PLOS Genetics

Sleep-like quiescence is an evolutionarily conserved state essential for physiological homeostasis; however, its dysregulation can lead to sleep disorders such as narcolepsy, which can be caused by abnormal neuropeptide signaling. In Caenorhabditis elegans, the G-protein-coupled receptor NPR-14 belongs to the orexin/allatotropin receptor family and has been proposed as a homolog of mammalian orexin receptors. Using npr-14 loss-of-function (lf) mutants, we demonstrate that NPR-14 promotes arousal and inhibits sleep-like quiescence. npr-14(lf) mutants exhibit prolonged quiescence, reduced locomotion, impaired sensory responses, and metabolic defects including elevated fat accumulation and decreased feeding and egg-laying. NPR-14 is expressed in ASH and ASI sensory neurons and in GABAergic DD, VD, and VC motor neurons, positioning it to modulate both sensory-motor integration and motor output directly. Genetic epistasis analysis revealed that NPR-14 functions upstream of EGL-4/protein kinase G (PKG): egl-4 loss-of-function suppressed the enhanced quiescence of npr-14 mutants, while egl-4 gain-of-function phenotypes were not enhanced by loss of npr-14. Caffeine treatment partially suppressed npr-14 mutant quiescence, suggesting convergence with adenosine-sensitive arousal pathways. These findings establish NPR-14 as a wake-promoting GPCR that inhibits EGL-4/PKG signalling to regulate quiescence and arousal. The NPR-14-EGL-4 axis suggests functional parallels to arousal regulation in other systems.

Meiotic recombination in many vertebrate lineages is directed to genomic regions by the DNA-binding protein PRDM9. To date, PRDM9 research has focused primarily on mammals, and its role in recombination localization has only recently been established in salmonids. PRDM9 binding specificity is determined by a tandemly repeated zinc-finger array that exhibits extensive allelic diversity within and between species. However, the extent to which PRDM9 variation shapes recombination landscapes in salmonids remains poorly understood. Here, we performed large-scale genotyping of PRDM9 in an aquaculture population of Atlantic salmon (Salmo salar) using long-read sequencing. By integrating PRDM9 genotypes with pedigree information and genome-wide recombination data, we generated PRDM9-specific linkage maps and sets of inferred crossover events. We show that the presence of specific PRDM9 alleles is associated with differences in recombination localization and identify patterns consistent with dominance interactions between alleles. Using population-averaged recombination rate estimates, we further link a previously described sequence motif enriched in European recombination hotspots to the presence of a common PRDM9 zinc-finger array allele (RPT6a). Together, our results demonstrate functional differences between PRDM9 alleles which contribute to divergence in recombination landscapes in Atlantic salmon, paralleling patterns observed in mammals. The broad geographic distribution of Atlantic salmon, combined with extensive pedigree data generated through aquaculture, highlights its potential as a powerful model for studying PRDM9 function and evolution beyond mammals.

Development requires the complex coordination of gene regulatory networks that must remain robust in the face of variable environmental cues. In Caenorhabditis elegans, the nuclear hormone receptor DAF-12 integrates metabolic cues and hormonal signals to control important life history decisions, including development, reproduction, and the rate of aging. Here, we tested the involvement of DAF-12 germline-to-soma signaling in two transgenerational longevity mutants, wdr-5 and jhdm-1. We have previously shown that both mutant populations gradually accumulate repressive H3K9me2 over multiple generations, which is necessary and sufficient for their lifespan extension. We find that daf-12 activity was required for the epigenetic establishment of longevity in both mutant populations, but was only necessary for maintaining longevity in a wdr-5 mutant background. Because DAF-12 also functions as a key regulator of dauer diapause, an alternative developmental stage triggered by environmental stress, we also tested the genetic relationship at earlier points in development. Surprisingly, mutations in either wdr-5 or jhdm-1 rescued the dauer defect of daf-12 mutants, and we found a synergistic effect on unchallenged larval development in wdr-5; daf-12 double mutants. These differing epistatic relationships indicate that, although the acquisition of longevity in both wdr-5 and jhdm-1 mutant populations shares a common mechanism, the impacts on somatic phenotypes (including lifespan extension) proceed via distinct pathways. Together, these results show how heritable chromatin states can co-opt existing developmental programs to influence key developmental decisions. ARTICLE SUMMARYHow do early experiences influence development and aging? In this study, we explore this question by testing the genetic interaction between the DAF-12 signaling pathway and heritable chromatin landscapes. Previously, we showed that two C. elegans mutants can accumulate heterochromatin over multiple generations to acquire longevity. We find that DAF-12 is required to establish this epigenetic trait but is not necessary to maintain it. We also find that chromatin landscapes bypass DAF-12s role earlier in development, including during the decision to enter dauer diapause. Overall, this study shows how chromatin states co-opt existing developmental programs to influence key life history decisions.

Transforming Growth Factor beta (TGF-{beta}) signaling helps orchestrate multiple organismal traits in animals by regulating target gene expression. However, how this pathway's transcriptional regulators, called Smads, control target gene expression to generate different traits is not well understood. Using the C. elegans system, we identified the master chromatin remodeler B-lymphocyte maturation protein-1 (BLMP-1, a Kruppel-like zinc finger protein homologous to human PRDM1/BLIMP1) as a partner in Smad-mediated gene expression regulation. Previous research showed BLMP-1/PRDM1 controls organismal traits that the C. elegans TGF-{beta} superfamily member DBL-1 also affects. We identified genetic interactions between the DBL-1 pathway and blmp-1 for these traits. While BLMP-1/PRDM1 and DBL-1 pathway signaling had an additive effect on body size, blmp-1 mutants were epistatic to DBL-1 pathway mutants for male tail development, hermaphrodite gonad development, brood size, lipid levels, movement, and survival traits. We showed DBL-1 signaling transcriptionally regulates blmp-1 expression. We also identified a physical interaction between the DBL-1 pathway Smads and BLMP-1/PRDM1 using yeast-two hybrid analyses. Using bioinformatics and qPCR analysis, we showed that Smads and BLMP-1/PRDM1 regulate expression of common downstream target genes. Our work identifies novel interactions between the DBL-1 signaling pathway and BLMP-1, two conserved major transcriptional regulators, that ultimately influence a spectrum of organismal traits. We propose a model whereby BLMP-1/PRDM1 regulates DBL-1 signaling by acting as a gatekeeper, remodeling the chromatin architecture to control the access of the Smad complex to target genes. Together, our results reveal a direct link between a TGF-{beta} signaling pathway and a PRDM1-family master transcription regulator and offer clues to how they interact to control larval and adult traits. Our work suggests a conserved mechanism of transcriptional control of developmental traits by the Smad-PRDM axis.

Adipose tissue is a key metabolic organ for carbohydrate and lipid metabolism. Multiple nutrient sensing pathways and metabolic enzymes operate in adipocytes to control energy production and lipid mobilization in response to physiological conditions. Important regulators of glycolytic and lipid metabolism in many species are members of the estrogen-related receptor (ERR) family of nuclear receptors. We previously showed that ERR is required for transcriptional regulation of glycolytic and pentose phosphate pathway enzymes in adult Drosophila females, consistent with what is observed in ERR mutant males and larvae. However, the cell-type specific targets of ERR in adipose and other tissues have not been fully elucidated. Here, using a modified targeted DamID approach (NanoDam), we identified ERR occupancy specifically in adult adipocytes at the loci that encode genes involved in glycolysis, the pentose phosphate pathway, and fatty acid metabolism. Overall, our results predict that ERR centrally functions in adipose tissue to regulate multiple metabolic pathways.

Restricting the localization of centromere-specific histone H3 variant Cse4 (CENP-A in humans) to centromeric chromatin is essential for chromosome segregation. Mislocalization of overexpressed Cse4/CENP-A to non-centromeric regions contributes to chromosomal instability (CIN) in model organisms and human cells. CIN is an important hallmark of many cancers and hence defining mechanisms that prevent mislocalization of Cse4 is clinically significant. Here we report a role for YRA2 (Yeast RNA Annealing Protein 2) in ubiquitin mediated proteolysis of Cse4 to prevent its mislocalization for chromosomal stability. YRA2 was identified in a genome-wide screen for gene deletions that exhibit synthetic dosage lethality (SDL) upon overexpression of CSE4 (GALCSE4). We determined that yra2{Delta} strains exhibit increased Cse4 stability, enriched Cse4 chromatin association, reduced Cse4 ubiquitination, Cse4 mislocalization, and CIN. Defects in interaction of E3 ubiquitin ligase Psh1 with Cse4 contributes to stability of Cse4 in yra2{Delta} strains. Consistent with these results, overexpression of PSH1 suppresses GALCSE4 SDL in yra2{Delta} strain. We determined that Yra2 mediated proteolysis of Cse4 is independent of its RNA related functions as strain deleted for the C-terminal ChTOP domain of Yra2 with an intact N-terminal RNA binding domain exhibits GALCSE4 SDL and defects in Cse4 proteolysis. Furthermore, poly(A)+ RNA export mutants in YRA1 (yra1-2) and MEX67 (mex67-5), that interact with Yra2, do not exhibit GALCSE4 SDL and defects in RNA export are not observed in yra2{Delta} cells. In summary, we have defined a key role for Yra2 in preventing mislocalization of Cse4 by facilitating its proteolysis to preserve chromosomal stability. Article summaryAccurate segregation of chromosomes during cell division is essential because segregation errors are linked to cancer and developmental disorders. We investigated how cells prevent mislocalization of centromere-specific histone H3 variant Cse4, which is essential for faithful chromosome segregation. We found that the yeast RNA annealing protein Yra2 prevents Cse4 mislocalization by promoting Psh1 mediated ubiquitination and degradation of Cse4. Cells lacking Yra2 showed increased stability of Cse4, enhanced chromatin enrichment with mislocalization to non-centromeric regions and CIN. These defects were suppressed by induction of Psh1. Our findings reveal a novel role for Yra2 in regulating Cse4 levels for chromosomal stability.

Cilia and flagella perform essential physiological functions in eukaryotes, and defects in these organelles cause several human diseases, including cancer and ciliopathies. The architecture of cilia is highly organized. The ciliary compartment is separated from the cytoplasm by the transition zone (TZ). The severity of ciliopathies linked to TZ assembly defects highlights the TZ's critical role. Although several core conserved complexes are involved in TZ assembly, variations in TZ composition are associated with structurally and functionally diverse cilia. Here, we identify Cfap410a as a novel component of the ciliary TZ in the two Drosophila ciliated tissues, male germ cells and sensory neurons. Cfap410a is one of the two Drosophila paralogs (Cfap410a and Cfap410b) of human CFAP410, whose mutations are associated with axial spondylo-metaphyseal dysplasia, retinitis pigmentosa and amyotrophic lateral sclerosis. We show here that Cfap410a is a proximity partner of Cby and that they act cooperatively in the hierarchy of the TZ assembly program by bridging the CEP290 and MKS transition zone modules. Simultaneous loss of Cfap410a and Cby halts ciliary growth by disrupting TZ formation in multiple types of Drosophila ciliated cells, each of which exhibiting varying dependence on these two proteins. Interestingly, the function of Cfap410a and Cfap410b are not functionally redundant, indicating that the two proteins have evolved towards specific functions. In summary, our results propose a novel role for CFAP410a at the TZ and provide an explanation for how deregulation of conserved TZ components could lead to tissue-specific ciliopathies.

The nematode trapping fungus Arthrobotrys oligospora transitions from saprophytic growth to a predatory lifestyle by forming adhesive traps in response to nutrient limitation and nematode derived cues. How nutrient availability integrates with prey sensing to control trap formation remains unclear. The presence of glucose can suppress trap formation and we found that Cre1, a conserved transcription factor that regulates the carbon catabolite repression pathway in fungi is essential for trap formation. Comparative transcriptomics and functional studies identified SMT1, which encodes a sphingolipid C9 methyltransferase, as a Cre1-dependent target that is sufficient to restore trap formation defect in the cre1 mutant. Smt1 contributes to the formation of sterol-enriched membrane domain at the tip of a growing trap hyphae and thus affects trap morphogenesis. We further discovered that the expression of SMT1 depends on both Cre1 and another transcription factor Ste12 that acts downstream of the pheromone response MAPK pathway critical for prey-sensing. These findings reveal functional crosstalk between Cre1 and Ste12 where both transcription factors are required for the expression of SMT1 and demonstrate that a predatory fungus integrates nutrient and prey-derived signals to regulate predatory lifestyle switching.

During meiosis, homologous chromosomes exchange segments in a process termed crossover recombination. Crossovers are non-randomly distributed along chromosomes, and in many eukaryotes, including plants, meiotic chromosome architecture and chromatin states control recombination landscapes. Whether these two components genetically interact has remained underexplored. To address this question, we combined Arabidopsis thaliana, hereinafter, Arabidopsis, mutations that disrupt meiotic chromosome architecture by depleting the meiotic chromosome axis (asy1/+) or synaptonemal complex (zyp1) with mutations in the DNA methyltransferases MET1 and CMT3 (met1/+ and cmt3), which lead to a loss of cytosine DNA methylation, the hallmark of heterochromatin, in the CG and CHG contexts, respectively. We quantified crossovers in telomere- and centromere-proximal chromosome intervals using fluorescent seed-based reporters and found that DNA methylation and meiotic chromosome architecture proteins can have distinct or cooperative roles in crossover control depending on the chromosome interval and DNA methylation context. We demonstrate that axis and synaptonemal complex act together with CG DNA methylation to control crossovers, while CHG DNA hypomethylation cannot fully restore a loss of centromere-proximal recombination caused by the depletion of ASY1 or ZYP1. Remarkably, increasing ASY1 dosage promotes crossovers within the pericentromere, representing a new non-epigenetic route to upregulate pericentromeric recombination. Author summaryMeiotic crossovers reshuffle genetic variation and are essential for evolution and crop breeding. However, crossovers occur unevenly along chromosomes, limiting genetic exchange in pericentromeric regions. Here, we investigate the genetic interactions between cytosine DNA methylation and meiotic chromosome architecture and show that, although heterochromatin depletion can permit pericentromeric crossovers, the structural integrity of the meiotic chromosome axis and the synaptonemal complex are essential to drive recombination. Remarkably, modulating the dosage of a chromosome axis protein provides a non-epigenetic strategy to increase pericentromeric crossovers, revealing new opportunities to reshape recombination landscapes in model and crop plants.

Insect pigmentation is an ecologically critical trait influencing many physiological processes. In Drosophila melanogaster, abdominal pigmentation is sexually dimorphic: males have fully pigmented posterior segments, while females exhibit a posterior melanin stripe. Pigmentation relies on the expression of pigmentation genes that encode enzymes involved in pigment synthesis. These genes are tightly regulated during pupal and young adult stages. To expand the gene regulatory network of pigmentation genes, we conducted an RNAi screen using the yellow-Gal4 driver, expressed during the pupal stage in abdominal epidermis. One of the candidates from this screen, Kdm5, encodes a histone demethylase erasing the H3K4me3 histone mark catalyzed by the histone methyl-transferase Trithorax (Trx). We show that Kdm5 down-regulation reduces abdominal pigmentation, mimicking trx down-regulation. Kdm5 activates melanin production through regulation of the pigmentation gene tan. Transcriptomic analyses reveal that Kdm5 and Trx share many targets in pupal abdominal epidermis, including piRNA pathway components such as piwi and aubergine. These piRNA components, originally associated with transposon silencing in the germline, also function in some somatic tissues such as the nervous system, the fat body or the gut. We demonstrate that Piwi and Aubergine participate in female abdominal pigmentation establishment, without evident piRNA production. We also show that Kdm5 and Piwi act not only in pupal abdominal epidermis but also in pupal fat body. This study therefore expands the regulatory network of pigmentation genes. It identifies a new somatic function for Kdm5 and Piwi and reveals a role for pupal fat body in female abdominal pigmentation regulation.

Retrotransposons are mobile genetic elements that can impair genome integrity, and their insertions and dysregulation have been implicated in various diseases. However, growing evidence suggests that retrotransposons may play important physiological roles. At the Drosophila larval neuromuscular junction (NMJ), the ViSyToR (Viral Synaptic Transfer of RNA) pathway requires the active retrotransposon copia as a key negative regulator of synaptogenesis. Here, we identify a long non-coding RNA, Statera (Stae), as a regulator of copia, initially discovered through its physical association with the Copia protein. Stae is highly expressed in the central nervous system and body wall muscles of Drosophila larvae. CRISPR knockout or RNAi knockdown of Stae leads to a general decrease of bouton number at the NMJ, indicating its role in promoting synaptogenesis. Furthermore, copia is highly upregulated in Stae mutants, suggesting that Stae functions to repress copia. Mechanistically, Stae reduces copia RNA stability and limits copia DNA copy number. Additional knockdown of copia in motor neuron-specific Stae RNAi animals rescues the abnormal NMJ morphology. Together, our findings reveal an unexpected role for a long non-coding RNA in promoting synaptogenesis by repressing a retrotransposon.

Epigenetic information is required for the maintenance of gene expression states through cell division. Some epigenetic information can also persist through generations, raising the possibility that epigenetic differences may arise in populations and contribute to evolutionary processes such as drift and natural selection. Evaluating this requires characterising the properties of such epimutations, so that their rate, stability and genome-wide distribution can be assessed. Recent experiments in many organisms have demonstrated that epimutations occur, but have limited stability relative to DNA sequence mutations. However, the extent to which epimutations contribute to evolution is still unclear, in part because it is not clear whether epimutations respond dynamically to environmental conditions. Here, we use the fission yeast S. pombe, in which evolutionarily relevant epimutations have been observed, but not yet systematically characterised, to test whether a physiologically relevant stress, ethanol exposure, leads to changes in the properties of epimutations. Using laboratory evolution experiments with repeated population bottlenecks to minimise selection, we show that epimutations associated with changes in small interfering (si)RNAs occur at a greater rate in ethanol. Ethanol-induced epimutations are enriched at transposable element loci and correlate with changes in transposon expression. Ethanol exposure also increases gene expression noise genome-wide and variability in growth rate; importantly, both these increases are suppressed in mutants lacking siRNAs. Together, these results demonstrate that stress can alter the generation of heritable epigenetic information, and suggest that siRNAs may have a role in promoting phenotypic variability in response to environmental stress.

Cohesin is a large multisubunit protein complex that plays essential roles in cell proliferation, genome organisation, and gene regulation in metazoans. Germline mutations in cohesin subunits or regulators cause a group of human developmental disorders collectively known as cohesinopathies. Increasing evidence indicates that individual cohesin subunits can confer distinct molecular functions to the complex; for example, STAG1 and STAG2 have both overlapping and non-overlapping roles in genome organisation. The zebrafish tailbud provides an excellent developmental model for investigating the coordination of cell proliferation and differentiation, processes in which cohesin has crucial functions. We previously demonstrated that loss of Stag2 disrupts Wnt signalling and mesoderm patterning in the zebrafish tailbud. Here, we show that, unlike mammals, zebrafish can tolerate complete loss of Stag1 from embryogenesis through to adulthood. In contrast to Stag2 deficiency, loss of Stag1 impairs cell cycle progression, activates p53 signalling, and induces a metabolic shift towards catabolism. BMP signalling is reduced in Stag1-deficient embryos and is accompanied by expansion of BMP antagonist chordin expression. Stag1 loss also alters chromatin accessibility at the chordin locus and affects accessibility at chromatin domain boundaries. We propose that modulation of growth and signalling pathways compensates for the absence of Stag1, allowing embryonic development to proceed correctly. Together, these findings reveal distinct contributions of Stag1 and Stag2 to cell-cycle regulation, chromatin architecture, and developmental signalling during vertebrate embryogenesis.

Huntingtons disease is a severe neurodegenerative condition arising from an abnormal CAG repeat expansion in the HTT gene, which leads to the production of a mutant Huntingtin protein carrying an extended polyglutamine stretch. Although the field has largely centred on the toxic effects gained by this mutant protein, growing evidence points to the loss of normal wild-type Huntingtin function as an additional contributor to disease progression. Despite this, the cell-intrinsic roles of wild-type Huntingtin in neuronal biology remain poorly defined, in part because disentangling its specific contributions from broader network-level effects has proven technically challenging. To address this knowledge gap, we took advantage of the Drosophila huntingtin homolog (htt) and selectively manipulated its expression in the small lateral ventral neurons (sLNvs), a discrete cluster of just eight circadian pacemaker neurons that govern behavioral rhythmicity and sleep. Through targeted genetic knock-down, we show that reducing htt levels in sLNvs weakens the robustness of free-running circadian rhythms and substantially increases sleep in female flies. These behavioral changes are not rooted in developmental abnormalities, as restricting htt knock-down to adult flies reproduces the sleep phenotype across both beam-crossing and video-based locomotion assays. At the cellular level, htt loss disrupts dense core vesicle trafficking along sLNv axons, altering the fraction of motile vesicles and their velocity, and abolishing the time-of-day-dependent fluctuations in vesicle dynamics observed in these neurons. Complementary electrophysiological recordings using whole-cell patch-clamp further reveal that htt knock-down lowers action potential firing rates without perturbing resting membrane potential. Together, these results identify huntingtin as a cell-autonomous regulator of neuropeptide trafficking, neuronal excitability and circadian output. Beyond advancing our understanding of wild-type huntingtin physiology, this work carries direct relevance for HD therapeutic strategies, particularly those involving huntingtin-lowering approaches, by highlighting functions that may be unintentionally compromised.

Vacuolar ATPases (V-ATPases) are highly conserved multi-subunit proton pumps that drive the acidification of intracellular vesicles, especially endosomes and lysosomes. By regulating progressive acidification of the endolysosomal pathway, V-ATPase activity impacts signaling transduction pathways both positively (e.g., internalization and activation of receptor-ligand complexes in endosomes) and negatively (e.g., degradation of pathway mediators in lysosomes). While the role of V-ATPases in human neurodegenerative diseases and cancer has been extensively studied, the requirement for these proteins in intestinal restitution remains poorly understood. Here, we use Drosophila to study the role of V-ATPases in regulating intestinal-injury and repair driven by excessive oxidative stress. We find that RNAi driven depletion of multiple subunits of the V-ATPase complex suppressed oxidative stress-induced lethality. By contrast, depletion of the main lysosomal catabolic enzyme in Drosophila (Cathepsin-D) had no effect. On a cellular level, these effects map to absorptive enterocytes (ECs) of the Drosophila intestine. Molecular analysis of intestines following injury by oxidative stress compared to uninjured controls reveals increased cell death, increased JNK-pathway activity, and increased IMD/NF-{kappa}B pathway signaling reporter expression compared to uninjured controls. Depletion of Vha44 (subunit C of the V1 complex) was sufficient to suppress the increased cell death, JNK pathway, and IMD/NF-{kappa}B pathway markers induced by oxidative stress in the intestine. Furthermore, overexpression of the MAP3K TAK1 enhanced death, JNK pathway and IMD/NF-{kappa}B pathway activation in a Vha44 dependent manner. These findings suggest that inhibition of V-ATPase activity can protect against intestinal injury caused by excessive oxidative stress. On a molecular level, we find that attenuation of endolysosomal acidification dampens pro-apoptotic JNK and IMD/NF-{kappa}B pathways, highlighting endosomal acidification as a potential amplifier of excessive oxidative stress.

Many neurological diseases are caused by mutations in broadly-expressed genes, but the basis for their neuron-specific manifestation is unclear. In Spinal Muscular Atrophy (SMA), loss of the ubiquitously-expressed spliceosome assembly factor SMN1 causes selective degeneration of motor neurons, leading to progressive neuromuscular decline. We explored the mechanisms of this cell-specific vulnerability using SMA models in the nematode C. elegans, which likewise exhibit progressive neuromuscular defects upon loss of smn-1. Surprisingly, our results show that the intestine - not neurons or muscle - is the selectively-vulnerable tissue causing smn-1 phenotypes. RNA-Seq reveals that loss of intestinal smn-1 causes specific global splicing defects, accompanied by robust transcriptional activation of the Intracellular Pathogen Response (IPR), a stress pathway enriched for ubiquitin-proteostasis genes. Consistent with this, smn-1 mutants exhibit elevated levels of proteasome activity. Pharmacological proteasome inhibition rescues many of the smn-1 mutant defects, as does deletion of specific components of the IPR pathway. These results reveal how the ubiquitously-expressed SMN-1 protein is required in a single tissue to avoid degenerative defects caused by hyperactive proteasome activity, contributing to our understanding of how mutations in ubiquitously-expressed genes can cause highly cell-specific pathologies. SIGNIFICANCE STATEMENTMany ubiquitously expressed genes cause highly selective neurodegenerative diseases, such as Huntingtons disease and Amyotrophic Lateral Sclerosis. The basis for this cell-specific vulnerability remains unclear. We address this question for smn-1 in C. elegans. We show that smn-1 is indeed required in a cell-specific manner, but unexpectedly not in neurons, but rather in the intestine. Both survival defects and behavioral phenotypes originate from intestinal loss of smn-1. We show that these defects are caused by hyperactive protein degradation and immune responses, and that mutant defects can be resolved by reducing these proteostasis and immune pathways using genetics or pharmacology. These results shed light on how a single tissue/cell can dictate the effects of a systemic genetic disease.

While ultra-rare missense variants in UMOD cause highly penetrant autosomal dominant tubulointerstitial kidney disease, a more frequent UMOD T62P variant conveys intermediate risk with variable penetrance. To determine whether age or polygenic risk contributes to the variable penetrance of T62P, we combined genotype and phenotype data from 882,306 individuals across the UK Biobank (discovery cohort) and the All of Us and MyCode biobanks (validation cohorts). We also analyzed the impact of aging on uromodulin processing and cellular stress in stably transfected kidney tubular cells expressing wild-type or mutant UMOD. We compared the effects of the GPS on risk of CKD between T62P carriers and non-carriers and tested for the GPS-by-T62P interaction. The UMOD T62P variant was reproducibly associated with increased risk of CKD in an age-dependent manner. Compared to wild-type, clones of T62P-expressing cells exhibited a defective uromodulin maturation profile, causing endoplasmic reticulum retention and stress. We also observed significant T62P-by-GPS interaction, with T62P carriers in the top quintile of the GPS having over 5-fold higher risk of CKD compared to population average (OR 5.17, 95%CI: 2.94-9.08, P=1.0E-08). In summary, we demonstrate that the penetrance of kidney disease in T62P carriers is strongly modified by both age and polygenic risk.

Metabolic alterations commonly accompany neurodevelopmental disorders and may contribute to their pathophysiology. Neurofibromatosis type 1 (OMIM 162200) is a genetic disorder that results from mutations in the NF1 gene and its encoded neurofibromin protein (Nf1). The disorder is multisystemic, affecting multiple aspects of development, physiology, and brain function. In addition, recent evidence suggests that Nf1 deficiency alters metabolic function in both humans and animal models. Whether the metabolic alterations result from changes in neurodevelopment is not known. Here we approach this question in Drosophila melanogaster, which expresses a conserved NF1 gene, exhibits phenotypes reminiscent of the human disease, and shares key developmental mechanisms with humans. Flies with nf1 mutations or RNAi-mediated knockdown exhibit altered metabolism in adulthood. Conditional Nf1 inactivation revealed that the adult metabolic phenotype resulted from loss of Nf1 in neurons during a developmental critical period (third instar larva/pupa), which corresponded to the period of nervous system maturation. Prior to the developmental critical period, nf1 mutants did not exhibit metabolic difference - rather, the metabolic alterations appeared only after the critical period. This suggests that the adult phenotype results from the onset of the developmental alteration during the critical period. High-resolution respirometry on adult mitochondria revealed no differences in complex I/II function or fatty acid oxidation between nf1 mutants and controls, suggesting that the metabolic alterations localize upstream of the electron transport chain at the cellular level. Overall, these data suggest that loss of Nf1 alters adult metabolism via effects during a critical period of nervous system development.

One hallmark of sex chromosome evolution is recombination suppression driven by inversions. The resulting non-recombining sex-linked regions accumulate deleterious mutations and functionally degenerate. The question therefore arises: why does selection not favor the reestablishment of recombination? Two (non-exclusive) explanations for this have been proposed: 1) selection to maintain linkage between the Primary Sex Determination Locus (PSDL) and sexually antagonistic loci - loci with alleles that are beneficial to one sex but detrimental to the other; and 2) the rarity of reversions - structural mutations that reverse the inversion that initially suppressed recombination. Empirical perspectives are sorely needed to evaluate the relevance of these models. Here, we characterised the intermediate stages of sex chromosome evolution in the blackspotted stickleback (Gasterosteus wheatlandi). We generated high-quality, phased assemblies and annotations for the X and Y chromosomes, as well as population-level sequencing. Using these data, we inferred distinct recombination loss events and their associated inversions. Most significantly, we find support from multiple lines of evidence for a [~]2 Mb recombination event that likely occurred via double crossover within an existing non-recombining inversion. This result highlights that rare recombination can occur within sex-linked inversions. Simulations suggest that such histories of gene flux may allow for a novel empirical framework, adapted from work on autosomal inversions, to infer evolutionary processes at work within sex-linked non-recombining regions and distinguish between models to explain the maintenance of recombination suppression on sex chromosomes. Significance StatementSex chromosomes have evolved countless times across eukaryotes and often lose the ability to recombine, causing them to degenerate over time. Why then, does recombination not restart to purge harmful mutations? By generating a high-quality genome assembly of the blackspotted stickleback, we discovered the strong empirical evidence of a sex chromosome undergoing a double-crossover event within a "non-recombining" region, which reset the degenerative process. This finding challenges the view that sex chromosome decay is a one-way street. Furthermore, using forward evolutionary simulations, we demonstrate that the genetic signatures left by such events could help identify the selective forces acting within non-recombining sex chromosomes, thereby explaining the maintenance of recombination suppression.

Chromosomes in Drosophila melanogaster are organized into distinct topologically associated domains delimited by boundaries bound by insulator proteins. The insulator protein BEAF (Boundary Element-Associated Factor of 32kDa) plays roles in both chromatin organization and transcriptional regulation, yet its precise molecular mechanisms remain elusive. To examine the role of BEAF in insulator function we used yeast 2-hybrid assays, pull-down assays with bacterially expressed proteins, and bimolecular fluorescence complementation assays in S2 cells to characterize interactions between BEAF and three co-insulator proteins: CP190, Pzg, and Chro. Our studies pinpoint minimal regions of CP190, Pzg, and Chro that directly interact with BEAF, as well as parts of BEAF that are crucial for its interactions with these co-insulator proteins. Functional analyses in transfected S2 cells revealed distinct regulatory roles for BEAF in association with CP190, Pzg, and Chro. CP190 showed a weak interaction with BEAF, and CP190 bound 2.3 kb upstream of promoter-proximal BEAF could not loop out the intervening DNA to effectively communicate with BEAF for luciferase reporter gene activation. In contrast, more robust interactions were observed between BEAF and both Pzg and Chro. Both could also effectively interact with BEAF from a distance to activate the reporter gene. It is likely that the role of CP190 in long-range insulator interactions is mediated by insulator proteins other than BEAF, although BEAF could help stabilize interactions. On the other hand, we propose that BEAF can directly collaborate with Pzg and Chro to mediate long-range chromatin interactions.