Biology subjects

Anbalagan, S.

Publications and source records attributed to Anbalagan, S..

6 recordsLinked to original sources

bioRxiv2024

Targeted blocking of gene splicing can dysregulate intron-embedded microRNAs

ASOs (antisense oligonucleotides) are a promising therapeutic approach for suppression, induction of gene expression or the correction of aberrant splicing. Addressing whether ASOs targeting genes embedded with intronic noncoding RNAs (ncRNAs) affect the expression and function of intronic ncRNAs is of importance to the success of ASOs in clinical trials. While studying the development of the zebrafish posterior pituitary (neurohypophysis), an important neuroendocrine interface, we observed that an ASO targeting the splice site, in contrast to the one targeting the translation site of the gene slit3, disrupts neurohypophyseal axonal morphogenesis. In addition to altered slit3 splicing, we also observed an increase in the expression of slit3 and slit3 intron-embedded primary mir218a-1 transcripts. The ASO-induced phenotype was not observed when mature mir218a-1 was blocked by an ASO or in mir218a-1-/- mutants. In addition, we also found that previously reported phenotypes due to ASOs targeting the splice site of pank2 and dnm2a were partially rescued when the mature mir103 and mir199-5p embedded in their introns, respectively, were blocked by ASOs. Our observation that ASOs targeting splice sites can affect intronic microRNA expression and function warrants further validation for other classes of ncRNAs. In addition, the idiosyncratic phenotypes when using translation and splice-blocking ASOs can be potentially used as a marker to identify the role of intronic ncRNAs.

molecular biology↗

bioRxiv2022

A ligand-receptor interactome atlas of the zebrafish

Studies in zebrafish can unravel the functions of cellular communication and thus identify novel bench-to-bedside drugs targeting cellular communication signaling molecules. Due to the incomplete annotation of zebrafish proteome, the knowledge of zebrafish receptome, secretome and tools to explore their interactome is limited. To address this gap, we de novo predicted the cellular localization of zebrafish reference proteome using deep learning algorithm. We combined the predicted and existing annotations on cellular localization of zebrafish proteins, and created repositories of zebrafish secretome, receptome, and interactome as well as associated diseases and targeting drugs. Unlike other tools, our interactome atlas is primarily based on physical interaction data of zebrafish proteome. The resources are available as R and Python scripts (https://github.com/DanioTalk). DanioTalk provides a novel resource for researchers interested in targeting cellular communication in zebrafish, as we demonstrate in applications studying synapse and axo-glial interactome.

developmental biology↗

bioRxiv2022

Regulation of mannitol metabolism in Enterococcus faecalis and association with parEF0409 toxin-antitoxin locus function.

The parEF0409 type I toxin-antitoxin locus is situated between genes for two paralogous mannitol-family phosphoenolpyruvate phosphotransferase systems (PTS). In order to address the possibility that parEF0409 function was associated with sugar metabolism, genetic and phenotypic analyses were performed on the flanking genes. It was found that the genes were transcribed as two operons; the downstream operon essential for mannitol transport and metabolism and the upstream operon performing a regulatory function. In addition to genes for the PTS components, the upstream operon encodes a gene similar to mtlR, the key regulator of mannitol metabolism in other Gram-positive bacteria. We confirmed that this gene is essential for regulation of the downstream operon and identified putative phosphorylation sites required for carbon catabolite repression and mannitol-specific regulation. Genomic comparisons revealed that this dual operon organization of mannitol utilization genes is uncommon in enterococci and that association with a toxin-antitoxin system is unique to E. faecalis. Finally, we consider possible links between parEF0409 function and mannitol utilization. ImportanceEnterococcus faecalis is both a common member of the human gut microbiota and an opportunistic pathogen. Its evolutionary success is partially due to its metabolic flexibility: in particular, its ability to import and metabolize a wide variety of sugars. While a large number of phosphoenolpyruvate phosphotransferase sugar transport systems have been identified in the E. faecalis genome bioinformatically, the specificity and regulation of most of these systems remains undetermined. Here we characterize a complex system of two operons flanking a type I toxin-antitoxin system required for the transport and metabolism of the common dietary sugar mannitol. We also determine the phylogenetic distribution of mannitol utilization genes in the enterococcal genus and discuss the significance of association with toxin-antitoxin systems.

microbiology↗

bioRxiv2022

Stress resilience is established during development and is regulated by complement factors

Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently, others are susceptible to the same stressors. However, it remains challenging to identify resilience in mammalian embryos to determine if stress resilience is established as a trait during development or acquired later in life. Using a new behavioural paradigm in zebrafish larvae, we show that resilience is a trait that is determined and exhibited early in life. Resilient and susceptible individuals retained these traits throughout life and passed them on to the next generation. Resilient larvae showed higher expression of resilience-associated genes and larvae lacking neuropeptide Y and miR218 were significantly under-represented in the resilient population. Unbiased transcriptome analysis revealed that multiple factors of the innate immune complement cascade were downregulated in resilient larvae in response to stressors. Pharmacological inhibition and genetic knockouts of critical complement factors led to an increase in resilience. We conclude that resilience is established early during development as a stable trait, and that neuropeptides and the complement pathway play positive and negative roles in determining resilience respectively. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/478444v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@359261org.highwire.dtl.DTLVardef@11d1e62org.highwire.dtl.DTLVardef@b5d346org.highwire.dtl.DTLVardef@141bae1_HPS_FORMAT_FIGEXP M_FIG C_FIG Why some individual individuals recover better than others from stressful situations is unclear. We show that resilience to stress is established during zebrafish development as a stable and heritable trait. Resilience is augmented by brain-derived neuropeptides and attenuated by innate immune complement factors specifically expressed in the liver. HighlightsO_LIWildtype zebrafish larvae show differences in their dynamics of recovering from stress, with some being more resilient than others. C_LIO_LIResilience is a stable and heritable trait. C_LIO_LIResilient fish show specific stress-responsive transcriptional changes. C_LIO_LINeuropeptide Y and miRNA218 positively affect resilience, while innate immune complement factors attenuate resilience. C_LI

neuroscience↗

bioRxiv2020

Genetic variation in the social environment affects behavioral phenotypes of oxytocin receptor mutants in zebrafish

Oxytocin-like peptides have been implicated in the regulation of a wide range of social behaviors across taxa. On the other hand, the social environment, which is composed of conspecifics genotypes, is also known to influence the development of social behavior, creating the possibility for indirect genetic effects. Here we used a knockout line for the oxytocin receptor in zebrafish to investigate how the genotypic composition of the social environment (Es) interacts with the oxytocin genotype (G) of the focal individual in the regulation of its social behavior. For this purpose, we have raised wild-type or knock-out zebrafish in either wild-type or knock-out shoals and tested different components of social behavior in adults. GxEs effects were detected in some behaviors, highlighting the need to control for GxEs effects when interpreting results of experiments using genetically modified animals, since the social environment can either rescue or promote phenotypes associated with specific genes.

ecology↗

bioRxiv2019

Robo2 regulates synaptic oxytocin content by affecting actin state

The regulation of neuropeptide level at the site of release is essential for proper neurophysiological functions. We focused on a prominent neuropeptide, oxytocin (OXT), and used the zebrafish as an in vivo model to visualize and quantify OXT content at the resolution of a single synapse. We found that OXT-loaded synapses were surrounded by polymerized actin. Perturbation of actin filaments by cytochalasin-D resulted in decreased synaptic OXT levels. Live imaging of the actin probe, Lifeact-EGFP, showed reduced mobility in OXT synapses in robo2 mutants, which displayed decreased synaptic OXT content. Using a novel transgenic reporter line allowing real-time monitoring of OXT-loaded vesicles, we showed that robo2 mutants display slower rate of vesicles accumulation. OXT-specific expression of dominant-negative Cdc42, which is a key regulator of actin dynamics and a downstream effector of Robo2, led to a dose-dependent increase in OXT content in WT, and a dampened effect in robo2 mutants. Our results link Robo2-Cdc42 signalling, which controls local actin dynamics, with the maintenance of synaptic neuropeptide levels.

developmental biology↗