Biology subjects

Patop, I. L.

Publications and source records attributed to Patop, I. L..

8 recordsLinked to original sources

bioRxiv2025

"Remote and partial clocks expand the circadian neuronal network, driving widespread molecular rhythmicity in Drosophila"

Circadian clocks orchestrate daily physiology and behavioral rhythms, yet the extent to which cells lacking canonical clock components exhibit robust temporal regulation remains unclear. Here we addressed this question using a two-step strategy. First, we systematically mapped core clock gene expression at single-cell resolution across the Drosophila brain and body. Second, leveraging these data and performing targeted experiments, we uncovered cells that lack most or all canonical clock components yet display strong mRNA rhythms. We found that lamina wide-field neurons show high-amplitude tim mRNA cycling even in constant darkness conditions (DD) despite minimal expression of other clock genes, suggesting a partial or noncanonical oscillator. In addition, C2 and C3 optic lobe neurons, which do not express core clock components, exhibit hundreds of circadian and daily cycling transcripts. Notably, circadian rhythms in C3 neurons coincide with oscillations of activity-regulated genes (ARGs), whereas C2 neurons cycle independently of ARGs, indicating distinct non-cell-autonomous mechanisms. These findings reveal a spectrum of circadian regulation, from autonomous to remote, input-driven rhythms and expand the circadian landscape to include strategies for generating and distributing temporal information across neuronal and non-neuronal cell types.

neuroscience↗

bioRxiv2025

Neuronal development shapes activity-dependent gene expression in a stimulus-specific manner

Neuronal activity-dependent gene expression is fundamental to a wide variety of brain functions. However, how development progress and stimulation modalities specifically affect neuron transcription is not fully understood. In this work, we first investigate the influence of development on neuronal firing and activity-driven transcription. We used an RNA sequencing approach over 7 days in vitro (DIV) or mature 21 DIV neurons, comparing neuronal depolarization with potassium chloride (KCl) versus Biccuculine application, a synaptic modality to induce neuronal activity. To further investigate how different activity patterns influence gene transcription in mature neurons, we compared global gene expression in neurons treated with three different and extensively used activation protocols: KCl, Bicuculine (Bic), and TTX withdrawal (TTXw). Our results demonstrate a strong influence of development on activity-dependent gene expression, and showed that different patterns of neuronal activity induce different transcriptional profiles and exhibit distinct temporal dynamics for the same genes. These findings offer novel insights into the complex relationship between neuronal activity and gene expression, shedding light on the context-dependent nature of activity-dependent transcriptional responses.

neuroscience↗

bioRxiv2024

Circular RNAs exhibit exceptional stability in the aging brain and serve as reliable age and experience indicators

Circular RNAs (circRNAs) comprise a large class of stable RNAs produced through backsplicing. While circRNAs have been shown to be very stable in cell culture, it is unknown how stable they are in vivo. Interestingly, studies across various animal systems demonstrated that circRNAs levels increase with age in neural tissue. However, the underlying reasons for this age-related accumulation are still unclear. To address these questions, we profiled circRNAs from fly heads at six timepoints across their lifespan. We found that circRNA levels increase linearly with age, independent of changes in mRNA levels, overall transcription, intron retention, or host genes splicing. This indicates that the age-related accumulation is attributed to their extraordinary stability in neural tissue rather than changes in biosynthesis. Furthermore, exposure to environmental stimuli like different temperatures, resulted in the increase but not decrease of circRNAs subsets, further confirming their stability in vivo. This exceptional stability implies that circRNAs can serve as markers of environmental experience. Indeed, flies subjected to a ten-day regimen at 29{degrees}C exhibit higher levels of specific brain circRNAs even six weeks after returning to standard conditions, indicating that circRNAs can reveal past environmental stimuli. Additionally, circRNA half-life measurements revealed values exceeding 20 days, with some showing no degradation over the animals lifetime. These findings demonstrate the extreme stability of circRNAs in vivo and their use as markers for aging, stress and life experiences.

neuroscience↗

bioRxiv2023

Organismal landscape of clock cells and circadian gene expression in Drosophila

BackgroundCircadian rhythms time physiological and behavioral processes to 24-hour cycles. It is generally assumed that most cells contain self-sustained circadian clocks that drive circadian rhythms in gene expression that ultimately generating circadian rhythms in physiology. While those clocks supposedly act cell autonomously, current work suggests that in Drosophila some of them can be adjusted by the brain circadian pacemaker through neuropeptides, like the Pigment Dispersing Factor (PDF). Despite these findings and the ample knowledge of the molecular clockwork, it is still unknown how circadian gene expression in Drosophila is achieved across the body. ResultsHere, we used single-cell and bulk RNAseq data to identify cells within the fly that express core-clock components. Surprisingly, we found that less than a third of the cell types in the fly express core-clock genes. Moreover, we identified Lamina wild field (Lawf) and Ponx-neuro positive (Poxn) neurons as putative new circadian neurons. In addition, we found several cell types that do not express core clock components but are highly enriched for cyclically expressed mRNAs. Strikingly, these cell types express the PDF receptor (Pdfr), suggesting that PDF drives rhythmic gene expression in many cell types in flies. Other cell types express both core circadian clock components and Pdfr, suggesting that in these cells, PDF regulates the phase of rhythmic gene expression. ConclusionsTogether, our data suggest three different mechanisms generate cyclic daily gene expression in cells and tissues: canonical endogenous canonical molecular clock, PDF signaling-driven expression, or a combination of both.

molecular biology↗

bioRxiv2021

SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1,000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.

molecular biology↗

bioRxiv2020

An in vivo strategy for knockdown of circular RNAs

Exonic circular RNAs (circRNAs) are highly abundant and evolutionarily conserved RNAs generated mostly from exons of protein-coding genes. Assaying the functions of circRNAs is not straightforward as common approaches for circRNA depletion tend to also alter the levels of mRNAs generated from the hosting gene. Here we describe a methodology for specific knockdown of circRNAs in vivo with tissue and cell resolution. We also describe an experimental and computational platform for determining the potential off-target effects as well as for verifying the obtained phenotypes. Briefly, we utilize miRNA-derived shRNAs targeted to the circRNA-specific back-splice junction to specifically downregulate the circRNA. We utilized this methodology to downregulate five circRNAs that are highly expressed in the fly nervous system. There were no effects on levels of the linear RNA or any RNA with complementarity to the expressed shRNA. Interestingly, downregulation of circCtrip resulted in developmental lethality that was recapitulated with a second shRNA. Moreover, we found that downregulation of individual circRNAs caused specific changes in the fly head transcriptome, suggesting roles for these circRNAs in the fly nervous system. Together, our results provide a methodological approach that enables the comprehensive study of circRNAs at the organismal and cell levels.

molecular biology↗

bioRxiv2018

Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila

Circadian rhythms are generated by the cyclic transcription, translation and degradation of clock genes, including timeless (tim). Currently, little is known about the mechanisms by which the circadian clock senses and adapts to temperature changes. Here we show that temperature dramatically changes the splicing pattern of tim. We found that at 18{degrees}C TIM protein levels are diminished due to the induction of two cold-specific splicing isoforms (tim-cold and tim-short&cold). At 29{degrees}C, another isoform, tim-Medium is strongly upregulated. We found that this isoform switching mechanism allows flies to regulate the levels and activity of TIM by setting miRNA-dependent thresholds for expression as well as by expressing isoforms with specific functions. Flies in which the production of tim-short&cold is abrogated display altered patterns of locomotor activity and altered tim expression. Interestingly, the introns of tim carry the information for the temperature sensitivity, suggesting that tim splicing per se is the temperature sensor.

neuroscience↗

bioRxiv2018

An in vivo knockdown strategy reveals multiple functions for circMbl

Circular RNAs (circRNAs) are highly abundant and evolutionary conserved RNAs of mostly unknown functions. circRNAs are enriched in the brain and accumulate with age in flies, worms and mice. Despite their abundance, little is known about their functions, especially in the context of whole organisms. Here we report the development and use of shRNAs to knock down and study the function of circMbl, the most abundant circRNA in Drosophila. This circRNA is highly conserved through evolution and is generated from the locus of the essential splicing factor muscleblind (mbl). Briefly, we generated flies in which circMbl is reduced more than 90% without measurable off-target effects in the hosting gene as well as in other RNAs. These flies display specific defects that suggest roles of circMbl in muscle and neural tissues during development and in adult flies. More specifically, whole organism downregulation of circMbl leads to male developmental lethality, altered gene expression, behavioral defects, wing posture- and flight defects. Moreover, these phenotypes are recapitulated by a second shRNA targeting circMbl. Importantly, knockdown and overexpression of circMbl affect mostly the same genes but in the opposite direction. Last but not least, downregulation of circMbl in the fly central nervous system caused abnormal synaptic function. Together, our results demonstrate the functionality of circMbl at the organismal level likely by acting in multiple tissues. Moreover, here we provide the first proof of functionality of circRNAs in Drosophila as well as a methodological approach that enables the comprehensive study of circRNAs in vivo.\n\nSIGNIFICANCE STATEMENTCircular RNAs (circRNAs) are highly abundant and evolutionary conserved RNAs of mostly unknown functions. Here we report the development and use of a shRNA-based system to knockdown specific circRNAs in vivo. We generated flies in which circMbl, the most abundant circRNA is reduced more than 90% without measurable off-target effects. These flies display male developmental lethality, altered gene expression, behavioral defects, wing posture- and flight defects. These phenotypes are recapitulated by a second shRNA targeting circMbl. Moreover, downregulation of circMbl in the fly central nervous system caused abnormal synaptic function. Together, our results demonstrate the functionality of circMbl at the organismal level and provide a methodological approach that enables the comprehensive study of circRNAs in vivo.

molecular biology↗