMEcf) the B chromosome, using caudal fin tissue collected through nonlethal procedures. These cultures were compared in terms of cell proliferation and in response to environmental stress (pH and temperature) using the MTT and RT-qPCR assay.</p><p><strong>Results: </strong>The AMEcf and AMEcfB cell lines exhibited karyotypic stability and high proliferative potential, demonstrating their suitability for diverse scientific applications. The B chromosome, found exclusively in a subpopulation of AMEcfB cells, influenced cell physiology by affecting cell division dynamics. Experiments under extreme pH and temperature conditions revealed differences in cell viability and gene expression between the two lines, highlighting the role of the B chromosome in modulating environmental responses.</p><p><strong>Conclusion: </strong>These findings align with previous reports on the effects of B chromosomes in living organisms. Thus, the A. mexicanus cell cultures established here represent a promising resource for investigations into B chromosome biology, offering significant ethical, economic, and methodological advantages.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"59-69"},"PeriodicalIF":1.7,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301348","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":"Atypical Presence of Interstitial Telomeric Sequences in Thamnophilus Species (Passeriformes: Thamnophilidae).","authors":"Vitor Oliveira de Rosso, Victoria Tura, Hybraim Severo Salau, Lilian de Oliveira Machado, Fabiano Pimentel Torres, Ricardo José Gunski, Analía Del Valle Garnero","doi":"10.1159/000545469","DOIUrl":"10.1159/000545469","url":null,"abstract":"<p><strong>Introduction: </strong>Thamnophilidae (typical antbirds) are a diverse family of insectivorous passerine birds restricted to neotropical forests, encompassing 237 species, of which only 5 have been studied cytogenetically.</p><p><strong>Methods: </strong>To investigate the chromosomal evolution of this group, we applied classical and molecular cytogenetic techniques, including conventional staining, C-banding, and fluorescence in situ hybridization with probes for repetitive telomeric sequences (TTAGGG)5 and 18S rDNA, in two representative species: Thamnophilus caerulescens and Thamnophilus ruficapillus.</p><p><strong>Results: </strong>The karyotypes of T. caerulescens and T. ruficapillus comprise 80 and 82 chromosomes, respectively. In addition to a possible fission in T. ruficapillus, morphological differences suggest the occurrence of pericentric inversions in the chromosomes of this species. The patterns of constitutive heterochromatin differed between the species: both showed centromeric markings and heterochromatin on the W chromosome, but T. ruficapillus also exhibited interstitial markings on seven chromosomal pairs. Both species presented interstitial telomeric sequences (ITSs) in the first seven pairs, which corresponded to constitutive heterochromatin in T. ruficapillus. The 18S rDNA probe hybridized to a single pair of microchromosomes in T. caerulescens and two pairs in T. ruficapillus.</p><p><strong>Conclusion: </strong>This study revealed novel patterns of constitutive heterochromatin in T. ruficapillus and ITSs in both species, which have not been previously observed in Passeriformes. The correspondence between constitutive heterochromatin and ITSs in T. ruficapillus suggests that these sequences are composed of repetitive DNA highly similar to telomeric sequences and/or are remnants of pericentric inversions, whereas in T. caerulescens, other mechanisms seem to be involved. The differences in observed patterns highlight distinct chromosomal evolution between these species, emphasizing the diversity within the family Thamnophilidae and the genus Thamnophilus, in contrast to the conserved patterns typically observed in the class Aves.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"1-11"},"PeriodicalIF":1.7,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794396","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":"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":"Kallmann Syndrome due to Balanced X Chromosomal Pericentric Inversion Disrupting ANOS1.","authors":"Michihiko Aramaki, Takashi Hamajima, Erina Suzuki, Maki Fukami, Keiko Matsubara","doi":"10.1159/000545695","DOIUrl":"10.1159/000545695","url":null,"abstract":"<p><strong>Introduction: </strong>Kallmann syndrome (KS) is a rare congenital disorder characterized by hypogonadotropic hypogonadism and anosmia/hyposmia. KS primarily results from nucleotide substitutions and copy number variations in known causative genes. Only one balanced X chromosomal inversion involving ANOS1 has been identified in a patient.</p><p><strong>Case presentation: </strong>We encountered a boy with typical clinical features of KS. G-banding showed a 46,Y,inv(X)(pter→p22.32::q21.1→p22.32::q21.1→qter) karyotype, and whole genome sequencing and array-based comparative genomic hybridization detected a copy number neutral pericentric inversion involving a 72-Mb region. The breakpoints were mapped to ANOS1 intron 3 and an intergenic region at Xq21.1. The two breakpoints shared a 3-bp complementary sequence but were not associated with repetitive elements or nucleotide insertions at the fusion junction.</p><p><strong>Conclusion: </strong>These results indicate that KS-causative inversions on the X chromosome can arise from replication-based errors. Furthermore, our data provide evidence that balanced X chromosomal inversions constitute a rare monogenic cause of KS.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"93-98"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973424","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 situ and in silico Localization of Major Satellite DNAs in the Genome of the Red-Eared Slider (<italic>Trachemys scripta elegans</italic>, Emydidae, Testudines).","authors":"Svetlana Romanenko, Svetlana A Romanenko, Dmitry Yu Prokopov, Sergey A Marchenko, Maria M Kulak, Arina V Ilina, Natalia A Serdyukova, Svetlana A Galkina, Vladimir A Trifonov","doi":"10.1159/000544908","DOIUrl":"10.1159/000544908","url":null,"abstract":"<p><strong>Introduction: </strong>Satellite DNA is an important component of the eukaryotic genome. Some satellite DNAs plays an important role in various biological processes. The red-eared slider (Trachemys scripta elegans, 2n = 50, C = 1.43 pg) belongs to the American freshwater turtle family and is recognized as one of the world's most invasive species. In the T. s. elegans chromosome-level genome assembly, which has been recently published, satellite DNAs comprise only 0.1%. From the repetitive repertoire of the T. elegans genome, only ribosomal DNA genes and telomeric repeats have been localized on the species' chromosomes.</p><p><strong>Methods: </strong>Using publicly available short-read sequencing data, we conducted de novo identification of the most abundant satellite DNAs in T. s. elegans using the TAREAN pipeline. We combined bioinformatics (using blastn) and chromosome mapping by fluorescence in situ hybridization to describe the distribution of major tandem repetitive DNAs. The diversity and distribution of satDNA in the assembled genome of T. s. elegans were explored using the SatXplor pipeline.</p><p><strong>Results: </strong>Six major satellite sequences occupying approximately 0.8% of the genome were identified in the genome data, all of which were successfully localized both in situ and in silico on T. s. elegans chromosomes and in silico on chromosomal scaffolds. We revealed a complex structural organization of these sequences: monomers may be moderately or highly variable and they may contain regions homologous to retrotransposons. Cytogenetic mapping showed the accumulation of satellite DNAs in the pericentromeric regions of most chromosomes and in the distal regions of the short arms of submetacentric chromosomes. Comparisons between cytogenetic maps and genome assembly data revealed discrepancies in the number and chromosomal locations of the identified satellite DNA clusters.</p><p><strong>Conclusion: </strong>The red-eared slider genome has a greater proportion of satellite DNA than was previously reported. These satellites demonstrate no specificity for either macrochromosomes or microchromosomes. Differences between in situ and in silico results indicate the challenges of repetitive sequence assembly, as well as discrepancies between chromosome numbering in the current chromosome-level genome assembly and the physical chromosome map.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":" ","pages":"162-174"},"PeriodicalIF":1.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604274","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}