Biology subjects

Ozel, M. N.

Publications and source records attributed to Ozel, M. N..

7 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

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↗

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

Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images

BackgroundFilopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells. ResultsTo address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing. ConclusionTo facilitate simple application within Amira or other frameworks, we share the source code, which is available at https://github.com/zibamira/filopodia-tool.

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↗

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↗

bioRxiv2018

Serial synapse formation through filopodial competition for synaptic seeding factors

Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a serial synapse formation model, where at any time point only a single synaptogenic filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin- leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial winner-takes-all mechanism that ensures the formation of an appropriate number of synapses.

neuroscience↗