Search Results (124)

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited treatment options. Patients are treated with DNA damaging chemotherapies which act by inducing DNA damage in rapidly dividing tumor cells. Unfortunately, these tumors frequently develop treatment resistance, underscoring the need to understand resistance mechanisms in order to develop better treatment strategies. DNA damage response (DDR) detects and repairs DNA damage, and the DDR pathway has been shown to contribute to chemoresistance. Another factor known to drive chemoresistance in PDAC is the dense stroma, composed of extracellular matrix proteins secreted by cancer-associated fibroblasts (CAFs). Our recent work identified a CAF-induced resistance mechanism involving N-myc downstream regulated gene 1 (NDRG1). CAF-induced signaling resulted in the phosphorylation of NDRG1 and NDRG1-dependent DNA repair and protection from chemotherapies. Loss of NDRG1 resulted in increased chemotherapy-induced DNA damage and decreased replication fork speed and recovery. Methods: To gain insight into the molecular mechanism of NDRG1-mediated DNA repair and replication, we performed a BioID screen to identify binding partners of NDRG1. We further assessed the mechanistic roles of the identified interaction partners on DNA repair using DNA replication and repair assays such as the Comet assay and DNA fiber assays. Results: Our BioID screen identified meiotic recombination 11 (MRE11) protein, a nuclease involved in DDR, as a putative NDRG1 interacting protein. Interaction between MRE11 and NDRG1 was enriched during the late S/early G2 cell cycle phases and under replication stress. However, this interaction is likely indirect as the interaction only occurred in a cellular context and not with in vitro purified proteins. Blocking NDRG1 phosphorylation or blocking MRE11 exonuclease activity both resulted in protection of newly synthesized DNA at stalled replication forks. In NDRG1 knockout cells, blocking MRE11 led to decreased protection of nascent DNA, suggesting that NDRG1 and MRE11 may be acting in the same pathway and that NDRG1 is required for MRE11’s activity at stalled forks. Conclusions: In summary, our work has uncovered a protein complex between NDRG1 and MRE11 that may play a key role in chemoresistance due to its role in the processing of stalled replication forks. Full article

Background: Compensatory mutations offer clues in deciphering the role of a particular protein in cellular processes. Here, we investigate an unknown compensatory mutation, present in the BEAF^NP6377 fly line, that provides sufficient rescue of the defective ovary phenotype caused by null BEAF alleles to allow the maintenance of fly stocks lacking the chromatin domain insulator proteins Boundary Element-Associated Factors BEAF-32A and BEAF-32B. We call this dominant mutation Tofu. Methods: We employ both classical genetics and genomic sequencing to attempt to identify the mutation. Results: We find evidence that points to a mutation in a predicted Polycomb response element (PRE) upstream of the ribbon transcription factor gene. This may lead to aberrant rib expression, which is otherwise not expressed in adult ovaries. BEAF and Rib colocalize to a set of promoters, suggesting overlap in gene regulation. Conclusions: Tofu could be a PRE mutation leading to the aberrant activation of rib in the ovaries. This could allow Rib to compensate for a lack of BEAF to activate one or more coregulated genes necessary for egg production in flies. Full article

Sexual reproduction in yeasts is a fundamental biological process that promotes genetic recombination and phenotypic diversification, enabling adaptation to fluctuating and stressful environments. Sporulation and subsequent mating generate novel allele combinations that enhance evolutionary potential; however, many domesticated industrial strains exhibit reduced sporulation capacity, limiting their use in breeding programs and constraining the generation of new diversity. This represents one of the major bottlenecks for improving yeast performance in industrial fermentations, particularly under the harsh conditions characteristic of bioethanol production. In this study, we exploited meiotic recombination and mass-mating strategies to expand genetic and phenotypic diversity in S. cerevisiae. By mass-mating haploid spores derived from genetically distinct parental strains, we generated highly heterogeneous hybrid populations in a single step, overcoming the limitations imposed by conventional breeding approaches, such as micromanipulation. These populations were subsequently screened to identify strains with enhanced fermentative performance and increased tolerance to industrial stressor media associated with bioethanol production. Our results demonstrate that sexual reproduction combined with mass-mating represents an efficient strategy to unlock hidden genetic potential and generate superior industrial yeast phenotypes. This work highlights the value of utilizing the natural reproductive biology of S. cerevisiae to accelerate strain improvement and develop robust yeasts adapted to challenging fermentation environments. Full article

Chromosome dynamics, recombination, and nucleolar organization intersect during meiotic prophase I, yet how the recombination context influences nucleolar architecture remains unclear. We analyzed the nucleolar pool of Cdc14 in Saccharomyces cerevisiae under matched prophase I gating and a uniform, frame-based operational definition of transient two-focus episodes. In a prophase-arrest reference, Cdc14–mCherry formed a predominant single nucleolar focus with occasional, reversible two-focus episodes that Nop56–GFP placed within the nucleolar compartment (nucleolar splitting). Splitting rose sharply when interhomolog recombination was compromised and remained elevated when Spo11 catalytic activity was abolished, indicating that increased DSB formation is not required and pointing instead to the homolog engagement state as a key variable. Population checkpoint readouts did not map onto the phenotype: Hop1 phosphorylation differed strongly across genotypes, yet splitting remained high in recombination-defective and DSB-free contexts and low in the reference. Timing analyses showed that events concentrated early and declined in the reference, whereas recombination-defective and DSB-free backgrounds retained activity into later windows across thresholds. We propose that nucleolar splitting reflects a rheological response of the nucleolus to chromosome-scale forces that vary with homolog engagement, consistent with contributions from DSB-independent chromosome dynamics such as telomere clustering, telomere-led rapid prophase movements, and centromere coupling/pairing. Together, these data support the nucleolus as a mesoscale, mechanically sensitive readout of meiotic chromosome dynamics. Full article

Background/Objectives: The majority of chromosome 22q11.2 deletions are de novo, resulting from meiotic non-allelic homologous recombination (NAHR). While 22q11.2 deletion syndrome (22q11.2DS)-associated phenotypes are well characterized, risk factors leading to NAHR are poorly understood, including the possible relationship with assisted reproductive technology (ART). Here we examined the prevalence of ART conceptions and medical comorbidities in patients with 22q11.2DS vs. spontaneously conceived (SC) patients with 22q11.2DS. Methods: Retrospective analysis, under IRB approval, of medical records on 1184 patients with laboratory-confirmed de novo chromosome 22q11.2 deletions was performed. ART conceptions included IVF with and without ICSI. Deletion size and obstetric, family, and medical histories were examined. Results: We identified 30 pregnancies conceived using ART (2.57%) compared with the U.S. general population rate of 2.3% (p-value = 0.6603). ART and SC sub-cohorts demonstrated no significant differences in deletion size or perinatal outcomes, including preterm birth, multiples, polyhydramnios, or congenital heart disease. Controlling for these factors, neonates conceived via ART were more likely to be admitted to the ICU (aOR = 6.3). Conclusions: Pregnancies conceived via ART, and later found to have 22q11.2DS, demonstrated no significant differences in prevalence or perinatal outcomes compared with the U.S. general population. Moreover, NAHR is unrelated to ART in this population. Likewise, associated phenotypic features are unrelated. These data will be reassuring to those families where ART was employed to conceive children who were later found to have 22q11.2DS. Full article

The germline-restricted chromosome (GRC) is a unique and enigmatic element found exclusively in the germ cells of passerine birds, with its function and evolutionary dynamics still largely unresolved. This study utilizes cytogenetic analysis of the Eurasian bullfinch (Pyrrhula pyrrhula) to explore the meiotic behavior of the GRC. We report the novel discovery of naturally occurring tetraploid and octoploid spermatocytes in this species. Remarkably, in these polyploid cells, the GRC exhibited normal meiotic processes, including full synapsis and recombination. Recombination was restricted to the H3K9me3-negative proximal half of the GRC bivalent, implicating a chromatin-based regulation mechanism. The standard chromosome set in the polyploid cells showed orderly chromosome synapsis. The number of recombination nodules in tetraploid and octoploid nuclei was approximately equal to the standard value for diploids multiplied by 2 and 4, respectively. These findings suggest that polyploidy does not completely hinder meiotic progression in birds and offer new insights into GRC regulation during meiosis. Full article

Male infertility affects nearly 15% of couples worldwide, with chromosomal abnormalities representing a major underlying cause. This review explores how numerical and structural chromosomal anomalies, along with environmental exposures, lifestyle factors, and age-related genetic changes, disrupt spermatogenesis and contribute to infertility. It synthesizes findings from cytogenetic, molecular, and clinical studies, with particular focus on mechanisms such as meiotic nondisjunction, spindle assembly checkpoint dysfunction, and alterations in cohesin and synaptonemal complex proteins. Chromosomal abnormalities, both numerical and structural, emerge as key contributors to male infertility by impairing chromosomal segregation and recombination, often leading to azoospermia or oligospermia. Meiotic checkpoint failures and recombination errors further exacerbate the production of aneuploid sperm. Environmental toxins, oxidative stress, and poor nutrition disrupt hormonal balance and chromatin integrity, while advancing paternal age is associated with increased sperm aneuploidy and impaired meiotic control, with implications for assisted reproduction. Specific syndromes, including AZF deletions, Kallmann syndrome, and 46,XX testicular DSD, exemplify the direct genetic impact on male fertility. Overall, chromosomal abnormalities are central to the pathophysiology of male infertility, arising from intrinsic meiotic errors as well as extrinsic environmental and lifestyle factors. Integrating cytogenetic diagnostics, genetic counseling, and lifestyle interventions is essential for comprehensive fertility assessment and management. Further research into molecular biomarkers and targeted therapies could enhance diagnosis, improve treatment strategies, and lead to better reproductive outcomes. Full article

Specific expression of genes is fundamental for defining the identity and the functional state of cells. Sequence-specific transcription factors interpret the information contained in DNA sequence motifs and recruit cofactors to modify chromatin and control RNA polymerases. This multi-step process typically involves several transcription factors and cofactors with different enzymatic activities. Post-translational modifications (PTMs) of histones are one key mechanism to control chromatin structure and polymerase activity and thus gene transcription. The methylation of histone H3 at lysine 4 (H3K4) is a modification of accessible chromatin, including enhancers and promoters, and also sites of recombination and some forms of DNA damage. H3K4 methylation is catalyzed by six lysine methyltransferase complexes, referred to as KMT2 or COMPASS-like complexes. These are important in processes related to transcription and contribute to recombination in T and B cells. PRDM9 and ASH1L are H3K4 methyltransferases involved in meiotic recombination and DNA repair, respectively. In transcription, H3K4 mono- and tri-methylation are located at enhancers and promoters, respectively. These modifications, either alone or in combination with other histone PTMs, provide binding sites for transcriptional cofactors. Through these sites, H3K4 methylation affects chromatin accessibility and histone PTMs, typically resulting in a favorable environment for transcription. H3K4 tri-methylation also recruits and regulates RNA polymerase II (RNAPII) complexes, which interact with KMT2 complexes, generating positive feedforward loops to promote transcription. Thus, H3K4 methylation has broad activities that are key to different chromatin-associated processes. Full article

Introduction: Genes in the endolysosome and autophagy pathways are major contributors to hereditary spastic paraplegia (HSP). A pathogenetic link between HSP and Alzheimer disease (AD) involving macroautophagy is well established. Sortilin-related receptor 1 (SORL1), an endosomal trafficking protein, plays a key role in glutamatergic neuron homeostasis and white matter tract integrity. Until now, SORL1 has only been associated with dominant AD and cerebral amyloid angiopathy. Methods: A case of HSP with cerebroretinal vasculopathy (CRV) negative on exome sequencing was further investigated using whole-genome sequencing. RNA-seq, Western blot, and immunofluorescence imaging were performed to explore a potential loss-of-function mechanism. Results: Sequencing revealed a biallelic SORL1 splice donor variant (c.1211 + 1G > A). Transcriptomics confirmed nonsense-mediated decay and aberrant splicing, predicting a disrupted reading frame. Reduced SORLA protein levels and significant enlargement of endolysosomes in patient-derived fibroblasts further cemented the pathogenicity of the variant. Conclusions: The probability that SORL1 acts as a recessive disease-causing gene gathers support from the following data: SORL1 genomic constraint score pRec = 1, high meiotic recombination rates on the locus, phenotype of Sorl1^−/− mice reminiscent of HSP with CRV, and endolysosomal enlargement in SORL1^−/− glutamatergic neurons in vitro. Taken together, SORL1 is probably a new candidate for a recessive form of complicated HSP. Full article

Our understanding of the molecular mechanisms by which DNA meiotic recombination occurs has significantly increased in the past decades. A more representative molecular model has also undergone repeated revisions and upgrades with the continuous expansion of experimental data. Considering several apparent issues in the field, we intend to make necessary upgrades to previous models and reanalyze those data, exploring structural details and molecular mechanisms of DNA meiotic recombination. Eligible studies were identified from PubMed/Medline (up to June 2024). Key related publications and experimental data were retrieved from eligible studies, displaying five major issues. Meanwhile, the biophysical modeling method was used to establish an enlacement model. Then, the model was used to wholly reanalyze the collected data. An updated molecular model was supplemented. In the current model, a copy choice mechanism can initiate DNA meiotic recombination. The copy choice is based on a branched structure of DNA, which results from relative motion between homologous single strands. The reanalysis of previous experimental data based on this model can lead to new interpretations that can better address the discrepancies between previous experimental observations and theoretical models, including (1) the intertwinement model having embodied the particular characteristics of the SDSA model; (2) hDNA arising from JM resolution rather than being followed by a JM; (3) strand specificity of hDNA mismatch repair seeming to be an illusion and copy choice more likely to be the actual state; (4) parity in resolution patterns of a dHJ leading to parity of gene conversion; (5) the cooperation of multiple HJs readily generating a high correlation between gene conversion and crossover; and (6) transpositional recombination and site-specific recombination seeming to have a common pathway to meiotic recombination. The results indicate that both revisions and reanalysis are necessary. The novel interpretations would be critical to the understanding of the mechanisms of DNA recombination as well as its role in DNA repair. Additionally, the work could have implications for how the field views the importance of factors such as Spo11 or the mechanisms that drive meiotic pairing. Full article

To overcome reproductive dysfunctions, recombinant gonadotropin hormones have been synthesised in different fish species. We were interested in gaining further insight into the effects of recombinant follicle-stimulating hormone (rFsh) in meagre Argyrosomus regius spermatogenesis and in improving the existing knowledge on the role of testicular apoptosis. Germ cell composition and testicular apoptosis were compared in pre-pubertal fish treated with rFsh (PreP-Fsh) and controls (PreP-C), and adult meagre with testes in the proliferative (Adult-Pro) and meiotic (Adult-Meio) spermatogenesis phases. A lower density of committed spermatogonia was observed in PreP-Fsh compared with PreP-C and in Adult-Meio compared with Adult-Pro. In pre-pubertal fish and in Adult-Pro, apoptosis affected mainly individual germ cells and Sertoli cells. In Adult-Meio, a high number of cysts containing apoptotic germ cells was observed, and apoptosis often involved entire clones of germ cells. rFsh reduced testicular apoptosis in pre-pubertal fish, whereas the advancement of spermatogenesis in adults was associated with an increased density of apoptotic cells. The present study corroborated previous observations on the effects of rFsh on spermatogenesis in pre-pubertal meagre and provided further insights on the changing role of apoptosis in the pre-pubertal phase versus different phases of spermatogenesis. Full article

South African cattle comprise diverse breeds with distinct evolutionary histories, potentially reflecting differences in recombination landscapes. This study assessed genome-wide recombination rates and hotspots in Bonsmara (n = 190) and Nguni (n = 119) cattle using three-generation half-sib pedigrees genotyped with the Illumina Bovine SNP50 BeadChip. Phasing across 29 autosomes was conducted using SHAPEIT v2, and crossover events were inferred using the DuoHMM algorithm. The total number of crossover events detected was higher in Nguni (n = 8982) than in Bonsmara (n = 7462); however, the average recombination rate per 1 Mb window was significantly higher in Bonsmara (0.31) compared to Nguni (0.18) (p < 0.01). This apparent discrepancy reflects differences in genomic distribution and crossover clustering across breeds, rather than overall recombination frequency. A critical limitation of the study is the reliance on half-sib families with small family sizes, which may underestimate recombination rates due to limited meiotic sampling and increased variance in crossover detection. We identified 407 recombination hotspots in Bonsmara and 179 in Nguni, defined as intervals exceeding 2.5 standard deviations above the mean recombination rate. Genes such as PDE1B and FP which are associated with productions traits were located within hotspot-enriched regions. However, functional causality between these genes and local recombination activity remains unverified. Our results provide statistically supported evidence for breed-specific recombination patterns and hotspot distributions, underscoring the importance of incorporating recombination architecture into genetic improvement strategies for South African cattle. Full article

Gonadal development and spermatogenesis critically influence fish reproductive performance. Neomales (genetically female but functionally male) are indispensable for generating all-female populations, yet their spermatogenesis remains understudied. In the present study, we systematically investigated gonadal maturation in neomales of the large yellow croaker (Larimichthys crocea), an economically important marine species exhibiting sexually dimorphic growth. We examined the growth performance and gonadal development throughout the maturation process in neomales and control males. Results showed comparable growth performance but a temporal divergence in gonadal development: the gonadosomatic index (GSI) of neomales was significantly higher than control males at 400 and 430 days post-hatching (dph), but not at 460 dph during the reproductive period. Histological, ultrastructural (TEM), and immunofluorescence analyses collectively demonstrated that neomale testes contained all major spermatogenic cell types. Their morphological characteristics and expression patterns of key markers—germ cells (vasa), Sertoli cells (sox9a), and meiotic recombination (dmc1)—were similar to control males. These findings enhance understanding of gonadal development and spermatogenesis in neomales, providing a theoretical and technical foundation for large-scale production of all-female large yellow croaker. Full article

Meiotic recombination is a key evolutionary process that generates novel allele combinations during prophase I of meiosis, promoting genetic diversity and enabling the selection of desirable traits in livestock breeding. Although its molecular mechanisms are well-characterised in model organisms such as humans and mice, studies in African indigenous cattle, particularly South African breeds, remain scarce. Key regulators of recombination, including PRDM9, SPO11, and DMC1, play essential roles in crossover formation and genome stability, with mutations in these genes often linked to fertility defects. Despite the Bonsmara and Nguni breeds’ exceptional adaptability to arid and resource-limited environments, little is known about how recombination contributes to their unique genetic architecture and adaptive traits. This review synthesises the current knowledge on the molecular basis of meiotic recombination, with a focus on prophase I events and associated structural proteins and enzymes. It also highlights the utility of genome-wide tools, particularly high-density single nucleotide polymorphism (SNP) markers for recombination mapping. By focusing on the underexplored recombination landscape in South African beef cattle, this review identifies key knowledge gaps. It outlines how recombination studies can inform breeding strategies aimed at enhancing genetic improvement, conservation, and the long-term sustainability of local beef production systems. Full article

The wolf fish Hoplias malabaricus is a Neotropical species characterized by remarkable karyotypic diversity, including seven karyomorphs (KarA-G) with distinct sex chromosome systems. This study investigated the homologous XY (KarF) and XY₁Y₂ (KarG) sex chromosome systems present in this species by integrating cytogenetics and genomics to examine sex chromosomes’ composition through characterization of repeatome (satellite DNA and transposable elements) and sex-linked markers. Our analysis indicated that both karyomorphs are little differentiated in their sex chromosomes content revealed by satDNA mapping and putative sex-linked markers. Both repeatomes were mostly composed of transposable elements, but neither intra- (male versus female) nor interspecific (KarF x KarG) variations were found. In both systems, we demonstrated the occurrence of sex-specific sequences probably located on the non-recombining region of the Y chromosome supported by the accumulation of sex-specific haplotypes of HmfSat10-28/HmgSat31-28. This investigation offered valuable insights by highlighting the composition of homologous XY and XY₁Y₂ multiple sex chromosomes. Although homologous, the large Y chromosome in KarF corresponds to two separate linkage groups (Y₁ and Y₂) in KarG implying a specific meiotic arrangement involving the X chromosome in a meiotic trivalent chain. This scenario likely influenced recombination rates and, as a result, the genomic composition of these chromosomes. Full article