Biology subjects

Khalil, V.

Publications and source records attributed to Khalil, V..

6 recordsLinked to original sources

bioRxiv2026

Single-cell chromatin tracing reveals multimodal molecular programs during memory formation

Experience-dependent activity is converted to coordinated molecular programs in neuronal ensembles during memory formation. However, due to the sparsity of the ensembles and the transience of immediate early gene (IEG) expression, it is unclear how IEGs engage downstream secondary response genes (SRGs) to regulate learning-specific neuroplasticity. Here, we generated a single-cell multiomic atlas of aversive learning and developed ChromTRAP, which retrospectively identifies recently activated neuronal ensembles from AP-1 (FOS/JUN)-centred chromatin traces. We integrated transcription, chromatin accessibility, histone modifications, and FOS occupancy across the amygdala, hippocampus, and prefrontal cortex. This revealed regulatory programs of learning-associated genes (LAGs), defined as SRGs preferentially induced by associative learning relative to baseline activity or independent stimulus exposure. These programs followed a brain-region- and cell-type-specific proximal-distal regulatory logic: gene-proximal Polycomb-associated H3K27me3 remodeling and AP-1-bound H3K27ac-marked distal enhancers. LAGs were further associated with enhanced intercellular signaling and MEF-family activity. Our findings establish a single-cell multiomic framework for linking learning experience to layered epigenetic regulation during activity-dependent neuroplasticity.

neuroscience↗

bioRxiv2025

Whole-genome single-cell multimodal history tracing to reveal cell identity transition

Advances in single-cell sequencing have deepened our understanding of cellular identities. However, because they inherently capture only static snapshots, after which no further observations are possible, we cannot compare past and present profiles within the same cell. Thus, multi-time-point whole-genome profiling at single-cell resolution has been a long-standing goal. Here, we introduce the History Tracing-sequencing (HisTrac-seq) platform, which enzymatically labels genomic DNA adenine to "bookmark" gene regulatory statuses. This first enabled the profiling of transcriptomic and epigenetic states in the mouse brain over a period of two months. Furthermore, extending HisTrac-seq to single-cell multi-omics sequencing, we demonstrated the simultaneous mapping of past and present profiles of the same single cells. Analyzing over 93,000 cells, we discovered unexpected, drastic cell identity transitions on a large scale ("identity jumps"). This phenomenon was previously unobservable with current technologies and revealed a hidden layer of developmental plasticity. HisTrac-seq offers a powerful approach to "temporal multi-omics" for disentangling dynamic biological processes involved in development, plasticity, aging, and disease progression.

genomics↗

bioRxiv2023

Recombinase-Independent AAV for Anterograde Transsynaptic Tracing

Viral transsynaptic labeling has become indispensable for investigating the functional connectivity of neural circuits. Adeno-associated virus serotype 1 (AAV1) allows for anterograde transneuronal labeling and manipulation of postsynaptic neurons. However, it is limited to delivering an AAV1 expressing a recombinase which relies on using transgenic animals or genetic access to postsynaptic neurons. We reasoned that a strong expression level could overcome this limitation. To this end, we used a self-complementary AAV1 (scAAV1) under a strong promoter (CAG). We demonstrated the anterograde transneuronal efficiency of scAAV1 by delivering a fluorescent marker in mouse retina-superior colliculus and thalamic-amygdala pathways in a recombinase-independent manner. In addition to investigating neuronal connectivity, scAAV1.CAG may be suitable for functional manipulation and imaging.

neuroscience↗

bioRxiv2023

Non-Hebbian plasticity produces long-lasting associative memories

The dominant models of learning and memory, such as Hebbian plasticity, propose that experiences are transformed into memories through input-specific synaptic plasticity at the time of learning. However, synaptic plasticity is neither strictly input specific nor restricted to the time of its induction. The impact of such forms of non-Hebbian plasticity on memory has been difficult to test, hence poorly understood. Here, we demonstrate that synaptic manipulations can deviate from the Hebbian model of learning, yet produce a lasting memory. First, we established a weak associative conditioning protocol in mice, where optogenetic stimulation of sensory thalamic input to the amygdala was paired with a footshock, but no detectable memory was formed. However, when the same input was potentiated minutes before or after, or even 24 hours later, the associative experience was converted to a lasting memory. Importantly, potentiating an independent input to the amygdala minutes but not 24 hours after the pairing produced a lasting memory. Thus, our findings suggest that the process of transformation of a transient experience into a memory is neither restricted to the time of the experience nor to the synapses triggered by it; instead, it can be influenced by past and future events.

neuroscience↗

bioRxiv2023

Distinct representations of innate and learned threats within the thalamic-amygdala pathway

Behavioral flexibility and timely reactions to salient stimuli are essential for survival. The subcortical thalamic-basolateral amygdala (BLA) pathway serves as a shortcut for salient stimuli ensuring rapid processing. Here, we show that BLA neuronal and thalamic axonal activity mirror the defensive behavior evoked by an innate visual threat as well as an auditory learned threat. Importantly, perturbing this pathway compromises defensive responses to both forms of threats, in that animals fail to switch from exploratory to defensive behavior. Despite the shared pathway between the two forms of threat processing, we observed noticeable differences. Blocking beta-adrenergic receptors impair the defensive response to the innate but not the learned threats. This reduced defensive response, surprisingly, is reflected in the suppression of the activity exclusively in the BLA, as the thalamic input response remains intact. Our side-by-side examination highlights the similarities and differences between innate and learned threat-processing, thus providing new fundamental insights.

neuroscience↗

bioRxiv2020

TRACE: An unbiased method to permanently tag transiently activated inputs

A fundamental interest in circuit analysis is to parse out the synaptic inputs underlying a behavioral experience. Toward this aim, we have devised an unbiased strategy that specifically labels the afferent inputs that are activated by a defined stimulus in an activity-dependent manner. We validated this strategy in four brain areas receiving known sensory inputs. This strategy, as demonstrated here, accurately identifies these inputs.

neuroscience↗