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Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

ABSTRACT: Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

PROVIDER: PRJNA1163431 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR30755200_1.fastq.gz	Fastqsanger.gz
	SRR30755200_2.fastq.gz	Fastqsanger.gz
	SRR30755201_1.fastq.gz	Fastqsanger.gz
	SRR30755201_2.fastq.gz	Fastqsanger.gz

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Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

Project description:Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.

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Project description:We present DOGMA-plex, a novel cellular barcoding systems that enable multiplexed analysis of multiple independent samples within a single experiment through a combination of viral barcodes and antibody-based plate-barcodes. Using this platform, we successfully profiled around 1,200 drug-dose responses across 475 surface proteins, chromatin accessibility, and the whole transcriptome in human treated with around 300 different chromatin inhibitors, demonstrating the method's ability to capture multi-modal cellular responses to chemical perturbations.

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Project description:In the cerebral cortex, projection neurons and interneurons work coordinately to establish functional neural networks and to control the balance between excitatory versus inhibitory synaptic activities for normal cortical functions. While the specific mechanisms that control productions of projection neurons and interneurons are beginning to be revealed, a global characterization of the molecular differences between these two groups of neurons is in need for a more comprehensive understanding of their developmental specifications as well as their cortical functions. Previous studies have shown that the majority of cortical projection neurons are produced by radial glial cells (RGCs) through intermediate progenitor cells (IPCs) which can be marked by the expression of transcription factor Tbr2(Eomes). In this study, taking advantage of lineage tracing power of combining Tbr2(Eomes)-GFP and DCX-mRFP transgenic reporter mice, we prospectively separated IPC-derived neurons (IPNs) from non-IPC-derived neurons (non-IPNs) of the embryonic cortex. Molecular characterizations revealed that IPNs and non-IPNs were enriched with projection neurons and interneurons, respectively. Transcriptome analyses documented distinct groups of genes differentially expressed between these two groups of neurons. These data present a useful resource for further investigation of the molecular regulations and functions of projection neurons and interneurons.

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Projection-defined amygdala neurons encode emotional memory through distinct transcriptomic programs

Project description:The amygdala is crucial for emotional memory, but the molecular programs that enable its distinct circuits to encode different memory features remain unclear. Combining single-cell RNA sequencing with retrograde tracing, we investigated transcriptomic dynamics of amygdala neurons projecting to nucleus accumbens (NAc) or auditory/temporal association cortex (AuC/TeA) during formation and long-term retention of fear and reward memories. We found that memory engages pathway-specific transcriptional programs of synaptic genes determined by valence, temporal stage, and projection target. Notably, the AMY→AuC/TeA pathway, previously considered a fear circuit, showed robust modulation during reward memory retention, and chemogenetic silencing confirmed its essential role in reward memory. Projection-defined neurons are transcriptionally and functionally heterogeneous: some subpopulations encode a single feature of emotional memory, such as an AMY→NAc subpopulation for reward memory formation and retention, and an AMY→AuC/TeA subpopulation for retention of fear and reward memories. Most subpopulations, however, encode multiple features via largely non-overlapping gene programs. We further identified Dcn as a selective marker for an AMY→NAc subpopulation preferentially recruited during fear memory formation. Our findings reveal a principle of projection-, valence-, and time-dependent transcriptional programming, demonstrate how subpopulations multiplex memory features via dynamic gene networks, and provide a comprehensive resource for dissecting amygdala function.

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