Cytogenetic and Genome Research最新文献

Introduction: Pericentric inversions (PEIs) are rare intrachromosomal balanced structural abnormalities. To achieve complete synapsis and recombination during meiosis, the pairing of normal and inverted chromosomes requires the formation of an inversion loop. A crossover within this inversion loop leads to the production of two complementary recombinant chromosomes, which may contain both duplicated and deleted segments, including regions distal to the inversion. The clinical relevance of inverted chromosomes is significant, as they can result in the generation of recombinant gametes that may lead to early miscarriages, stillbirths, or congenital abnormalities in the progeny of carriers. The empirical frequencies of recombinant spermatozoa in men heterozygous for inv(19)(p13.3q12) were estimated. Additionally, the presence of the interchromosomal effects (ICEs) on chromosomes 13, 18, 21, X, and Y was evaluated.

Methods: Fluorescence in situ hybridization (FISH) was performed on sperm nuclei using DNA probes for the subtelomeric regions of the short (p) and long (q) arms of chromosome 19, the centromeric regions of chromosome 18, X, and Y as well as DNA probes for the regions 13q14 and 21q22.

Results: The inverted segment on chromosome 19 measures 31.5 Mb, which represents 53.3% of the total length of the affected chromosome. FISH analysis of 2,923 sperm nuclei revealed no detection of recombinant chromosomes. ICE on chromosomes 13, 18, 21, X, and Y were not observed.

Conclusion: Empirical data have been obtained for the first time regarding the frequency of gametes containing recombinant chromosomes, as well as the absence of ICEs on chromosomes 13, 18, 21, X, and Y during the meiotic segregation of the PEI of chromosome 19, inv(19)(q13.3q12). It was demonstrated that the extremely low risk of recombinant chromosome formation, falling below the detectable threshold (with 95% confidence intervals), is associated with inv(19)(p13.3q12). We hypothesize that the meiotic behavior of PEIs is influenced not only by the relative size of the inverted segment but also by the morphological characteristics of the affected chromosome. Further studies are needed to explore the factors that influence the meiotic behavior of PEIs.

Introduction: The Phasianidae family belongs to Galliformes, which is basal to other Neognathae. Despite the availability of chromosome-level genome assemblies for many Phasianidae species, the karyotypes for some species remain poorly investigated.

Methods: In this study, we described karyotypes using classical, differential, and molecular cytogenetic (BAC-FISH) methods. To compare chromosome-level genomes of 10 Galliformes species dot-plot analysis was performed.

Results: We provide the first comprehensive description of the karyotype of two Tetraonini species: the western capercaillie (Tetrao urogallus, 2n = 78) and the hazel grouse (Tetrastes bonasia, 2n = 80). We mapped chicken BAC clones (CHORI-261) with known coordinates to the chromosomes of the western capercaillie and Japanese quail (Coturnix japonica, 2n = 78) to anchor physical chromosomes to chromosome-level assemblies. Finally, we performed dot-plot comparisons of ten available chromosome-level genome assemblies to identify inter- and intrachromosomal rearrangements in Galliformes.

Conclusion: We show that the centromeric fusion of orthologs of GGA6 and GGA8 is shared by all analyzed species in the tetraonid clade: T. urogallus, T. bonasia, and Lagopus muta. We identified linage-specific intrachromosomal rearrangements on chromosomes orthologs to chicken Z (Phasianinae and Tetraoninae), 7 and 12 (Phasianinae and Tetraoninae), 5 and 13 (Perdicinae), 22 (Alectoris). Our study shows that analysis of the genomes of several closely related species allows us to identify chromosomal rearrangements characteristic of individual evolutionary lines.

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.

Background: The Y chromosome microdeletions are common genetic cause of male infertility. Mechanisms of impaired spermatogenesis and meiosis, as well as phenotypic variability, have not been sufficiently studied.

Objective: The paper provides results of the spermatogenesis and meiotic study based on the analysis of synaptonemal complex (SC) in the spermatocyte nuclei in infertile men with Y chromosome microdeletions.

Materials and methods: Examined cohort consisted of 9 male patients 27-32 years old with primary infertility with non-obstructive azoospermia. The patients had a 46,XY karyotype, complete (n = 4) and partial AZFc (n = 2) deletions, and complete AZFb (n = 2) and AZFb+c (n = 1) deletions. Semen analysis was performed and assessed according to the WHO guidelines (WHO, 2010). The AZF deletions were detected by multiplex PCR, analyzing Y-specific loci in accordance with the guidelines for molecular diagnosis of the Y chromosome microdeletions. Testicular biopsy was performed by with the TESE technique. Testicular tissue fragments were assessed under a light microscope for the presence of spermatocytes, spermatids, spermatozoa, atypical and degenerating germ cells in the suspension and analyzed by histopathology. Immunostaining was performed using antibodies to the SYCP3, γH2AFX, RAD51, and MLH1 proteins.

Results: In 6 examined patients, spermatocytes were found at following stages of the prophase I of meiosis: leptotene - 32.3 ± 39.4 (0-100)%, zygotene - 17.4 ± 20.1 (0-63.6)%, pachytene - 48.6 ± 38.2 (0-100)%, diplotene - 1.8 ± 2.2 (0-5.6)%. Percentage of germ cells at these stages was very close between patients with AZFb, AZFb+c, and AZFc deletions. Meiotic arrest at the zygotene stage with atypical SCs and incomplete synapsis in all nuclei was found in patient with complete AZFb+c deletion. Complete meiotic arrest at early-mid-pachytene was characterized for complete AZFc and AZFb deletions. Azoospermic patients with partial AZFc (gr/gr) deletions had incomplete meiotic arrest at the mid-pachytene stage.

Conclusion: Our own and literature data indicate more severe spermatogenesis and meiosis failures in patients with AZFb+c and AZFb deletions in comparison with AZFc deletions. Meiotic arrest at early-mid-pachytene was common, but some variability was found in the severity of spermatogenesis abnormalities in patients with complete AZFc deletions that requires further research.

Introduction: Meiotic recombination is one of the major sources of genetic diversity. Understanding the cytogenetic basis for recombination rate alterations is essential to explain the patterns of variation observed between different groups of species. Common degu (Octodon degus) is a South American rodent of the speciose and highly chromosomal variable Ctenohystrica clade, on which relatively few cytogenetic studies have been carried out. It has a mostly bi-armed karyotype, making it an interesting model for cytogenetic research.

Methods: Using immunolocalization of key meiotic proteins and electron microscopy in pachytene spermatocytes, we determined the frequency and distribution of recombination events along a number of chromosome bivalents and the characteristics of sex chromosome synapsis.

Results: Recombination rate of common degu was the highest among the Hystricognathi species studied. In contrast to most mammals, no pronounced recombination peaks near the telomeres were observed in degu. We detected late recombination nodules in the pericentromeric regions of some bivalents, which is a highly extraordinary pattern due to the centromere effect. Within the heterochromatic blocks located on the chromosome arms and marked by H3K9me3, one of the major constitutive heterochromatin marks, we observed a significant decrease in recombination frequency. We describe for the first time the bridge between X and Y in the late pachytene stage in common degu and the absence of late MLH1-dependent recombination nodules in the sex bivalent.

Conclusion: We can assume that the absence of H3K9me3 signaling at centromeres is unrelated to the presence of MLH1 near the centromere. Findings on potential achiasmatic meiosis in common degu were discussed in relation to sex chromosome evolution.

Introduction: Infertility and recurrent pregnancy loss are serious health problems often associated with genetic abnormalities such as chromosomal rearrangements. Although conventional cytogenetics plays a crucial role in this kind of diagnostics, it fails to detect submicroscopic changes, especially in the pericentromeric regions of acrocentric chromosomes, which are potentially prone to rearrangement. To overcome this limitation, this study aimed to identify such subtle changes that can lead to reproductive disorders using fluorescence in situ hybridization (FISH) technique and newly developed fluorescence probes that specifically target these regions.

Methods: The study group consisted of 50 couples who, despite having unprotected sexual intercourse, had been unable to conceive for more than a year or had suffered two or more miscarriages and had been unable to carry a pregnancy to term. After exclusion of cytogenetically visible chromosomal alterations, patients were subjected to FISH analysis with three newly designed probe sets that stain the centromere and pericentromere regions of acrocentric chromosomes 13 and 21 (SET-I), 14 and 22 (SET-II), and 15 (SET-III).

Results: FISH analysis of SET-II and SET-III probes revealed a cryptic reciprocal translocation between chromosomes 15 and 22 in a 33-year-old male. His female cousin was also found to be a carrier of the same translocation and had a dysmorphic child due to adjacent II missegregation.

Conclusion: Subtle chromosomal changes, such as reciprocal translocations in our patients, may be one of the underlying causes of unbalanced gametes in reproductive disorders. The use of three newly designed FISH probe sets may need to be considered to offer comprehensive prenatal and preimplantation genetic testing to couples with reproductive failure.

Introduction: The chromosome region 15p11.2-15q11.2 contains heterochromatic and euchromatic DNA segments. Heteromorphisms in 15p11.2-15q11.1 have been reported, as has been a euchromatic variant (EV) region in 15q11.2.

Methods: Fluorescence in situ hybridization (FISH) was used to examine the genomic regions 15p11.2-15q11.2 in parallel and at the single-cell level. A total of 44 cases with normal chromosomes 15 were examined, including 38 cases with a small supernumerary marker chromosome 15 (sSMC(15)). Combined five-color FISH probe sets A and B were developed, which include probe mixtures for the positions 8.7-20.7 Mb and 22.262115-23.863963 Mb (GRCh37/hg19).

Results: Therefore, the frequencies of the 15p11.2-15q11.1 heteromorphisms for D15Z1, D15Z3, and D15Z4 were determined at 16%, 7.4%, and 13.5%, respectively. Copy number gains or losses in the EV region 15q11.2 were most frequently observed at positions 22.262115-22.826598 (GRCh37/hg19); overall, copy number variants in 15q11.2 were observed in 41% of the chromosomes 15 examined. Furthermore, it became clear that more attention needs to be paid to the exact characterization of breakpoints in sSMC(15) cases. It was shown that the breakpoint clusters involved in sSMC formation differ from those responsible for microdeletions associated with Prader-Willi/Angelman syndrome. Interestingly, at least 25% of the sSMC(15) cases studied here were formed by an interchromosomal U-type exchange. This group also included two previously unrecognized asymmetric sSMCs.

Conclusion: In summary, the detailed investigation of the chromosomal regions 15p11.2-15q11.2 using molecular cytogenetics has provided new insights into the formation of sSMC(15) and submicroscopic variations in this region.

Background: Tandemly repeated satellite DNA sequences are an important part of animal genomes. They are involved in chromosome interactions and the maintenance of the integral structure of the nucleus, regulation of chromatin conformation and gene expression, and chromosome condensation and movement during cell division. Satellite DNAs located in the centromeric heterochromatin evolve rapidly and likely affect hybrid fertility and fitness. However, their studies are taxonomically highly biased. In lacertid lizards, satDNA has been extensively studied in the subfamily Lacertinae, but the subfamily Eremiadinae has been largely overlooked.

Results: In this work, we describe a novel 177-bp-long centromeric satDNA family EremSat177, which is present in all studied species of the genus Eremias, but not in related genera. EremSat177 is not homologous to any previously identified centromeric satellites. Using fluorescence in situ hybridization, we demonstrate its centromeric localization in E. velox and E. arguta. We also show its tandem organization and intra-genomic homogenization by in silico analysis in the genome of E. argus. The phylogenetic analysis of consensus EremSat177 sequences from 12 Eremias species demonstrates that the same monomer subfamily is the most abundant in all these species, and its evolution mainly follows the species phylogeny as revealed by the mtDNA sequences.

Conclusion: The EremSat177 represents a novel, lineage-specific centromeric satellite DNA, and its role in centromere functioning should be revealed in further research.