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

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.

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.

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.

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 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.

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.

Maintaining genome integrity in the germline is critical for fertility and organismal survival. Here, we identify C. elegans PARP-2 as an essential and non-redundant regulator of replication-coupled DNA repair. PARP-2 localizes to chromatin during germline development and is also present in the nucleolus; replication stress is associated with changes in its nucleolar distribution, linking fork perturbation to nucleolar signaling and ribosomal homeostasis. Loss of PARP-2 leads to embryonic lethality, larval arrest, and hypersensitivity to replication-blocking and crosslinking agents, accompanied by accumulation of recombination intermediates. Strikingly, a catalytic-dead mutant (E509K) causes even more severe defects than the null allele, including hyperactivation of DNA damage pathways and elevated apoptosis, revealing that PARP-2 enzymatic activity not only executes repair but also restrains excessive stress responses. Chromatin profiling further shows enrichment of PARP-2 at promoter-proximal, fragile loci, suggesting a constitutive surveillance role. Together, these findings establish PARP-2 as a multifunctional genome guardian that integrates catalytic and structural roles to maintain genome stability and nucleolar function, with implications for understanding PARP-associated disease mutations.

Circadian rhythms are prevalent on Earth and temporally organize behaviour and physiology of organisms to occur in species-specific 'temporal niches'. However, species differ in how strictly individuals are controlled by their circadian clock, suggesting that it may offer a selective advantage for an individual to extend its temporal niche under certain circumstances, for example during stressful environmental conditions. A potential mechanism controlling temporal niche adherence involves the evolutionary capacitor and chaperon protein HSP90, known to assist the proper folding of important signalling molecules. If HSP90 becomes rate limiting (e.g., under environmental stress) hidden genetic variation will be expressed, producing novel and potentially beneficial phenotypes for the individual. While this role of HSP90 is well established for morphological traits, we show here that it extends to regulation of temporal behavioural patterns. We show that within a small subset of clock neurons in the fly brain, HSP83, the fly homologue of HSP90, mitigates inter-individual behavioural variability. We provide evidence for the requirement of HSP83 for efficient transcription of the gene encoding the circadian neuropeptide Pigment Dispersing Factor (PDF), and for correct PDF accumulation in central clock neurons. Strikingly, Hsp83 mutants affect synchronized oscillations of the clock protein PERIOD (PER) in subsets of circadian clock neurons in the same way as flies without PDF, further supporting a role of Hsp83 in regulating Pdf. Our findings therefore provide a mechanistic explanation for HSP83 function in regulation of behavioural variability, and offer an explanation for how to restrict temporal niche extension to stressful environmental conditions.

Long term laboratory-based evolution experiments are a powerful tool that are increasingly being used to study fundamental aspects of evolution and to identify genes that contribute to overall fitness under different conditions. However, even with automation, the time that they take to execute limits the extent to which evolution experiments can be used as part of a high throughput approach to understand the links between genotype and phenotype. Mutations that lead to genetic loss of function (LoF) are frequently selected for in evolution experiments. Thus, in principle these experiments could be done more rapidly by starting not with clonal isolates but with dense transposon libraries that will contain loss of function mutations in all non-essential genes. Here, we test this hypothesis by comparing the results of long term (5 month) evolution experiment, in which E. coli was grown with daily transfers in unbuffered LB starting at pH 4.5, with short term (5 and 10 day) experiments on a high-density transposon library in the same strain and under the same conditions. We show that there is a overlap in the genes and pathways identified using the two methods, as well as identifying other gene of interest whose LoF contributes to fitness. This approach has the potential to complement laboratory-based evolution, enabling rapid, higher throughput, testing of a wide range of parameters that may have an influence on evolutionary trajectories.