The interferon response is a signalling pathway unique to vertebrates that links the innate and adaptive immune responses. Interferons signal through a cascade of factors including the JAK-STAT pathway to induce the transcription of hundreds of interferon-stimulated genes (ISGs). Although the main interferon signal transduction pathways and ISGs have been elucidated, translational regulation of ISG transcripts is not fully understood. Prior work demonstrated that ribosomal protein RPL28 negatively regulates a subset of ISGs; however, we find that this effect may be due to a reduction in overall ribosome abundance. Multi-omics analysis of RNA-seq and LC-MS/MS data reveal proteins, including several ISGs, that are translationally up-regulated in IFN-β-stimulated cells depleted of ribosome biogenesis factor BOP1. Analysis of codon usage demonstrates a significant reduction in codon optimality for proteins that are translationally up-regulated during BOP1 knockdown and IFN-β stimulation. Using reporter constructs, we demonstrate that codon nonoptimal reporters are translated more than codon-optimized reporters in BOP1-depleted IFN-β cells. We propose that ribosome biogenesis may in part regulate the translational fine-tuning of integral ISG protein production to ensure optimal interferon responses, with potential effects extending beyond this pathway.

The regulatory network governed by CDX/Caudal family transcription factors plays critical roles in shaping embryonic neural development. In C. elegans, we found that proper expression of pal-1, the C. elegans Caudal homologue, is required for correct positioning of motor neuron cell bodies in the first larval stage ventral nerve cord (VNC). We identified an upstream regulatory region within the pal-1 promoter that drives pal-1 expression in a subset of DD and DA neuronal progenitors. We also show that SEX-1, a nuclear hormone receptor, is required for motor neuron positioning in the VNC. Loss of sex-1 results in neuronal positioning defects similar to those observed in pal-1 mutants. This is in part due to a requirement for SEX-1 in promoting pal-1 expression in DD and DA neuronal progenitors during VNC assembly. Double mutant analysis further suggests that sex-1 also has pal-1-independent functions. Together, these findings define a transcriptional hierarchy in which the SEX-1 nuclear hormone receptor regulates the tissue-specific activity of PAL-1 to promote proper motor neuron positioning in the VNC and highlight a conserved role for NHR and CDX/Caudal family proteins in central nerve cord formation.

All viruses must co-opt the host translational machinery for viral protein synthesis. The dicistrovirus intergenic region internal ribosome entry site (IGR-IRES) utilizes the most streamlined translation mechanism by adopting a triple pseudoknot structure that directly recruits and binds within the intersubunit space of the ribosome and initiates translation from a non-AUG codon. The origin of this unprecedented mechanism is not known. Using a bioinformatics pipeline to examine the diversity and function of IRESs across RNA viromes, we searched for IRES-like RNA structures using RNA covariance models for multiple IRES sub-types, and tested functional IRES by using a dual-fluorescent lentiviral library reporter screen. We identified over >4,700 dicistro-like genomes with ~32% containing putative IRES structures, including novel viral genome arrangements with multiple IRESs and IRESs embedded within open-reading frames (ORFs). Predicted IRESs bound directly to purified ribosomes and supported internal ribosome entry activity in vitro and in vivo. Moreover, internal IRESs embedded within an ORF of monocistronic genomes were functional and operated simultaneously to produce the downstream ORF. We also identified IRES-like structures within non-dicistrovirus viral genomes, including in the families Tombusviridae and Narnaviridae that bound to ribosomes directly and a subset can direct internal ribosome entry. This study provides a framework to map the origin of factorless IRES mechanisms and study the diverse viral strategies utilizing RNA-based mechanisms.

Two percent of patients with X-linked intellectual disability (XLID) exhibit loss-of-function mutations in the enzyme, ZDHHC9. One of the main anatomical deficits observed in these patients is a decrease in corpus callosum volume and a concurrent disruption in white matter integrity. In this study, we demonstrate that deletion of Zdhhc9 in mice disrupts the balance of mature oligodendrocyte subtypes within the corpus callosum. While overall mature oligodendrocyte numbers are unchanged, there is a marked increase in MOL5/6 cells that are enriched in genes associated with cell adhesion and synapses, and a concomitant decrease in MOL2/3 cells that are enriched in genes associated with myelination. In line with this, we observed a decrease in the density of myelinated axons and disruptions in myelin compaction in the corpus callosum of Zdhhc9 knockout mice. RNA sequencing and proteomic analysis further revealed a reduction in genes and proteins essential for lipid metabolism, cholesterol synthesis, gene expression, and myelin compaction, offering insights into the underlying mechanisms of the pathology. These findings reveal a previously underappreciated and fundamental role for ZDHHC9 and protein palmitoylation in regulating oligodendrocyte subtype determination and myelinogenesis, offering mechanistic insights into the deficits observed in white matter volume in patients with mutations in ZDHHC9.

Inositol phosphates (IPs) are essential for the development and function of the nervous system. Loss-of-function studies, which demonstrate the importance of specific IP isomers, show their critical role in proper neural tube formation. In this study, we show that inositol pentakisphosphate 2-kinase (IPPK-1), the kinase that phosphorylates IP5 to generate IP6, is involved in assembling the ventral nerve cord (VNC) in C. elegans. We show that mutations in ippk-1 lead to the mispositioning of motor neurons along the VNC of newly hatched larvae. These positioning defects reflect disruption of VNC assembly during embryogenesis, as VNC neuronal progenitors in ippk-1 embryos display a more compact organization after arising on the left and right sides of the embryo, delays in rosette-mediated convergent extension, and defects in cell intercalation. We further show that injection of exogenous IP6 into the gonads of ippk-1 mutants can rescue both embryonic and neuron positioning defects. Our findings indicate that IP isomers, particularly IP6, are important for ventral nerve cord formation in C. elegans. Along with their role in neural tube formation in vertebrates, these results suggests that IP isomers play an ancient role in central nerve cord development.

BACKGROUND & AIMS:GATA family transcription factors are somatically variable (SV) in esophageal adenocarcinomas (EAC) and inducible by simulated reflux. Our study examines the mechanisms whereby GATA family members (GATA4, GATA6, and the atypical TRPS-1) influence oncogenesis during the Barrett's esophagus (BE) metaplasia-dysplasia transition preceding EAC. METHODS:RNAseq analyses of esophageal cell lines and lesion-derived adult stem cells (ASCs) in conjunction shRNA- or CRISPR-facilitated gene silencing, together with reanalysis of The Cancer Genome Atlas data, spatial transcriptomics, and organ-on-a-chip studies were used. RESULTS:Although a gastroesophageal reflux disease history positively correlated with GATA4/6 somatically variable and a columnar-associated gene signature (ANPEP/GATA4) in The Cancer Genome Atlas EAC cases, it negatively associated with a squamous lineage-linked signature (TP63/SOX15) containing TRPS1. In experimental data, opposing effects on regulators of squamous and columnar lineage identity were uncovered between TRPS1 and classical GATA factors (GATA4/6). Interrogation of this GATA "fulcrum" defined further genes (CGN, IL6R, and GPRC5B) targeted for TRPS1-mediated suppression or GATA4/6 activation. A novel spatial transcriptomic signature of BE-associated high-grade dysplasia (HGD) captured GATA fulcrum action, through GPRC5B expression. Functionally, GPRC5B was found to be low-pH-responsive, to increase proliferative and colony formation rates, and when overexpressed facilitate a hyperproliferative HGD-like transformation of BE-ASCs. Using an organ-on-a-chip platform, cellular overgrowth, reduced luminal villus structures, lower goblet cell numbers, and loss of intestine-associated marker gene expression (TFF3/MUC2) were observed following GPRC5B overexpression in BE-ASCs, mirroring HGD. CONCLUSIONS:This study identifies critical GATA factor-mediated processes underlying cellular phenotype in the BE-HGD-EAC transition and identifies GATA-inducible GPRC5B as a functional marker and possible driver of progression through HGD to EAC.

We investigated the clinical and functional role of the miR-106a-363 cluster in adult acute myeloid leukemia (AML). LAML miRNA-Seq TCGA analyses revealed that high expression of miR-106a-363 cluster members was associated with inferior survival, and miR-106a-5p and miR-20b-5p levels were significantly elevated in patients with adverse risk AML. Overexpression of the miR-106a-363 cluster and its individual members in a murine AML model significantly accelerated leukemogenesis. Proteomics analysis of leukemic bone marrow cells from these models emphasized the deregulation of proteins involved in intracellular transport, protein complex organization and mitochondrial function, driven predominantly by miR-106a-5p. These molecular alterations suggested mitochondrial activation as a potential mechanism for the observed increase in leukemogenicity. High-resolution respirometry and STED microscopy confirmed that miR-106a-5p enhances mitochondrial respiratory activity and increases mitochondrial volume. These findings demonstrate that the miR-106a-363 cluster, and particularly miR-106a-5p, contribute to AML progression through modulation of mitochondrial function and deregulation of mitochondria-coordinated pathways.

In tumor cells, protein glycosylation patterns are often dramatically altered compared to normal cells. This leads to the emergence of novel neo-antigens on the tumour cell surface. Podocalyxin is a heavily glycosylated transmembrane sialomucin that is overexpressed in many solid tumors, with higher expression being significantly correlated with poor prognosis. We have developed a candidate therapeutic monoclonal antibody called PODO447 that binds to a tumor-associated altered glycoform of podocalyxin (Canals Hernaez et al., J Immunother Cancer. 2020 Nov;8(2):e001128). Clinically, the glycopeptide epitope recognized by PODO447 is present on a significant subset of podocalyxin-positive tumors and high expression of the epitope is associated with an aggressive ‘cold’ immune phenotype in patient tumors (Brassard et al., Front Oncol. 2023 Dec 21:13:1286754.). An antibody drug conjugate (ADC) that contains PODO447 as its targeting arm has shown promising results for tumor-killing efficacy in pre-clinical models of pancreatic and ovarian carcinoma (Canals Hernaez et al., Front Oncol. 2022 May 4:12:856424). As the expression of the PODO447 glycoepitope associates with aggressive tumor types, we assessed the phenotype of PODO447-expressing cells to better elucidate the potential role of the emergence of this novel epitope in tumor progression. The CFPAC-1 pancreatic ductal adenocarcinoma-derived cell line, while being universally podocalyxin-positive, contains subpopulations of cells that express either high or low levels of the PODO447 epitope. We were able to sort these two populations through fluorescent-activated cell sorting (FACS) and performed bulk RNA-seq, comparing expression patterns between these two populations. Interestingly, we found genes that are known markers of epithelial to mesenchymal transition (EMT) to be upregulated in PODO447High cells, including transcription factors (TWIST1, ZEB1, ZEB2) and extracellular matrix components and remodelling factors (FN1, ITGA5, COL1A1, MMP2, MMP13). CFPAC-1 PODO447High cells also have elevated N-cadherin levels compared to PODO447Low cells. In addition, while E-cadherin mRNA and total protein levels are unchanged, we found that the localization of E-cadherin is altered in PODO447High cells, being restricted to the intracellular compartment, compared to a junctional, cell surface localization in PODO447Low cells. Furthermore, the PODO447High cells have a more mesenchymal morphology and increased single-cell motility. Collectively, these data suggest that the emergence of the PODO447 epitope is associated with the acquisition of a partial EMT (p-EMT) phenotype that may functionally contribute to tumor progression. Targeting this tumor-specific podocalyxin epitope clinically with our antibody may prove effective in preventing disease progression. Pamela Austin Dean, Erin M. Bell, Stephane Flibotte, Anjali Parthasarathy, Lydia Liu, Aileen Liman, Julyanne Brassard, Kelly M. McNagny, Calvin D. Roskelley. The therapeutic candidate antibody PODO447 recognizes a glycopeptide on podocalyxin-expressing tumor cells that have undergone a partial epithelial-mesenchymal transition [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr C108.

Mechanistic target of rapamycin (mTOR) functions in mTOR complex 1 (mTORC1) with raptor to match metazoan metabolism to available nutrients to regulate multiple cellular, physiological, and pathological processes. Hypoxic cellular injury is influenced by the mTORC1 pathway, but whether its activity promotes or prevents injury is unclear, and which mTORC1-regulated mechanisms control hypoxic injury are obscure. Here, we report the discovery of a hypoxia-resistant, temperature-sensitive raptor mutant in an unbiased forward mutagenesis screen in C. elegans. This raptor mutant is both hypoxia resistant and long lived at intermediate temperatures, while unable to develop at higher temperatures. Temperature-shift experiments show that the conditional hypoxia resistance can be induced in the raptor mutant immediately prior to the hypoxic insult. At these intermediate temperatures, the raptor mutation selectively reduces protein synthesis without affecting autophagy, and epistasis experiments implicate mTOR-targeted translation regulators as components of the hypoxia resistance mechanism. Using the conditional developmental arrest phenotype in a selection for suppressors of raptor loss of function, we isolated multiple second-site raptor missense mutants, whose mutated residue is predicted to interact with RagA, a raptor-binding protein. These suppressor mutations restore normal protein synthesis, hypoxic sensitivity, and lifespan and thereby implicate raptor-RagA interactions as critical to these biological processes.

The Poly(A) Tail Length (PATL) of mRNAs of certain cell-cycle regulatory genes undergo significant trimming during M-phase, however the functional importance is unknown. The Ccr4-Not and PAN complexes account for the majority of cytoplasmic poly(A) deadenylation, but their potential roles in regulation of cell-cycle mRNA PATLs has not been investigated. We find that under conditions of microtubule stress in yeast, loss of PAN deadenylase activity leads to arrest in M phase, defective spindles, and increased cell death. PAN consists of the catalytic subunit Pan2 and the RNA binding subunit Pan3. Consistent with a role in mitosis, PAN2 interacts genetically with tubulin genes, prefoldin complex genes and the cyclins CLB1 and CLN3 . PAN2 knockdown in human cultured cells disrupts mitosis and results in spindle fragmentation leading to abnormal cell division, while expression of human PAN2 in yeast rescues pan2 Δ cell-cycle phenotypes. Hence, we reveal an important highly conserved role for PAN in ensuring proper mitosis when cells are under microtubule stress. We propose PAN regulates PATLs of mRNAs of key cell-cycle/mitotic proteins in response to defective spindles.### Competing Interest StatementThe authors have declared no competing interest.

Abstract Pancreatic ductal adenocarcinoma (PDAC) it though to develop through induction of different precursor lesions, however, the normal cell type that gives rise to these precancerous lesions and PDAC is unclear. Recent studies using mouse models and ex vivo cultured human cells suggest that the cellular origin of PDAC may be either acinar or ductal cells. Potential transcriptional markers associated with PDAC of different cellular origins have been identified. Here, we interrogate whether these markers are predictive of cellular of origin across models using mouse models where acinar and ductal cells (Ptf1aCreER or Sox9CreER) expressing oncogenic Kras in the absence of Trp53 or Pten give rise to PDAC tumors. We found that acinar- and ductal-cell-derived PDAC exhibit transcriptional differences both in vivo and in vitro when comparing within one genotype or sample source type (e.g. bulk tumor or primary cell lines). However, previously predicted markers of cellular origin had variable expression across models and sample types suggestive of differences specific to those sample sets. Using our larger sample sets and multiple genotypes and source types, we proposed a more comprehensive set of cell of origin markers for consideration. Application of these markers to our own data sets, however, failed to properly segregate acinar- and ductal-cell-derived PDAC into separate groups. This suggests that the transcriptional heterogeneity observed in our sample set was not driven by the tumors arising from different cellular origins. We also examined the relationship between cell of origin and patient PDAC transcriptional subtypes using our mouse model datasets. Our findings support previous research indicating that mouse models of acinar-cell-derived PDAC favor those of a classical subtype. However, our mouse PDAC samples all express similar or very low levels of the genes denoting the basal subtype, suggesting that the basal subtype was not strongly present in any of the datasets we examined. In summary, our data suggest that acinar and ductal cells converge into a very similar PDAC transcriptional state and that, if differences can be identified, they will likely be identified by non-transcript based readouts. Citation Format: Ken Chu, Alex Lee, Karnjit Sarai, Yan Dou, Wesley Hunt, Emma Croft, Atefeh Samani, Farnaz Taghizedeh, Claire Dubois, Stephane Flibotte, Janel Kopp. Cell of origin does not underlie transcription heterogeneity in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A025.

Genetic balancers in Caenorhabditis elegans are complex variants that allow lethal or sterile mutations to be stably maintained in a heterozygous state by suppressing crossover events. Balancers constitute an invaluable tool in the C. elegans scientific community and have been widely used for decades. The first/traditional balancers were created by applying X-rays, UV, or gamma radiation on C. elegans strains, generating random genomic rearrangements. Their structures have been mostly explored with low-resolution genetic techniques (e.g., fluorescence in situ hybridization or PCR), before genomic mapping and molecular characterization through sequencing became feasible. As a result, the precise nature of most chromosomal rearrangements remains unknown, whereas, more recently, balancers have been engineered using the CRISPR-Cas9 technique for which the structure of the chromosomal rearrangement has been predesigned. Using short-read whole-genome sequencing (srWGS) and tailored bioinformatic analyses, we previously interpreted the structure of four chromosomal balancers randomly created by mutagenesis processes. Here, we have extended our analyses to five CRISPR-Cas9 balancers and 17 additional traditional balancing rearrangements. We detected and experimentally validated their breakpoints and have interpreted the balancer structures. Many of the balancers were found to be more intricate than previously described, being composed of complex genomic rearrangements (CGRs) such as chromoanagenesis-like events. Furthermore, srWGS revealed additional structural variants and CGRs not known to be part of the balancer genomes. Altogether, our study provides a comprehensive resource of complex genomic variations in C. elegans and highlights the power of srWGS to study the complexity of genomes by applying tailored analyses.

Short-chain fatty acids (SCFAs) are key molecules produced by gut bacteria in the intestine, that are absorbed into the bloodstream and strongly influence human health. SCFA disruption and imbalances have been linked to many diseases; however, they are seldom used diagnostically as their detection requires extensive sample preparation and expensive equipment. In this work, an electrochemical sensor was developed to enable real-time, quantitative measurement of SCFAs from complex samples in liquid phase without the need for extraction, evaporation, or destruction. An impedance-based sensor for in vitro detection of acetic acid, propionic acid, and butyric acid (accounting for more than 95% of SCFAs in the intestine) was fabricated by the deposition of a ZnO and polyvinyl alcohol (PVA) on the surface of a microfabricated interdigitated gold electrode. The sensor was first exposed to a broad, physiologically relevant range of concentrations of SCFAs in isolation (0.5–20 mg/ml) and unlike previously published SCFA sensors that could detect only in gas form with the aid of evaporation, it was able to detect them directly in the liquid phase at room temperature. Electrochemical impedance spectroscopy analysis was then applied to the mixture of SCFAs prepared at different ratios and in complex media at concentrations ranging from 0.5 to 10 mg/ml, which showed the capability of the sensor to measure SCFAs in experimentally relevant mixture. The recorded faradaic responses were then used to train a fit-to-data model to utilize the sensor to screen human bacterial isolates and detect which species secrete SCFAs in vitro . This work will allow for the rapid and non-destructive determination of the levels of SCFAs in complex biological samples, providing a miniaturized, highly stable, and highly sensitive sensor for real-time monitoring applications.

The reversible lipid modification protein S-palmitoylation can dynamically modify the localization, diffusion, function, conformation and physical interactions of substrate proteins. Dysregulated S-palmitoylation is associated with a multitude of human diseases including brain and metabolic disorders, viral infection and cancer. However, the diverse expression patterns of the genes that regulate palmitoylation in the broad range of human cell types are currently unexplored, and their expression in commonly used cell lines that are the workhorse of basic and preclinical research are often overlooked when studying palmitoylation dependent processes. We therefore created CellPalmSeq ( https://cellpalmseq.med.ubc.ca ), a curated RNAseq database and interactive webtool for visualization of the expression patterns of the genes that regulate palmitoylation across human single cell types, bulk tissue, cancer cell lines and commonly used laboratory non-human cell lines. This resource will allow exploration of these expression patterns, revealing important insights into cellular physiology and disease, and will aid with cell line selection and the interpretation of results when studying important cellular processes that depend on protein S-palmitoylation.

Abstract Soluble Se compounds are of great concern in mine influenced water (MIW) from many coal and metal mines due to Se bioaccumulation in aquatic environments and toxicity to birds and fish. Biological treatment to remove soluble Se to regulated levels, which are on the orders of µg-Se/L, is challenging due to the chemical and biological complexity of MIW. For instance, co-contaminant nitrate can inhibit selenate reduction. Native bacteria consortia from mine impacted aquatic environments are sources for known and novel selenate reducing bacteria. In this study, two consortia of native bacteria enriched from different locations on a coalmine known to exhibit elevated release of Se were tested for their ability to remove soluble Se from a typical MIW in sequencing batch bioreactors. One consortium, enriched from an impacted natural vegetated wetland known to harbour native microorganisms involved in selenate-Se reduction, when inoculated into MIW achieved limited soluble Se removal in the presence of nitrate. The other consortium enriched from a disused tailing storage facility achieved greater removal of soluble Se in the presence of nitrate. Genome-resolved metagenomics were used to identify and track consortium members and identify putative novel selenate reducing microorganisms.

Abstract Soluble Se compounds are of great concern in mine influenced water (MIW) from many coal and metal mines due to Se bioaccumulation in aquatic environments and toxicity to birds and fish. Biological treatment to remove soluble Se to regulated levels, which are on the orders of µg-Se/L, is challenging due to the chemical and biological complexity of MIW. For instance, co-contaminant nitrate can inhibit selenate reduction. Native bacteria consortia from mine impacted aquatic environments are sources for known and novel selenate reducing bacteria. In this study, two consortia of native bacteria enriched from different locations on a coalmine known to exhibit elevated release of Se were tested for their ability to remove soluble Se from a typical MIW in sequencing batch bioreactors. One consortium, enriched from an impacted natural vegetated wetland known to harbour native microorganisms involved in selenate-Se reduction, when inoculated into MIW achieved limited soluble Se removal in the presence of nitrate. The other consortium enriched from a disused tailing storage facility achieved greater removal of soluble Se in the presence of nitrate. Genome-resolved metagenomics were used to identify and track consortium members and identify putative novel selenate reducing microorganisms.

During nervous system development, axons navigate complex environments to reach synaptic targets. Early extending axons must interact with guidance cues in the surrounding tissue, while later extending axons can interact directly with earlier "pioneering" axons, "following" their path. In Caenorhabditis elegans, the AVG neuron pioneers the right axon tract of the ventral nerve cord. We previously found that aex-3, a rab-3 guanine nucleotide exchange factor, is essential for AVG axon navigation in a nid-1 mutant background and that aex-3 might be involved in trafficking of UNC-5, a receptor for the guidance cue UNC-6/netrin. Here, we describe a new gene in this pathway: ccd-5, a putative cdk-5 binding partner. ccd-5 mutants exhibit increased navigation defects of AVG pioneer as well as interneuron and motor neuron follower axons in a nid-1 mutant background. We show that ccd-5 acts in a pathway with cdk-5, aex-3, and unc-5. Navigation defects of follower interneuron and motoneuron axons correlate with AVG pioneer axon defects. This suggests that ccd-5 mostly affects pioneer axon navigation and that follower axon defects are largely a secondary consequence of pioneer navigation defects. To determine the consequences for nervous system function, we assessed various behavioral and movement parameters. ccd-5 single mutants have no significant movement defects, and nid-1 ccd-5 double mutants are less responsive to mechanosensory stimuli compared with nid-1 single mutants. These surprisingly minor defects indicate either a high tolerance for axon guidance defects within the motor circuit and/or an ability to maintain synaptic connections among commonly misguided axons.

Animal development is a complex yet robust process that can withstand lengthy and variable interruptions. In Caenorhabditis elegans, adverse conditions can trigger entry into dauer, a stress-resistant, developmentally arrested diapause stage that occurs midway through larval development. Favorable conditions promote recovery from dauer, and post-dauer larvae develop normally. During larval development, epidermal seam cells are multipotent and divide at each stage. At adulthood, seam cells differentiate and express the adult-specific COL-19 collagen. The progression of cell fates is controlled by a network of genes called the heterochronic pathway, including the LIN-29 transcription factor that directly activates col-19 expression, and the let-7 microRNA that indirectly promotes lin-29 expression. Notably, most known heterochronic genes that oppose adult cell fate act only during continuous development; these genes are dispensable after dauer. We performed a genetic screen for heterochronic genes that act after dauer and identified ztf-16, encoding a zinc finger transcription factor in the hunchback/Ikaros- like family. We found that ztf-16 is required to prevent precocious expression of the adult cell fate marker col-19p::gfp equally during both life histories, making ztf-16(-) the first precocious heterochronic mutant to be unaffected by dauer. Our data indicate that ztf-16 regulates col-19p::gfp via a novel, lin-29- independent mechanism. Endogenous ztf-16b::gfp expression is regulated by let-7 and ztf-16 acts genetically downstream of let-7, but lin-29 is not required for col-19p::gfp expression in ztf-16 mutant larvae or adults. Finally, mRNA-seq experiments identified genes whose expression is regulated by ztf-16 in each life history. Taken together, this work illuminates a novel aspect of the heterochronic pathway relevant to both dauer and non-dauer development.

Dynamic protein S-palmitoylation is critical for neuronal function, development, and synaptic plasticity. Synaptic activity-dependent changes in palmitoylation have been reported for a small number of proteins. Here, we characterized the palmitoylome in the hippocampi of male mice before and after context-dependent fear conditioning. Of the 121 differentially palmitoylated proteins identified, just over half were synaptic proteins, whereas others were associated with metabolic functions, cytoskeletal organization, and signal transduction. The synapse-associated proteins generally exhibited increased palmitoylation after fear conditioning. In contrast, most of the proteins that exhibited decreased palmitoylation were associated with metabolic processes. Similar results were seen in cultured rat hippocampal neurons in response to chemically induced long-term potentiation. Furthermore, we found that the palmitoylation of one of the synaptic proteins, plasticity-related gene-1 (PRG-1), also known as lipid phosphate phosphatase-related protein type 4 (LPPR4), was important for synaptic activity-induced insertion of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) into the postsynaptic membrane. The findings identify proteins whose dynamic palmitoylation may regulate their role in synaptic plasticity, learning, and memory.