Satellite DNAs (satDNAs) are among the least resolved components of telomere-to-telomere (T2T) genome assemblies despite recent advances in long-read sequencing. Among mammals, camelids provide an excellent system to study satDNA evolution because of their exceptional karyotypic conservation despite more than 11 million years of independent evolution. Here, we systematically characterize the satDNA landscape of the chromosome-level alpaca reference genome VicPac4 by combining bioinformatic reference-guided repeat identification, PCR validation, and fluorescence in situ hybridization (FISH). Cross-species PCR analysis of 13 candidate satDNAs revealed two major conservation patterns: six families amplified across all camelids, whereas seven were restricted to South American camelids (SACs). FISH further demonstrated distinct chromosomal organization of nine satDNA families: four showed widespread chromosomal distribution; three localized near centromeres of a subset of chromosomes; one was primarily associated with chromosome 26 but had lower copy number on additional chromosomes, and one exclusively mapped to chromosomes 27 and 36 in all SACs. The latter displayed consistent and prominent copy number differences between species, individuals and homologous chromosomes, suggesting naturally occurring variation in satellite array expansion. This satellite amplified by PCR across Camelidae, whereas FISH detected expanded arrays only in SACs, suggesting differences in satellite organization between SAC and Camels. Beyond satDNA identification, the proposed workflow facilitated the discovery and comparative analysis of pseudogene-rich repetitive blocks in the alpaca genome and their absence in Camels’ genome assemblies. These findings substantially expand the alpaca satDNAs catalogue and provide a cytogenetic framework for future T2T genome refinement and comparative studies across Camelidae.
Chromatin is a DNA–protein polymer that ensures the safekeeping and realization of genetic information in eukaryotic cells. The genome of higher eukaryotes is packed into a relatively small nuclear volume and organized in a non-random yet non-deterministic manner, exhibiting a high degree of complexity and flexibility. Despite the dense packing of chromatin, the cell effectively controls transcription, replication, and DNA repair. Genomic approaches, direct visualization, and computer modeling have allowed to accumulate a large amount of data on the structure and behavior of chromatin in various functional states. However, many of these techniques rely on chemical cross-linking, membrane permeabilization, or altered ionic conditions, which may perturb native chromatin structure. This has led to contradictory views on chromatin organization in situ. Cryo-electron microscopy (Cryo-EM) ensures preservation of the cellular structures in a close to native hydrated state and provides high resolving power, thus becoming a tool of choice for studying organization of chromatin at the nucleosomal and supranucleosomal scales. This review summarizes how cryo-EM has advanced our understanding of chromatin organization and function, considers the limitations of the method, and discusses future directions and perspectives in the field.
Background Prophylactic total gastrectomy (PTG) is a risk-reducing strategy considered in individuals at high risk for diffuse gastric cancer (DGC) associated with germline CDH1 pathogenic variants. Methods A systematic literature search (PubMed, Scopus) was conducted to identify studies that performed PTGs in CDH1 carriers. Data were analysed using a random-effects generalised linear mixed model. Cochran's Q test was used to assess the heterogeneity between studies. Forest plots were used to display study-specific estimates, and the pooled estimates were calculated within three subsequent cohort periods (2001-2010; 2011-2020; 2021-2025). Statistical analyses were performed using R software. Results A total of 21 studies were considered out of 302 originally identified, including a total of 967 CDH1 carriers. PTG was performed in 62.9% of CDH1 pathogenic variant carriers. Advanced DGC (>pT1a) was detected in 1.1% and <= pT1a in 79% in postoperative PTG specimens. The majority of PTGs were reported from North America (58.9%). The pooled proportion of PTG decreased from 83.2% (95% CI 61.0% to 94.0%) in 2001-2010 to 71.0% (95% CI 59.0% to 80.7%) in 2011-2020 and to 67.5% (95% CI 48.9% to 81.8%) in 2021-2025 (p for trend=0.12). Conclusion About 60% of PTGs were reported from North America. The majority of the lesions were classified as pT1a. PTG indication has been progressively and constantly decreasing during the last years considered. This can be related to the recent genetic analyses reporting a lower DGC risk in CDH1 carriers and with the improvement in detection of early lesions during endoscopy. PROSPERO registration number CRD420261368873.
Background Mainstreaming, in which genetic testing is shifted outside clinical genetics, can improve access to genetic testing. This is being explored in several countries, including Canada, the USA and the UK. However, standardised practice within a jurisdiction helps ensure equitable high-quality access. This study aimed to evaluate consistency in the implementation of cancer genetics mainstreaming across Ontario, Canada.Methods Adult cancer genetics centres in Ontario were emailed an online survey in June 2025, which was completed by mainstreaming implementation leads. Results were anonymised and analysed in aggregate.Results Of 18 centres contacted, 13 responded; 12/13 reported having implemented cancer genetics mainstreaming. All mainstreaming centres offered pathways for breast, ovarian, prostate and pancreatic cancers, primarily based on personal history criteria. Most centres did not mainstream for other cancer sites but were planning to expand. A 19-gene hereditary breast/ovarian/prostate panel was most commonly ordered. There was variation in the timepoint of genetics service involvement. Turnaround times for expedited results were relatively consistent (median 21 days, IQR 18-22), whereas turnaround times for routine results varied widely (median 50 days, IQR 36-94).Conclusion Across Ontario, centres were generally consistent in mainstreaming the most common indications. Opportunities to improve quality and equity include reducing variability in routine turnaround time, standardising management pathways for negative results and streamlining ordering to align with eligibility criteria. Some centres cited limited genetics knowledge as an implementation barrier, though engagement improved over time. Ongoing evaluation of mainstreaming can support consistent access to care.
Satellite DNAs (satDNAs) are repetitive sequences that play important structural and functional roles in vertebrate genomes; however, their genomic composition and behavior during meiosis remain poorly understood in geckos. Here, we investigated the satellitome of the Central American banded gecko (Coleonyx mitratus) using bioinformatic and cytogenetic approaches. We identified fifteen candidate satDNA sequences representing at least fourteen satDNA families and mapped their distribution on mitotic and meiotic chromosomes. Most satellites were concentrated in constitutive heterochromatin regions. One of the satDNA families, CmitSat-10-58, showed compact signals associated with the core of the synaptonemal complex on most chromosomes and co-localized with anti-centromere antibodies, suggesting a possible role in centromeric function. A heterochromatin region on chromosome 6 containing two satDNA families showed delayed synapsis and excessive stretching during the pachytene stage. Differences in satDNA composition between the X and Y chromosomes may be associated with their delayed synapsis. Our results provide new insight into the organization, chromosomal distribution, and potential functional significance of satellite DNA in gecko genomes, and support further investigation of the relationship between repetitive DNA, heterochromatin organization, and chromosome dynamics during meiosis.
