PLOS Genetics: New Articles

Canalization of neural dynamics by δ-protocadherins in the developing zebrafish optic tectum

2026-06-01T14:00:00Z

by Sayantanee Biswas, Michelle R. Emond, Grace S. Philip, James D. Jontes

Brain dynamics are constrained by the underlying topology of neuronal networks. How genes collaborate to organize these neural networks during development remains an enduring mystery. In humans, large numbers of genes have been implicated in neurodevelopmental disorders that are characterized by variable and overlapping phenotypes. The complexity of the brain and the heterogeneity of the disorders makes understanding the relationships between genes, development and neural function challenging (Lee PH, Anttila V, Won H, et al. Cell. 179. p. 1469–82.e11. 2019, Hyman SE. Philos Trans R Soc Lond B Biol Sci. 373(1742). p. 20170031. 2018, de Masfrand S, Cogné B, Nizon M, et al. Eur J Med Genet. 69. p. 104932. 2024). Beginning in the 1940s, Waddington suggested the concept of canalization to describe the role of genes as buffering developmental trajectories against genetic and environmental variation, leading to precise outcomes (Waddington CH. Nature. 150(3811). p. 563–5. 1942). Here, we show that members of the δ-protocadherin family of homophilic cell adhesion molecules, Protocadherin-19 and Protocadherin-17, contribute to developmental canalization of neural dynamics in the visual system of larval zebrafish. We provided oriented visual stimuli to zebrafish larvae and performed in vivo 2-photon calcium imaging in the optic tectum. The latent dynamics resulting from the population activity were remarkably conserved among different wild type larvae, allowing quantitative comparisons within and among genotypes. In both Protocadherin-19 and Protocadherin-17 mutants, the latent dynamics diverged stochastically from wild type, suggesting that the loss of these adhesion molecules leads to stochastic phenotypic variability and introduced disruptions of circuit organization that varied among individual mutants. These results are consistent with the developmental canalization of a vertebrate neural circuit, and suggest a framework for understanding the observed variability in complex brain disorders.

Sequence context and methylation interact to shape germline mutation rate variation at CpG sites

2026-06-01T14:00:00Z

by Sheel Chandra, Ziyue Gao

A prominent example of sequence context-dependent mutation rate variation is the elevated transition rate at CpG sites, which is largely attributed to cytosine methylation. CpGs with different flanking sequences also exhibit mutation rate variation, but this variation is only partially correlated with context-specific methylation level. Here, we quantify the CpG mutation rate and mutagenic effect of methylation across sequence contexts. Using a regression framework that accounts for recurrent mutations, we analyze human polymorphisms from the gnomAD dataset to estimate mutation rates of unmethylated and methylated CpGs separately in each unique 4-mer or 6-mer context. We find that CpG mutation rate variation in the human genome is shaped by methylation at the focal cytosine, the flanking nucleotides, and interactions between them, suggesting distinct context-dependent mutation patterns for unmethylated and methylated cytosines. Our analysis further reveals that the context effects are driven by largely independent effects of upstream and downstream sequences. Notably, an upstream adenine markedly increases CpG mutation rates regardless of methylation status or downstream sequences. Furthermore, upstream and downstream sequences have similar effects in chimpanzee and rhesus macaque, indicating that some conserved, intrinsic sequence features shape CpG mutability. On the other hand, some inter-species differences, which are especially pronounced at methylated sites on the chimpanzee lineage, point to recent evolutionary changes, possibly in context-specificity of proteins governing DNA demethylation and repair processes.

Yap1 regulates motility and vertebral development and prevents kyphoscoliosis in zebrafish

2026-05-28T14:00:00Z

by Victoria C. Williams-Ward, Kees Wanders, Simon M. Hughes

Scoliosis affects 2–3% of people, often developing during and after adolescence, and currently has a lifetime chance of surgical intervention of ~0.1% in high income countries. Understanding of causal genetic and environmental factors is improving, with mechanical feedback interactions between the neuromuscular and skeletal systems thought to be important. While examining mechanosignalling in the zebrafish musculoskeletal system, we observed transient expression of yap1 mRNA in precursor cells of muscle and notochord and wwtr1 mRNA accumulation in differentiated muscle. Yap1 and Wwtr1/Taz are transcriptional coactivators that mediate Hippo pathway signalling, often in response to mechanosignals. Loss of function mutation of either gene alone transiently altered early larval motility and reduced survival to adulthood, but mutation of yap1 specifically diminished overall growth without an obvious histological muscle defect. Yap1 mutants had a temperature-sensitive phenotype of oedema in cardiac and other tissues, which could be rescued by rearing at low temperature. Rescued yap1 mutants showed focal defects in hypochordal col8a1a mRNA expression at 1–2 days post-fertilisation (dpf), an early motility defect at 5 dpf and subsequently developed a fully penetrant vertebral dysmorphology, reflected by a decrease in posterior vertebral height. Thereafter, frank kyphoscoliosis accompanied by additional vertebral defects developed in around a third of the surviving yap1 mutants and was first detected at 11 dpf. Thus, the mild initial vertebral defect can, in a predisposing genetic or environmental background, gradually develop into full kyphoscoliosis through a positive feedback mechanism, analogous to the Hueter-Volkmann ‘Law’. Although the cell type/s of cell autonomous yap1 action remain unclear, we hypothesise that Yap1 mechanosensation mediates feedback between bone, muscle and tendon to restrain vertebral overgrowth and protect against the development of kyphoscoliosis.

Species-specific coevolution of RecA–RecN interfaces governs DNA double-strand break repair in Escherichia coli

2026-05-28T14:00:00Z

by Mizuki Inoue, Genki Akanuma, Masafumi Hayashi, Takashi Hishida

DNA double-strand breaks (DSBs) threaten genome stability and cell survival but can be faithfully repaired through homologous recombination (HR). RecN, a bacterial protein closely related to the structural maintenance of chromosomes family, cooperates with RecA in HR-dependent DSB repair, yet the molecular basis and physiological relevance of their interaction remain unclear. Here, we investigated the functional interplay between RecA and RecN during DSB repair by heterologously expressing Pseudomonas aeruginosa RecA (paRecA) and RecN (paRecN) in Escherichia coli. We found that in E. coli ∆recA ∆recN cells, co-expression of paRecA and paRecN fully restored MMC resistance, whereas co-expression of E. coli RecA (ecRecA) with paRecN conferred partial resistance to mitomycin C (MMC), demonstrating species-specific compatibility. Expression analysis revealed that paRecN was poorly expressed in E. coli, but codon optimization significantly enhanced its abundance and repair activity. We further identified gain-of-function paRecN mutants (I73T and R453H) that restored repair without increased expression. These mutants displayed species-specific adaptation, which improved compatibility with ecRecA but reduced functionality with paRecA. Fluorescence microscopy revealed that MMC-induced nucleoid localization was increased in paRecN^I73T and paRecN^R453H compared with paRecN. Collectively, these findings demonstrate that coevolution optimizes the RecA–RecN interface to ensure efficient DSB repair.

FabF and FadM cooperate to recycle fatty acids and rescue ∆plsX lethality in Staphylococcus aureus

2026-05-27T14:00:00Z

by Paprapach Wongdontree, Milya Palmier, Clara Louche, Vincent Leguillier, Carine Machado Rodrigues, Karine Gloux, David Halpern, Céline Henry, Jamila Anba-Mondoloni, Alexandra Gruss

Phospholipids are essential components of most cell membranes. In Staphylococcus aureus, PlsX acyltransferase is considered indispensable for initiating phospholipid synthesis, unless exogenous fatty acids (FAs) are available to bypass this requirement. We report that S. aureus can capture internal FA sources to overcome PlsX essentiality in a ∆plsX mutant via point mutations in either of two genes: fabF, which encodes the FA synthesis enzyme 3-oxoacyl-(acyl-carrier-protein) synthase II, or fadM, which encodes an understudied bifunctional acyl-CoA thioesterase and ACP binding protein. Despite growth rescue, both ∆plsX suppressors differ from the parental strain by producing phospholipids with shortened FA lengths, suggesting that both suppressors lead to premature FA release during synthesis. Additionally, both suppressors display increased sensitivity to β-lactam antibiotics. The similar behavior of both suppressors led us to show that fabF suppressors require the presence of fadM, indicative of FabF-FadM cooperation. We propose that reduced processivity of FabF suppressor variants, or greater availability of FadM for ACP binding in FadM variants, facilitates FA release from FabF-acyl-ACP intermediates. A FabF-FadM relay leading to FA release may contribute to homeostasis between FASII and phospholipid synthesis pathways.

Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii

2026-05-27T14:00:00Z

by Francois D. Rouleau, Alexandre K. Dubé, Alicia Pageau, Lyne Désautels, Philippe Dufresne, Christian R. Landry

Pneumocystis jirovecii is an opportunistic fungal pathogen responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients. Antifolate drugs targeting the dihydrofolate reductase (DHFR), including trimethoprim (TMP), remain central to treatment, but studying the effects of mutations in DHFR on resistance to treatment is limited by our inability to culture this organism in vitro or in animal models. We expressed P. jirovecii DHFR (PjDHFR) in Saccharomyces cerevisiae and performed deep mutational scanning (DMS) on this protein to measure the effects of all single amino-acid substitutions on enzyme function and resistance to methotrexate (MTX), a model antifolate which shares structural features with TMP. We integrated experimental results with structural and evolutionary features from multiple biophysical modeling approaches, and by using an interpretable machine-learning framework, we trained a random forest model to classify MTX resistance-conferring mutations in PjDHFR. We then leveraged this framework as a prediction tool to model the effects of mutations on resistance to TMP, which cannot be directly assayed experimentally. Functional measurements from DMS were the strongest contributors to resistance prediction and generally outperformed purely computational features. Resistance-conferring mutations were constrained by function, revealing a functional–resistance trade-off within this essential protein. Feature contribution analyses highlighted key predictors such as distance to ligand, flexibility, stability, and functional trade-off as determinants of resistance. When extrapolated to TMP, the model identified candidate resistance mutations consistent with known biochemical constraints of DHFR. We demonstrate how experimentally measured functional landscapes can be combined with biophysical modeling to help understand and predict antifolate resistance in an unculturable fungal pathogen. Our results provide biological insight into the constraints affecting the evolution of resistance in PjDHFR, and support that resistance arises from mutations altering drug interactions while preserving function. We illustrate how DMS data can enable generalizable, mechanistically interpretable models of drug resistance across structurally related antifolates.

mFABIO: An integrative multi-tissue TWAS fine-mapping approach to prioritize potentially causal genes and tissues underlying binary traits

2026-05-27T14:00:00Z

by Haihan Zhang, Kevin He, Lam C. Tsoi, Xiang Zhou

Recent advances in transcriptome-wide association study (TWAS) fine-mapping have enabled the joint modeling of multiple genes to improve causal gene prioritization. However, existing methods have been developed primarily for quantitative traits and most of them rely on gene expression data from a single tissue. Here, we present mFABIO, a multi-tissue TWAS fine-mapping method specifically designed for binary traits. mFABIO employs a probit model to directly link genetically regulated expression (GReX) of genes within a locus across multiple tissues to a binary outcome, while accounting for correlations in GReX across genes and tissues. As a result, mFABIO offers substantial power gains for binary traits, while maintaining robust control of false discovery rates (FDR). We evaluated mFABIO through extensive simulations and applied it to an in-depth analysis of six binary disease traits (asthma, breast cancer, gout, hypertension, prostate cancer, and rheumatoid arthritis) in the UK Biobank, using expression data spanning 38 Genotype-Tissue Expression (GTEx) tissues. mFABIO identified an average of 42 likely causal genes and 65 tissue-gene pairs per disease (FDR < 0.05). Notably, 60.9% of the genes and 77.2% of the gene-tissue pairs were supported by existing TWAS or GWAS evidence. This represented at least a 14.9% increase in evidence-supported genes and a 14.8% increase in evidence-supported gene-tissue pairs, compared to existing approaches. Additionally, mFABIO was also able to narrow down the list of potentially causal candidates by at least 51.3% for genes, and 50.8% for gene-tissue pairs, compared to single-tissue approaches. Leveraging its improved power, mFABIO successfully prioritized multiple potentially causal gene-tissue pairs associated with these diseases, with biological support. Notable examples include D2HGDH in lung tissue for asthma, CYBRD1 in breast mammary tissue for breast cancer, and CCR6 in spleen tissue for rheumatoid arthritis. Overall, mFABIO serves as an effective tool for multi-tissue TWAS fine-mapping of binary traits.

Pre-cuticle DPY-6 acts as a blueprint for aECM periodic organization in C. elegans

2026-05-26T14:00:00Z

by Sophie Mazzoli, Thomas Sonntag, Emma Cadena, Claire Valotteau, Susanna K. Birnbaum, Meera V. Sundaram, Nathalie Pujol

Apical extracellular matrices (aECMs) are essential for tissue integrity and function in multicellular organisms, but there is limited understanding of how such matrices are assembled and organized in the extracellular environment. The Caenorhabditis elegans cuticle, a model aECM that undergoes morphogenesis during each of the worm’s four larval molts, requires periodic circumferential furrows for structural integrity and immune regulation. Here, we show that furrow collagens must be cleaved from their N-terminal transmembrane domain for secretion and depend on the mucin-like pre-cuticle protein DPY-6 for their periodic assembly. While DPY-6 is dispensable for initial embryonic furrow formation, it acts as a mold during subsequent molts, ensuring pattern replication via its C-terminal cysteine cradle domain. These results reveal a central role for a transient matrix factor in organizing a complex periodically structured aECM.

MR2G: A novel framework for causal network inference using GWAS summary data

2026-05-26T14:00:00Z

by Zhaotong Lin, Wei Pan, Haoran Xue

Inferring a causal network among multiple traits is essential for unraveling complex biological relationships and informing interventions. Mendelian randomization (MR) has emerged as a powerful tool for causal inference, utilizing genetic variants as instrumental variables (IVs) to estimate causal effects. However, when the directions of causal relationships among traits are unknown, reconstructing the underlying causal network becomes challenging. In particular, the presence of cycles or feedback loops, which are common in biological systems, poses additional challenges for causal network inference, and remains largely under-studied with standard MR approaches and existing IV-based network inference methods. To address these issues, we introduce MR2G, a new statistical framework that enables robust inference of causal networks, including those with cycles, directly from GWAS summary statistics. MR2G is built on a formally defined recursive causal graph model that rigorously links direct causal effects to (univariable) MR estimands. It recovers a biologically interpretable causal network from pairwise MR effect estimates, while incorporating a network-informed IV screening strategy to reduce pleiotropic bias and improve robustness. Through realistic simulations, MR2G demonstrates superior accuracy and robustness in recovering complex causal structures, including those involving feedback loops. We apply MR2G to GWAS summary statistics for six complex diseases and nine cardiometabolic risk factors. MR2G not only recovers well-established causal pathways but also uncovers multiple feedback relationships, highlighting its utility in disentangling complex and biologically plausible causal networks from large-scale genetic data.

ZBP1 Drives CD8⁺ T cell-mediated anti-tumor immunity in head and neck squamous cell carcinoma

2026-05-26T14:00:00Z

by Yu Min, Ge Song, Lianlian Yang, Ling He, Shihong Xu, Kun Gao, Zheran Liu, Xingchen Peng, Lei Dai

Head and neck squamous cell carcinoma (HNSCC) frequently resists PD-1 blockade due to an immunologically “cold” tumor microenvironment (TME). Here, we identify Z-DNA binding protein 1 (ZBP1) as a key immunoregulator that reprograms immune-suppressive TMEs. Integrated TCGA/SangerBox analyses revealed ZBP1 as a hub gene strongly correlated with cytotoxic CD8⁺ T cells (r = 0.48, p < 0.0001) and M1 macrophages (r = 0.39, p < 0.0001). Multi-model validation in 92 HNSCC specimens revealed elevated ZBP1 expression versus normal tissues (p < 0.01), co-localized with infiltrating CD8⁺/CD4⁺ T cells and CD68⁺ macrophages through multiplex immunofluorescence. Clinically, high ZBP1 predicted improved survival (HR = 0.61 for overall survival; HR = 0.45 for disease specific survival; p < 0.0001) and early-stage presentation (p = 0.004). Mechanistically, ZBP1 overexpression in SCC-7/MOC2 models suppressed tumor growth while enhancing IFN-γ⁺ CD8⁺ T cell activation and reducing M2 polarization (CD206⁺: 16.91% vs 38.19% in ZBP1-high vs control, p < 0.001). Single-cell transcriptomics uncovered ZBP1-driven TME remodeling through chemokine signaling networks and expanded effector T cell compartments, validated by 1.49-fold increased CD8⁺ T cell infiltration via flow cytometry. Spatial analysis revealed ZBP1 overexpression amplified immune cell crosstalk (1.65-fold interaction increase, p < 0.001), upregulating CD8⁺ T cell chemotaxis (CXCR3/CCR5-CCL5 axis) and effector functions (p < 0.0001). Concurrently, it suppressed immunosuppressive pathways (ARG1 ↓ /IDO1↓) through metabolic reprogramming, establishing ZBP1 as a dual regulator synchronizing lymphocyte recruitment and myeloid suppression. Our integrative approach bridges computational biology with functional validation, demonstrating ZBP1’s capacity to convert “cold” tumors into immunologically active niches. This work positions ZBP1 as both a stratification biomarker for checkpoint inhibitor response and a therapeutic target for TME reprogramming in HNSCC.

An intronic variant in Ferredoxin Reductase (FDXR) creates a cryptic exon in Quarter Horses with Equine Juvenile Spinocerebellar Ataxia

2026-05-20T14:00:00Z

by Briana N. Brown, Anna R. Dahlgren, Sharmila Ghosh, Blythe Durbin-Johnson, Andrew Willis, Cassandra Olivas, Daniel York, Robert Grahn, Rebecca R. Bellone, Gino A. Cortopassi, Andrew D. Miller, C. Titus Brown, Kevin Woolard, Carrie J. Finno

Equine Juvenile Spinocerebellar Ataxia (EJSCA) is a novel autosomal recessive neurologic disease in Quarter Horses. Affected foals display a progressive proprioceptive ataxia by 1–5 weeks of age, leading to recumbency and necessitating euthanasia. Whole genome sequencing was performed on 7 EJSCA cases and unaffected horses that included 4 obligate carriers, 4 unaffected half or full-siblings, and 28 unrelated, unaffected control Quarter Horses. An 82 kb region of association was identified (EquCab3.0, chr11: 6963986–7045999), containing 9 candidate SNPs across four genes (FADS6, FDXR, GRIN2C and TMEM104). Decreased FDXR mRNA expression and a cryptic exon was identified in spinal cord tissue from EJSCA cases via RNA-sequencing. One of the 9 associated SNPs (FDXR-203 c.177 + 1778G > C) was the eighth base pair of this cryptic exon. Affected foals were all homozygous for the variant. Protein concentrations of FDXR were lower in EJSCA cases in spinal cord and liver compared to unaffected controls. The FDXR-203 c.177 + 1778G > C mutation represents the first non-coding neurological genetic variant in horses. Additionally, this is the first genetic cause of a degenerative axonopathy in the horse and a spontaneous disease model to study FDXR pathology in humans.

Comparative whole-genome analyses of articular chondrocytes and skin fibroblasts reveal distinct genome instability landscapes in mesenchymal cell types

2026-05-20T14:00:00Z

by Safia Mahabub Sauty, Jacqueline Shine, Hamed Bostan, Jian-Liang Li, Piotr A. Mieczkowski, Richard F. Loeser, Brian O. Diekman, Dmitry A. Gordenin

DNA damage lesions can result in mutations and genome rearrangements that are associated with cellular aging and diseases. The landscape of somatic mutations in individual tissue and cell types are dictated by their unique physiological states, cellular functions, mutagenic exposures, and efficiency of DNA repair. Articular chondrocytes and skin fibroblasts are two cell types of mesodermal origin with distinct exposure to internal and external sources of DNA damage. While somatic genome instability features of skin fibroblasts have been well detailed, knowledge about mechanisms underlying genome changes in chondrocytes is scarce. Here, we took a whole-genome sequencing approach to evaluate the load, sources, and patterns of genome changes in 18 primary human chondrocyte clones from donors with and without osteoarthritis (OA). Findings in chondrocyte clones largely agreed with a recent study of 100 single-cell sequenced chondrocytes. We compared genome changes in chondrocytes with clonally-expanded human skin fibroblasts sequenced in our previous studies. We demonstrated that skin fibroblasts show a higher burden of somatic mutations, with an increased rate of mutation accumulation per cell division. Motif-centered analyses of mutation catalogues identified only endogenous sources of mutations in chondrocytes, as opposed to skin fibroblasts which also showed a heavy burden of UV-induced mutations. Spontaneous deamination of meCpG and mutagenesis by exposure to small epoxides and S_N2 electrophiles showed higher mutagenic activities in chondrocytes compared to skin fibroblasts. Chondrocytes showed ubiquitous prevalence of indels in homonucleotide runs of ≥5 bases, while skin fibroblasts showed high contributions of UV-associated deletions of ≥5 bp not in repeats. Structural variants in rearrangement hotspots colocalized with human common fragile sites in skin fibroblasts, but not in chondrocytes. Together, our study comprehensively recorded genome instability features in chondrocytes and highlighted the unique mutagenesis landscapes of two mesenchymal cell types.

Correction: Alanine-scanning mutagenesis library of MreB reveals distinct roles for regulating cell shape and viability

2026-05-20T14:00:00Z

by Suman Maharjan, Ryan Sloan, Jada Lusk, Rose Bevienguevarr, Jacob Surber, Randy M. Morgenstein

Correction: Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses

2026-05-19T14:00:00Z

by Chris Wallace

Why recombination hotspots?

2026-05-19T14:00:00Z

by Julien Joseph, Thomas Brazier, Marie Raynaud, Sylvain Glémin, Frédéric Baudat, Bernard de Massy, Nicolas Lartillot, Laurent Duret

Meiotic recombination is the process by which DNA is exchanged between parental chromosomes during the production of gametes in eukaryotes. This phenomenon has important implications for fertility, genetic diversity and genome stability. Intriguingly, not all regions of the genome are equally susceptible to recombine during meiosis. Instead, in many eukaryotes, recombination events are concentrated in short genomic segments called recombination hotspots. Since the first discovery of recombination hotspots, several theories have emerged to explain their existence. In this review, we discuss the relevance of these theories in regards of recent advances in characterizing the diversity and determinants of fine-scale recombination landscapes. Finally, we outline new research avenues for elucidating the evolutionary origins of recombination hotspots.

Cas9-expressing HC-04 hepatocytes facilitate CRISPR-based analysis of Plasmodium falciparum sporozoite-host interactions

2026-05-18T14:00:00Z

by Lisa H. Verzier, Eva Hesping, Marcel Doerflinger, Marco J. Herold, Justin A. Boddey

Sporozoites of Plasmodium falciparum, the deadliest malaria parasite, are injected into the skin by infected mosquitoes and must reach the liver to initiate infection. There, they invade hepatocytes and develop into exoerythrocytic merozoites that eventually enter the bloodstream and invade erythrocytes, causing malaria. The sporozoite’s journey requires cell traversal, where sporozoites transiently enter and exit host cells, lysing membranes to move deeper into tissue and evade immune cell destruction. After reaching the liver and traversing several hepatocytes, sporozoites productively invade a final hepatocyte to establish an exoerythrocytic form. The molecular mechanisms underlying traversal, invasion, and intracellular development remain incompletely understood, particularly with respect to host factors. To address this, we engineered human HC-04 hepatocytes, the only known cell line supporting P. falciparum liver-stage development, to express Cas9-mCherry, enabling CRISPR-based functional genomics studies. We validated Cas9 activity of HC-04.2B3 and demonstrated successful guide-RNA-directed gene disruption via non-homologous end joining. Optimized traversal and invasion assays led to a robust cytometric readout suitable for screening human genes involved in P. falciparum infection. Disruption of 10 human genes previously implicated in infection by bacterial and viral pathogens confirmed utility of this platform. This study provides the basis for genome-wide CRISPR screens to uncover hepatocyte biology and host determinants of infection.

Spatiotemporal characterization of single-stranded DNA intermediates after UV irradiation: II. Rapid growth and effects of recA and recJ

2026-05-14T14:00:00Z

by Remy A. A. Ripandelli, Elizabeth A. Wood, Andrew Robinson, Antoine M. van Oijen, Michael M. Cox

Irradiation of E. coli with UV light results in the formation of post-replication gaps and induction of the SOS response. Here, we investigate the dynamics of single strand gap formation and resolution in cells growing with a 50 min doubling time within specially designed microfluidic chips, making observations on fluorescent gap markers in individual cells over the course of 8 hours. In cells proficient for gap repair, irradiation with UV at 5 J/m² triggers an immediate increase in the number and intensity of gap markers. Cells lacking recF, recO, or recA cannot repair gaps via the canonical gap repair pathway and exhibit elevated gap numbers and intensities over many hours. Major conclusions include: (1) Post-replication gaps are a major feature of DNA metabolism after UV irradiation. (2) The long-lived, high-intensity foci observed in recF, recO, or recA mutants are completely dependent on the RecJ nuclease. In the absence of other RecFOR pathway functions, RecJ-mediated enlargement of many gaps continues unabated for extended periods. (3) In the absence of RecA or other RecFOR pathway functions, cells accumulate repair intermediates that are bound by large numbers of SSB molecules. (4) In the absence of RecJ, other pathways, perhaps involving TLS, displace SSB in gaps. Our results also confirm, using a different experimental setup and protocol, that: (a) UV-related repair activities, including nucleotide excision repair of at least some lesions, may continue for multiple cell generations after exposure; and (b) we again see no evidence that RecF facilitates lesion skipping. Overall patterns of gap formation and resolution under rapid growth conditions are consistent with a burst of post-replication gap formation following UV irradiation, postulated in the accompanying report to rapidly trigger the SOS response.

Spatiotemporal characterization of single-stranded DNA Intermediates after UV Irradiation: I: Post-replication gaps formed during slow growth

2026-05-14T14:00:00Z

by Nischal Sharma, Megan E. Cherry, Camille Henry, Elizabeth A. Wood, Andrew Robinson, Antoine van Oijen, Harshad Ghodke, Michael M. Cox

When E. coli cells are UV irradiated, replisome encounters with some DNA lesions lead to lesion skipping and formation of ssDNA gaps. These gaps are protected by SSB and repaired through the RecFOR recombinational DNA repair pathway. However, many questions about this pathway remain unanswered. Here, we used a fluorescent SSB fusion that supports normal growth in the absence of WT SSB under most conditions to directly visualize the real-time formation and resolution of ssDNA intermediates in cells lacking factors (RecB, RecJ, RecF, and RecO), that facilitate recombinational DNA repair pathways under slow growth conditions. Upon DNA damage, SSB-bound features of various sizes increased within these cells. In WT cells, ssDNA gaps appeared and were resolved at a steady state level that persisted for hours. Formation of most ssDNA gaps was not dependent on RecB function. Large increases in ssDNA gaps were observed in cells lacking RecFORJ functions, particularly in the absence of RecO. These findings indicate that: (a) When hundreds of UV lesions are introduced into the genome, at least some lesions remain unaddressed by nucleotide excision repair (NER) for several hours under slow growth conditions. (b) Replisome encounters with DNA lesions rapidly generate ssDNA gaps. (c) A relatively small portion of the ssDNA foci appearing in WT cells may reflect breaks processed by the RecBCD system. (d) Most prominent SSB features reflect post-replication gaps repaired by RecFORJ. Lack of RecFORJ functions leads to accumulation of unresolved gaps over time. (e) RecF is not required for post-replication gap formation. Overall, the results provide direct visualization of complex UV-induced changes in DNA metabolism caused by replisome encounters with UV-generated pyrimidine dimers. Combined with a decades-long literature of related results and proposals, a unified view of how E. coli responds to UV irradiation can be put forward.

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation

2026-05-08T14:00:00Z

by Guillermo Reales, Jeffrey M. Pullin, Ichcha Manipur, Elena Vigorito, Chris Wallace

Colocalisation analysis integrates GWAS and molecular QTL datasets to identify candidate effector genes. Even with a wide range of molecular QTLs, 40% or more of GWAS loci remain unexplained, leaving a “colocalisation gap”. We systematically characterised two large-scale eQTL colocalisation studies, to describe the determinants of this gap and ultimately inform the selection and design of eQTL studies to close the gap. We analyse over 1.3 million colocalisation tests from Open Targets Genetics (OTG) and perform and analyse colocalisations from 14 immune-mediated disease (IMD) GWAS and 12 diverse immune cell eQTL studies, selected to cover a range of cellular granularities and sample sizes. We find that 50% of GWAS peaks in OTG and 34% in IMDs colocalised and were more likely to colocalise if they were located nearer to genes and had a more common lead variant. Colocalisation was also more likely to occur in disease relevant tissues. The lowest granularity immune cell eQTL studies had the largest sample sizes, the greatest eQTL discovery and produced the largest number of colocalisations, particularly for lower-frequency variants. However, while higher resolution eQTL studies detected fewer eQTLs, each of those eQTLs was more likely to colocalise with a GWAS peak, emphasising the importance of cell specific eQTLs. Indeed, over 50% of colocalisations were found in only one cell type. Overall, our results suggest that a diverse set of cells in different contexts, and large, high granularity studies will be needed to identify remaining colocalisations. In addition, we observed that 47% of GWAS peaks colocalised with multiple genes in OTG and 37% in IMDs. Through simulations, sensitivity analyses, and integration of enhancer-promoter capture data we find that multiple colocalisations likely represent coregulation. While disentangling causality from horizontal pleiotropy will ultimately require experimental perturbation, triangulation using different sources of observational data is likely to be necessary for gene prioritisation.

Simulated sample splitting approach to address biases due to instrument selection and participant overlap in two-sample Mendelian Randomization studies

2026-05-08T14:00:00Z

by Amanda Forde, Gibran Hemani, John Ferguson

Mendelian randomization (MR) is a popular statistical technique that uses genetic variants to explore causal relationships in observational epidemiology. Summary-level MR, the most common form, relies on published GWAS summary statistics to estimate causal effects between exposures and outcomes. However, empirical analyses tend to ignore issues relating to Winner’s Curse of instrument effects, weak instrument bias and sample overlap. Our simulations and empirical analyses using the UK Biobank indicate that such mechanisms can induce substantial bias in routine MR approaches. We propose MR Simulated Sample Splitting (MR-SimSS), a novel method that corrects this bias requiring no additional data beyond GWAS summary statistics for the exposure and outcome of interest. It operates by simulating statistically independent sets of summary statistics, analogous to what would be produced by splitting the individual-level data into independent subsets, which can then be plugged into existing two-sample MR methods. With sufficient instrument variants, MR-SimSS is robust to a range of sample overlap scenarios, providing a practical and modular solution to Winner’s Curse and weak instrument bias.

Tumour-driven lipid accumulation in oenocytes reflects systemic lipid alterations

2026-05-07T14:00:00Z

by Chang Liu, Sofya Golenkina, Natasha Fahey, Priya Kumar, Louise Y. Cheng

Cancer cachexia is a multifactorial syndrome characterized by systemic metabolic dysfunction, including liver steatosis. In this study, we examined the role of larval oenocytes - hepatocyte-like cells, in a Drosophila model of cancer cachexia. We found that oenocytes in tumour-bearing larvae accumulate lipid droplets in response to tumour-secreted signals, Gbb and ImpL2. This lipid accumulation reflects systemic changes in lipid metabolism, responding to lipid metabolism manipulations in either the fat body or the muscle. Disrupting lipid synthesis/breakdown (via FASN1 and Bmm), storage (via Lsd2), or trafficking (via apolipoproteins) in these tissues significantly modulated lipid droplet accumulation in oenocytes. Moreover, oenocyte-specific knockdown of FASN1 reduced their lipid content and non-autonomously affected lipid droplet size in the fat body, suggesting cross-regulatory interactions between these tissues. Cachectic oenocytes also exhibited altered signaling profiles, characterized by reduced PI3K signalling. Enhancing PI3K signalling through Akt overexpression restored oenocyte size and reduced lipid levels; however, these changes did not significantly improve muscle integrity. Together, our data suggests that dynamic exchange of lipids occur between the fat body, oenocytes and the muscle during cancer cachexia. While the fat body and muscle lipid pools are key regulators of muscle integrity, oenocytes - despite their metabolic responsiveness, do not appear to play an active role in preserving muscle function during cachexia.

Tissue-specific transfer learning improves functional variant and therapeutic target discoveries in breast and prostate cancer

2026-05-06T14:00:00Z

by Qing Li, Dinghao Wang, Zilong Zhang, Deshan Perera, Zhishan Chen, Wanqing Wen, M. Ethan MacDonald, Weijia Cai, Jun Yan, Xiao-Ou Shu, Wei Zheng, Xingyi Guo, Quan Long

DNA foundation models trained on large-scale genomic and epigenetic datasets have shown promise for regulatory variant interpretation, yet their application to tissue-specific contexts remain limited. Here, we present a transfer learning (TL) framework to adapt Enformer, a deep neural network trained on 5,313 multi-omics tracks, to breast and prostate cancer using 275 and 357 tissue-specific transcription factor (TF) ChIP–seq tracks, respectively. We computed tissue-specific cis-regulatory activity (tCRA) scores for millions of single-nucleotide variants (SNVs) in genome-wide association study (GWAS) datasets and prioritized high-impact SNV subsets (1M, 1.5M, and 2M). These TL-prioritized variants demonstrated consistently greater enrichment in tissue-specific enhancers, cancer GWAS risk variants, and ClinVar pathogenic variants compared to the original Enformer model. Transcriptome-wide association studies (TWAS) using TL-based SNVs identified more cancer-relevant genes, many of which exhibited functional essentiality (DepMap), therapeutic tractability (drug databases), and disease relevance (DisGeNET). Notably, TL models outperformed the base model in identifying genes enriched for drug targets and clinically relevant disease associations. Our results show that TL-derived tCRA scores enhance regulatory variant prioritization and improve susceptibility gene discovery in a tissue-specific manner. Our study provides a generalizable framework for tailoring foundation models to disease-relevant contexts, with implications for variant interpretation, therapeutic target discovery, and precision medicine.

Correction: The foraging gene coordinates brain and heart networks to modulate socially cued interval timing in Drosophila

2026-05-05T14:00:00Z

by Hongyu Miao, Wenjing Li, Yongwen Huang, Woo Jae Kim

KAT6A is essential for developmental control gene expression in neural stem and progenitor cells

2026-05-04T14:00:00Z

by Anne K. Voss, Samantha Eccles, Johannes Wichmann, Waruni Abeysekera, Maria I. Bergamasco, Alexandra L. Garnham, Nishika Ranathunga, Yuqing Yang, Rory Bowden, Gordon K. Smyth, Tim Thomas

Heterozygous variants in the KAT6A gene encoding the histone lysine acetyltransferase KAT6A (MOZ, MYST3) cause Arboleda-Tham syndrome, a cognitive impairment syndrome. Histone acetylation is generally associated with active gene transcription. Genetic deletion of both alleles of the Kat6a gene in mice causes developmental defects including anterior homeotic transformation, cleft palate, interrupted aortic arch and cardiac septal defects. Loss of KAT6A impairs expression of HOX, DLX and TBX genes, which are essential for body segment identity specification, palate, heart and aortic arch development. However, the effects of loss of KAT6A on chromatin modifications and gene expression in neural cells, which are relevant to normal brain development and function, is still poorly understood. In this study, we used an automated high-throughput chromatin profiling method and RNA sequencing in mouse neural system and progenitor cells to assess the effects of loss of one or two alleles of Kat6a on gene expression, histone acetylation and methylation. We also assessed occupancy by a trithorax group protein and RNA polymerase II. Our data suggests two modes of action for KAT6A: (1) acetylation of histone H3 on lysine 23 at promoters and enhancers and (2) recruitment of the trithorax group protein MLL1 (KMT2A) to promote the expression of developmental genes, including SOX and homeodomain genes. Together, these two functions appear to be required for normal gene expression in neural progenitors and essential for proliferation and neuronal differentiation.

A novel role of tRNA-derived fragments in porcine granulosa-oocyte cell communication and cuproptosis

2026-04-30T14:00:00Z

by Linyuan Shen, Xue Zhao, Shuang Wu, Yuhang Lei, Shuang Liang, Saihao Wang, Haodong Dai, Yan Wang, Lei Chen, Ye Zhao, Mailin Gan, Shijun Xiao, Guangbin Zhou, Li Zhu

Copper is essential for reproductive function, yet its accumulation can lead to cytotoxicity and cuproptosis. However, the specific molecular mechanisms underlying granulosa cell cuproptosis and follicular atresia remain unclear. Particularly, the molecular pathway by which tRNA-derived fragments (tRFs), recognized as crucial epigenetic regulators, are involved in the regulation of granulosa cell cuproptosis requires further elucidation. In this study, we indicated that copper accumulation disrupted mitochondrial respiration and protein lipoylation, resulting in impaired mitochondrial TCA cycling and subsequent cellular metabolic imbalance. Furthermore, a direct correlation was identified between tRFs and copper homeostasis. Functional analysis demonstrated that tRF-Gly-M3, produced by angiopoietin (ANG) splicing, was significantly upregulated in granulosa cells cuproptosis, and impaired mitochondrial function to induce cuproptosis by silencing the expression of GLS mRNA. tRF-Gly-M3 in exosomes secreted by cuproptosis-induced granulosa cells was high expression, and these exosomes could be delivered into oocytes. tRF-Gly-M3 also impaired oocytes mitochondrial metabolic function, inhibited oocytes maturation, first polar body extrusion and parthenogenesis via silencing GLS mRNA. Overall, our findings indicated that tRFs from granulosa cells could be intercellularly delivered to oocytes, effectively regulating oocyte development.

INS-17 acts as a nutrient deprivation signal to mediate adult IIS-regulated associative behaviors in C. elegans

2026-04-28T14:00:00Z

by Emily J. Leptich, Priyadharshini Vijayakumar, Edward W. Pietryk, Meredith I. Williams, Rachana Rajupalem, Rachel N. Arey

Insulin/Insulin-like growth factor 1 (IGF-1) signaling (IIS) is a pleiotropic signaling pathway that functions across tissues to coordinate phenotypic changes in response to nutrient status. Thus, the ubiquity of the IIS pathway hinders efforts to elucidate the mechanisms driving specific IIS-related phenotypes. Previous research in the nematode worm C. elegans has demonstrated that loss of function of the IIS transmembrane receptor (IR) ortholog, DAF-2, results in a doubled lifespan and enhanced learning and memory behaviors in young and aged animals. However, these findings are the result of reducing DAF-2 receptor function rather than modulating ligand-receptor interactions. In the current study, we aimed to dissect ligand-receptor interactions that may regulate associative behaviors apart from canonical IIS lifespan phenotypes in C. elegans. To this end, we performed targeted genetic screening of Insulin-like Peptides (ILPs) previously identified as DAF-2 antagonists to test their role in learning and memory phenotypes. We discovered that only a single uncharacterized ILP, INS-17, is required for learning and memory. We also demonstrate that INS-17 is sufficient to confer extended memory ability and can promote the maintenance of learning and memory with age. Additionally, we observe that INS-17 regulates associative behaviors independent of lifespan, uncoupling some IIS-mutant phenotypes. We find that regulation of the ins-17 genetic locus explains its unique requirement among ILPs for learning and memory behaviors. Finally, we found that INS-17 acts to signal a state of nutrient deprivation. This activity is required to properly process stimulus valence to promote advantageous behaviors. Our findings deepen the understanding of how IIS can regulate specific phenotypic outputs in response to changes in internal metabolic states.

A positive feedback loop between sensory and octopaminergic neurons underlies nociceptive plasticity in Drosophila larvae

2026-04-28T14:00:00Z

by Jean-Christophe Boivin, Yi Q. Zhao, Jiayi Zhu, Jared T. Dakin, Jing Ning, Tomoko Ohyama

Adaptive modulation of nociceptive behaviour based on prior experience is essential for responding effectively to environmental threats. In Drosophila larvae, nociceptive escape behaviours are robust and stereotyped, yet emerging evidence suggests this can be modulated by experience and internal state. Here, we demonstrate that repeated activation of nociceptive sensory neurons enhances both the likelihood and intensity of nocifensive rolling, reflecting a form of behavioural sensitization. This heightened responsiveness is accompanied by a sustained increase in activity within nociceptive sensory neurons, suggesting that plasticity arises, at least in part, within the sensory compartment. We identified the neuromodulator octopamine as a critical regulator of the sensitization: signalling through the octopamine receptor OAMB is required to sustain elevated nociceptive gain, and feedback from one of octopaminergic neurons class, the ventral unpaired median (VUM) neurons, amplifies sensory neuron output. Together, these findings reveal an experience-dependent positive feedback loop in the nociceptive system, where neuromodulatory circuits tune behavioural output.

The RCAR12-CAP1-OST1 module controls ABA-mediated stomatal closure in Arabidopsis

2026-04-28T14:00:00Z

by Xiaoyi Li, Qian Zhang, Jiangjie Kang, Lianxin Jiang, Yihan Feng, Juan Du, Chaowen Xiao, Jianglan Wei, Qirong Wen, Ying Wang, Jianmei Wang, Yi Yang

Phytohormone abscisic acid (ABA) induces the stomatal closure in plants under drought stress, a process requiring actin reorganization. Yet how ABA perception couples with cytoskeletal dynamics in stomatal closure remains unclear. In this study, we report that Arabidopsis cyclase-associated protein 1 (CAP1) functions as a negative regulator of ABA-induced drought responses through modulating actin network organization in Arabidopsis. Further analyses demonstrate that CAP1 interacts with RCAR12 suppresses actin filaments (F-actin) disassembly, whereas ABA disrupts the CAP1-RCAR12 interaction, thus recovering CAP1’s depolymerization activity. Further, ABA-activated OST1 (OPEN STOMATA 1) phosphorylates CAP1 in Arabidopsis. OST1-mediated phosphorylation of CAP1 attenuates CAP1 binding to ADF4 and inhibits the ADF4-CAP1 complex. This inhibition leads to F-actin stabilization, which in turn maintains stomata in a closed state. This study demonstrates that CAP1 orchestrates ABA-induced stomatal closure under drought stress in Arabidopsis. Specifically, CAP1 acts by coupling ABA signaling to dynamic reorganization of actin cytoskeleton.

Correction: Functional redundancy and formin-isoform independent localization of tropomyosin paralogs in Saccharomyces cerevisiae

2026-04-28T14:00:00Z

by The PLOS Genetics Staff

Potential Rad54 separation of function mutation highlights unique roles during homologous recombination

2026-04-27T14:00:00Z

by Jingyi Hu, David Moraga, Amanda Xu, Lauren Peysakhova, J. Brooks Crickard

Homologous recombination (HR) is a DNA repair pathway that utilizes a template-based approach to repair double-strand breaks within the genome. Template use requires the exchange of individual DNA strands, which members of the RecA family of recombinases facilitate. Rad51 is a primary strand exchange factor in eukaryotes. During regular mitotic DNA repair, Rad51 is aided by the DNA translocase Rad54, which acts as a motor to remodel the template DNA and stabilize primary-strand exchange intermediates. The regulation of this activity remains incompletely understood. Here, we have identified a conserved site within the C-terminal region of Rad54. The mutation of this site creates a separation of function at early strand-exchange intermediates in vivo. Using this mutant protein, we identify a novel intermediate essential for stabilizing displacement loop (D-loop) structures. This precedes the removal of Rad51 and DNA extension. Based on our experiments, we hypothesize that this Rad54 mutant cannot stabilize Rad51-mediated strand-exchange intermediates due to slippage during translocation, leading to failure in DNA remodeling. Identifying a mutant that disrupts this intermediate before Rad51 removal unifies existing models of Rad54-mediated D-loop formation and extension.

PLOS Genetics: New Articles

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Sequence context and methylation interact to shape germline mutation rate variation at CpG sites

Yap1 regulates motility and vertebral development and prevents kyphoscoliosis in zebrafish

Species-specific coevolution of RecA–RecN interfaces governs DNA double-strand break repair in Escherichia coli

FabF and FadM cooperate to recycle fatty acids and rescue ∆plsX lethality in Staphylococcus aureus

Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii

mFABIO: An integrative multi-tissue TWAS fine-mapping approach to prioritize potentially causal genes and tissues underlying binary traits

Pre-cuticle DPY-6 acts as a blueprint for aECM periodic organization in C. elegans

MR2G: A novel framework for causal network inference using GWAS summary data

ZBP1 Drives CD8+ T cell-mediated anti-tumor immunity in head and neck squamous cell carcinoma

An intronic variant in Ferredoxin Reductase (FDXR) creates a cryptic exon in Quarter Horses with Equine Juvenile Spinocerebellar Ataxia

Comparative whole-genome analyses of articular chondrocytes and skin fibroblasts reveal distinct genome instability landscapes in mesenchymal cell types

Correction: Alanine-scanning mutagenesis library of MreB reveals distinct roles for regulating cell shape and viability

Correction: Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses

Why recombination hotspots?

Cas9-expressing HC-04 hepatocytes facilitate CRISPR-based analysis of Plasmodium falciparum sporozoite-host interactions

Spatiotemporal characterization of single-stranded DNA intermediates after UV irradiation: II. Rapid growth and effects of recA and recJ

Spatiotemporal characterization of single-stranded DNA Intermediates after UV Irradiation: I: Post-replication gaps formed during slow growth

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation

Simulated sample splitting approach to address biases due to instrument selection and participant overlap in two-sample Mendelian Randomization studies

Tumour-driven lipid accumulation in oenocytes reflects systemic lipid alterations

Tissue-specific transfer learning improves functional variant and therapeutic target discoveries in breast and prostate cancer

Correction: The foraging gene coordinates brain and heart networks to modulate socially cued interval timing in Drosophila

KAT6A is essential for developmental control gene expression in neural stem and progenitor cells

A novel role of tRNA-derived fragments in porcine granulosa-oocyte cell communication and cuproptosis

INS-17 acts as a nutrient deprivation signal to mediate adult IIS-regulated associative behaviors in C. elegans

A positive feedback loop between sensory and octopaminergic neurons underlies nociceptive plasticity in Drosophila larvae

The RCAR12-CAP1-OST1 module controls ABA-mediated stomatal closure in Arabidopsis

Correction: Functional redundancy and formin-isoform independent localization of tropomyosin paralogs in Saccharomyces cerevisiae

Potential Rad54 separation of function mutation highlights unique roles during homologous recombination

ZBP1 Drives CD8⁺ T cell-mediated anti-tumor immunity in head and neck squamous cell carcinoma