Biology subjects

Jose, A. M.

Publications and source records attributed to Jose, A. M..

11 recordsLinked to original sources

bioRxiv2026

Two SID-1-dependent genes sensitive to heritable epigenetic changes can also impact reproduction

Import of double-stranded RNA (dsRNA) into the germ line can have consequences that last for many generations. However, the role of such transgenerational regulation by extracellular dsRNA is unclear. In the nematode C. elegans, entry of dsRNA into the cytosol requires the transmembrane protein SID-1 and loss of SID-1 for a few generations causes changes in gene expression that can persist for hundreds of generations. Here we report an expanded number of such SID-1-dependent genes (SDGs) and analyze two germline-expressed SDGs: sdg-1 and sdg-2. Deleting sdg-1 reduces brood size in some lineages. An endogenous SDG-1::mCherry fusion protein shows conditional enrichment within nuclei, colocalization with perinuclear germ granules, and colocalization with microtubules. Although animals with SDG-1::mCherry have a normal brood size, they have fewer early progeny with some animals showing defective germline morphology. Deleting the sdg-1 open reading frame eliminates defects in most but not all the animals that express mCherry in a now sdg-1(-) background, suggesting transgenerational consequences of SDG-1::mCherry that persist in some siblings lacking sdg-1. Deleting sdg-2 also reduces brood size in some lineages. An endogenous SDG-2::mCherry fusion protein is constitutively detectable in the cytoplasm and nucleus. The sequence and predicted structure of SDG-2 suggest that it can interact with the Gli-type transcription factor TRA-1, which regulates spermatogenesis. Together, these results suggest that changes in SDG-1 or SDG-2 can impact reproduction. Therefore, the import of extracellular dsRNA or other SID-1 function(s) that regulate SDGs could have evolved to modulate the lingering impacts of ancestral epigenetic changes.

genetics↗

bioRxiv2024

Reliable odorant sensing but variable associative learning in C. elegans

Animals can move towards or away from an odorant. Such chemotaxis has been used as a paradigm for learning when coupled with pre-exposure to the sensed odorant. Here we develop an assay for the nematode C. elegans that avoids the typical use of chemical or physical immobilization when measuring the response of worms to odorants. Using two sets of rectangular arenas that are oriented such that worms in one set must move in the opposite direction to worms in the other set for the same response, we found that unfed worms show reproducible movement towards the odorants butanone and benzaldehyde, and away from the odorant nonanone. In addition to the use of opposing orientations to control for gradients of unknown cues outside the arena, we introduce a measure of dispersal to control for locomotion defects and unknown cues within the arena. Since this assay avoids the use of paralytics or physical constraints, it is useful for the analysis of graded responses to a variety of chemicals and the discovery of underlying molecular mechanisms. Using this setup, we found that pre-exposure of unfed worms to butanone to induce an association of starvation with butanone resulted in different extents of such associative learning during different trials - from no learning to learned avoidance. Given this variation in associative learning despite the artificially controlled lab setting, we speculate that in dynamic natural environments such learning might be rare and highlight the challenge in discovering evolutionarily selected mechanisms that could underlie learning in the wild.

animal behavior and cognition↗

bioRxiv2024

Selecting genes for analysis using historically contingent progress

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 C. 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 was 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.

bioinformatics↗

bioRxiv2024

Evidence for multiple forms of heritable RNA silencing

Heritable gene silencing has been proposed to rely on DNA methylation, histone modifications, and/or non-coding RNAs in different organisms. Here we demonstrate that multiple RNA-mediated mechanisms with distinct and easily detectable molecular signatures can underlie heritable silencing of the same open-reading frame in the nematode C. elegans. Using two-gene operons, we reveal three cases of gene-selective silencing that provide support for the transmission of heritable epigenetic changes through different mechanisms of RNA silencing independent of changes in chromatin that would affect all genes of an operon equally. Different heritable epigenetic states of a gene were associated with distinct populations of stabilized mRNA fragments with untemplated poly-UG (pUG) tails, which are known intermediates of RNA silencing. These pUG signatures provide a way to distinguish the multiple mechanisms that can drive heritable RNA silencing of a single gene.

genetics↗

bioRxiv2023

Heritable epigenetic changes are constrained by the dynamics of regulatory architectures

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. Such stable changes can (1) alter steady-state levels while preserving the architecture, (2) induce different architectures that persist for many generations, or (3) collapse the entire architecture. Architectures that are otherwise unstable can become heritable through periodic interactions with external regulators, which suggests that the evolution of mortal somatic lineages with cells that reproducibly interact with the immortal germ lineage could make a wider variety of regulatory 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 C. elegans, which range from permanent silencing to recovery from silencing within a few generations and subsequent resistance to silencing. 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.

systems biology↗

bioRxiv2023

Target-specific requirements for RNA interference can be explained by a single regulatory network

Since double-stranded RNA (dsRNA) is effective for silencing a wide variety of genes, all genes are typically considered equivalent targets for such RNA interference (RNAi). Yet, loss of some regulators of RNAi in the nematode C. elegans can selectively impair the silencing of some genes. Here we show that such selective requirements can be explained by an intersecting network of regulators acting on genes with differences in their RNA metabolism. In this network, the Maelstrom domain-containing protein RDE-10, the intrinsically disordered protein MUT-16, and the Argonaute protein NRDE-3 work together so that any two are required for silencing one somatic gene, but each is singly required for silencing another somatic gene, where only the requirement for NRDE-3 can be overcome by enhanced dsRNA processing. Quantitative models and their exploratory simulations led us to find that (1) changing cis-regulatory elements of the target gene can reduce the dependence on NRDE-3, (2) animals can recover from silencing in non-dividing cells and (3) cleavage and tailing of mRNAs with UG dinucleotides, which makes them templates for amplifying small RNAs, is enriched within pUG zones matching the dsRNA. Similar crosstalk between pathways and restricted amplification could result in apparently selective silencing by endogenous RNAs.

genetics↗

bioRxiv2021

Intercellular transport of RNA can limit heritable epigenetic changes

RNAs in circulation carry sequence-specific regulatory information between cells in plant, animal, and host-pathogen systems. Such RNA can cross generational boundaries, as evidenced by somatic double-stranded RNA (dsRNA) in the nematode C. elegans silencing genes of matching sequence in progeny. Here we dissect the intergenerational path taken by dsRNA from parental circulation and discover that cytosolic import through the dsRNA importer SID-1 in the parental germline and/or developing progeny varies with developmental time and dsRNA substrates. Loss of SID-1 enhances initiation of heritable RNA silencing within the germline and causes changes in the expression of the sid-1-dependent gene sdg-1 that last for more than 100 generations after restoration of SID-1. The SDG-1 protein is enriched in perinuclear germ granules required for heritable RNA silencing but is expressed from a retrotransposon targeted by such silencing. This auto-inhibitory loop suggests how retrotransposons could persist by hosting genes that regulate their own silencing.

genetics↗

bioRxiv2020

The FDA-approved drugs ticlopidine, sertaconazole, and dexlansoprazole can cause morphological changes in C. elegans

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 morphologically distinct pharyngeal defects 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.

pharmacology and toxicology↗

bioRxiv2018

Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference

Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematode C. elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissue-specific - EGO-1 in the germline and RRF-1 in somatic cells. Here we analyze instances of silencing in somatic cells that lack RRF-1. By varying dsRNA sources and target genes, we find that silencing in the absence of RRF-1 is most obvious when dsRNA from neurons is used to silence genes in intestinal cells. This silencing requires EGO-1, but the lineal identity of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. As a result, all cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against the use of a few molecules as proxies for predicting the behavior of a cell.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC=\"FIGDIR/small/393074v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@f61659org.highwire.dtl.DTLVardef@3535c2org.highwire.dtl.DTLVardef@15c59d0org.highwire.dtl.DTLVardef@ca4ef_HPS_FORMAT_FIGEXP M_FIG C_FIG Random sets of cells can either receive different amounts of double-stranded RNA from neurons or use different RdRPs - RRF-1 only versus RRF-1 or EGO-1 - to perform the same function.

genetics↗

bioRxiv2017

Cell code: the evolving arrangement of molecules that perpetuates life

Life is perpetuated through a single-cell bottleneck between generations in many organisms. Here, I highlight that this cell holds information in two distinct forms: in the linear DNA sequence that is replicated during cell divisions, and in the three-dimensional arrangement of molecules that can change during development but that is recreated at the start of each generation. These two interdependent stores of information - one replicating with each cell division and the other cycling with a period of one generation - coevolve while perpetuating an organism. Unlike the genome, the cycling arrangement of molecules, which could include RNAs, proteins, sugars, lipids, etc., is not well understood. Because this arrangement and the genome are together transmitted from one generation to the next, analysis of both is necessary to understand evolution, origins of inherited diseases, and consequences of genome engineering. Recent developments suggest that tools are in place to examine how all the information to build an organism is encoded within a single cell, and how this cell code is reproduced in every generation.

developmental biology↗

bioRxiv2017

Mating can cause transgenerational gene silencing in Caenorhabditis elegans

Changes in gene expression that last for multiple generations without changes in gene sequence have been reported in many plants and animals1-3. Cases of such transgenerational epigenetic inheritance (TEI) could support the ancestral origins of some diseases and drive evolutionary novelty. Here, we report that stably expressed sequences in C. elegans have features that provide a barrier against TEI. By using double-stranded RNA (dsRNA) targeting the same sequence in different genes, we show that genes typically recover from silencing within the germline in a few generations. A rare recombinant two-gene operon containing this target sequence that recovered poorly from induced silencing enabled us to delineate mechanisms that can perpetuate silencing. Parental exposure to dsRNA targeting one gene within this operon reveals two distinct phases of the resulting TEI: only the matching gene is silenced in early generations, but both can become silenced in later generations. However, silencing of both genes can be initiated within one generation by mating, which perturbs intergenerational RNA-based mechanisms such that silencing dominates for more than 250 generations. This stable RNA silencing can also reduce the expression of homologous sequences in different genes in trans within the germline, but the homologous genes recover expression after a few generations. These results suggest that stably expressed sequences are subject to feedback control that opposes TEI initiated by multiple mechanisms within the germline. We speculate that similar homeostatic mechanisms that enable recovery from epigenetic changes underlie the observed preservation of form and function in successive generations of living systems.

genetics↗