Biomedical subjects

Chenxi Zhou

Publications and source records attributed to Chenxi Zhou.

3 recordsLinked to original sources

PubMed2026

Cumulus cells enhance oocyte genomic quality control by promoting DNA damage-induced meiotic arrest.

Cumulus cells are known to maintain oocyte arrest at prophase I through gap junction-mediated cAMP signalling, but their role after meiotic resumption remains unclear. Here, we show that cumulus cells enhance oocyte genomic quality control by sensitizing mouse oocytes to DNA damage-induced meiotic arrest. Time-lapse imaging of SiR-tubulin-labelled spindles revealed that oocytes from cumulus-oocyte complexes (COCs) matured faster than denuded oocytes (DOs). Upon mild DNA damage induced by low-dose etoposide, COC oocytes arrested at metaphase I, whereas DOs completed maturation despite similar levels of DNA lesions. This arrest required spindle assembly checkpoint (SAC) activity, as reversine rescued polar body extrusion and BubR1 and Mad2 were elevated in COCs but not DOs. Disruption of gap junctions or inhibition of mTOR signalling abolished the checkpoint response. Notably, cumulus cells did not enhance oocyte response to minor spindle perturbations. These findings reveal a previously unrecognized role of cumulus cells in mediating DNA damage-induced SAC activation, providing post-GVBD genomic surveillance beyond prophase I arrest.

Animals↗

PubMed2025

Genome size estimation from long read overlaps.

MOTIVATION: Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existing tools are primarily optimized for short-read data. RESULTS: We present LRGE, a novel tool that uses read-to-read overlap information to estimate genome size in a reference-free manner. LRGE calculates per-read genome size estimates by analysing the expected number of overlaps for each read, considering read lengths and a minimum overlap threshold. The final size is taken as the median of these estimates, ensuring robustness to outliers such as reads with no overlaps. Additionally, LRGE provides an expected confidence range for the estimate. We validate LRGE on a large, diverse bacterial dataset and confirm it generalizes to eukaryotic datasets. On bacterial genomes, LRGE outperforms k-mer-based methods in both accuracy and computational efficiency and produces genome size estimates comparable to those from assembly-based approaches, like Raven, while using significantly less computational resources. AVAILABILITY AND IMPLEMENTATION: Our method, LRGE (Long Read-based Genome size Estimation from overlaps), is implemented in Rust and is available as a precompiled binary for most architectures, a Bioconda package, a prebuilt container image, and a crates.io package as a binary (lrge) or library (liblrge). The source code is available at https://github.com/mbhall88/lrge and an archive at https://doi.org/10.5281/zenodo.17183812 under an MIT license.

Genome Size↗

PubMed2025

Forty new genomes shed light on sexual reproduction and the origin of tetraploidy in Microsporidia.

Microsporidia are single-celled, obligately intracellular parasites with growing public health, agricultural, and economic importance. Despite this, Microsporidia remain relatively enigmatic, with many aspects of their biology and evolution unexplored. Key questions include whether Microsporidia undergo sexual reproduction, and the nature of the relationship between tetraploid and diploid lineages. While few high-quality microsporidian genomes currently exist to help answer such questions, large-scale biodiversity genomics initiatives, such as the Darwin Tree of Life project, can generate high-quality genome assemblies for microsporidian parasites when sequencing infected host species. Here, we present 40 new microsporidian genome assemblies from infected arthropod hosts that were sequenced to create reference genomes. Out of the 40, 32 are complete genomes, eight of which are chromosome-level, and eight are partial microsporidian genomes. We characterized 14 of these as polyploid and five as diploid. We found that tetraploid genome haplotypes are consistent with autopolyploidy, in that they coalesce more recently than species, and that they likely recombine. Within some genomes, we found large-scale rearrangements between the homeologous genomes. We also observed a high rate of rearrangement between genomes from different microsporidian groups, and a striking tolerance for segmental duplications. Analysis of chromatin conformation capture (Hi-C) data indicated that tetraploid genomes are likely organized into two diploid units, similar to dikaryotic cells in fungi, with evidence of recombination within and between units. Together, our results provide evidence for the existence of a sexual cycle in Microsporidia, and suggest a model for the microsporidian lifecycle that mirrors fungal reproduction.

Genome, Fungal↗