PLOS Genetics: New Articles

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.

Translation control by altered start codon usage as a means of modulating the general stress response and virulence in Listeria monocytogenes

2026-04-06T14:00:00Z

by Jialun Wu, Claire Kelly, Duarte N. Guerreiro, Brenda Chanza, Ashley Reade, Catherine M. Burgess, Conor O’Byrne

In the food-borne pathogen Listeria monocytogenes, SigB is the central regulator of general stress response (GSR) and it mediates host entry by promoting acid resistance and epithelial cell attachment. However, mutations can readily arise to disable regulators of SigB (Rsb proteins), which suggests a considerable genetic plasticity in the GSR. To further investigate this, we defined the complete genome sequence of a clinical isolate and elucidated how sequential mutations within sigB operon (rsbX N77K and rsbU Q317*) impacted fitness through modulation of SigB activity. To investigate the plasticity of the GSR, we followed its genetic adaptation to lethal acidic challenge (mimicking the selective pressure encountered during entry into the host). Acid resistance developed rapidly and all 6 acid resistant derivatives (ARDs) selected for analysis had acquired mutations in rsbW, which encodes an antagonist of SigB that suppresses SigB activity during non-stress conditions. These mutations resulted in non-canonical start codons (rsbW^ATG to rsbW^ATA or rsbW^ATT) or premature translation termination (rsbW^-) and all were found to result in increased SigB activity. A translational reporter assay demonstrated distinct differences in translation efficiency between three start codons: ATG > ATA > ATT, suggesting that a perturbation of RsbW:SigB stoichiometry alters SigB activity. We then analysed start codon usage for all conserved genes in 60,692 L. monocytogenes genomes. This analysis revealed flexible usage of start codons associated with genetic clades in 39 conserved genes, 13 of which are involved in virulence and stress response. Further, we show that flexible use of canonical start codons (ATG and GTG) can also mediate different levels of expression of virulence and stress response genes. Taken together, we show the genetic plasticity of GSR regulation in a model pathogen, and highlight the importance of translational control as a means of fine-tuning gene expression during short-term adaptation and long-term evolution for optimal fitness.

System drift in the evolution of plant meristem development

2026-04-03T14:00:00Z

by Pjotr L. van der Jagt, Steven Oud, Renske M. A. Vroomans

Developmental system drift (DSD) is a process where a phenotypic trait is conserved over evolutionary time, while the genetic basis for the trait changes. DSD has been identified in models with simpler genotype-phenotype maps (GPMs), such as RNA folding, however the extent of DSD in more complex GPMs, such as developmental pattern formation, is debated. To investigate the occurrence of DSD in complex developmental GPMs, we constructed a multi-scale computational model of the evolution of gene regulatory networks (GRNs) governing plant meristem (stem cell niche) development. We found that, during adaptation, some regulatory interactions became essential for the correct expression of stem cell niche genes. These regulatory interactions were subsequently conserved for thousands of generations. Nevertheless, we observed that these deeply conserved regulatory interactions could be lost over an extended period of stabilising evolution. These losses were compensated by changes elsewhere in the GRN, which then became conserved as well. This gain and loss of regulatory interactions resulted in a continual cis-regulatory rewiring in which accumulated changes caused changes in the expression of several genes. Using two publicly available datasets we found frequent changes in conserved non-coding sequences across six evolutionarily divergent plant species, and showed that these changes do not correlate with changes in gene expression patterns, demonstrating the occurrence of DSD. These findings align with the results from our computational model, showing that DSD is pervasive in the evolution of complex developmental systems.

DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A

2026-04-02T14:00:00Z

by Ioannis Kafetzopoulos, Francesca Taglini, Moira Pasquier, Hazel Davidson-Smith, Christine J. Rodger, Lucia Puchades Gimeno, Andrew A. Malcolm, Duncan Sproul

Loss of DNA methylation is a hallmark of cancer that is proposed to promote carcinogenesis through gene expression alterations, retrotransposon activation and induction of genomic instability. Cancer-associated hypomethylation does not occur across the whole genome but leads to the formation of partially methylated domains (PMDs). However, the mechanisms underpinning PMD formation remain unclear. PMDs replicate late in S-phase leading to the hypothesis that they become hypomethylated due to incomplete re-methylation by the maintenance methyltransferase DNMT1 during cell division. Here we investigate the role of DNMT1 in shaping the cancer methylome by conducting whole genome bisulfite sequencing (WGBS), repli-seq and ChIP-seq on DNMT1 knockout HCT116 colorectal cancer cells (DNMT1 KO cells). We find that DNMT1 loss leads to preferential hypomethylation in late replicating, heterochromatic PMDs marked by the constitutive heterochromatic mark H3K9me3 or the facultative heterochromatic mark H3K27me3. However, we also observe that a subset of H3K9me3-marked PMDs gain methylation in DNMT1 KO cells. We find that, in DNMT1 KO cells, these hypermethylated PMDs remain late replicating but DNMT3A localises to them. This is accompanied by loss of heterochromatic H3K9me3, specific gain of euchromatic H3K36me2 and some gene upregulation. These same domains also have more variable DNA methylation than other PMDs in colorectal tumours in vivo. Our observations suggest that hypermethylated PMDs lose their heterochromatic state, enabling their methylation by DNMT3A and the establishment of a hypermethylated, non-PMD state, despite their late replication timing. More generally, our findings suggest that differential de novo DNMT activity plays a key role in establishing domain level DNA methylation patterns in cancer cells.

Delta family protocadherins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb

2026-04-01T14:00:00Z

by Daniel T. Barnes, Ezekiel M. D. Crenshaw, Matthew J. Curran, Jessica B. Herr, Emily S. Devereaux, Carly D. Seligman, Jonathan A. Raper

To understand how neural circuits are assembled, it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single-cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance-related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non-clustered delta-protocadherin family of adhesion molecules. We found that two members of the delta1-protocadherin family, pcdh7b and pcdh11, are most highly expressed in sensory neurons that project to a specific identifiable neuropil in the early olfactory bulb called the DZ protoglomerulus. Knocking down either one of these protocadherins impairs the ability of sensory axons to terminate within the DZ protoglomerulus. Knockdown does not affect the ability of other sensory axons from terminating normally in a separate neuropil called the CZ protoglomerulus. In contrast, two members of the delta2-protocadherin family, pcdh10b and pcdh17, are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. We conclude that delta1-protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus, while delta2-protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus.

ADNP regulates chromatin architecture and lineage fidelity during neural differentiation

2026-04-01T14:00:00Z

by Phillip Wulfridge, Nathaniel Rell, John Doherty, Kuo-Chen Fang, Michelle Lee Lynskey, Kavitha Sarma

Transition from a pluripotent to a differentiated cell state is accompanied by significant changes in genome organization. Activity dependent neuroprotective protein (ADNP) is a chromatin regulator with critical roles in neurodevelopment and limits the genomic occupancy of CTCF, a master architectural protein in genome organization, in embryonic stem cells. However, ADNP localization, function, and relationship with CTCF in differentiated neural lineages are not well studied. Here we develop a dual degron model which allows us to acutely deplete ADNP in neural progenitor cells (NPCs). We find that ADNP depletion does not impact NPC survival in the short term, but results in a genome organization switch, which favors the formation of short-range chromatin looping interactions coinciding with CTCF accumulation. Furthermore, ADNP localizes to active gene promoters in NPCs that are unoccupied by CTCF, where it prevents over-expression of genes that are activated upon neurodifferentiation and represses those involved in commitment to other lineages. Our findings uncover CTCF-dependent as well as CTCF-independent regulatory mechanisms of ADNP in NPC-specific chromatin organization and gene expression programs that may underlie its essential function in neurodevelopment.

The geometry of G × E: How scaling and endogenous treatment effects shape interaction direction

2026-04-01T14:00:00Z

by Michal Sadowski, Andy W. Dahl, Noah Zaitlen, Richard Border

Gene-environment interaction (G × E) studies hold promise for identifying genetic loci mediating the effects of environmental risk on disease. However, interpretation of G × E effects is often confounded by two fundamental issues: the dependence of interaction estimates on outcome scale and the presence of endogenous treatment effects, in which genetic liability influences environmental exposure. These factors can induce apparent G × E signals—even when genetic and environmental contributions are purely additive on an unobserved scale. In this work, we demonstrate that any monotone convex transformation of an outcome induces sign-consistent G × E effects: the sign of the interaction term aligns with the sign of the corresponding main genetic effect. Convex transformations are a broad class of functions that include many commonly used data transformations, such as exponential and logarithmic functions, the square root, and other power transformations. We further show that endogenous treatment effects, modeled as threshold-based interventions, generate G × E effects with a similar directional signature. Exploiting this property, we propose a simple diagnostic: sign consistency across G × E estimates can signal when interactions are driven by outcome scaling or exposure endogeneity. We validate our framework in the UK Biobank using transcriptome-wide interaction studies (TxEWAS) across multiple trait–environment pairs, observing widespread sign consistency in some settings—suggesting confounding by scaling or treatment bias. Our results provide both a theoretical foundation and a practical tool for interpreting G × E findings, enabling researchers to assess whether the observed G × E signal may depend substantially on outcome scaling or be influenced by exposure endogeneity.

Characterization of EOP-1 reveals cell autonomous oscillations preceding somatic cell fusion in Neurospora crassa

2026-03-31T14:00:00Z

by Anne Geertje Oostlander, Marcel René Schumann, Lina Strzelczyk, Lucas Well, Ulrike Brandt, Marco Leiterholt, Stefan Jakschies, Tina Rietschel, Josef Wissing, Lothar Jänsch, André Fleißner

Cell fusion is a fundamental process essential for the development and proliferation of eukaryotic organisms. In the ascomycete fungus Neurospora crassa, germinating spores undergo chemotropic interactions and fusion to merge into a supracellular unit, which gives rise to the mycelial colony. Within mature colonies, hyphal branches fuse to form anastomoses between leading hyphae, enhancing the overall connectivity of the mycelium. Both germling and hyphal fusion rely on the same molecular machinery. The MAP kinase MAK-2 and the fungal-specific protein SO have been identified as key regulators of these processes, and their alternating recruitment to the plasma membrane at interacting cell tips suggests a dialog-like cell communication mechanism involving dynamic switches between signal sending and receiving. However, the mechanisms that trigger the onset of this intercellular communication are still not understood. This study identifies EOP-1 as an interaction partner of the SO protein and functionally characterizes its role in cell communication and fusion. Deletion of the eop-1 gene abolished germling fusion and chemotropic interactions, while live-cell imaging showed EOP-1 oscillating at interacting cell tips, coinciding with SO recruitment. Intriguingly, EOP-1 displayed a similar dynamic, oscillatory tip recruitment also in isolated, non-interacting germlings, setting it apart from previously characterized fusion factors in N. crassa. This observation suggests for the first time that spore germlings of N. crassa exhibit fusion related cell-autonomous oscillatory behavior and implicates EOP-1 in initiating intercellular communication. The oscillatory recruitment pattern of EOP-1 was dependent on the presence of SO, MAK-1, MAK-2, BEM1 and HAM-14 in the cell. Loss of EOP-1 strongly reduced MAK-1 phosphorylation, placing EOP-1 upstream of MAK-1 pathway activation. This work offers new insight into how genetically and developmentally identical cells initiate and coordinate their communication and mutual attraction.

The adapt-to-nutrient NRPS-like secondary metabolite gene cluster facilitates Verticillium dahliae adaptation to different nutrient environments

2026-03-31T14:00:00Z

by Ying-Yu Chen, Lea S. Steglich, Nadja Spasovski, Marcel H. W. Franzius, Merle Aden, Isabel Maurus, Rebekka Harting, Gerhard H. Braus

Filamentous fungi produce a wide range of secondary metabolites to adapt to changing environments. RNA sequencing revealed that nine biosynthetic gene clusters (BGCs) of the phytopathogenic Verticillium dahliae react to different nutrient environments. The adapt-to-nutrient NRPS-like (ANN) cluster contributes to antibacterial activity and developmental processes important for the early biotrophic life cycle, but is dispensable for virulence on tomato (Solanum lycopersicum). Transcription of the core biosynthetic enzyme-encoding ANN3 is highly induced in nutrient-poor environment. ANN3 is transcriptionally controlled by global and in-cluster transcription factors. ANN3 is activated by early colonisation transcription factors Som1 and Vta2, but repressed by Mtf1, which governs late stages of disease progression. The in-cluster transcription factor Ann1, which represses ANN3, is less abundant in nutrient-poor environment or when V. dahliae encounters antagonists. Ann1 promotes resting structure formation but suppresses conidiation and antibacterial activity. Possible products of the ANN cluster were revealed by comparing metabolites extracted from ANN3 regulator mutants and from the bacterial-fungal interaction zone. Our findings revealed that V. dahliae perceives different nutrient environments and changes its survival strategy by differential expression of the ANN secondary metabolite gene cluster.

Correction: How convincing is a matching Y-chromosome profile?

2026-03-30T14:00:00Z

by Mikkel M. Andersen, David J. Balding

Mms4 chromosomal association reveals functional relationships between meiotic crossover pathways in budding yeast

2026-03-30T14:00:00Z

by Amamah Farzlin Farnaz, Sameer Joshi, Praseetha Sarath, Girija Jogwar, Koodali T. Nishant

Meiotic crossovers are generated from the repair of programmed DNA double-strand breaks (DSBs). In the budding yeast Saccharomyces cerevisiae and mammals, most crossovers are generated through the Class I pathway, involving the mismatch-repair related complex Msh4-Msh5, while a smaller fraction is produced by the Mms4-Mus81 endonuclease (Class II pathway). We present the first report on the genome-wide localization of the Mms4 protein during meiosis in S. cerevisiae. Surprisingly, Mms4 localization showed a trend towards weak DSB sites, unlike the localization of the Class I crossover protein -Msh5, which is biased towards strong DSB sites. This preference for weaker DSB hotspots was retained in a msh5∆ mutant, arguing against competitive models of Mms4 and Msh5 association on meiotic chromosomes. The chromosomal association of Mms4 does not require the formation of meiotic DNA breaks but is facilitated by chromosome axis assembly. These results suggest Mms4 is primarily associated with chromosomal axis regions positioned near recombination intermediates. Mms4 binding is also largely insensitive to heterozygosity, unlike Msh5, consistent with its independence from recombination for localization. Together, these findings support a model in which Mms4-Mus81 enhances the robustness of meiotic recombination with a trend towards binding DSB hotspots that are weaker or are located in regions with sequence divergence that may be processed less efficiently by the Class I pathway.

Post-translational modifications of GlmR integrate metabolic and stress signals to maintain cell envelope homeostasis in Bacillus subtilis

2026-03-30T14:00:00Z

by Logan B. Suits, Sebastian J. Khan, Dipanwita Bhattacharya, Silviya Dimitrova, Prahathees J. Eswara

The metabolic networks of most life forms integrate cost-benefit analysis to properly budget carbon and other essential nutrients. Bacillus subtilis is a Gram-positive model bacterium found in diverse ecological niches such as soil, marine environments, and the human gut. As such, B. subtilis cells fine-tune metabolic pathways by monitoring signals indicating the presence of nutrients and stressors. A highly conserved protein, GlmR, is a key player in rationing carbon for the production of cell envelope precursors. This function of GlmR can be attributed to its role in cell shape regulation and antibiotic resistance. Given its central position in carbon utilization, GlmR is under post-translational regulation by phosphorylation and UDP-N-acetylglucosamine (UDP-GlcNAc) binding. GlmR is also linked to cyclic-di-AMP (c-di-AMP), a nucleotide second messenger involved in osmotic and cell wall stress response. In this study, we probed the importance of GlmR in cell morphogenesis, c-di-AMP signaling, and investigated the physiological significance of post-translational regulation. Our results reveal that cells lacking glmR exhibit: (i) increased susceptibility to tunicamycin, a cell envelope targeting antibiotic; (ii) impaired division site positioning; and (iii) reduced intracellular c-di-AMP concentration. Furthermore, we show that the function of GlmR is fine-tuned by UDP-GlcNAc binding, phosphorylation, and acetylation. Additionally, we provide evidence showing that the recently discovered uridyltransferase activity of GlmR is integral for its function. We show that GlmR is a cell width determinant and propose a model suggesting close cooperation with an actin-like protein, MreB. Overall, our studies highlight the importance of the enzymatic function of GlmR and elucidate the mechanism behind the multiple post-translational means to regulate this crucial protein which is at the crux of carbon flux with an important role in maintaining cell envelope integrity.

mTOR signaling regulates demand-adapted hematopoiesis and metabolic reprogramming required for an effective cellular immune response in Drosophila melanogaster larvae

2026-03-24T14:00:00Z

by Ines Anderl, Jens-Ola Ekström, Tea Tuomela, Mika Rämet, Tiina Susanna Salminen, Laura Vesala

The evolutionarily conserved mechanistic Target of Rapamycin (mTOR) pathway connects energy and nutrient availability to growth, proliferation, differentiation, immunity and survival. Here, we investigated the role of the mTOR pathway in Drosophila hematopoiesis and immunity using genetic and transcriptomic analyses of peripheral larval blood cells (hemocytes). We show that blood cell-directed mTor expression induced lamellocyte differentiation as seen after parasitoid wasp infection. Genetic epistasis revealed that lamellocyte hematopoiesis downstream of mTor is mediated by the JNK and p38 pathways. Transcriptomic profiling showed largely similar changes in gene expression patterns of wasp infected and mTor overexpressing hemocytes. While mTOR signaling is necessary for proper lamellocyte differentiation, mTOR Complex 1 (mTORC1) activity is suppressed in mature lamellocytes. Our transcriptome data indicated that hemocyte activation is accompanied by a shift in metabolism towards aerobic glycolysis for energy production, the oxidative pentose phosphate pathway for NADPH recycling, ROS production and detoxification as well as glutaminolysis for glutathione production. Our data highlight the key role of mTOR in controlling blood cell fate in Drosophila.

Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans

2026-03-24T14:00:00Z

by Maddy Comerford, Davide M. Vespasiani, Navya Shukla, Laura E. Cook, Danat Yermakovich, Michael Dannemann, Matthew Leavesley, Christopher Kinipi, François-Xavier Ricaut, Nicolas Brucato, Murray P. Cox, Irene Gallego Romero

Interbreeding between anatomically modern humans and archaic hominins has contributed to the genomes of present-day human populations. However, our understanding of the specific gene regulatory consequences of Neanderthal, and particularly, Denisovan introgression is limited. Here, we used a massively parallel reporter assay to investigate the regulatory effects of 25,869 high-confidence introgressed SNPs segregating in present-day individuals of Papuan genetic ancestry in immune cell types. Overall, 8.22% of Denisovan and 8.58% of Neanderthal sequences showed active regulatory activity, and 9.22% of these displayed differential activity between archaic and modern alleles. We found no association between introgressed allele frequency on activity regardless of introgression source, but introgressed Denisovan alleles at higher frequencies were less likely to be differentially active than expected, suggesting introgression is under some degree of selective constraint. Both activity and differentially activity were associated with distance to the nearest transcription start site, while differential activity was additionally associated with differential transcription factor binding. Genes predicted to be regulated by differentially active sequences included IFIH1 and TNFAIP3, key immune genes and known examples of archaic introgression. Overall, this work provides experimental validation of regulatory activity for thousands of archaic variants in populations with the highest levels of Denisovan ancestry worldwide, revealing how human evolutionary history actively shapes present-day genetic diversity and immune function.

Genetic and functional characterization of AMH Signaling in Zebrafish - Evidence for Roles of Amh-Bmpr2a-Bmpr1bb Pathway in Controlling Gonadal Homeostasis

2026-03-23T14:00:00Z

by Yiming Yue, Chu Zeng, Xin Zhang, Chao Bian, Zhiwei Zhang, Kun Wu, Weiting Chen, Xianqing Zhou, Ling Lu, Nana Ai, Wei Ge

Anti-Müllerian hormone (AMH), a member of the TGF-β superfamily, plays a crucial role in Müllerian duct regression in mammals. AMH signals through a specific type II receptor (AMHRII) and a type I receptor to activate the downstream Smad1/5/9 signaling pathway. Interestingly, non-mammalian vertebrates, including teleosts, also express AMH despite lacking Müllerian ducts. Accumulating evidence indicates that AMH influences gonadal development and function across vertebrates. Intriguingly, zebrafish, a popular model organism, possesses AMH (Amh/amh) but lacks specific type II receptor (Amhr2). Based on our previous studies and data from others, we propose that Amh may signal through a novel pathway in zebrafish involving the BMP type II receptor Bmpr2a and type I receptor Bmpr1bb. In this study, we provide genetic and functional evidence for the existence of the Amh-Bmpr2a-Bmpr1bb signaling pathway in zebrafish and its role in controlling gonadal homeostasis. Our experimental data excluded the participation of Bmpr2b and Bmpr1ba, paralogues of Bmpr2a and Bmpr1bb respectively, in Amh signaling. Additionally, we also provide genetic evidence that the phenotypes exhibited by amh, bmpr2a, and bmpr1bb mutants, i.e., gonadal hypertrophy, were all dependent on gonadotropin signaling, and that the two gonadotropins (FSH and LH) showed similar potency in driving the development of hypertrophic gonadal growth resulting from dysfunction in the Amh-Bmpr2a-Bmpr1bb signaling pathway. In summary, the present study provides comprehensive evidence for Amh signaling through Bmpr2a-Bmpr1bb pathway and its interplay with gonadotropins in controlling germ cell proliferation and differentiation.

An evaluation of age-varying genetic effects underlying body-mass index and blood pressure in the UK Biobank

2026-03-20T14:00:00Z

by Genevieve M. Leyden, Panagiota Pagoni, Grace M. Power, David Carslake, Tom G. Richardson, Kate Tilling, Gibran Hemani, George Davey Smith, Eleanor Sanderson

Genome-wide association studies (GWAS) are conventionally conducted in cohorts spanning a wide age-range. These studies typically assume that genetic associations are constant across different ages. Some traits, however, may have age-varying genetic associations. This has implications for the interpretation of genetic effects derived in downstream applications, such as Mendelian randomization (MR) analyses. In this study we conducted a series of age-stratified GWAS on individuals aged 40–69 years in the UK Biobank, for body-mass index (BMI) and three blood pressure traits (systolic, diastolic and pulsatile pressure (PP)) in 2-year age strata (N up to 26,330). We used a meta-regression approach to systematically identify single nucleotide polymorphisms (SNPs) with evidence for age interaction effects among trait-associated GWAS signals and additional loci genome-wide. Within an MR framework, we examine the relationship between BMI and blood pressure traits on cardiovascular and cardiometabolic outcomes (type-2 diabetes (T2D), stroke, peripheral artery disease (PAD), heart failure, coronary heart disease and atrial fibrillation). Next, we describe the effect of the SNP*Age interaction on those relationships in a modified inverse-variance weighted (ivw) analysis. We identified differential enrichment of age-interaction effects, which was trait dependent. For example, 10.3% of BMI discovery SNPs had evidence for an age-interaction in our data compared to 44.7% for PP (at P < 0.05). Our downstream MR and modified ivw analyses highlight the influence of age on the genetically predicted relationship between PP and adverse cardiovascular outcomes. For example, our results indicated that an increased rate of change in genetically predicted PP across the age period is associated with higher susceptibility to PAD (interaction odds ratio = 2.71; P = 1.82x10^-13; 95%-CI: 2.08-3.53). The data generated in this project provides a valuable resource for further exploration of mechanisms relevant to the genetic architecture of complex traits and all summary data has been made accessible to the research community.

A scaffold attachment factor PHM-2 regulates synaptic transmission through SLO-2 potassium channel in C. elegans

2026-03-19T14:00:00Z

by Longgang Niu, Karthika Murugasen, Shannon Hanggodo, Sakia Ferdousy, Lishuang Zhu, Bojun Chen

Scaffold attachment factor B (SAFB) proteins are evolutionarily conserved DNA/RNA binding proteins that are involved in multiple processes of gene expression. These proteins are broadly expressed with particular high expression observed in the nervous system. However, their physiological roles in neurons are largely unclear. Here we show that PHM-2, the sole SAFB ortholog in C. elegans, regulates synaptic transmission at the neuromuscular junctions through an effect on SLO-2 potassium channel. We found that phm-2 mutants suppress a sluggish phenotype of worms expressing a hyperactive SLO-2 channel, greatly reduces SLO-2-mediated neuronal whole-cell currents, and enhances neuromuscular synaptic transmission. In addition, we found that PHM-2 genetically interacts with another DNA/RNA binding protein, HRPU-2/hnRNP U, to control SLO-2 expression through a posttranscriptional mechanism. These results reveal a novel function of a SAFB protein in regulating neuronal activity, and may help understand the physiological roles of SAFB proteins in the nervous system of other species.

Plagl1 regulates the retinal progenitor cell to Müller glial cell transition

2026-03-18T14:00:00Z

by Yacine Touahri, Alissa Pak, Luke Ajay David, Joseph Hanna, Hedy Liu, Yucheng Xiao, Lauren Belfiore, Yaroslav Ilnytskyy, Edwin van Oosten, Nobuhiko Tachibana, Lata Adnani, Jiayi Zhao, Mary Hoffman, Rajiv Dixit, Dawn Zinyk, Cynthia J. Guidos, Volker Enzmann, Pengpeng Bi, Isabelle Aubert, Laurent Journot, Igor Kovalchuk, Yves Sauvé, Jeff Biernaskie, Chao Wang, Satoshi Okawa, Antonio del Sol, Carol Schuurmans

Müller glia arise from late-stage retinal progenitor cells (RPCs) as a distinct lineage that diverges from neurogenic trajectories. Here, we identify the maternally imprinted gene Plagl1 as a key transcriptional regulator of gliogenesis in the murine retina. Plagl1 is expressed during the RPC-to-glia transition and is dynamically regulated in Müller glia following injury. To define its developmental role, we analyzed Plagl1^⁺/⁻pat null mutant retinas at postnatal day 7 (P7), when central retinal gliogenesis is complete. In the absence of Plagl1, Sox9 ⁺ glial/precursor cells were displaced and proliferated ectopically, with structural dysmorphologies, reactive gliosis, and impaired visual processing persisting into later postnatal stages. Bulk RNA-seq and ATAC-seq revealed widespread reductions in chromatin accessibility and transcriptional dysregulation affecting epigenetic modifiers, translational machinery, fate-specifying transcription factors, cell cycle regulators, and signaling pathways. Single-cell pseudobulk analysis showed that Plagl1 loss disrupts chromatin, transcriptional, and translational programs specifically within Sox9 ⁺ cells, encompassing Müller glia and precursor populations, pinpointing these cells as the source of defects in Plagl1^⁺/⁻pat retinas. Notch signaling was elevated in Plagl1-deficient glia, and genetic activation at P14 displaced Sox9 ⁺ glial cells, without inducing proliferation. Similarly, conditional deletion of Plagl1 in postnatal Müller glia at P14 disrupted positioning and not cell cycle exit, confirming a cell-autonomous requirement for Müller glia positioning that is independent of proliferation control. Since these conditional manipulations could only be performed at P14 at the earliest, they reveal Plagl1’s later functions in postmitotic glia and complement, rather than mirror, the earlier P7 mixed RPC/glial null phenotype. Together these findings establish Plagl1 as a critical regulator of the late-stage RPC to Müller glia transition, acting through coordinated control of chromatin accessibility and gene expression programs to ensure timely cell cycle exit. This function aligns with Plagl1’s broader tumor suppressor role in stabilizing postmitotic, differentiated cell states across tissues.

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

2026-03-17T14:00:00Z

by Marie-Claire Harrison, David C. Rinker, Abigail L. LaBella, Dana A. Opulente, John F. Wolters, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas

Antifungal drug resistance is a major challenge in fungal infection management. Numerous genomic changes are known to contribute to acquired drug resistance in clinical isolates of specific pathogens, but whether they broadly explain natural resistance across entire lineages is unknown. We leveraged genomic, ecological, and phenotypic trait data from naturally sampled strains from nearly all known species in subphylum Saccharomycotina to examine the evolution of resistance to eight antifungal drugs. The phylogenetic distribution of drug resistance varied by drug; fluconazole resistance was widespread, while 5-fluorocytosine resistance was rare, except in Lipomycetales. A random forest algorithm trained on genomic data predicted drug-resistant yeasts with 54–75% accuracy. Fluconazole resistance was consistently predicted with the highest accuracy (75.2%). Furthermore, fluconazole resistance prediction accuracy was similar between models trained on genome-wide variation in the presence and number of InterPro protein annotations across Saccharomycotina (75.2%) and those trained on amino acid sequence alignment data of Erg11, a protein known to be involved in fluconazole resistance (74.3-74.9%). Interestingly, the top Erg11 residues for predicting fluconazole resistance across Saccharomycotina do not overlap with, are not spatially close to, and are less conserved than those previously linked to resistance in clinical isolates of Candida albicans. In silico deep mutational scanning of the C. albicans Erg11 protein reveals that amino acid variants implicated in clinical cases of resistance are almost universally destabilizing while variants in our most informative residues are energetically more neutral, explaining why the latter are much more common than the former in natural populations. Importantly, previous experimental analyses of C. albicans Erg11 have shown that amino acid variation in our most informative residues, despite having never been directly implicated in clinical cases, can directly contribute to resistance. Our results suggest that studies of natural resistance in yeast species never encountered in the clinic will yield a fuller understanding of antifungal drug resistance.

Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells

2026-03-17T14:00:00Z

by Marleen T. Aarts, Anna Nordin, Claudio Cantù, Antonius L. van Boxtel, Renée van Amerongen

Gene expression is controlled by complex transcriptional networks in which transcription factors and their cognate enhancer elements integrate developmental and environmental cues. The progesterone receptor (PR), a hormone-activated transcription factor, is essential for breast development and physiology, yet how it engages with the chromatin and lineage-specific cofactors remains unclear. Using an unbiased approach, we identify the epithelial transcription factor grainyhead-like 2 (GRHL2) as a key co-regulator of PR activity in hormone responsive breast cancer cells. We show that GRHL2 interacts with PR in a progesterone-independent manner. Upon progesterone stimulation, GRHL2 and PR are both recruited to distal enhancer elements of target genes. Furthermore, GRHL2- and PR-bound elements connect spatially through chromatin looping to regulate shared targets. These findings uncover a previously unrecognized mechanism by which GRHL2 and PR coordinate gene regulation through both chromatin binding and 3D genome architecture modification, positioning GRHL2 as a crucial modulator of steroid hormone receptor function.

Functional interrogation of candidate cis-regulatory elements at the LDLR locus

2026-03-17T14:00:00Z

by Kyle Leix, Candilianne Serrano-Zayas, Hitarthi S. Vyas, Sarah E. Graham, Brian T. Emmer

Regulation of LDLR gene expression plays an important role in the development of atherosclerotic diseases including heart attack and stroke. Although LDLR regulation by sterol response elements has been well characterized, the functional significance of other noncoding regions at the LDLR locus remains poorly defined. In this study, we developed and applied a high throughput CRISPR screen to test the functional importance of candidate LDLR cis-regulatory elements (CREs) in their native genomic context. In total, we found 25 discrete regions to exhibit a significant impact on LDLR expression. For one of these regions with particularly strong activity in the first intron, we validated the presence of an enhancer by confirming that its disruption reduced endogenous LDLR expression while its insertion upstream of a minimal promoter augmented reporter gene expression. We then applied a massively parallel reporter assay to fine map enhancer activity within this region to a 129 bp interval that is highly conserved among vertebrates, exhibits biochemical hallmarks of enhancer activity, is enriched for transcription factor binding motifs, and contains a common genetic variant (rs57217136) that has been associated with human LDL cholesterol levels by genome-wide association studies. Overall, these findings demonstrate the power of CRISPR screening to interrogate candidate CREs and clarify the functional landscape of noncoding sequences at the LDLR locus.

Simplifying causal gene identification in GWAS loci

2026-03-17T14:00:00Z

by Marijn Schipper, Jacob Ulirsch, Danielle Posthuma, Stephan Ripke, Karl Heilbron

Genome-wide association studies (GWAS) help to identify disease-linked genetic variants, but pinpointing the most likely causal genes in GWAS loci remains challenging. Existing GWAS gene prioritization tools are powerful but often use complex black box models trained on datasets containing biases. Here, we used a data-driven approach to construct a truth set of causal genes in 200 GWAS loci. We found that a simple logistic regression model performed as well as a more complex XGBoost model, and that many commonly-used gene prioritization features could be removed without meaningfully affecting performance (e.g., expression quantitative trait locus colocalization and Mendelian randomization). We present CALDERA, a gene prioritization tool that uses a logistic regression model and uses just four input features. In independent benchmarking datasets of resolved GWAS loci, CALDERA achieved state-of-the-art performance in comparison with other methods (FLAMES, L2G, and cS2G). CALDERA outputs causal gene probabilities for all genes in a given GWAS locus and we show that these probabilities are well-calibrated. Applying CALDERA to 93 UK Biobank traits, we predicted 11,956 putative causal genes, potentially resolving up to 52% of loci. Overall, CALDERA provides a powerful solution for prioritizing potentially causal genes in GWAS loci that minimizes the data processing required to construct input features and generates an easily-interpretable output score.

Estimating the distribution of fitness effects of loss of heterozygosity (LOH) events using an engineered library of Saccharomyces cerevisiae

2026-03-16T14:00:00Z

by Yi-Hong Ke, Michelle Orozco-Quime, Josh Bauman, Tamilie Carvalho, Grant A. Landry, Shuhua Ge, Anuj Kumar, Timothy Y. James

Loss of heterozygosity (LOH) is a large contributor of genetic variation in natural populations or lab-evolved asexual diploids. However, its contribution to adaptation is uncertain, because the full spectrum of its fitness effects remains largely uncharacterized. To systematically investigate the distribution of fitness effects (DFE) of LOH, we engineered a diverse, barcoded library of heterozygous diploid Saccharomyces cerevisiae strains, each containing randomly induced LOH events. By employing competitive fitness assays and barcode sequencing (Bar-seq) across seven distinct environments, including various stressors from chemicals, temperature, and an in vivo host model, we quantified the fitness consequences of LOH events. Our results reveal that the DFE of LOH is predominantly neutral to deleterious, with a general trend of decreasing fitness correlated with larger cumulative lengths of LOH tracts. However, the fitness effects were variable and the fitness landscape was highly environment-dependent. While beneficial LOH events were rare and of small effect in standard rich media, they were common and conferred substantial fitness gains in novel or stressful conditions. A key finding was the prevalence of antagonistic pleiotropy where over 75% of strains exhibited fitness trade-offs, gaining an advantage in one environment at the cost of fitness in others. The magnitude of these trade-offs was also found to correlate with longer LOH tracts. Overall, this work demonstrates that LOH plays a dual role in evolution. While it often imposes a genetic burden, it also provides a powerful mechanism for rapid, environment-specific adaptation, driving specialization by trading general robustness for niche-specific advantages.

Evolutionary turnover of key amino acids explains conservation of function without conservation of sequence in transcriptional activation domains

2026-03-16T14:00:00Z

by Claire J. LeBlanc, Jordan Stefani, Melvin Soriano, Angelica W. Y. Lam, Marissa A. Zintel, Sanjana R. Kotha, Emily P. Chase, Giovani Pimentel-Solorio, Aditya Vunnum, Gean Hu, Katherine L. Flug, Aaron Fultineer, Niklas Hummel, Max V. Staller

In folded protein domains, protein function is frequently more conserved than amino acid sequence because highly diverged sequences can fold into equivalent 3D structures with identical function. During evolution, intrinsically disordered protein regions (IDRs) often experience rapid amino acid sequence divergence, but because they do not fold into stable 3D structures, it remains largely unknown when and how function is conserved. As a model system for studying the evolution of IDRs, we examined transcriptional activation domains, the regions of transcription factors that bind to coactivator complexes. We systematically identified activation domains on 502 homologs of the transcriptional activator Gcn4 spanning 600 MY of fungal evolution in the Ascomycota. We found that the central activation domain shows strong conservation of function without conservation of sequence. This conservation of function without conservation of sequence arises from evolutionary turnover (gain and loss) at two length scales. Within the central activation domain, we see turnover of acidic and aromatic residues, but primarily loss of short linear motifs. In the full-length transcription factor, we see turnover of entire activation domains. Stabilizing selection and evolutionary turnover at multiple length scales are likely a general mechanism for conservation of function without conservation of sequence in IDRs.

Topological stratification of continuous genetic variation in large biobanks

2026-03-16T14:00:00Z

by Alex Diaz-Papkovich, Shadi Zabad, Hannah Snell, Chief Ben-Eghan, Luke Anderson-Trocmé, Georgette Femerling, Vikram Nathan, Jenisha Patel, Simon Gravel

Biobanks now contain genetic data from millions of individuals. Dimensionality reduction, visualization and clustering are standard when exploring data at these scales; while efficient and tractable methods exist for the first two, clustering remains challenging because of the many ways in which demography and sampling can affect structure. In practice, clustering is commonly performed by drawing shapes around dimensionally reduced data or assuming populations have “type” genomes or allele frequencies that represent a population. We propose to use dimensionality reduction with UMAP followed by clustering with HDBSCAN to identify sets of points forming relatively dense subsets in genotype space. The approach is fast, easy to implement, and integrates with existing pipelines. When applied to simulated data or data from three biobanks, the approach identifies groups of individuals enriched for shared features correlated with ancestry, including country of birth, ethnicity, and sampling location, without requiring strong assumptions about the number or size of clusters, or the sources of population structure. Because it does not rely on proximity to a specific point in genetic space, this topological approach can form clusters that continuously span long distances in genetic space. This can help distinguish admixed populations, which can exhibit wide ancestry variation within populations and overlap of ancestry proportions across populations. Such clusters can highlight and account for interpretable sources of genetic, demographic, or sampling heterogeneity in a dataset that would otherwise have required a range of specialized techniques. We illustrate how topological genetic strata can further help us understand structure within biobanks, evaluate distributions of genotypic and phenotypic data, examine polygenic score transferability, identify potential influential alleles, and perform quality control.

Nucleosome positioning shapes cryptic antisense transcription

2026-03-13T14:00:00Z

by Jian Yi Kok, Zachary H. Harvey, Elin Axelsson, Frédéric Berger

Maintaining transcriptional fidelity is essential for precise gene regulation and genome stability. Despite this, cryptic antisense transcription, occurring opposite to canonical coding sequences, is a pervasive feature across all domains of life. How such potentially harmful cryptic sites are regulated remains incompletely understood. Here, we show that nucleosome arrays within gene bodies play a key role in suppressing cryptic transcription. Using the fission yeast Schizosaccharomyces pombe as a model, we demonstrate that the CHD-family chromatin remodeler Hrp3 coordinates with the transcription elongation machinery, via the transcriptional regulator Prf1/RTF1, to position nucleosomes at sites of cryptic transcription initiation within gene bodies. In the absence of Hrp3, AT-rich sequences within gene bodies lose nucleosome occupancy, exposing promoter-like sequences that drive cryptic initiation. While cryptic transcription is generally detrimental, we identify a subset of antisense transcripts that encode critical meiotic genes, suggesting that cryptic transcription can also serve as a source of regulatory innovation. These findings define an elongation‑coupled chromatin pathway that preserves transcriptional fidelity and reveal how nucleosome remodeling shapes antisense transcription, cellular homeostasis, and adaptive potential.

COG5 deficiency disrupts cellular copper homeostasis and underlies the impaired mitochondrial OXPHOS function

2026-03-13T14:00:00Z

by Yuwei Zhou, Keyi Li, Ruowei Zhu, Xue Ma, Xinfei Ye, Mengqing Mao, Ding Li, Xiaofei Zeng, Zhehui Chen, Jing Wu, Liqin Jin, Xiaohua Tang, Yanling Yang, Jianxin Lyu, Xiaoting Lou

COG5, a subunit of the conserved oligomeric Golgi (COG) complex, plays a critical role in retrograde trafficking within the Golgi apparatus. Dysfunction of COG5 is associated with various human disorders, yet the underlying pathogenic mechanisms remain poorly understood. To investigate the mechanisms, we conducted proteomic analyses using COG5-deficient and rescue cell models, which revealed a potential link between COG5 dysfunction and mitochondrial oxidative phosphorylation (OXPHOS) deficiency. Using COG5-deficient cell models and patient-derived cells harboring COG5 variants, we biochemically validated the involvement of COG5 in mitochondrial OXPHOS, particularly in the regulation of complex I content. These models also exhibited elevated cellular copper levels. Notably, the significant reduction in OXPHOS complexes could be rescued by either restoring COG5 expression or administering a copper chelator. We further demonstrated that excessive cellular copper disrupts the function of mitochondrial iron-sulfur clusters, potentially leading to complex I assembly defects. Additionally, we identified a patient with biallelic COG5 variants presenting with a distinct subtype of mitochondrial disease (Leigh syndrome), a phenotype not previously associated with COG5-related disorders. These findings provide novel mechanistic insights into the role of COG5, extending beyond its established function in Golgi-mediated glycosylation modifications. Our results underscore the importance of COG5 in mitochondrial function through a copper-dependent pathway, offering new perspectives on its contribution to cellular homeostasis and disease pathogenesis.

Wanted: A population genetic theory of biological noise regulation

2026-03-13T14:00:00Z

by Daniel M. Weinreich, Tom Sgouros, Yevgeniy Raynes, Hlib Burtsev, Edison Chang, Sanyu Rajakumar, Ignacio G. Bravo, Csenge Petak

Classical population genetics provides a robust, quantitative framework for modeling how natural selection acts on alleles that influence phenotypes with invariant fitness consequences for their carriers, such as running speed or drug resistance. By contrast, modifier theory considers the evolution of alleles that influence population genetic parameter values in their carriers, such as mutation or recombination rates. This is a more complicated problem. First, the fitness effects of modifier alleles reflect independently realized stochastic phenotype perturbations they induce in their carriers. And second, the association between modifier alleles and their induced phenotypes can decay over generations. Consequently, general results in modifier theory have been few. Here, we propose recasting modifier theory as exploring the evolution of alleles that influence the amount of stochasticity in inheritance, be it genetic, epigenetic, cytoplasmic or somatic transmission. We then present a toy model that predicts the existence of a selectively optimal amount of such “reproductive noise,” which depends on the rate of environment change, the timescale of association between noise allele and induced phenotype, and population size. Next, we suggest that the same framework can be applied to the evolution of alleles that influence “developmental noise,” i.e., the amount of stochastic phenotypic variation among genetically identical organisms reared in identical environments. This theoretical connection is timely, because high throughput assays are now demonstrating widespread heritability in the amount of developmental noise. Our approach also resolves the long-standing teleological criticism of the hypothesis that evolvability can evolve by natural selection. Taken together, this work demonstrates the opportunities for a robust, quantitative population genetic theory of alleles that influence the amount of biological noise.