Biology subjects

Prahlad, V.

Publications and source records attributed to Prahlad, V..

6 recordsLinked to original sources

bioRxiv2025

piRNAs safeguard splicing and RNA fidelity during heat shock

Piwi-interacting RNAs (piRNAs) silence transposons and foreign sequences; yet, for poorly understood reasons, they also extensively target endogenous mRNAs. Here, we demonstrate that this targeting preserves transcript isoform fidelity by regulating pre-mRNA splicing in C. elegans. Using the heat shock response to provoke rapid transcriptional changes, we found that piRNAs and PIWI/PRG-1 direct the production of endogenous antisense 22G-RNAs from newly induced transcripts. These endo-siRNAs associate with RNA Polymerase II, spliceosome protein MOG-7/C2orf3/Ntr2, and nascent RNAs to delay splice completion and regulate splice-site selection. Long-read transcriptome sequencing revealed that loss of piRNAs accelerates splice completion but compromises accurate splice-site selection, increasing the production of aberrant transcript isoforms that are normally eliminated by alternative splicing coupled to nonsense-mediated decay (AS-NMD). Consequently, piRNA pathway mutants are profoundly reliant on NMD for embryonic survival, development, and proteostasis maintenance. Together, our findings identify a previously unrecognized role for the piRNA pathway in coordinating splicing with RNA quality control to preserve proteome integrity. We propose that this unexpected role for the piRNA pathway may have evolved from its ancestral function in recognizing transposable elements, which frequently introduce cryptic splice sites and undergo exonization, to generate novel transcripts that require elimination by NMD.

cell biology↗

bioRxiv2024

Robustness and variability in Caenorhabditis elegans dauer gene expression

Both plasticity and robustness are pervasive features of developmental programs. The dauer in Caenorhabditis elegans is an arrested, hypometabolic alternative to the third larval stage of the nematode. Dauers undergo dramatic tissue remodeling and extensive physiological, metabolic, behavioral, and gene expression changes compared to conspecifics that continue development and can be induced by several adverse environments or genetic mutations that act as independent and parallel inputs into the larval developmental program. Therefore, dauer induction is an example of phenotypic plasticity. However, whether gene expression in dauer larvae induced to arrest development by different genetic or environmental triggers is invariant or varies depending on their route into dauer has not been examined. By using RNA-sequencing to characterize gene expression in different types of dauer larvae and computing the variance and concordance within Gene Ontologies (GO) and gene expression networks, we find that the expression patterns within most pathways are strongly correlated between dauer larvae, suggestive of transcriptional robustness. However, gene expression within specific defense pathways, pathways regulating some morphological traits, and several metabolic pathways differ between the dauer larvae. We speculate that the transcriptional robustness of core dauer pathways allows for the buffering of variation in the expression of genes involved in adaptation, allowing the dauers induced by different stimuli to survive in and exploit different niches.

bioinformatics↗

bioRxiv2022

Neuronal IL-17 controls C. elegans developmental diapause through p53/CEP-1

During metazoan development, how cell division and metabolic programs are coordinated with nutrient availability remains unclear. Here, we show that nutrient availability signaled by the neuronal cytokine, ILC-17.1 switches C. elegans development between reproductive growth and dormancy by controlling the activity of the tumor suppressor p53 ortholog, CEP-1. Specifically, upon food availability, ILC-17.1 signaling by amphid neurons promotes glucose utilization and suppresses CEP-1/p53 to allow growth. In the absence of ILC-17.1, CEP-1/p53 is activated, upregulates cell-cycle inhibitors, decreases phosphofructokinase and cytochrome C expression, and causes larvae to arrest as stress-resistant, quiescent dauers. We propose a model whereby ILC-17.1 signaling links nutrient availability and energy metabolism to cell cycle progression through CEP-1/p53. These studies describe ancestral functions of IL-17s and the p53-family of proteins and are relevant to our understanding of neuroimmune mechanisms in cancer. They also reveal a DNA damage-independent function of CEP-1/p53 in invertebrate development and support the existence of a previously undescribed C. elegans dauer pathway. During metazoan development, nutrient availability is coordinated with the division, growth and metabolic activity of individual cells through cell-cell communication. This is also the case in the invertebrate C. elegans, a free-living bacterivore, which displays a dramatic developmental plasticity to ensure that its growth and reproduction match available resources(1-10). When C. elegans larvae hatch under optimal conditions (at 20{degrees}C, low population densities, on abundant food) they develop continuously into reproducing adults. However, if they hatch under suboptimal conditions, such as in the paucity of food, at high population densities, or high ambient temperatures, larvae implement an alternative developmental program and arrest as quiescent, stress-resistant larvae called dauer larvae. Dauer larvae display metabolic and organismal phenotypes specialized for dispersal and survival, and can remain arrested in this state for months to resume development into reproductive adults when favorable conditions return(1-10). Previous studies have identified molecular pathways that mediate the dauer decision, showing that growth promoting molecules like insulins, transforming {beta} growth factor (TGF{beta}/DAF-7) and lipid based dafachronic acid hormones are released by sensory neurons and other cells to license continued development; adverse environments inhibit these growth promoting signals and trigger dauer arrest(1-11). A number of quantitative trait loci (QTL) also modulate dauer (12). Yet, how the dauer entry decision results in a coordinated change in cell fates across different tissues and is linked with the systemic shut-down of anabolic pathways remains poorly understood. An important group of proteins that mediate cell-cell communication and metabolism in metazoa are secreted proteins called cytokines(13, 14). The IL-17 cytokines constitute a family of proinflammatory cytokines, highly conserved across animal phyla. In mammals, these cytokines are released by specialized immune cells to activate immune surveillance, enhance barrier function, promote wound healing, and play crucial immunometabolic roles in maintaining energy homeostasis(15). In humans, IL-17s also promote cancers and autoimmune disease such as psoriasis(16, 17). Here, we show that the C. elegans IL-17 ortholog, ILC-17.1, signals food availability, and coordinates cell division with metabolism by controlling the activity of the C. elegans tumor suppressor p53 ortholog, CEP-1. Specifically, neuronal ILC-17.1 suppresses CEP-1/p53 activity in the presence of food to license growth. Upon the loss of ILC-17.1 signaling, CEP-1/p53 is activated, and remarkably, this switches whole organism development from continuous growth to dormancy. The p53-like tumor suppressor genes are found in all multicellular animals where they prevent the transmission of damaged DNA by activating a multifaceted program that controls cell cycle checkpoints, mediates reversible growth arrest or apoptosis, and controls metabolic flux (18-22). Our studies show that these functions of CEP-1/p53 also act, in the absence of DNA damage, to control developmental quiescence of C. elegans, suggesting that the developmental function of the p53-gene family could have shaped their evolution(23-25). SignificanceDevelopment in a metazoan requires that the division and differentiation of diverse cells be coordinated with nutrient availability. We show that one mechanism by which this occurs in C. elegans is through signaling by the neuronal IL-17 cytokine, ILC-17.1, and its control over p53/CEP-1. In the presence of food, ILC-17.1 release suppresses p53/CEP-1 and allows reproductive growth; decreased ILC-17.1 signaling activates p53/CEP-1-dependent transcription and metabolic programs, leading to the reversible arrest of larvae as quiescent dauers. Our studies suggest an ancestral function of IL-17 is linking nutrient availability to energy metabolism and growth. They reveal a DNA damage-independent function of p53/CEP-1 in invertebrate development. Finally, our studies support the existence of a previously undescribed dauer pathway in C. elegans.

developmental biology↗

bioRxiv2021

Germline activity of the heat shock factor HSF-1 programs the insulin-receptor daf-2 in C. elegans

The mechanisms by which maternal stress alters offspring phenotypes remain poorly understood. Here we report that the heat shock transcription factor HSF-1, activated in the C. elegans maternal germline upon stress, epigenetically programs the insulin-like receptor daf-2 by increasing repressive H3K9me2 levels throughout the daf-2 gene. This increase occurs by the recruitment of the C. elegans SETDB1 homolog MET-2 by HSF-1. Increased H3K9me2 levels at daf-2 persist in offspring to downregulate daf-2, activate the C. elegans FOXO ortholog DAF-16 and enhance offspring stress resilience. Thus, HSF-1 activity in the mother promotes the early life programming of the insulin/IGF-1 signaling (IIS) pathway and determines the strategy of stress resilience in progeny. One Sentence SummaryHSF-1 recruits MET-2 to silence daf-2 and mediate early life programming of C. elegans upon stress

cell biology↗

bioRxiv2020

Serotonin signaling by maternal neurons upon stress ensures progeny survival

Germ cells are vulnerable to stress. Therefore, how organisms protect their future progeny from damage in a fluctuating environment is a fundamental question in biology. We show that in Caenorhabditis elegans, serotonin released by maternal neurons during stress ensures the viability and stress tolerance of future offspring by enabling the transcription factor HSF1 to alter chromatin in soon-to-be fertilized germ cells by recruiting the histone chaperone FACT, displacing histones, and initiating protective gene expression. Without maternal serotonin signaling by neurons, FACT is not recruited by HSF1 in germ cells, transcription occurs but is delayed, and progeny of stressed C. elegans mothers fail to complete development. Serotonin acts through a signal transduction pathway conserved between C. elegans and mammalian cells to facilitate HSF1 to recruit FACT. These studies uncover a novel mechanism by which stress sensing by neurons is coupled to transcription response times of germ cells to protect future offspring.

cell biology↗

bioRxiv2017

Olfactory learning modulates the expression of molecular chaperones in C. elegans

Learning, a process by which animals modify their behavior as a result of experience, allows organisms to synthesize information from their surroundings to acquire resources and predict danger. Here we show that prior encounter with the odor of pathogenic bacteria prepares Caenorhabditis elegans to survive actual exposure to the pathogen by increasing HSF-1-dependent expression of genes encoding molecular chaperones. Learning-mediated enhancement of chaperone gene expression requires serotonin. Serotonin primes HSF-1 to enhance the expression of molecular chaperone genes by promoting its localization to RNA polymerase II-enriched nuclear loci, even prior to transcription. HSF-1-dependent chaperone gene expression ensues, however, only if and when animals encounter the pathogen. Thus, learning equips C. elegans to better survive environmental dangers by pre-emptively and specifically initiating transcriptional mechanisms throughout the whole organism. These studies provide one plausible basis for the protective role of environmental enrichment in disease.

cell biology↗