PLOS Genetics: New Articles

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 epigenomic 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.

The pos-1 3′ untranslated region governs germline specification and proliferation to ensure reproductive robustness

2026-04-27T14:00:00Z

by Haik V. Varderesian, Juliet N. Utaegbulam, Hannah E. Brown, Beverly Ramirez, Melina Velcani, Sean P. Ryder

During fertilization, haploid gametes combine to form a zygote. The male (sperm) and female (oocyte) gametes contribute a similar amount of DNA, but the oocyte contributes nearly all the cytoplasm. Oocytes are loaded with maternal mRNAs thought to be essential for embryonic patterning after fertilization. A conserved suite of RNA-binding proteins (RBPs) regulates the spatiotemporal translation and stability of maternal mRNAs. POS-1 is a CCCH-type tandem zinc finger RBP expressed in fertilized Caenorhabditis elegans zygotes from maternally supplied mRNA. POS-1 accumulates in the posterior of the embryo where it promotes posterior cell fate. Here, we show that the pos-1 3′ untranslated region (UTR) is essential for POS-1 patterning and contributes to maximal reproductive fecundity. We engineered a pos-1 mutant where most of the endogenous pos-1 3′UTR was removed using CRISPR genome editing. Our results show that the 3′UTR represses POS-1 expression in the maternal germline but increases POS-1 protein levels in embryos after fertilization. In a wild-type background, POS-1 repression via the 3′UTR has little impact on fertility. In a sensitized background, the deletion mutant has a complex pleiotropic phenotype where most adult homozygous progeny lack either one or both gonad arms. Most phenotypes become more penetrant at elevated temperature. Together, our results support an emerging model where the 3′UTRs of maternal transcripts, rather than being essential, contribute to reproductive robustness during stress.

The transcription factor TaWRKY58 coordinates growth and drought sensitivity in wheat by repressing TaLRR and TaBCS1

2026-04-24T14:00:00Z

by Yazhou Zhang, Xinyao Cheng, Xinyu Yu, Anyu Gu, Xufei Zhao, Mei Deng, Guoyue Cheng, Qiang Xu, Qiantao Jiang, Yuming Wei

Balancing growth and stress adaptation is essential for optimizing crop productivity, yet the transcriptional mechanisms underlying this trade-off in wheat remain poorly understood. Here, we identify the WRKY transcription factor TaWRKY58 as a key repressor coordinating plant architecture and drought response. Loss-of-function mutants of TaWRKY58 exhibit increased plant height and early flowering, accompanied by elevated gibberellin levels, while overexpression restores wild-type phenotypes. Under drought stress, TaWRKY58 represses soluble sugar accumulation, and its mutants show enhanced drought tolerance. Using DAP-seq, we identified genome-wide binding sites of TaWRKY58 and uncovered a W-box-like motif enriched in its target promoters. Electrophoretic mobility shift and dual-luciferase assays confirmed that TaWRKY58 directly binds to and represses two key targets: TaLRR, encoding a leucine-rich repeat protein, and TaBCS1, encoding a mitochondrial AAA^⁺ ATPase. Mutants of TaLRR and TaBCS1 display dwarfism and drought hypersensitivity, respectively, mirroring aspects of the TaWRKY58 overexpression phenotype. Our data support a model in which TaWRKY58 functions as a transcriptional repressor in a coherent regulatory module that fine-tunes growth and stress adaptation by modulating signaling and energy metabolism. This mechanism offers a potential strategy for breeding wheat with optimized yield stability under fluctuating environments.

Nebivolol suppresses glioblastoma progression via dual modulation of mitochondrial metabolism and AKT/mTOR/4EBP1 signaling axis

2026-04-24T14:00:00Z

by Lingni Zhou, Hongyu Che, Hongyan Jiang, Luxin Yin, Yongang Jiang, Yuhui Zhang, Haoran Liang, Rutong Yu, Xu Zhang, Xuejiao Liu

Emerging evidence reveals the pivotal involvement of mitochondrial metabolic dysregulation in glioblastoma (GBM) pathogenesis, considering mitochondrial metabolism as a potential therapeutic target. Nebivolol, a third-generation β-adrenergic receptor antagonist clinically employed in cardiovascular diseases, has recently exhibited notable anti-neoplastic properties. Nevertheless, its therapeutic efficacy and mechanistic underpinnings in GBM remain largely unexplored. In this investigation, we comprehensively assessed the impact of nebivolol on GBM cellular proliferation and elucidated its molecular mechanisms. Our findings revealed that nebivolol markedly suppressed the proliferation and clonogenic abilities of multiple GBM cell lines, concomitant with cell cycle arrest and apoptotic induction. Mechanistically, nebivolol impaired mitochondrial respiratory chain complex I activity, diminished adenosine triphosphate (ATP) synthesis, and augmented ROS production, collectively precipitating neoplastic cell apoptosis. Furthermore, nebivolol attenuated AKT/mTOR/4EBP1 signaling cascade activation, thereby impeding GBM malignant proliferation. In vivo studies corroborated these observations, demonstrating that nebivolol administration significantly attenuated orthotopic GBM xenograft progression and extended survival in tumor-bearing murine models. This study delineates a novel dual mechanism whereby nebivolol exerts anti-GBM effects through concurrent modulation of mitochondrial bioenergetics and AKT/mTOR/4EBP1 signaling transduction. These results provide robust preclinical evidence supporting nebivolol’s clinical repurposing for GBM therapy.

Correction: Regulatory rewiring drives intraspecies competition in Bacillus subtilis

2026-04-21T14:00:00Z

by Margarita Kalamara, Alistair Bonsall, Jonathan Griffin, Joana Carneiro, Marek Gierlinski, Lukas Eigentler, David Stevenson, Amy Wood, Michael Porter, Helge C. Dorfmueller, Cait E. MacPhee, James C. Abbott, Nicola R. Stanley-Wall

Inducible gene deletion reveals essentiality of protein kinases and a septation initiation network in Candida albicans

2026-04-21T14:00:00Z

by Bernardo Ramírez-Zavala, Ines Krüger, Sonja Schwanfelder, Johannes Lackner, Thomas Krüger, Olaf Kniemeyer, Joachim Morschhäuser

Protein kinases are key components of many signaling pathways that regulate cellular activities, and some of them are indispensable for the viability of cells. We used inducible gene deletion to assess the importance of a set of putative essential protein kinases for growth and viability of the pathogenic yeast Candida albicans and to get clues about the functions of uncharacterized essential kinases. We found that bud32Δ, ctk1Δ, rio1Δ, and rio2Δ mutants were viable but grew very slowly, explaining previous failures to generate homozygous deletion mutants. PTK2 was essential, but under certain conditions ptk2Δ mutants remained viable and over time could acquire suppressor mutations in the Ptk2-dependent plasma membrane ATPase Pma1 that restored growth. Deletion of the uncharacterized orf19.5376 was lethal and the null mutants formed pseudohyphae that lacked normal septa and eventually lysed, a phenotype that was phenocopied by auxin-induced protein depletion. The mutants were defective in septin organization, indicating that the orf19.5376-encoded kinase is functionally similar to the nonessential kinase Elm1 of Saccharomyces cerevisiae, but is indispensable for viability in C. albicans. Mutants lacking orf19.3456, which does not have a homolog in S. cerevisiae, were also nonviable and grew as aseptate, sometimes multinucleate hyphae before cell death. Co-immunoprecipitation followed by liquid chromatography-mass spectrometry identified a protein, encoded by the uncharacterized orf19.193, as a candidate regulatory subunit of the orf19.3456-encoded kinase, as mutants lacking this protein exhibited the same terminal phenotype as orf19.3456 mutants. These results provide strong evidence that instead of using a mitotic exit network (MEN) with only two kinases (Cdc15 and Dbf2), as was previously thought, C. albicans regulates septum formation and cytokinesis via a septation initiation network (SIN), known from fission yeast and filamentous fungi, which contains a protein kinase cascade consisting of the upstream kinase Cdc15, the orf19.3456-encoded kinase, and the downstream kinase Dbf2.

Epigenetic gene regulation is controlled by distinct regulatory complexes utilizing specialized paralogs of TELOMERE REPEAT BINDING FACTORS

2026-04-21T14:00:00Z

by Maik Mendler, Kristin Krause, Simone Zündorf, Prathamesh Sannak, Petra Tänzler, Sara Stolze, Hirofumi Nakagami, Franziska Turck

Epigenetic regulators shape chromatin landscapes, allowing cells to express distinct gene sets depending on cell-type, developmental stage or environmental cues. These regulatory complexes rely on interactions with sequence-specific DNA binding proteins, such as the small family of TELOMERE REPEAT BINDING FACTORS (TRBs). TRBs are components of chromatin regulatory complexes with opposing functions, such as the epigenetic repressors Polycomb Repressive Complex 2 (PRC2) and a JMJ14/NAC complex that respectively add and removes the repressive H3K27me3 and positive H3K4me3 modification, but also with the plant-specific PEAT complex that is linked to histone acetylation and gene activation. We dissected the partial redundancy between TRB1, TRB2 and TRB3 in target gene selection and interaction with different chromatin regulatory complexes. High redundancy of TRBs is suggested by major phenotypic changes that are only observed trb triple mutants; however, we found different target site preference between TRB1-3 and preferred partnership with chromatin complexes. Furthermore, TRB paralogs interacted with the NuA4 histone acetylation complex, both together with and in absence of PEAT. Among the three paralogs, TRB1 had more unique binding sites and correlated stronger with PEAT and NuA4 functions. In contrast, TRB2 and TRB3 were more dependent on the presence of bona fide telo-box motifs and were more likely to be found at PRC2 associated sites. Overall, we provide insight into the diverse roles of TRBs in epigenetic gene regulation and how their diversification contributes to their apparent redundancy, as well as their observed activating and repressing effects on gene expression.

Dominance modifiers at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical pathways

2026-04-20T14:00:00Z

by Rita A. Batista, Eléonore Durand, Monika Mörchen, Jacinthe Azevedo-Favory, Samson Simon, Manu Dubin, Vinod Kumar, Eléanore Lacoste, Corinne Cruaud, Christelle Blassiau, Matteo Barois, Anne-Catherine Holl, Chloé Ponitzki, Nathalie Faure, William Marande, Sonia Vautrin, Isabelle Fobis-Loisy, Jean-Marc Aury, Sylvain Legrand, Ute Krämer, Thierry Lagrange, Xavier Vekemans, Vincent Castric

Self-incompatibility in flowering plants is a common mechanism that prevents self-fertilization and promotes outcrossing. In Brassicaceae, the self-incompatibility locus is highly diverse, with many alleles arranged in a complex dominance hierarchy and exhibiting monoallelic expression in heterozygote individuals. Monoallelic expression of the pollen self-incompatibility gene is achieved through the action of sRNA precursors that resemble miRNAs, although the underlying molecular mechanisms remain elusive. Here, we engineered Arabidopsis thaliana lines expressing components of the Arabidopsis halleri self-incompatibility system, and used a reverse genetics approach to pinpoint the pathways underlying the function of these sRNA precursors. We showed that they trigger a robust decrease in transcript abundance of the recessive self-incompatibility genes, but not through the canonical transcriptional or post-transcriptional gene silencing pathways. Furthermore, we observed that single sRNA precursors are typically processed into hundreds of sRNA molecules with a variety of sizes, abundance levels and ARGONAUTE loading preferences. Our results suggest that these seemingly arbitrary processing characteristics are essential for establishing the self-incompatibility dominance hierarchy, as they enable a single sRNA precursor from a dominant allele to effectively repress multiple recessive alleles, thus providing a unique example of how small RNAs mediate gene silencing within a highly complex regulatory network.

Whole-genome sequencing reveals a possible molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro

2026-04-20T14:00:00Z

by Aoi Kudoh, Satoshi Natsume, Yu Sugihara, Hiroaki Kato, Akira Abe, Kaori Oikawa, Motoki Shimizu, Kazue Itoh, Mai Tsujimura, Yoshitaka Takano, Toshiyuki Sakai, Hiroaki Adachi, Atsushi Ohta, Mina Ohtsu, Takuma Ishizaki, Toru Terachi, Hideki Innan, Ryohei Terauchi

Dioecious plants, which have distinct male and female individuals, constitute ~5% of angiosperm species and have emerged frequently and independently from hermaphroditic ancestors. Although recent molecular studies of sex determination have started to reveal the diversity of the genetic systems underlying dioecy, research on the evolution of dioecy is limited, especially in monocots. Here, we explore the molecular basis of sex determination in the monocot Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Chromosome-scale and haplotype-resolved genome assemblies and linkage analysis suggested that this plant has a male heterogametic sex-determination (XY) system, with sex-determination regions located on chromosome 3. Sequence comparison between the X- and Y-chromosomes and read coverage analysis revealed X- and Y-specific regions in putative pericentromeric chromosome regions. Within the Y-specific region, we propose two candidate genes that are likely involved in sex determination: BLH9, encoding a homeobox protein, and HSP90, encoding a molecular chaperone. BLH9 functions in a similar way as AtBLH9 in Arabidopsis thaliana. BLH9 could be involved in suppression of female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants.

Examining the association between fetal HLA-C, maternal KIR haplotypes and birth weight

2026-04-20T14:00:00Z

by Caitlin Stephanie Decina, Nicole M. Warrington, Robin N. Beaumont, Beilei Bian, Caroline Brito Nunes, Geng Wang, William L. Lowe Jr, David Squire, Damjan Vukcevic, Stephen Leslie, Rachel M. Freathy, David M. Evans

Human birth weight is under stabilizing selection, seeking balance between extremes of high and low, thereby reducing fetal and maternal perinatal mortality risk. Certain combinations of maternal killer immunoglobulin-like receptor (KIR) and paternally derived fetal human leuokocyte antigen-C (HLA-C) alleles were previously associated with higher risk of high and low birth weight in a study with limited sample size (n = 1,316). Using recently developed methods to impute HLA and KIR haplotypes using single nucleotide polymorphism (SNP) genotype data, we tested associations of fetal HLA and maternal KIR genotypes with offspring birth weight in a large sample. We imputed KIR haplotypes using the KIR*IMP imputation software in 10,602 mother-offspring pairs of European descent from singleton pregnancies from five studies. Using mixed linear regression models to account for mothers with multiple children, we tested associations between maternal KIR A vs B haplotypes (AA, AB/BA, BB genotypes) as well as copy number of activating receptor gene KIR2DS1 (0, 1, 2 copies of the gene) in the presence of fetal HLA C1/C2 alleles, and offspring birth weight. Associations were analyzed in each cohort before performing a meta-analysis to estimate the interaction effects between maternal KIR and fetal HLA-C2 on birth weight across the entire sample. The KIR haplotypes achieved imputation accuracy estimated at >95% in most of the cohorts. No interaction effects were observed between either the maternal A vs. B haplotype or the maternal KIR2DS1 locus and fetal HLA-C. When specifically trying to replicate the previously associated combination of maternal KIR2DS1 and paternally inherited fetal HLA-C2, there was a negligible change in offspring birth weight for each additional KIR2DS1 allele and HLA-C2 of paternal origin (7g lower birth weight per allele [95% CI: -54, 40], P = 0.78). We found little evidence of association between birth weight and maternal KIR haplotypes or fetal HLA-C2 and were unable to replicate previously reported findings. Our observations reinforce the importance of replication and the use of large sample sizes in the validation of genetic associations.

Constitutively active RAS prolongs Cdc42 signalling, while MAPK signalling is attenuated during fission yeast mating

2026-04-17T14:00:00Z

by Emma J. Kelsall, Akatsuki Kimura, Ábel Vértesy, Kornelis R. Straatman, Mishal Tariq, Raquel Gadea, Chandni Parmar, Gabriele Schreiber, Shubhchintan Randhawa, Takashi Y. Ida, Cyril Dominguez, Edda Klipp, Kayoko Tanaka

The small GTPase RAS is a signalling hub activating multiple pathways, which may respond differently to a constitutively active RAS mutation. We explored this issue in fission yeast, where RAS-mediated pheromone signalling (PS) activates two downstream pathways: the MAPK^Spk1 and Cdc42 pathways. We observed that the yeast RAS mutation ras1.G17V, an equivalent of the mammalian ras.G12V oncogenic mutation, causes prolonged Cdc42 activation, whereas MAPK^Spk1 activation was transient and attenuated. To explain this observation, we generated a PS framework by conducting genetic epistasis analysis of PS mutants and biochemical analysis of two Ras1 effectors, Cdc42-GEF^Scd1 and MAPKKK^Byr2, each of which triggers activation of the Cdc42 and MAPK^Spk1 pathways, respectively. Cdc42-GEF^Scd1 and MAPKKK^Byr2 directly interacted with Ras1 in vitro in a competitive manner, and overexpression of the Ras binding domain of either Cdc42-GEF^Scd1 or MAPKKK^Byr2 in cells inhibited both downstream pathways, confirming that Ras1 signalling branches into the MAPK^Spk1 and Cdc42 pathways. In conjunction with the genetic epistasis analysis, we developed the PS framework-based mathematical model to test which network structures can explain the transient MAPK^Spk1 activation profile. Incorporating a negative-feedback circuit acting on pheromone production or sensing enabled the model to quantitatively reproduce MAPK^Spk1 dynamics in the wild type and 20 additional PS mutants. The predicted PS negative-feedback was experimentally confirmed by deleting Sxa2, the carboxypeptidase that degrades one of the mating pheromones, which led to hyperactivation of both MAPK^Spk1 and Cdc42. Our study provides a holistic understanding of the fission yeast pheromone signalling network, explaining how RAS signalling propagates differently through two downstream pathways. Our PS mathematical model may serve as a valuable reference framework for analysing other RAS signalling systems.

Oocyte vitrification disrupts zygotic genome activation in embryos by impairing maternal spliceosome translation and Crxos splicing

2026-04-15T14:00:00Z

by Jianpeng Qin, Ao Ning, Jian Han, Xiangyi Chen, Beijia Cao, Yujun Yao, Xiaoqing He, Bo Pan, Yaozong Wei, Kunlin Du, Shuqi Zou, Jiangfeng Ye, Guozhi Yu, Qiuxia Liang, Jie Qiao, Jie Yan, Guangbin Zhou

Oocyte vitrification is indispensable in assisted reproduction, yet its link to compromised embryonic development remains mechanistically unresolved. Here, this study demonstrate through integrated transcriptome and translatome analysis that vitrification disrupts maternal mRNA translation—sparing global transcriptional output—in mouse oocytes. This translational perturbation prominently suppresses genes encoding spliceosome components, including Phf5a, leading to persistent and widespread alternative splicing defects in subsequent 2-cell embryos. Importantly, aberrant splicing specifically depletes the functional full-length transcript of the essential zygotic genome activation (ZGA) regulator Crxos (Egam1) while elevating a truncated, non-functional variant (Egam1^ΔEXON3). Functional analyses confirm that loss of Crxos in 2‑cell embryos not only compromises developmental progression but also reduces global transcriptional activity, likely via impaired RNA Pol II recruitment and elongation at ZGA genes. Together, this work delineates a linear pathological cascade triggered by oocyte vitrification, comprising maternal translational suppression, spliceosome impairment, Crxos aberrant splicing, impaired ZGA, and developmental compromise, thereby offering a mechanistic basis for refining cryopreservation protocols in reproductive medicine.

Correction: Transcriptional repression of reaper by Stand still ensures female germline development in Drosophila

2026-04-15T14:00:00Z

by The PLOS Genetics Staff

Worm orthologues of cytokinesis-associated proteins CIT and ASPM regulate neuronal microtubule dynamics and polarity in C. elegans

2026-04-15T14:00:00Z

by Sunanda Sharma, Keerthana Ponniah, Ishanee Bandyopadhyay, Devyani Vadawale, Sandhya P. Koushika, Anindya Ghosh-Roy

The polarized architecture of neurons is intricately associated with the modulation of microtubule dynamics. Over the years, several microtubule-associated factors that regulate neuronal polarity have been identified. However, the precise details of how microtubule arrangement and stability are established in axons and dendrites are not clearly understood. To uncover the relevant factors involved in the biological pathways governing microtubule regulation in neurons, we conducted a suppressor screen using the neuronal ectopic extension phenotype caused by the loss of the kinesin-13 family microtubule depolymerizing protein KLP-7 in C. elegans. Interestingly, apart from eleven variants of α (mec-12) and β (mec-7) tubulins, we isolated a variant of cytokinesis-associated protein, W02B8.2/citk-1, the suggested kinase-less orthologue of mammalian citron-rho interacting kinase (CIT). Little is known about the role of CIT in microtubule regulation in post-mitotic neurons. In this study, we found that the kinase-less worm orthologues of CIT, citk-1 and citk-2, redundantly modulate microtubule stability in the axon-like anterior process and maintain the population of plus-end-out microtubules in the dendrite-like posterior process of the PLM mechanosensory neurons in a cell-autonomous manner. In the absence of citk-1 and citk-2, PLM neurons exhibit variable morphological defects, including neurite growth and synaptic branch defects. Moreover, we find that CITK-1/2 work in the same genetic pathway as ASPM-1 (the worm homolog of mammalian ASPM (abnormal spindle-like microcephaly-associated protein)) to modulate plus-end dynamics of microtubules in PLM neurons. Our findings suggest that the cytokinesis-associated CITK-1/2 and ASPM-1 have non-mitotic roles in regulation of microtubules in differentiated PLM neurons.

Chronic replication stress-mediated genomic instability disrupts placenta development in mice

2026-04-13T14:00:00Z

by Mumingjiang Munisha, Rui Huang, Jordan Khan, John C. Schimenti

Abnormal placentation drives many pregnancy-related pathologies and poor fetal outcomes, but the underlying molecular causes are understudied. Here, we show that persistent replication stress due to mutations in the MCM2–7 replicative helicase disrupts placentation and reduces embryo viability in mice. MCM-deficient embryos exhibited normal morphology, but their placentae had a drastically diminished junctional zone (JZ). Whereas cell proliferation in the labyrinth zone (LZ) remained unaffected, it was reduced in the JZ during development. MCM2–7 deficient trophoblast stem cells (TSCs) failed to maintain stemness, suggesting that replication stress affects the initial trophoblast progenitor pool in a manner that preferentially impacts the developing JZ. In contrast, pluripotency of mouse embryonic stem cells (ESCs) with MCM2–7 deficiency were not affected. Developing female mice deficient for FANCM, a protein involved in replication-associated DNA repair, also had placentae with a diminished JZ. These findings indicate that replication stress-induced genomic instability compromises embryo outcomes by impairing placentation.

ZmSKIP enhances drought tolerance by reducing stomatal aperture in maize

2026-04-13T14:00:00Z

by Yao Wang, Yujiao Zhou, Qimeng Li, Yanyan Zhang, Li Yang, Qiao Zhou, Wen Xu, Tianhong Liu, Yaxi Liu, Fengkai Wu, Guangchao Sun, Wei Guo, Yanli Lu, Jie Xu

SKI-INTERACTING PROTEINS (SKIPs), primarily known as splicing factors, control gene expression at the post-transcriptional level in stress responses in plants. However, little is known about SKIPs in regulating plant drought stress at the transcriptional level, particularly in maize (Zea mays L.). Here, we discover that ZmSKIP enhances drought tolerance in maize. ZmSKIP transgenic plants were generated to study how ZmSKIP positively regulates drought tolerance. Overexpression of ZmSKIP promoted stomatal closure and reduced water loss, whereas the opposite effect was observed in skip-aa mutants. ZmSKIP directly binds to the “TAATA” motif in the promoter of B-cell lymphoma 2-associated athanogene 8 (ZmBAG8). bag8 mutants exhibit the decreased water loss and reduced stomatal aperture phenotype under drought stress. Additionally, ZmSKIP can be recruited by ZmBAG8 in stress granules (SGs) to decrease its protein abundance in the nucleus. Increased ZmBAG8 expression leads to larger stomatal aperture and normal plant growth. Under drought stress, the interaction between ZmSKIP and ZmBAG8 was abolished, while ZmSnRK2.3 phosphorylates ZmSKIP at Ser²³⁶ and Ser²⁴⁴ to enhances drought tolerance by strengthening the ability of ZmSKIP to suppress ZmBAG8 expression. Thus, our findings demonstrate that ZmSnRK2.3-mediated phosphorylation of ZmSKIP reduces ZmBAG8 expression and stomatal aperture, thereby enhancing drought tolerance in maize.

Correction: An essential gene screening identifies yeast Mot1 as a suppressor of R-loops and genome instability

2026-04-10T14:00:00Z

by María E. Soler-Oliva, Rocío A. Domínguez-Sierra, Hélène Gaillard, Andrés Aguilera

Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina

2026-04-08T14:00:00Z

by Mohita Gaur, Matthew J. Brooks, Xulong Liang, Ke Jiang, Anjani Kumari, Milton A. English, Paolo Cifani, Maria C. Panepinto, Jacob Nellissery, Robert N. Fariss, Laura Campello, Claire Marchal, Anand Swaroop

High aerobic glycolysis in retinal photoreceptors, as in cancer cells, is implicated in mitigating energy and metabolic demands. Lactate, a product of glycolysis, can exert epigenetic regulation through histone lactylation in cancer. Here, we show that enhanced ATP production during mouse retinal development is achieved primarily through increase in glycolysis. Histone lactylation, especially H3K18La, parallels increased glycolysis and lactate levels in the developing retina. Multi-omics analyses, combined with confocal imaging, reveal the localization of H3K18La near H3K27Ac in the euchromatin at promoters of active retinal genes. In mouse retinal explants, glucose metabolism is associated with lactate levels as well as H3K18La and consequently gene expression. However, inhibition of glycolysis with 2-deoxyglucose (2-DG) reduces global H3K18La and H3K27Ac marks with somewhat distinct transcriptional changes. Evaluation of accessible chromatin at H3K18La-marked promoters uncovers an enrichment of GC-rich motifs for transcription factors of SP, KMT and KLF families, among others, indicating the specificity of H3K18La-mediated gene regulation. Our results indicate glycolysis/lactate/H3K18La as a potential axis for transcriptional response to changing metabolic conditions in the retina, especially photoreceptors.

Establishment of a congenic strain for the oyster mushroom reveals the structure and evolution of mating-type loci

2026-04-08T14:00:00Z

by Yi-Yun Lee, Guillermo Vidal-Diez de Ulzurrun, Rebecca J. Tay, Yen-Ping Hsueh

Pleurotus ostreatus, a widely cultivated edible oyster mushroom, is an ecologically versatile species with applications in biotechnology, agriculture, and food production. It functions as a decomposer and in nutrient-limited conditions it enhances its survival by using a potent toxin to prey on nematodes. Its adaptability is further regulated by sexual reproduction, which follows a tetrapolar mating system governed by two unlinked, multiallelic loci, matA and matB. The two mating-compatible monokaryotic strains PC9 and PC15, derived from the parental dikaryon strain N001, exhibit significant physiological differences. PC9 grows robustly in laboratory conditions, whereas PC15 grows more slowly, making PC9 the preferred strain for research. To advance P. ostreatus as a genetic model, we characterized the mating-type (MAT) loci of both monokaryon strains and developed a congenic strain. We analyzed the MAT loci in multiple P. ostreatus strains, and identified 11 A and 12 B alleles among twelve haplotypes, confirming their multiallelic nature. Using 10 rounds of backcrossing, we introgressed the matA and matB loci from PC15 into the PC9 genetic background to generate the congenic strain PC9.15. After sequencing and assembling a high-quality and contiguous genome for PC9.15, we confirmed that the genomes of PC9.15 and PC9 are 99% similar, with the only major difference placed at the matA and matB loci.