Biology subjects

Rajesh, R.

Publications and source records attributed to Rajesh, R..

8 recordsLinked to original sources

bioRxiv2026

Temporal regulation of a spatial patterning factor in Drosophila neurogenesis

A central question in neurobiology is how the transient programs that pattern neural progenitors are translated into the enormous, stable diversity of neuronal types. Spatial and temporal cues act only briefly, yet each neuron's identity is defined and maintained for life by terminal selector transcription factors (TFs). How a neuron's developmental origin is read out into a particular selector code remains poorly understood. Some current models propose that spatial and temporal origins are inherited independently through separate selectors. We show instead that, in the Drosophila optic lobe, the same selector can be activated by different patterning axes through physically distinct enhancers, even within the same lineage. Visual system homeobox (Vsx1) spatially patterns a central neuroepithelial domain and later acts as a terminal selector in dozens of neuronal types, most originating exclusively from that domain. However, in Dm2 neurons that are produced from every domain, it is regulated not by neuroepithelial Vsx1 but by the neuroblast temporal TF BarH1, through an enhancer distinct from its domain-specific ones. Combining in vivo reporters with sequence-to-accessibility deep-learning models, we identify and disrupt the key binding sites in this enhancer, impairing its Dm2-specific activity. Reciprocally, the temporal TF Homeobrain (Hbn) acts as a terminal selector in the related neuron Mi21 independently of its neuroblast temporal window: its expression in these late-born neurons is instead placed under dorsoventral spatial control. Patterning inputs therefore need not be partitioned across separate selectors but converge combinatorially on the modular enhancers of shared ones, revealing a cis-regulatory logic that re-encodes this limited set of inputs into vast neuronal diversity.

neuroscience↗

bioRxiv2026

A habenula-enriched GPCR, GPR151, regulates behavioral sensitivity to inflammation

BackgroundInflammation-associated depression is a subtype of major depressive disorder that is often resistant to conventional pharmacotherapies, which act in a regionally non-specific manner and therefore also produce unwanted side effects. Here we test GPR151, an orphan GPCR associated with inflammation and highly expressed in the habenula--a region linked to negative valence and depression--as a therapeutic target for inflammation-associated depression. MethodsWe integrated mouse and human habenular expression analyses with genetic loss-of-function and adult habenular re-expression approaches in mice. Gpr151 knockout mice and littermate controls were exposed to lipopolysaccharide (LPS) inflammatory challenge and assessed for stress coping and motivated behavior, body weight loss, and peripheral immune activation. To test whether adult habenular GPR151 expression is sufficient to restore inflammation-associated behavioral vulnerability, GPR151 was re-expressed in the habenula of knockout mice. ResultsGPR151 was exceptionally enriched in the habenula and showed conserved topographic organization and similar expression relationships with habenular marker genes in mice and humans. Following LPS challenge, male Gpr151 knockout mice showed reduced passive coping despite body weight loss and immune activation comparable to littermate controls. Adult habenular GPR151 re-expression increased LPS-induced amotivation in male knockout mice without increasing LPS-induced weight loss or immune activation. Female Gpr151 knockout mice also showed reduced passive coping after LPS challenge; however, habenular GPR151 re-expression was insufficient to increase LPS-induced amotivation in females. ConclusionsThese findings identify GPR151 as a conserved, regionally enriched regulator of behavioral sensitivity to inflammatory challenge and support GPR151 as a candidate therapeutic target for inflammation-associated depression.

neuroscience↗

bioRxiv2026

Evolutionary rise of a synaptic mechanism for creating and diversifying key reinforcement signals

Most neurons release either excitatory or inhibitory neurotransmitters. However, multiple inputs to the lateral habenula (LHb) co-transmit glutamate and GABA, transmitters with opposing effects on LHb output. Although the LHb has an established role in reinforcement learning, the adaptive significance of glutamate/GABA co-release remains unclear. Using experimentally informed simulations, we show that GABA co-release is sufficient to produce temporal difference (TD)-like transformations of input activity, computations commonly used for reinforcement learning and behavioral optimization. Heterogeneous GABA-to-glutamate ratios, like those found among LHb neurons ex vivo, produce diverse TD-like computations linked to higher-order decision-making. Single-cell RNA-sequencing analysis and machine-learning image analysis further indicate that glutamate/GABA co-release expanded across vertebrate evolution, from fish to mice, rats, and monkeys. Evolutionary expansion of glutamate/GABA co-release may have supported increasingly sophisticated learning and decision-making that contribute to intelligent behavior.

neuroscience↗

bioRxiv2026

Phenology of 50 tree species across 9 years in a South Asian tropical rainforest indicates complex influence of climate, traits, and phylogeny

In relatively aseasonal tropical rainforests, few studies have explored long-term phenological patterns of a high diversity of tree species in relation to climate, phylogeny, and functional traits. In these systems, short-duration seasonal pulses of irradiance and water deficit are expected to provide narrower windows for leafing and flowering and wider windows for fruiting across prolonged wet seasons, potentially mediated by functional traits and phylogenetic relatedness. Here, we document leafing, flowering, and fruiting phenology of 50 tree species (920 - 1077 trees, 10 - 42 trees/species) monitored monthly over an 9-y period (2017 - 26) in a relatively aseasonal south Asian tropical rainforest in the Anamalai Hills, Western Ghats, India. We examined correlations between climatic variables (irradiance, daylength, temperature, precipitation) and tree phenology and Mantel correlations among similarity in monthly phenology, functional traits (wood density, seed size, and maximum height), and phylogenetic relatedness. We then investigated the phylogenetic signal of phenological traits (frequency, amplitude, duration, and peak month) using Pagels {lambda}. Leaf flushing and flowering showed distinct seasonality and negative associations with daylength and precipitation, whereas fruiting showed greater temporal spread and weaker associations with climate. Functional traits or phylogeny did not significantly influence leaf flushing and flowering, whereas dissimilarity in fruiting was correlated with phylogenetic distance and peak fruiting month showed a significant phylogenetic signal ({lambda} = 0.96). The results indicate that in relatively aseasonal tropical rainforests, proximate climatic cues more strongly influence leaf flushing and flowering, whereas phylogenetic constraints affect timing of fruiting and may cause lineage-specific vulnerabilities to climate change.

ecology↗

bioRxiv2025

Regulatory logic of neuronal identity specification in Drosophila

Combinations of terminal selector transcription factors (tsTFs) are thought to establish and maintain the unique identities of the numerous cell types found in nervous systems. However, it remains largely unclear how tsTF combinations are specified during development, and how they then coordinate the type-specific differentiation programs of each neuron. To investigate these regulatory mechanisms, we performed simultaneous single-cell RNA and ATAC sequencing on the Drosophila optic lobes at four stages of their development and identified over 250 distinct cell types. We characterized the common cis-regulatory features of neuronal enhancers and performed comprehensive inference of gene regulatory networks across cell types and stages. Our results reveal cell-type and stage-specific enhancers of many neuronal genes and the cooperative actions of tsTFs, pan-neuronal and ecdysone-responsive TFs on these enhancers. We show that the same effector genes are often regulated by different tsTF combinations acting through distinct enhancers in different neurons. During neurogenesis, tsTF codes are established within a brief critical period in newborn neurons, often through cell-type-specific enhancers that are not accessible in their progenitors. Accordingly, when neuroblast temporal patterning TFs are re-utilized as tsTFs in neurons, they are regulated independently through separate enhancers. Therefore, neuronal identity specification and differentiation is a multi-step regulatory program, wherein the same TFs enact distinct regulatory codes at different steps and across cell types.

neuroscience↗

bioRxiv2024

Morphological and functional convergence of visual projections neurons from diverse neurogenic origins in Drosophila

The Drosophila visual system is a powerful model to study the development of neural circuits. Projection neurons that relay visual information from the lobula part of the optic lobe to the central brain (the lobula columnar neurons-LCNs), are thought to encode different visual features relevant to natural behavior. There are [~]20 classes of LCNs whose projections form highly specific, non-overlapping synaptic domains in the brain called optic glomeruli. Although functional investigations of several LCN circuits have been carried out, very little is known about their developmental origin and the stem cell lineages that generate the LCN subtypes. To address their origin, we used single-cell mRNA sequencing to define the transcriptome of each LCN subtype and identified driver lines that are expressed in specific LCNs throughout development. We show that LCNs originate from neural stem cells in four distinct regions in the fly brain that exhibit different modes of neurogenesis, including the ventral and dorsal tips of the outer proliferation center (tOPC), the ventral tips of the inner proliferation center (vtIPC) and the central brain (CB). This convergence of similar neurons illustrates the complexity of generating neuronal diversity in the brain and likely reflects the evolutionary origin of each LCN subtype that detects a highly specific visual feature and influence behaviors that might be specific to each species.

neuroscience↗

bioRxiv2023

A PI(3,4,5)P3-dependent allosteric switch controls antigenic variation in trypanosomes

African trypanosomes evade host immune clearance by antigenic variation, causing persistent infections in humans and animals. These parasites express a homogeneous surface coat of variant surface glycoproteins (VSGs). They transcribe one out of hundreds of VSG genes at a time from telomeric expression sites (ESs) and periodically change the VSG expressed by transcriptional switching or recombination. The mechanisms underlying the control of VSG switching and its developmental silencing remain elusive. We report that telomeric ES activation and silencing entail an on/off genetic switch controlled by a nuclear phosphoinositide signaling system. This system includes a nuclear phosphatidylinositol 5-phosphatase (PIP5Pase), its substrate PI(3,4,5)P3, and the repressor-activator protein 1 (RAP1). RAP1 binds to ES sequences flanking VSG genes via its DNA binding domains and represses VSG transcription. In contrast, PI(3,4,5)P3 binds to the N-terminus of RAP1 and controls its DNA binding activity. Transient inactivation of PIP5Pase results in the accumulation of nuclear PI(3,4,5)P3, which binds RAP1 and displaces it from ESs, activating transcription of silent ESs and VSG switching. The system is also required for the developmental silencing of VSG genes. The data provides a mechanism controlling reversible telomere silencing essential for the periodic switching in VSG expression and its developmental regulation.

microbiology↗

bioRxiv2023

Using single-cell RNA sequencing to generate cell-type-specific split-GAL4 reagents throughout development

Cell-type-specific tools facilitate the identification and functional characterization of distinct cell types, which underly the complexity of neuronal circuits. A large collection of existing genetic tools in Drosophila relies on enhancer activity to label different subsets of cells. These enhancer-based GAL4 lines often fail to show a predicable expression pattern to reflect the expression of nearby gene(s), partly due to an incomplete capture of the full gene regulatory elements. While genetic intersectional technique such as the split-GAL4 system further improve cell-type-specificity, it requires significant time and resource to generate and screen through combinations of enhancer expression patterns. In addition, since existing enhancer-based split-GAL4 lines that show cell-type-specific labeling in adult are not necessarily active nor specific in early development, there is a relative lack of tools for the study of neural development. Here, we use an existing single-cell RNA sequencing (scRNAseq) dataset to select gene pairs and provide an efficient pipeline to generate cell-type-specific split-GAL4 lines based on the native genetic regulatory elements. These gene-specific split-GAL4 lines can be generated from a large collection of coding intronic MiMIC/CRIMIC lines either by embryo injection or in vivo cassette swapping crosses and/or CRISPR knock-in at the N or C terminal of the gene. We use the developing Drosophila visual system as a model to demonstrate the high prediction power of scRNAseq-guided gene specific split-GAL4 lines in targeting known cell types. The toolkit allows efficient cluster annotation in scRNAseq datasets but also the identification of novel cell types. Lastly, the gene-specific split-GAL4 lines are broadly applicable to Drosophila tissues. Our work opens new avenues for generating cell-type-specific tools for the targeted manipulation of distinct cell types throughout development and represents a valuable resource to the fly research community. Significance StatementUnderstanding the functional role of individual cell types in the nervous systems has remained a major challenge for neuroscience researchers, partly due to incomplete identification and characterization of underlying cell types. To study the development of individual cell types and their functional roles in health and disease, experimental access to a specific cell type is often a prerequisite. Here, we establish an experimental pipeline to generate gene-specific split-GAL4 guided by single-cell RNA sequencing datasets. These lines show high accuracy for labeling targeted cell types from early developmental stages to adulthood and can be applied to any tissues in Drosophila. The collection of gene-speicifc-split-GAL4 will provide a valuable resource to the entire fly research community.

developmental biology↗