Biology subjects

Coyne, R.

Publications and source records attributed to Coyne, R..

3 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↗