Cytogenetic and Genome Research最新文献

Introduction: 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.

Methods: 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.

Results: 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.

Conclusion: 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.

Introduction: Here we compare differences in the presence of telomeric signals (tDNA-FISH) among karyotypes of taxa having different whole-arm chromosomal rearrangements under the assumption of their participation in differentiation/integration processes during karyotype evolution. We analyzed the cytogenetic peculiarities of Robertsonian-like (centromeric) and tandem (telomere-involving) rearrangements using examples of the authors' recent research on comparative cytogenetics of mammals. New data on intra- and interspecific karyotype variation helped understand the nature of chromosomal rearrangements and their molecular features within and between species in two target mammalian taxa: representatives of two genera from two orders (insectivores and rodents).

Methods: To detect telomeric repeats in karyotypes of representatives of the Eurasian genus Sorex and Ethiopian endemic Stenocephalemys, G-banded metaphase chromosomes were hybridized in situ with a fluorescein-conjugated peptide nucleic acid probe and 5'-TAMRA-labeled (CCCTAA)₄ oligonucleotides.

Results: We compared the location of a molecular chromosomal trait - telomeric sequences - among karyotypes of taxonomically distinct individuals having different types of whole-arm chromosomal rearrangements. Along with the regular terminal location of the telomeric signal on all chromosomes, displays of interstitial telomeric sequences (ITSs) were detectable. This pattern was typical for a studied shrew specimen whose karyotype corresponded to a natural interracial F1 hybrid. This finding doubles the number (known to date) of S. araneus race-specific metacentrics having an identified telomeric signal. In karyotypes of Stenocephalemys specimens, we revealed individual differences in autosomes corresponding to tandem fusion rearrangements, possibly species-specific, for the first time. No intrachromosomal telomeric signal expected in this case was detectable in autosomes, whereas we registered ITSs in pericentromeric regions on X chromosomes near a short, completely heterochromatic (additional) arm.

Conclusion: The new data indicate a heterogeneous distribution of the telomeric signal (tDNA-FISH) on mitotic chromosomes that are involved in (typical for mammals) whole-arm chromosomal variation, thus representing two models of karyotype evolution: Robertsonian polymorphism and tandem fusions. In the analyzed examples of whole-arm chromosomal rearrangements, displays of the centromeric ITS signal more likely represent an integral feature of cytogenetic relatedness within a species (chromosomal races) or between species (in a genus or group of genera) than differentiation of taxa.

Introduction: 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.

Methods: 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.

Results: 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.

Conclusion: 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.

Introduction: 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.

Methods: 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.

Results: 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.

Conclusion: 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.

Introduction: 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.

Case presentation: 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.

Conclusion: 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.

Background: The study of gametogenesis in hybrids between intraspecific chromosomal forms or distinct species is mainly aimed at identifying the successful outcome of the process to produce balanced, viable gametes. At the same time, deviations from typical meiotic progression patterns may provide a pivotal mechanism for speciation.

Summary: The long history of studying the process of gametogenesis and the development of methodological approaches have helped clarify the cytological and molecular processes that occur during meiosis. Since the early 1980s, Prof. Oxana Kolomiets has been studying meiosis in various species, including mole voles Ellobius, with a focus on chromosome synapsis and other key events during prophase I. Research on hybrids from different chromosomal forms of mole voles has uncovered notable differences in how meiosis progresses and its impact on fertility. In cases where Robertsonian translocations exhibit incomplete homology, various chromosomal multivalents form during prophase I. These configurations are often so complex that the chance of producing balanced gametes appears minimal. Moreover, there were also variations in the formation of trivalents. These discrepancies are thought to arise due to the involvement of distinct chromosomes in Robertsonian translocations, which lead to alterations in the spatial structure of the nucleus. Autosomes and sex chromosomes can exhibit disparities in trajectories of movement, synapsis, and recombination in meiosis. These disparities manifest most distinctly in hybrids, where atypical interchromosomal interactions, including those between sex chromosomes and autosomes, occur. Such interactions are absent in normal meiocytes, highlighting the altered meiotic processes in hybrids.

Key messages: Chromosomal rearrangements, such as Robertsonian translocations, neocentromeres, and dicentric chromosomes, alter nuclear architecture, leading to meiotic irregularities that disrupt the progression of meiosis and gametogenesis. Meiotic irregularities cause variation in hybrid fertility. The analysis of meiosis I prophase turns out to be highly efficient for understanding the mechanisms of speciation.

Introduction: Small supernumerary marker chromosomes (sSMCs) are small structurally abnormal chromosomes whose origin and structure are difficult to determine by conventional cytogenetic banding techniques. The aims of the study were to analyze sSMCs discovered in prenatal diagnosis, explore the origin and clinical significance of fetal sSMCs, and inform genetic counseling and reproductive health care.

Methods: Karyotyping was performed on pregnant women who underwent prenatal diagnosis in a Chinese hospital between April 2018 and April 2024. The sSMC cases encountered were further analyzed using copy number variation sequencing (CNV-seq) to determine the origin of the sSMCs and assess their clinical significance. Uniparental disomy (UPD) was excluded in the families with de novo sSMC cases using multiplex fluorescence PCR and capillary electrophoresis.

Results: Out of 30,114 prenatal samples, 30 cases of sSMCs were identified, yielding a detection rate of 0.10%. Family analysis was performed on 23 of these cases, revealing 4 cases inherited and 19 cases of  de novo aberrations. CNV-seq was conducted on 27 cases, with 14 showing no abnormalities and 13 exhibiting CNVs. Among the 10 cases where the origin of the sSMC was clearly identified, the duplications involved chromosomes 4, 10, 12, 15, 18, X, and Y, with pathogenic CNVs accounting for 70.0% (7/10) and variants of uncertain clinical significance accounting for 30.0% (3/10). Out of the 30 women with sSMCs detected, 13 chose to terminate the pregnancy, representing 43.3% (13/30). A follow-up was conducted on 13 de novo sSMC cases that were negative for CNV-seq. Among the live-born fetuses, all except one, who presented with speech delay, showed normal clinical features. UPD testing was successfully performed on 3 families (including the 3-year-old girl with speech delay), and all results were negative.

Conclusion: Utilizing both karyotyping and molecular genetic testing is advantageous for effectively screening and identifying sSMCs. CNV-seq is recommended as an important supplementary method for sSMC identification, thereby providing more detailed genetic counseling for prenatal diagnosis.

Introduction: DNA helicases are vital for preserving genome integrity and ensuring the correct process of meiosis. Despite their recognized significance, the precise roles and spatial dynamics of these enzymes during meiotic prophase I remain largely unexplored.

Methods: The key methodology of this study consisted of immunocytochemical staining and statistical evaluation.

Results: Our results demonstrate that RTEL1 (Regulator of Telomere Elongation 1) helicase is present in regions that have just initiated synapsis, emphasizing that chromosome synapsis is essential for this helicase. Since RTEL1 and replication protein A (RPA) were previously shown to colocalize in somatic cells, we sought to assess this relationship in meiosis. During early pachytene, when RTEL1 and RPA levels are at their peak, several immuno-foci of these proteins exhibited complete or partial overlap, suggesting colocalization in some chromosomal regions, though some remained distinct. The earlier appearance of RPA in meiotic nuclei supports the notion that it may facilitate RTEL1 recruitment for DNA repair. As meiosis progresses from early pachytene to diplotene, the significant decrease in RTEL1 and RPA signals underscores their predominant involvement in early prophase I.

Conclusion: This study identifies RTEL1 as the third helicase, following BLM and FANCJ, to be detected in prophase I, suggesting that additional helicases may be added to this list in the future. Its unique synapsis-dependent behavior distinguishes it from the other two helicases, which do not exhibit such a pattern. Furthermore, our findings suggest that RTEL1 can demonstrate antirecombinase activity within synaptonemal complexes and functions as part of the meiotic helicase complex, which regulates critical aspects of meiotic processes.

Introduction: R1 and R2 retrotransposons specifically integrate into 28S rRNA genes, thereby disrupting many rDNA units within the nucleolar organizer region (NOR) of Drosophila. However, they also appear to play mutualistic roles, contributing to the maintenance of rDNA copy number and the regulation of nucleolar dominance. In addition to their presence in nucleolar rDNA, R1 elements are strongly enriched in the pericentromeric heterochromatin of the X chromosome, located distal to the NOR. This enrichment coincides with several enigmatic genetic phenomena - such as the ABO and cr phenotypes - whose molecular basis remains poorly understood. Notably, this region is one of the least characterized domains of the Drosophila melanogaster genome, lying outside the reference assembly and unresolved in metaphase chromosome preparations.

Methods: We performed cytological mapping of R1 and R2 retrotransposons in D. melanogaster heterochromatin using polytene chromosomes from Rif11 mutant, which suppresses under-replication of all types of heterochromatic sequences. These were combined with classical eu-heterochromatic inversions of the X chromosome.

Results and conclusion: We identified distinct clusters of both R1 and R2 elements within the X chromosome heterochromatin outside the NOR. R1 elements are highly enriched in the region between the heterochromatic Stellate (hSte) gene cluster and the NOR. This zone exhibits a unique response to Su(var)3-9 mutations, characterized by pronounced decondensation and the formation of a pseudo-puff. Proximal to the R1-enriched domain and adjacent to hSte cluster, we observed a region enriched in R2 elements. The edges of the NOR also show R2 enrichment, likely corresponding to intra-nucleolar domains that accumulate transcriptionally inactive rDNA units. In contrast, nucleolar R1 elements - which also mark inactive rDNA units - are more evenly distributed across the entire NOR. Based on these findings, we propose a refined cytological map of X chromosome heterochromatin in D. melanogaster.

Introduction: 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.

Methods: 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.

Results: 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.

Conclusion: 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.