Biology subjects

Haskell, D.

Publications and source records attributed to Haskell, D..

5 recordsLinked to original sources

bioRxiv2025

Insertion of rare autism variants in synaptic genes induce novel behavioral phenotypes in C. elegans

Neurodevelopmental conditions and disorders, including autism, involve a complex interplay of genetic, environmental, and developmental factors. Despite this complexity, genetic studies have identified more than 150 candidate genes that increase risk for autism and related neurodevelopmental and neuropsychiatric conditions. Unsurprisingly, synaptic genes are a large proportion of these genes, likely due to their roles in the formation and maintenance of synaptic architecture, function, and the plasticity of neurons and circuits. The association of synaptic genes with autism and similar conditions is driven by all types of genetic variation, including inherited and de novo rare variants that have unknown impacts on the function of the gene. Here we insert 4 conserved rare variants in the C. elegans orthologs of NLGN4X, NRXN1, and SHANK3, and define their impact on gene function compared to known loss of function variants using behavioral assays. We find that the rare variants impact multiple foraging behaviors, with each gene and variant having a unique pattern of behavioral changes and functional impact. The NLGN4X(A283T) variant induced clear loss of function, while NLGN4X(G84R) induces a loss of function in one behavior, but a gain of function in another behavior. The NRXN1(L18Q) variant induced remarkable loss and gain of functions with distinct impacts across each behavior. The SHANK3(L143P) variant induced partial loss of function in a single behavior. We also identify for the first time that loss of function of shn-1/SHANK3 alters social feeding and food response behaviors. We uncover a remarkably complex impact of rare variants in synaptic genes, with differential impacts across behaviors, highlighting the importance of broad behavioral analysis and the nuanced effects of missense variants compared to loss of function alleles. Together, we define the complex functional impact of each variant on gene function, compare the impact of variants and genes across multiple behaviors, and provide further support for the use of C. elegans to define the impact of genetic variation derived from human neurodevelopmental and neuropsychiatric disorders.

genetics↗

bioRxiv2025

Functional comparison of control and 3' deletion human NRXN1 isoforms in C. elegans

Heterozygous deletions in NRXN1, encoding the presynaptic adhesion molecule Neurexin 1, are among the most frequently identified rare variants in schizophrenia and other neuropsychiatric disorders. Patient sequencing has revealed that 3 deletions within NRXN1 generate novel isoforms not produced from the intact locus, yet whether these isoforms are functional, passively non-functional, or actively pathogenic in vivo is still not clear. To address this, we expressed eight human NRXN1 isoforms in C. elegans neurons including four control isoforms and four 3 deletion variant isoforms identified in schizophrenia patient cell lines, and characterized their effects on protein localization and two independent behaviors: a food deprivation response and social feeding behaviors. Most human isoforms showed expression and localization within the nerve ring and neurons similar to the C. elegans ortholog, NRX-1; however, several isoforms, particularly among the 3 deletion variants, displayed aberrant accumulation in neuronal cell bodies or as puncta in neuropil. Functionally, isoforms fell into one of three categories: no effect on nrx-1 loss-of-function behavioral phenotypes, partial rescue, or gain of function, with multiple isoforms showing differences between the behaviors. Strikingly, two 3 deletion isoforms produced gain-of-function behavioral phenotypes more severe than the nrx-1 null mutant, demonstrating that these patient-derived variants can be actively pathogenic. These results establish C. elegans as a tractable in vivo platform for dissecting the isoform-specific functional consequences of NRXN1 variants and suggest that strategies for NRXN1-associated neuropsychiatric diseases must account for both loss-of-function and gain-of-function isoform mechanisms.

neuroscience↗

bioRxiv2025

Variation in social feeding behavior and interactions among Caenorhabditis nematodes

The ability to respond to complex stimuli and environmental cues is essential for organisms to survive and reproduce. Responding to a wide range of stimuli requires a neuronal network that can integrate cues and execute behavioral responses. Evolution of behaviors occurs ubiquitously in most established ecological niches, even among closely related species. To uncover the genetic and neuronal drivers of evolving behaviors, we have taken advantage of the large and relatively ancient divergence in the Caenorhabditis genus to ask how different Caenorhabditis nematodes respond to environmental stimuli and whether behavioral traits are shared or distinct. Here, we assayed foraging behaviors of twelve members of the Caenorhabditis clade, including members of both the elegans and japonica supergroup, and the basal taxon C. monodelphis. For each species, we analyzed social feeding and bordering behaviors, which are well characterized in C. elegans. These behaviors are the functional readout of complex sensory integration of multiple sensory cues including pheromones, touch, O2/CO2 concentration, and attractive and noxious stimuli. We hypothesized that the evolutionary divergence between species would correlate to divergence in these behaviors. We observed a wide variation in social aggregate feeding and bordering behaviors of hermaphrodite and female animals, but the variation did not correlate with evolutionary relatedness of the species. Addition of male animals with female or hermaphrodite animals of the same species increased aggregation behavior of subset of species, but not others. Combination of a second species with C. elegans significantly reduced aggregate feeding behavior of C. elegans, but not the other species. Intraspecies and interspecies interactions therefore modifies behavioral paradigms. Overall, we find that foraging and social feeding behaviors vary widely across Caenorhabditis species, likely due to species-specific responses and integration of environmental and context sensory cues. In general, the clade represents a compelling model to dissect evolution of behavior across diverse environments and a large timescale.

evolutionary biology↗

bioRxiv2025

A noncanonical Pol III-dependent, Microprocessor-independent biogenesis pathway generates a germline enriched miRNA family

MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression. In canonical miRNA biogenesis, primary miRNAs are transcribed from intergenic loci or intronic regions by RNA polymerase II, sequentially cleaved by the Microprocessor complex and Dicer, and resulting mature miRNAs are loaded into Argonaute to repress target mRNAs. A minority of miRNAs are generated via noncanonical biogenesis pathways that bypass the Microprocessor and/or Dicer. Here, we describe a new Pol III-dependent, Microprocessor -independent, and Dicer-dependent biogenesis pathway exemplified by the mir-1829 family in C. elegans. Although the mir-1829 family loci reside in intronic regions of protein-coding genes, we show that the miRNAs are derived from independent Pol III transcripts. Unlike other Pol III-dependent miRNAs, the mir-1829 family small RNAs are the dominant species derived from their loci, rather than fragments of a larger functional noncoding RNA. These germline-enriched miRNAs are loaded in multiple miRNA Argonautes, including the recently-characterized germline Argonaute ALG-5, which we demonstrate is repressive when tethered to a reporter transcript. We extend these findings, identifying additional Pol III-transcribed and noncanonical small RNAs in C. elegans and human datasets, including human miR-4521. These young, noncanonical miRNAs may represent an early snapshot in the evolution of de novo miRNA genes.

molecular biology↗

bioRxiv2020

KH domain containing RNA-binding proteins coordinate with microRNAs to regulate Caenorhabditis elegans development

microRNAs (miRNAs) and RNA binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate and the precise mechanisms of their coordination are not well understood. RNA binding proteins often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K Homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs during Caenorhabditis elegans development, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonaute alg-1. Interestingly, two KH domain genes, predicted splicing factors sfa-1 and asd-2, genetically interacted with all of the miRNA mutants tested, while other KH domain genes exhibited functional interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of the C. elegans KH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that many C. elegans KH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.

genetics↗