Jose AM (2024) Elife "Heritable epigenetic changes are constrained by the dynamics of regulatory architectures."

Jose AM

[Elife, 2024]

Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. Here, I develop criteria for the heritability of regulatory architectures and use quantitative simulations of interacting regulators parsed as entities, their sensors, and the sensed properties to analyze how architectures influence heritable epigenetic changes. Information contained in regulatory architectures grows rapidly with the number of interacting molecules and its transmission requires positive feedback loops. While these architectures can recover after many epigenetic perturbations, some resulting changes can become permanently heritable. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of architectures heritable. Differential inhibition of the positive feedback loops that transmit regulatory architectures across generations can explain the gene-specific differences in heritable RNA silencing observed in the nematode <i>Caenorhabditis elegans</i>. More broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.

Jose AM (2020) Elife "The analysis of living systems can generate both knowledge and illusions."

Jose AM

[Elife, 2020]

Life relies on phenomena that range from changes in molecules that occur within nanoseconds to changes in populations that occur over millions of years. Researchers have developed a vast range of experimental techniques to analyze living systems, but a given technique usually only works over a limited range of length or time scales. Therefore, gaining a full understanding of a living system usually requires the integration of information obtained at multiple different scales by two or more techniques. This approach has undoubtedly led to a much better understanding of living systems but, equally, the staggering complexity of these systems, the sophistication and limitations of the techniques available in modern biology, and the need to use two or more techniques, can lead to persistent illusions of knowledge. Here, in an effort to make better use of the experimental techniques we have at our disposal, I propose a broad classification of techniques into six complementary approaches: perturbation, visualization, substitution, characterization, reconstitution, and simulation. Such a taxonomy might also help increase the reproducibility of inferences and improve peer review.

Jose AM et al. (2011) Nat Struct Mol Biol "Two classes of silencing RNAs move between Caenorhabditis elegans tissues."

Garcia GA, Hunter CP, Jose AM

[Nat Struct Mol Biol, 2011]

Organism-wide RNA interference (RNAi) is due to the transport of mobile silencing RNA throughout the organism, but the identities of these mobile RNA species in animals are unknown. Here, we present genetic evidence that both the initial double-stranded RNA (dsRNA), which triggers RNAi, and at least one dsRNA intermediate produced during RNAi can act as or generate mobile silencing RNA in C. elegans. This dsRNA intermediate requires the long dsRNA-binding protein RDE-4, the endonuclease DCR-1, which cleaves long dsRNA into double-stranded short-interfering RNA (ds-siRNA), and the putative nucleotidyltransferase MUT-2 (RDE-3). However, single-stranded siRNA and downstream secondary siRNA produced upon amplification by the RNA-dependent RNA polymerase RRF-1 do not generate mobile silencing RNA. Restricting intertissue transport to long dsRNA and directly processed siRNA intermediates rather than amplified siRNA may serve to modulate the extent of systemic silencing in proportion to available dsRNA.

Jose AM et al. (2012) Proc Natl Acad Sci U S A "Conserved tyrosine kinase promotes the import of silencing RNA into Caenorhabditis elegans cells."

Leal-Ekman S, Kim YA, Jose AM, Hunter CP

[Proc Natl Acad Sci U S A, 2012]

RNA silencing in Caenorhabditis elegans is transmitted between cells by the transport of double-stranded RNA (dsRNA). The efficiency of such transmission, however, depends on both the cell type and the environment. Here, we identify systemic RNAi defective-3 (SID-3) as a conserved tyrosine kinase required for the efficient import of dsRNA. Without SID-3, cells perform RNA silencing well but import dsRNA poorly. Upon overexpression of SID-3, cells import dsRNA more efficiently than do wild-type cells and such efficient import of dsRNA requires an intact SID-3 kinase domain. The mammalian homolog of SID-3, activated cdc-42-associated kinase (ACK), acts in many signaling pathways that respond to environmental changes and is known to directly associate with endocytic vesicles, which have been implicated in dsRNA transport. Therefore, our results suggest that the SID-3/ACK tyrosine kinase acts as a regulator of RNA import into animal cells.

Jose AM et al. (2009) Proc Natl Acad Sci U S A "Export of RNA silencing from C. elegans tissues does not require the RNA channel SID-1."

Hunter CP, Smith JJ, Jose AM

[Proc Natl Acad Sci U S A, 2009]

Double-stranded RNA (dsRNA) triggers RNA interference (RNAi) to silence genes of matching sequence. In some animals this experimentally induced silencing is transported between cells, and studies in the nematode Caenorhabditis elegans have shown that the dsRNA channel SID-1 is required for the import of such transported silencing signals. Gene silencing can also be triggered by endogenously expressed RNAi triggers, but it is unknown whether such silencing is transported between cells. Here, we show that, in C. elegans, SID-1 is required for efficient silencing of multicopy transgenes, indicating that mobile silencing signals contribute to transgene silencing. Further, most tissues can transport silencing initiated by the tissue-specific transgenic expression of RNAi triggers to other tissues, consistent with expressed RNAi triggers generating mobile silencing signals. Whereas the import of silencing signals requires SID-1, we found that mobile silencing signals generated by transgene-expressed RNAi triggers are exported to other tissues through a SID-1-independent mechanism. Furthermore, when RNAi triggers are expressed in ingested Escherichia coli, silencing signals can be transported to internal tissues from the gut lumen across gut cells that lack SID-1. Thus, C. elegans can transport endogenous and exogenous RNA silencing signals between many different tissues via at least 2 SID-1 independent export pathways.

Jose AM et al. (2005) J Biol Chem "Domains, amino acid residues, and new isoforms of Caenorhabditis elegans diacylglycerol kinase 1 (DGK-1) important for terminating diacylglycerol signaling in vivo."

Jose AM, Koelle MR

[J Biol Chem, 2005]

Diacylglycerol kinases (DGKs) inhibit diacylglycerol (DAG) signaling by phosphorylating DAG. DGK-1, the C. elegans ortholog of human neuronal DGKtheta;, inhibits neurotransmission and thus controls behavior. DGK-1, like DGKtheta;, has three cysteine-rich domains (CRDs), a pleckstrin homology (PH) domain, and a kinase domain. To identify DGK domains and amino acid residues critical for terminating DAG signaling in vivo, we analyzed 20 dgk-1 mutants defective in DGK-1 controlled behaviors. We found by sequencing that the mutations included nine amino acid substitutions and seven premature stop codons that impair the physiological functions of DGK-1. All nine amino acid substitutions are either in the second CRD, the third CRD, or in the kinase domain. Thus, these domains are important for the termination of DAG signaling by DGK-1 in vivo. Seven of the substituted amino acid residues are present in all human DGKs and likely define key residues required for the function of all DGKs. An ATP-binding site mutation expected to inactivate the kinase domain retained very little physiological function, but we found two stop codon mutants predicted to truncate DGK-1 before its kinase domain that retained significantly more function. We detected novel splice forms of dgk-1 that can reconcile this apparent conflict, as they skip exons containing the stop codons to produce DGK-1 isoforms that contain the kinase domain. Two of these isoforms lack an intact PH domain yet appear to have significant function. Additional novel isoform(s) account for all the DGK-1 function necessary for one behavior, dopamine response.

Jose AM et al. (2007) Genetics "A specific subset of transient receptor potential vanilloid-type channel subunits in Caenorhabditis elegans endocrine cells function as mixed heteromers to promote neurotransmitter release."

Jose AM, Koelle MR, Bany IA, Chase DL

[Genetics, 2007]

Transient receptor potential (TRP) channel subunits form homotetramers that function in sensory transduction. Heteromeric channels also form, but their physiological subunit compositions and functions are largely unknown. We found a dominant-negative mutant of the C. elegans TRPV (vanilloid-type) subunit OCR-2 that apparently incorporates into and inactivates OCR-2 homomers as well as heteromers with the TRPV subunits OCR-1 and -4, resulting in a premature egg-laying defect. This defect is reproduced by knocking out all three OCR genes, but not by any single knockout. Thus a mixture of redundant heteromeric channels prevents premature egg laying. These channels, as well as the G protein Galphao, function in neuroendocrine cells to promote release of neurotransmitters that block egg laying until eggs filling the uterus deform the neuroendocrine cells. The TRPV channel OSM-9, previously suggested to be an obligate heteromeric partner of OCR-2 in sensory neurons, is expressed in the neuroendocrine cells but has no detectable role in egg laying. Our results identify a specific set of heteromeric TRPV channels that redundantly regulate neuroendocrine function, and show a subunit combination that functions in sensory neurons is also present in neuroendocrine cells but has no detectable function in these cells.

Zhang H et al. (2024) Food Funct "Aronia melanocarpa extract extends the lifespan and health-span of Caenorhabditis elegans via mitogen-activated protein kinase 1."

Zhang H, Wei W, Li H, Gong Y, Du J, Yan X, Zhou H, Zhu Z, Chen L, Liu Z, Sheng L

[Food Funct, 2024]

Aging is a highly complex process and one of the largest risk factors for many chronic diseases. <i>Aronia melanocarpa</i> (AM) is rich in bioactive phytochemicals with antioxidant, anti-inflammatory, and anticancer properties. However, little is known about its effects on aging. The objective of this study was to evaluate the effects of AM extract on lifespan and health-span using <i>Caenorhabditis elegans</i> as a representative model. The mechanisms of its effects were explored using transcriptomics and untargeted metabolomics. Results showed that the lifespan of <i>C. elegans</i> was significantly extended by 22.2% after high-dose AM treatment. AM improved the behavior and physiological functions of <i>C. elegans</i> by increasing the pharyngeal pumping rate, decreasing lipofuscin accumulation and the reactive oxygen species level, enhancing resistance to oxidative stress, and increasing the activities of superoxide dismutase and catalase. Transcriptome analysis showed that the <i>pmk-1</i> gene (mitogen-activated protein kinase 1), which is involved in the MAPK signaling pathway, was the gene with the largest fold change after AM intervention. However, in the <i>C. elegans pmk-1(km25)</i> mutant, the beneficial effect of AM in improving nematode senescence disappeared. An untargeted metabolomics study showed that the levels of 4-hydroxyproline, rhamnose, and cysteine were increased after AM supplementation, and their extending effect on the lifespan and health-span of <i>C. elegans</i> were partly dependent on the <i>pmk-1</i> gene. In conclusion, our results revealed that AM can promote the lifespan and health-span of <i>C. elegans via</i> the PMK-1 pathway, highlighting the potential of AM as a dietary supplement to delay aging.

Lalit F et al. (2025) Nucleic Acids Res "Selecting genes for analysis using historically contingent progress: from RNA changes to protein-protein interactions."

Lalit F, Jose AM

[Nucleic Acids Res, 2025]

Progress in biology has generated numerous lists of genes that share some property. But advancing from these lists of genes to understanding their roles is slow and unsystematic. Here we use RNA silencing in Caenorhabditis elegans to illustrate an approach for prioritizing genes for detailed study given limited resources. The partially subjective relationships between genes forged by both deduced functional relatedness and biased progress in the field were captured as mutual information and used to cluster genes that were frequently identified yet remain understudied. Some proteins encoded by these understudied genes are predicted to physically interact with known regulators of RNA silencing, suggesting feedback regulation. Predicted interactions with proteins that act in other processes and the clustering of studied genes among the most frequently perturbed suggest regulatory links connecting RNA silencing to other processes like the cell cycle and asymmetric cell division. Thus, among the gene products altered when a process is perturbed could be regulators of that process acting to restore homeostasis, which provides a way to use RNA sequencing to identify candidate protein-protein interactions. Together, the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process.

Galford KF et al. (2020) Chemosphere "The FDA-approved drugs ticlopidine, sertaconazole, and dexlansoprazole can cause morphological changes in C.elegans."

Jose AM, Galford KF

[Chemosphere, 2020]

Urgent need for treatments limit studies of therapeutic drugs before approval by regulatory agencies. Analyses of drugs after approval can therefore improve our understanding of their mechanism of action and enable better therapies. We screened a library of 1443 Food and Drug Administration (FDA)-approved drugs using a simple assay in the nematode C.elegans and found three compounds that caused morphological changes. While the anticoagulant ticlopidine and the antifungal sertaconazole caused both accumulations that resulted in distinct distortions of pharyngeal anatomy and lethality upon acute exposure, the proton-pump inhibitor dexlansoprazole caused molting defects and required exposure during larval development. Such easily detectable defects in a powerful genetic model system advocate the continued exploration of current medicines using a variety of model organisms to better understand drugs already prescribed to millions of patients.