Cytogenetic and Genome Research最新文献

Introduction: Satellite DNA (satDNA) is an important component of eukaryotic genomes that influences chromosomal organization and evolution. This study investigates the sequence diversity, chromosomal distribution, and copy number variation of the CLA-SAT-149 satDNA family (149 bp) in four clariid catfish species, Clarias macrocephalus, C. gariepinus, C. batrachus, and C. nieuhofii, as well as in F₁ hybrids and backcross (BC) progeny.

Methods: Fluorescence in situ hybridization (FISH) was used to map CLA-SAT-149 on metaphase chromosomes. Quantitative PCR (qPCR) quantified copy number variation. Amplicon sequencing was applied to characterize sequence variants, and Bayesian clustering analysis was used to assess genetic relationships among subfamilies.

Results: Chromosome mapping showed species-specific signals present in C. macrocephalus and F₁ hybrids but absent in C. gariepinus and C. nieuhofii. qPCR revealed significantly higher copy numbers in C. macrocephalus. Two sequence variants were identified: the canonical 149-bp (subfamily A) and an 85-bp derivative (subfamily B). Bayesian analysis indicated multiple genetically distinct subgroups among species. F₁ hybrids and BC progeny exhibited unique sequence profiles and copy number patterns, while C. nieuhofii lacked CLA-SAT-149 entirely.

Conclusion: The results support lineage-specific expansion, amplification, and loss of CLA-SAT-149 in clariid catfish, consistent with the satDNA library model. These patterns provide insights into satDNA evolution and have potential applications in aquaculture genetics, hybrid identification, and species differentiation.

Introduction: The domestic guinea pig (Cavia porcellus, Caviidae) is an important laboratory species, model for human medical research, worldwide spread pet and a source of food in specific parts of South America. Data on chromosomal abnormalities in guinea pigs are really limited, probably due to the complexity of their karyotype (2n = 64).

Methods: G- and C-banding and fluorescence in situ hybridization (FISH) using human chromosome-specific painting probes were used to analyze the karyotype and identify chromosomes involved in a newly discovered Robertsonian translocation.

Results: Karyotype 63,XY,rob(13;19) was revealed in a phenotypically normal, fertile domestic guinea pig male. The chromosomes involved in the fusion were verified using FISH with human whole chromosome probes and known guinea pig - human chromosome synteny.

Conclusion: This finding adds to the limited cytogenetic data available on the guinea pig, and provides a basis for further investigation of their chromosomal variation and its biological significance. Our results indicate the need for chromosome studies in this cytogenetically mostly neglected species, especially in breeding populations used for biomedical research.

Introduction: Sex chromosomes often evolve through suppressed recombination and accumulation of transposable elements (TEs) on the sex-limited chromosome, leading to divergence and eventual degeneration. The clam shrimp Eulimnadia texana possesses proto-sex chromosomes (Z and W) at an early evolutionary stage, providing a unique opportunity to examine the initial genomic changes underlying sex chromosome differentiation. Additionally, both sex chromosomes are expressed in homogametic ZZ and WW shrimp, allowing a regular expression of both sex chromosomes in homozygotes.

Methods: We analyzed newly assembled ZZ (male) and previously published WW (hermaphrodite) genomes of E. texana. Sex-linked markers were mapped to identify the Z chromosome. TEs were annotated using a species-specific repeat library and RepeatMasker. The Z and W chromosomes were divided into bins and randomization tests compared TE accumulation between the sex chromosomes as well as between corresponding regions within these two chromosomes; the latter was focused on the putative sex-determining regions of both the Z and W. Kimura distance-based analyses were used to estimate TE age divergence.

Results: The Z chromosome showed no significant TE enrichment relative to autosomes but was enriched for DNA transposons. The W chromosome exhibited significantly higher retrotransposon (LTR and LINE) accumulation. Only the sex-determining region of the W showed significantly elevated retrotransposon content compared to the Z. TE age landscapes indicated recent bursts of retrotransposon activity on the W.

Conclusion: These findings support theoretical predictions that retrotransposons accumulate in non-recombining regions, while DNA transposons are associated with recombining chromosomes. The W chromosome of E. texana shows early signs of differentiation, with localized retrotransposon buildup, while the Z remains autosome-like. This study highlights E. texana as a valuable model for understanding the genomic mechanisms of early sex chromosome evolution.

Background: Ageing is a general, intrinsic, and progressively deleterious process that affects all cells, tissues, and organs albeit at different extent and rate in each individual. The complexity and universality of its phenotypic manifestations suggest a multifactorial origin. The autosomal recessive disorder Werner syndrome likely represents a segmental progeroid disorder since patients show several, but not all phenotypes of premature ageing.

Summary: Proliferative senescence of diploid cells in culture provided a model system in which ageing can be studied experimentally. Cultures of cells from patients with Werner syndrome experienced an extreme form of proliferative senescence and a clonal succession of translocations, known as variegated translocation mosaicism. In addition, Werner syndrome cells showed spontaneous deletion formation and a prolongation of and arrest in the S phase of the cell cycle. The WRN protein harbours a helicase, an exonuclease and a RecQ interaction domain. With the latter, the WRN protein may interact with NBS1, Replication Protein A (RPA), MRE11, TREX1, MUTYH, POT1, TRF1, FEN-1, PAPRP-1, p97/VCP, TRF2, DNA polymerase(beta), Ku76/80, EXO-1, NEIL1, and p53, which are key to DNA damage response pathways including canonical NHEJ, homologous recombination, base excision repair, and telomere maintenance. The WRN exonuclease domain is a target of WRNIP1 binding, which links WRN to resolution of stalled replication due to collision with transcription and the ATM-mediated cell cycle checkpoint. Patients with an incomplete complement of Werner syndrome phenotypes, called atypical Werner syndrome patients, were found to carry variants in LMNA, POLD1, SPRTN, MDM2, CTC1, SAMHD1.

Key messages: These findings broaden the genotypic landscape and the phenotypic spectrum of Werner syndrome. In this review potential molecular mechanisms underlying genomic instability in Werner syndrome, including chromothripsis due to asynchronous S phase traverse and telomere crises followed by bridge fusion breakage cycles are discussed. The participation of WRN in multiple gene networks is consistent with the multifactorial nature of ageing in general.

Background: The damselfishes, an extremely diverse group of herbivorous fish, stands out as an important and ubiquitous ecological component of coral reefs. In the Western South Atlantic, the genus Stegastes is the most representative, whose evolutionary paths and taxonomic status of insular endemic species have been better evaluated. To clarify the karyotypic evolution involved in the diversification of this group, cytogenetic analyses were performed in four nominal species (Stegastes variabilis and Stegastes fuscus, distributed in Brazilian coastal regions; Stegastes rocasensis and Stegastes sanctipauli, from Rocas Atoll and São Paulo and São Pedro Archipelago) and one subspecies (S. fuscus trindadensis, from Trindade and Martim Vaz Archipelago).

Results: Classical cytogenetic protocols and fluorescence in situ hybridization (FISH) with 18S and 5S rDNA probes were used for comparative analyses. All species had 2n = 48 chromosomes, with high FN values ranging from 88 to 92. Stegastes rocasensis and S. sanctipauli shared identical cytogenetic patterns, while S. f. trindadensis revealed a syntenic arrangement of 18S and 5S rDNA sites not found in S. fuscus from the Brazilian coast.

Conclusion: The karyotypic evolution of Stegastes was predominantly driven by multiple pericentric inversions (and/or centromere shifts), resulting in changes in the internal organization of chromosomes. S. rocasensis and S. sanctipauli have similar cytogenetical patterns, as well as S. fuscus and S. f. trindadensis indicating incipient evolutionary differentiation in insular species. Mapping other repetitive DNA sequences provided an exceptional opportunity to clarify chromosomal changes and their association with the evolutionary diversification of Stegastes species.

Introduction: DMRT1 on the Z chromosome is a conserved male sex-determining gene in birds. In chickens, a representative model species of Neognathae, the function of DMRT1 has been well characterized. In contrast, Palaeognathae species such as the emu possess less differentiated sex chromosomes and thus provide a valuable system for investigating avian sex determination, yet molecular studies remain limited. We investigated the timing of sex determination and the expression of key genes involved in gonadal differentiation in emu and further characterized DMRT1 variants.

Methods: Sex determination stage was identified by anatomical comparison of male and female embryonic gonads. Expression of seven genes (DMRT1, AMH, SOX9, NR5A1, FOXL2, CYP19A1, and RSPO1) was examined by mRNA-seq and RT-PCR. DMRT1 splicing variants were predicted by in silico analysis and 3' RACE was used to identify alternative polyadenylation (APA) variants.

Results: The gonadal differentiation occurred at HH25-28 based on gonadal morphology. Gene expression analysis revealed emu-specific patterns not observed in chickens. Notably, RSPO1 was highly expressed in females at HH24-25, preceding DMRT1 expression in males at HH28-29, suggesting ovarian differentiation begins earlier. We identified three splicing variants and four APA variants of DMRT1, with variant 1 predominant during gonadal development.

Conclusion: These findings suggest that while molecular sex differentiation mechanisms are largely conserved between Palaeognathae and Neognathae, they differ in parts. In particular, early RSPO1 expression may initiate ovarian differentiation prior to testis determination by DMRT1. The presence of emu-specific DMRT1 variants further indicates possible species-specific mechanisms in testis development.

Background: 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.

Summary: 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.

Key message: 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.

Background: 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.

Summary: 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.

Key messages: 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.

Background: 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.

Introduction: 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.

Case presentation: 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.

Conclusion: 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.