@article {68469, title = {Multimodal mapping of cell types and projections in the central nucleus of the amygdala}, journal = {eLife}, year = {2023}, month = {2023 Jan 20}, abstract = {

The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-Seq) to classify molecularly defined cell types in the CEA and identified marker-genes to map the location of these neuronal types using\ expansion\ assisted iterative fluorescence in\ situ\ hybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of \~{}30,000 molecularly defined CEA neurons. Our study revealed spatio-molecular organization of the CEA, with medial and lateral CEA associated with distinct cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker-gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.

}, doi = {10.7554/eLife.84262}, url = {https://doi.org/10.7554/eLife.84262}, author = {Yuhan Wang and Sabine Krabbe and Mark Eddison and Fredrick E. Henry and Greg Fleishman and Andrew L. Lemire and Lihua Wang and Wyatt Korff and Paul W. Tillberg and Andreas L{\"u}thi and Scott M. Sternson} } @article {67810, title = {A serotonergic axon-cilium synapse drives nuclear signaling to maintain chromatin accessibility}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Sep 01}, pages = {3390-3407}, abstract = {

Chemical synapses between axons and dendrites mediate much of the brain{\textquoteright}s intercellular communication. Here we describe a new kind of synapse {\textendash} the axo-ciliary synapse - between axons and primary cilia. By employing enhanced focused ion beam {\textendash} scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between the serotonergic axons arising from the brainstem, and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, 5-hydroxytryptamine receptor 6 (HTR6), whose mutation is associated with learning and memory defects. Using a newly developed cilia-targeted serotonin sensor, we show that optogenetic stimulation of serotonergic axons results in serotonin release onto cilia. Ciliary HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway. Ablation of this pathway results in nuclear actin and chromatin accessibility changes in CA1 pyramidal neurons. Axo-ciliary synapses serve as a distinct mechanism for neuromodulators to program neuron transcription through privileged access to the nuclear compartment.

}, doi = {10.1016/j.cell.2022.07.026}, author = {Shu-Hsien Sheu and Srigokul Upadhyayula and Vincent Dupuy and Song Pang and Andrew L. Lemire and Deepika Walpita and H. Amalia Pasolli and Fei Deng and Jinxia Wan and Lihua Wang and Justin Houser and Silvia Sanchez-Martinez and Sebastian E. Brauchi and Sambashiva Banala and Melanie Freeman and C. Shan Xu and Tom Kirchhausen and Harald F. Hess and Luke Lavis and Yu-Long Li and S{\'e}verine Chaumont-Dubel and David E. Clapham} } @article {68468, title = {Spatial organization of the 3D genome encodes gene co-expression programs in single cells}, journal = {bioRxiv}, year = {2022}, month = {2022 Oct 27}, abstract = {

Deconstructing the mechanism by which the 3D genome encodes genetic information to generate diverse cell types during animal development is a major challenge in biology. The contrast between the elimination of chromatin loops and domains upon Cohesin loss and the lack of downstream gene expression changes at the cell population level instigates intense debates regarding the structure-function relationship between genome organization and gene regulation. Here, by analyzing single cells after acute Cohesin removal with sequencing and spatial genome imaging techniques, we discover that, instead of dictating population-wide gene expression levels, 3D genome topology mediated by Cohesin safeguards long-range gene co-expression correlations in single cells. Notably, Cohesin loss induces gene co-activation and chromatin co-opening between active domains in\ cis\ up to tens of megabase apart, far beyond the typical length scale of enhancer-promoter communication. In addition, Cohesin separates Mediator protein hubs, prevents active genes in\ cis\ from localizing into shared hubs and blocks intersegment transfer of diverse transcriptional regulators. Together, these results support that spatial organization of the 3D genome orchestrates dynamic long-range gene and chromatin co-regulation in single living cells.

}, doi = {10.1101/2022.10.26.513917}, url = {https://doi.org/10.1101/2022.10.26.513917}, author = {Peng Dong and Shu Zhang and Liangqi Xie and Lihua Wang and Andrew L. Lemire and Arthur D. Lander and Howard Y. Chang and Zhe J. Liu} }