Biology subjects

Desplan, C.

Publications and source records attributed to Desplan, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-locus chromatin memory enables flexible spatial fate specification in the Drosophila visual system

Spatial patterning generates neuronal diversity by compartmentalizing progenitors into domains with distinct molecular identities. However, these patterning cues are often transient in neurogenic domains, raising the question of how spatial information can be preserved and how rigidly it constrains neuronal fates. Here we show that a single-locus chromatin memory in the Drosophila medulla enables spatial identity to be both faithfully executed and flexibly bypassed. Medulla progenitors are partitioned into three spatial domains marked by Vsx1, Optix and Bifid. Domain-resolved single-cell multiome profiling reveals that progenies from different neuroepithelial domains are nearly indistinguishable for both transcriptome and chromatin accessibility, although persistent, domain-specific accessibility is retained only at a single spatial-factor locus, either Vsx1/2 or Bifid. These same factors are absent when neuroepithelial cells are converted to neural stem cells but are re-expressed in postmitotic neurons to execute domain-specific fates. Because this bookmarking is so restricted, specific classes of neurons can skip the domain-specific re-expression program and default to a common ground state, adopting equivalent fates regardless of spatial origin. Other neurons reach the same domain-ignoring state by expressing Vsx1/2 through a program independent of their domain of origin. PRC2-mediated silencing restricts Vsx1 re-expression to its home domain, while temporal identity and Notch signaling in newborn neurons determine which neurons engage or bypass the spatial program. Thus, single-locus chromatin memory preserves spatial information without making it an obligatory determinant of every neuronal fate.

developmental biology↗

bioRxiv2026

A Lineage-Specific Peptide Suppresses Juvenile Hormone to Drive Reproductive and Longevity Reprogramming in Ants

In ants and other eusocial insects, reproductive division of labor is tightly regulated by juvenile hormone (JH), which suppresses reproduction in most individuals to maintain the worker caste. However, how social cues trigger systemic JH suppression to permit reproductive activation remains unclear. In the ant Harpegnathos saltator, workers respond to queen loss by engaging in sustained ritualistic dueling and transitioning into reproductive, long-lived pseudoqueens (gamergates). This provides a powerful model for investigating the molecular basis of socially induced plasticity. We examined the hemolymph proteome of transitioning ants and identified HCRG1, a lineage-restricted peptide upregulated during dueling, as a circulating factor that physically interacts with Hex70c, a broadly conserved JH-binding Hexamerin. HCRG1 promotes ovarian development by antagonizing JH signaling. Expression of ant HCRG1 in the heterologous solitary model Drosophila also extends lifespan. These findings identify an evolutionarily derived circulating factor that links social sensory perception to systemic JH suppression, enabling coordinated reproductive and longevity transitions in a social insect.

evolutionary biology↗

bioRxiv2026

Layered social competition coordinates reproductive hierarchy formation in ants

Social interactions establish reproductive hierarchies and regulate division of labor in eusocial insect colonies. In the ant Harpegnathos saltator, queen loss induces a subset of workers to transition into reproductive pseudo-queens, known as gamergates, through a ritualized antennal-dueling tournament that can last for more than a month. Gamergate transition is associated with sustained dueling engagement, yet the interaction networks and social dynamics that shape reproductive hierarchy formation remain unclear. Here, we combine long-term automated tracking with behavioral classifiers to systematically quantify social interactions, including antennal dueling and two distinct biting behaviors: aggressive grooming and mandible locking. We find that antennal dueling is organized into two activity states, an engaged state and a disengaged state, and that persistent maintenance of the engaged state, rather than transient entry into it, predicts successful transition to gamergate fate. Early access to abundant food shapes dueling activity and biases ants toward entry into the engaged state. Moreover, engaged-state individuals exhibit a strong assortative preference for dueling with one another and cluster spatially within the colony. We further show that mandible locking precedes transitions out of the engaged state, whereas aggressive grooming reinforces the disengaged state, together consistent with a role in stabilizing worker fate. Our findings reveal how structured social interactions organize reproductive hierarchy formation by regulating stable behavioral states associated with caste fate.

neuroscience↗

bioRxiv2025

RNA-RNA interactions coordinate GABA metabolism and signaling

How functionally related genes are coordinately expressed within a given cell type remains poorly understood. Here we reveal that the 3'UTR, beyond binding RNA-binding proteins and microRNAs, mediates heterotypic RNA-RNA interactions that confer cell type-specific gene expression, and demonstrate that this function is essential for GABAergic signaling in Drosophila. We show the vesicular GABA transporter VGAT is transcribed pan-neuronally but its translation is repressed in non-GABAergic neurons by miR-7 through three conserved 3'UTR sites. We identify a GABAergic neuron-specific lncRNA, GABA UnLocker (Gul), with sequences complementary to all three VGAT miR-7 sites that derepresses VGAT translation. Gul is co-expressed with the adjacent Gad1 gene, which produces GABA, in all GABAergic neurons, such that a single GABAergic neuron-specific transcriptional input instructs both GABA synthesis and, via Gul, the transporter for GABA release. Gul also targets other mRNAs in GABA metabolism, suggesting that it coordinates GABAergic gene expression through 3'UTR RNA-RNA interactions.

molecular biology↗

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↗

bioRxiv2025

Title: Retinal Calcium Waves Coordinate Uniform Tissue Patterning of the Drosophila Eye.

Optimal neural processing relies on precise tissue patterning across diverse cell types. Here, we show that spontaneous calcium waves arise among non-neuronal support cells in the developing Drosophila eye to drive retinal morphogenesis. These waves are initiated by Cad96Ca receptor tyrosine kinase signaling, triggering PLC{gamma}-mediated calcium release from the endoplasmic reticulum. A cell-type-specific Innexin code coordinates wave propagation through a defined gap junction network among non-neuronal retinal cells, excluding photoreceptors. Wave intensity scales with ommatidial size, triggering stronger Myosin II-driven apical contraction at interommatidial boundaries in larger ommatidia. This size-dependent mechanism compensates for early boundary irregularities, ensuring uniform ommatidial packing critical for precise optical architecture. Our findings reveal how synchronized calcium signaling among non-neuronal cells orchestrates tissue patterning in the developing nervous system.

developmental biology↗

bioRxiv2025

Temporal and Notch identity determine layer targeting and synapse location of medulla neurons

How specification mechanisms that generate neural diversity translate into specific neuronal targeting, connectivity, and function in the adult brain is not understood. In the medulla region of the Drosophila optic lobe, neural progenitors generate different neurons in a fixed order by sequentially expressing a series of temporal transcription factors as they age. Then, Notch signaling in intermediate progenitors further diversifies neuronal progeny. Using the Electron Microscopy reconstruction of the adult fly brain, we matched the temporal and Notch identity of medulla neurons with their adult targeting features across the different optic lobe neuropils at synapse resolution, and found that these specification mechanisms are significantly associated with the depth of neuropil targeting in the adult brain, for both local interneurons and projection neurons. We show that this temporal identity-dependent targeting of projection neurons unfolds early in development and is genetically determined. Notably, synapse location in the adult brain of putative medulla neurons can be used to predict their temporal origin. Moreover, synapses of neuronal types from different connectome-predicted functional subsystems are compartmentalized in the different neuropils, suggesting a link between synaptic stratification and specific visual functions. Finally, we show that candidate terminal selector TFs are significantly associated with a specific depth bias in the optic lobe neuropils, providing putative molecular determinants of this targeting. Together, we show that temporal identity and Notch status of medulla neurons can predict their neuropil synapse location, linking their developmental patterning with adult circuit architecture.

developmental biology↗

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↗

bioRxiv2024

High-throughput identification of the spatial origins of Drosophila optic lobe neurons using single-cell mRNA-sequencing

The medulla is the part of the Drosophila optic lobe with the greatest neuronal diversity, in which the identity of each neuronal type is specified in progenitors and newborn neurons via the integration of temporal, spatial, and Notch-driven patterning mechanisms. This identity is maintained in differentiating and adult neurons by the expression of neuronal type-specific combinations of terminal selectors, which are transcription factors expressed continuously during development and in the adult that are thought to control all neuronal type-specific gene expression. However, how the patterning mechanisms establish terminal selector expression is unknown. We have previously characterized the temporal and Notch origin of medulla neurons. Here we have used single-cell mRNA-sequencing to characterize their spatial origins and identified two new spatial subdomains. Together, this makes the medulla the first complex brain structure for which the patterning mechanisms specifying the identity of each neuronal type are known. This knowledge allowed us to identify correlations between patterning information, terminal selector expression and neuronal features. Our results suggest that different subsets of the patterning information accessible to a given neuronal type control the expression of each of its terminal selectors and of modules of terminal features, including neurotransmitter identity. Therefore, the evolution of new neuronal types could rely on the acquisition of modules of neuronal features pre-determined by their developmental origin.

developmental biology↗

bioRxiv2023

Spatial patterning regulates neuron numbers in the Drosophila visual system

Neurons must be made in the correct proportions to communicate with the appropriate synaptic partners and form functional circuits. In the Drosophila visual system, multiple subtypes of Distal medulla (Dm) inhibitory interneurons are made in distinct, reproducible numbers--from 5 to 800 per optic lobe. These neurons are born from a crescent-shaped neuroepithelium called the Outer Proliferation Center (OPC), which can be subdivided into specific domains based on transcription factor expression. We fate mapped Dm neurons and found that more abundant neural types are born from larger neuroepithelial subdomains, while less abundant subtypes are born from smaller ones. Additionally, morphogenetic Dpp/BMP signaling provides a second layer of patterning that subdivides the neuroepithelium into smaller domains to provide more granular control of cell proportions. Apoptosis appears to play a minor role in regulating Dm neuron abundance. This work describes an underappreciated mechanism for the regulation of neuronal stoichiometry.

developmental biology↗

bioRxiv2023

An Atlas of the Developing Drosophila Visual System Glia and Subcellular mRNA Localization of Transcripts in Single Cells

Glial cells are essential for proper nervous system development and function. To understand glial development and function, we comprehensively annotated the glial cells from two large single-cell mRNA-sequencing (scRNA-seq) atlases of the developing Drosophila visual system. This allowed us to identify all glial cell types from larval to adult stages and follow their developmental trajectories to understand how the diversity of glial types is generated during development. We show that whereas most glial types, such as chiasm glia, gradually change their transcriptome as they mature during development, neuropil glia that transcriptionally appears as a single cell class in larvae, splits into ensheathing (EG) and astrocyte-like (ALG) glia types during pupal stages. We have experimentally validated these developmental trajectories and identified the genetic markers expressed through the differentiation between EG and ALG classes. Unexpectedly, our analysis of scRNA-seq datasets allowed us to discover that the transcriptome of glial cell bodies can be distinguished from that of their processes. We have identified that processes are enriched for distinct mRNAs that were validated in vivo. This work provides the most detailed transcriptomic analysis of optic lobe glia during development and helps explain the expansion of glial diversity observed in the adult visual system. We also present an innovative computational approach to identify mRNA species that are differentially localized to cell bodies or cellular processes.

developmental biology↗

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↗

bioRxiv2022

Insulin signaling and extended longevity in ants

In most organisms, the cost of reproduction is a shorter lifespan. However, the reproductive caste in eusocial insect species (queen) exhibits an extraordinarily longer lifespan than non-reproductive castes (workers) despite having a similar genome, thus contradicting the aging dogma. In the absence of the queen, Harpegnathos saltator ants can undergo a caste switch from workers to reproductive pseudo-queens (gamergates). Gamergates exhibit a dramatically prolonged lifespan. When placed in the presence of a reproductive, they revert to worker status and their lifespan is then shortened accordingly. To understand this unique relationship between reproduction and longevity, we analyzed tissue-specific gene expression between castes. Insulin is upregulated in the gamergate brain that leads to oogenesis, but surprisingly correlates with extended longevity. This correlates with increased lipid synthesis and elevated production of vitellogenin in the fat body, which are both transported to the egg. We show that the production of vitellogenin in the fat body is due to the systemic activation of the MAPK branch of the insulin/IGF signaling (IIS)-pathway. In contrast, reduced expression of insulin receptors in the fat body of gamergates and the production in their developing ovary of an anti-insulin (Imp-L2) lead to the downregulation of the AKT/FOXO branch of the IIS-signaling pathway in the fat body, and to the dramatically extended longevity. This reveals a dual-pathway mechanism that reconciles increased longevity in the context of active reproduction in eusocial insects. One Sentence SummaryInsulin-dependent reproduction in ants correlates with extended longevity through insulin inhibition by anti-insulin Imp-L2.

physiology↗

bioRxiv2022

Coordinated control of neuronal differentiation and wiring by a sustained code of transcription factors

The enormous diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of [~]10 transcription factors that are continuously expressed by them. We show that targeted modifications of this selector code induce predictable conversions of cell fates between neurons in vivo. These conversions appear morphologically and transcriptionally complete, arguing for a conserved gene regulatory program that jointly instructs both the type-specific development and the terminal features of neurons. Cis-regulatory sequence analysis of open chromatin links one of these selectors to an upstream patterning gene in stem cells that specifies neuronal fates. Experimentally validated network models show that selectors interact with ecdysone signaling to regulate downstream effectors controlling brain wiring. Our results provide a generalizable framework of how specific fates are initiated and maintained in postmitotic neurons.

neuroscience↗

bioRxiv2021

A comprehensive series of temporal transcription factors in the fly visual system

The brain consists of thousands of different neuronal types that are generated through multiple divisions of neuronal stem cells. These stem cells have the capacity to generate different neuronal types at different stages of their development. In Drosophila, this temporal patterning is driven by the successive expression of temporal transcription factors (tTFs). While a number of tTFs are known in different animals and across various parts of the nervous system, these have been mostly identified by informed guesses and antibody availability. We used single-cell mRNA sequencing to identify the complete series of tTFs that specify most Drosophila medulla neurons in the optic lobe. We tested the genetic interactions among these tTFs. While we verify the general principle that tTFs regulate the progression of the series by activating the next tTFs in the series and repressing the previous ones, we also identify more complex regulations. Two of the tTFs, Eyeless and Dichaete, act as hubs integrating the input of several upstream tTFs before allowing the series to progress and in turn regulating the expression of several downstream tTFs. Moreover, we show that tTFs not only specify neuronal identity by controlling the expression of cell type-specific genes. Finally, we describe the very first steps of neuronal differentiation and find that terminal differentiation genes, such as neurotransmitter-related genes, are present as transcripts, but not as proteins, in immature larval neurons days before they are being used in functioning neurons; we show that these mechanisms are conserved in humans. Our results offer a comprehensive description of a temporal series of tTFs in a neuronal system, offering mechanistic insights into the regulation of the progression of the series and the regulation of neuronal diversity. This represents a proof-of-principle for the use of single-cell mRNA sequencing for the comparison of temporal patterning across phyla that can lead to an understanding of how the human brain develops and how it has evolved.

developmental biology↗

bioRxiv2019

Extrinsic cues cooperate with intrinsic temporal factors to increase neuronal diversity

Temporal patterning of neural progenitors leads to the sequential production of diverse neuronal types. To better understand how extrinsic cues interact with intrinsic temporal programs to contribute to temporal patterning, we studied the Drosophila mushroom body neural progenitors (neuroblasts). Each of these four neuroblasts divides ~250 times to sequentially produce only three main neuronal types over the course of ~9 days of development: {gamma}, followed by {beta}, and finally {beta} neurons. The intrinsic temporal clock is composed of two RNA-binding proteins, IGF-II mRNA binding protein (Imp) and Syncrip (Syp), that are expressed in opposing temporal gradients. Activin signaling affects the production of {beta} neurons but whether and how this extrinsic cue interacts with the intrinsic temporal program was not known. We show that the Activin ligand Myoglianin produced from glia regulates the levels of the intrinsic temporal factor Imp in mushroom body neuroblasts. In neuroblasts mutant for the Activin signaling receptor baboon, Imp levels are higher than normal during the {beta} temporal window, leading to the specific loss of the {beta} neurons. The intrinsic temporal clock still progresses but with a delay, skipping the {beta} window without affecting the total number of neurons produced: The number of {gamma} neurons increases, {beta} disappear and the number of {beta} neurons decreases. Our results illustrate that an extrinsic cue modifies an intrinsic temporal program to increase neuronal diversity.

developmental biology↗

bioRxiv2019

Coordination between stochastic and deterministic specification in the Drosophila visual system

Many sensory systems use stochastic fate specification to increase their repertoire of neuronal types. How these stochastic decisions are coordinated with the development of their target post-synaptic neurons in processing centers is not understood. In the Drosophila visual system, two subtypes of the UV-sensitive R7 color photoreceptors called yR7 and pR7 are stochastically specified in the retina. In contrast, the target neurons of photoreceptors in the optic lobes are specified through a highly deterministic program. Here, we identify subtypes of the main postsynaptic target of R7, the Dm8 neurons, that are each specific to the different subtypes of R7s. We show that during development the different Dm8 subtypes are produced in excess by distinct neuronal progenitors, independently from R7 subtype specification. Following matching with their respective R7 target, supernumerary Dm8s are eliminated by apoptosis. We show that the two interacting cell adhesion molecules Dpr11, expressed in yR7s, and its partner DIP{gamma}, expressed in yDm8s, are essential for the matching of the synaptic pair. Loss of either molecule leads to the death of yDm8s or their mis-pairing with the wrong pR7 subtype. We also show that competitive interactions between Dm8 subtypes regulate both cell survival and targeting. These mechanisms allow the qualitative and quantitative matching of R7 subtypes with their target in the brain and thus permit the stochastic choice made in R7 to propagate to the deterministically specified downstream circuit to support color vision.

neuroscience↗

bioRxiv2018

Phenotypic convergence in the brain: distinct transcription factors regulate common terminal neuronal characters

Transcription factors regulate the molecular, morphological, and physiological characters of neurons and generate their impressive cell type diversity. To gain insight into general principles that govern how transcription factors regulate cell type diversity, we used large-scale single-cell mRNA sequencing to characterize the extensive cellular diversity in the Drosophila optic lobes. We sequenced 55,000 single optic lobe neurons and glia and assigned them to 52 clusters of transcriptionally distinct single cells. We validated the clustering and annotated many of the clusters using RNA sequencing of characterized FACS-sorted single cell types, as well as marker genes specific to given clusters. To identify transcription factors responsible for inducing specific terminal differentiation features, we used machine-learning to generate a random forest model. The predictive power of the model was confirmed by showing that two transcription factors expressed specifically in cholinergic (apterous) and glutamatergic (traffic-jam) neurons are necessary for the expression of ChAT and VGlut in many, but not all, cholinergic or glutamatergic neurons, respectively. We used a transcriptome-wide approach to show that the same terminal characters, including but not restricted to neurotransmitter identity, can be regulated by different transcription factors in different cell types, arguing for extensive phenotypic convergence. Our data provide a deep understanding of the developmental and functional specification of a complex brain structure.

developmental biology↗