Cytogenetic and Genome Research最新文献

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.

Background: Robertsonian (Rb) chromosomal rearrangements are very common in mammals and are the primary basis of chromosome number variation between species. The fertility of heterozygotes has particular significance in understanding the mode of fixation of Rb rearrangements, and could have a role in the attainment of reproductive isolation by chromosomally differentiated species. Summary: Here we survey available data on fertility of Rb heterozygotes in mammals, comparing with homozygotes, and considering effects on litter size, frequencies of anaphase I nondisjunction, germ cell death and pachytene features associated with that germ cell death. We consider both simple heterozygotes which form trivalent configurations at meiosis I and complex heterozygotes which form longer configurations due to heterozygosity for different chromosomes with monobrachial homology. Two species have a particularly wide variety of Rb heterozygotes and have been well studied: the house mouse (the western subspecies) and the common shrew. The overall data confirm that heterozygosity for a single Rb metacentric may be associated with near-normal fertility in mammals, though not in every instance. Usually infertility is not going to be a substantial hindrance to fixation of Rb fusions or fissions. Nor is infertility in simple heterozygotes for one or a few Rb metacentrics on its own likely to promote reproductive isolation. However, simple heterozygotes forming many meiotic trivalents and complex heterozygotes forming long meiotic configurations may suffer substantial infertility or sterility. Even so, heterozygous house mice and common shrews forming the very longest meiotic chains and rings may produce some young. We discuss the implications of these findings with regards the role of Rb rearrangements in speciation. Key Messages: Infertility due to Rb heterozygosity on its own may rarely hinder fixation of Rb rearrangements nor be sufficient to cause a complete interruption to gene flow between hybridizing chromosomal forms. However, this does not rule out a role for Rb rearrangements in speciation. Reinforcement is possible, and Rb rearrangements have the potential to act in synergy with genic incompatibilities to promote reproductive isolation. There can also be the contrary process of despeciation. Natural selection may respond in various ways to a given degree of infertility.

Introduction: Spindles are microtubules-based machines whose primary function is to accurately segregate chromosomes in both mitotic and meiotic cell division. The structure of spindles is critical for their function; errors in morphology or attachment to chromosomes lead to aneuploidy, potentially resulting in disease, infertility, and lethality. Electron microscopy studies have yielded fine-detail spindle ultrastructures in many plant and animal species, but no studies have investigated the spindle of Zea mays, a critical crop, and cytogenetic model system.

Methods: Here we use electron tomography (ET), reconstruction, and modeling to obtain three-dimensional, nanometer-resolution of the Z. mays meiotic spindle. Structures such as microtubules, kinetochores, vesicles, membrane channels, and nuclear envelope were modeled through a partial spindle reconstruction, and confirmed using immunostaining and live fluorescence microscopy.

Results: ET revealed that maize spindles contain 8-18 kinetochore microtubules (kMTs) per kinetochore, which are approximately 776 nm in diameter and 316 nm in depth. Small ∼37 nm vesicles were identified, as well as larger (∼5 µm long, 800 nm wide) membrane structures with channels that allow spindle microtubules to pass through. These membrane channels stain positively for the ER-marker protein disulfide isomerase. Imaging of prophase meiotic cells revealed a cross-hatch microtubule arrangement in the perinuclear ring on the external surface of the nuclear envelope, which also contained type II nuclear grooves with transnuclear microtubules passing from the nucleus to the cytoplasm.

Conclusions: Z. mays meiotic spindles are similar to animal counterparts with a comparable number of kMTs and pre-spindle transnuclear microtubules but also plant-specific features such as Golgi-derived vesicles to assist cell plate formation, internal ER membrane channels, and a perinuclear microtubule ring that aids spindle assembly. Maize kinetochores have an electron-diffuse ball in cup morphology that is comparable in size to Drosophila kinetochores and larger than mammalian kinetochores.

Introduction: Telomeric sequences are stable parts of the genome and are widely conserved among higher level taxa (e.g., TTAGG in insects and other arthropods) although exceptions are known and their numbers are increasing with research. The true bug suborder Heteroptera (Hemiptera) includes more than 40,000 species in about 100 families, classified into seven infraorders. Four different telomeric motifs are currently known in Heteroptera, including (TTAGG)_n, (TTAGGGATGG)_n, (TTAGGGGTGG)_n, and (TTAGGGTGGT)_n. The canonical "insect" motif (TTAGG)_n was found in representatives of two infraorders, Nepomorpha and Cimicomorpha. Derived motifs were found in a few species previously known as TTAGG-negative in the evolutionarily advanced sister infraorders Cimicomorpha and Pentatomomorpha (= Terheteroptera). Here, we studied telomeric motifs in 20 species of true bugs belonging to 10 families of Terheteroptera.

Methods: We used fluorescence in situ hybridization with the "insect" telomeric probe (TTAGG)_n and an alternative probe (TTAGGGATGG)_n to map the distribution of telomeric sequences in the chromosomes of 8 species of Pentatomomorpha (from the families Pentatomidae, Rhopalidae, Lygaeidae, Geocoridae, and Blissidae). We also analyzed chromosome-level genome assemblies available in the NCBI database for another 4 species of Pentatomomorpha (from Alydidae, Coreidae, and Pentatomidae) and 8 species of Cimicomorpha (from Reduviidae, Miridae, and Anthocoridae).

Results: Overall, we identified telomeric sequences in all but one (Geocoris dispar; Geocoridae) species. The telomeric motif (TTAGGGATGG)_n was detected in both Cimicomorpha (in the families Anthocoridae and Miridae) and Pentatomomorpha (in Blissidae, Lygaeidae, Pentatomidae, and Rhopalidae); the motif (TTAGGGGTGG)_n was found only in Pentatomomorpha (in Alydidae, Coreidae, and Pentatomidae); and the canonical "insect" motif (TTAGG)_n was found in the family Reduviidae (Cimicomorpha). With our new data, telomeric motifs are now known for 40 species of true bugs from 30 genera, 13 families and 3 infraorders, including Nepomorpha, Cimicomorpha, and Pentatomomorpha. Noncanonical motifs are found so far only in the Terheteroptera clade and are dominant in this group, with (TTAGGGATGG)_n leading.

Conclusion: Our new data have expanded the understanding of telomere composition and evolution in Cimicomorpha and Pentatomomorpha and suggested that (TTAGGGATGG)_n telomeric sequences can be considered ancestral for the entire clade Terheteroptera.

Introduction: 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.

Methods: 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.

Results: 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.

Conclusion: 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.

Introduction: 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.

Methods: 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.

Results: 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.

Conclusion: 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.

Background: Various malignancies can be efficiently combated by focusing on glutathione. It is unclear how glutathione-related genes link to diffuse large B-cell lymphoma (DLBCL).

Methods: Clinical information was gathered from DLBCL patients, and differences in glutathione-related differentially expressed genes (DEGs) between DLBCL and healthy groups were found. Enrichment analysis was run on the DEGs associated with glutathione. We discovered hub genes in glutathione, confirmed hub genes' capacity for diagnosis and function prediction, and estimated drug sensitivity. Immune microenvironmental variations between healthy and DLBCL people were assessed, and hub genes for transcription factor (TF) targeting and miRNAs were found.

Results: The glutathione-related DEGs were linked to biological processes such as response to oxidative stress and response to xenobiotic stimulus, according to enrichment analysis. Out of DEGs associated with glutathione, six hub genes were chosen. In the DLBCL population, there was a notable upregulation of the six hub genes. All the genes' AUC values in the diagnostic ability category were more than 0.7, showing strong hub gene diagnostic capacity. The DLBCL population had a high level of T-cell infiltration, according to immune infiltration analysis techniques. Similar activities, such as the cell cycle G2/M phase transition and the negative control of organelle formation, are demonstrated by gene function prediction for hub. According to drug sensitivity prediction, there was a favorable link between KPNA2 with pracinostat, BRCA1 with B-7100, and LEE-011. The gene KPNA2 was shown to be concurrently targeted by many miRNAs and TFs, according to the miRNA-gene-TF interaction network.

Conclusion: The relationship between DLBCL and glutathione-related genes was uncovered by our research, and six glutathione genes were linked to DLBCL. These genes might be used as diagnostic biomarkers or targets for treatment for DLBCL patients.