51
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Identifying Inputs to Visual Projection Neurons in Drosophila Lobula by Analyzing Connectomic Data. eNeuro 2022; 9:ENEURO.0053-22.2022. [PMID: 35410869 PMCID: PMC9034759 DOI: 10.1523/eneuro.0053-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 11/21/2022] Open
Abstract
Electron microscopy (EM)-based connectomes provide important insights into how visual circuitry of fruit fly Drosophila computes various visual features, guiding and complementing behavioral and physiological studies. However, connectomic analyses of the lobula, a neuropil putatively dedicated to detecting object-like features, remains underdeveloped, largely because of incomplete data on the inputs to the brain region. Here, we attempted to map the columnar inputs into the Drosophila lobula neuropil by performing connectivity-based and morphology-based clustering on a densely reconstructed connectome dataset. While the dataset mostly lacked visual neuropils other than lobula, which would normally help identify inputs to lobula, our clustering analysis successfully extracted clusters of cells with homogeneous connectivity and morphology, likely representing genuine cell types. We were able to draw a correspondence between the resulting clusters and previously identified cell types, revealing previously undocumented connectivity between lobula input and output neurons. While future, more complete connectomic reconstructions are necessary to verify the results presented here, they can serve as a useful basis for formulating hypotheses on mechanisms of visual feature detection in lobula.
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52
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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53
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De Rop FV, Ismail JN, Bravo González-Blas C, Hulselmans GJ, Flerin CC, Janssens J, Theunis K, Christiaens VM, Wouters J, Marcassa G, de Wit J, Poovathingal S, Aerts S. Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads. eLife 2022; 11:e73971. [PMID: 35195064 PMCID: PMC8993220 DOI: 10.7554/elife.73971] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA-seq and single-cell assay for transposase-accessible chromatin (ATAC-seq) technologies are used extensively to create cell type atlases for a wide range of organisms, tissues, and disease processes. To increase the scale of these atlases, lower the cost and pave the way for more specialized multiome assays, custom droplet microfluidics may provide solutions complementary to commercial setups. We developed HyDrop, a flexible and open-source droplet microfluidic platform encompassing three protocols. The first protocol involves creating dissolvable hydrogel beads with custom oligos that can be released in the droplets. In the second protocol, we demonstrate the use of these beads for HyDrop-ATAC, a low-cost noncommercial scATAC-seq protocol in droplets. After validating HyDrop-ATAC, we applied it to flash-frozen mouse cortex and generated 7996 high-quality single-cell chromatin accessibility profiles in a single run. In the third protocol, we adapt both the reaction chemistry and the capture sequence of the barcoded hydrogel bead to capture mRNA, and demonstrate a significant improvement in throughput and sensitivity compared to previous open-source droplet-based scRNA-seq assays (Drop-seq and inDrop). Similarly, we applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes closely matching reference single-cell gene expression data. Finally, we leveraged HyDrop-RNA's high capture rate to analyze a small population of fluorescence-activated cell sorted neurons from the Drosophila brain, confirming the protocol's applicability to low input samples and small cells. HyDrop is currently capable of generating single-cell data in high throughput and at a reduced cost compared to commercial methods, and we envision that HyDrop can be further developed to be compatible with novel (multi) omics protocols.
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Affiliation(s)
- Florian V De Rop
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Joy N Ismail
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Carmen Bravo González-Blas
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Gert J Hulselmans
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Christopher Campbell Flerin
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Jasper Janssens
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Koen Theunis
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Valerie M Christiaens
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Jasper Wouters
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Gabriele Marcassa
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Synapse Biology, Department of Neurosciences, KU LeuvenLeuvenBelgium
| | - Joris de Wit
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Synapse Biology, Department of Neurosciences, KU LeuvenLeuvenBelgium
| | | | - Stein Aerts
- VIB-KU Leuven/VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory of Computational Biology, Department of Human Genetics, KU LeuvenLeuvenBelgium
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54
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Cellular diversity and gene expression profiles in the male and female brain of Aedes aegypti. BMC Genomics 2022; 23:119. [PMID: 35144549 PMCID: PMC8832747 DOI: 10.1186/s12864-022-08327-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/18/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Aedes aegypti is a medically-important mosquito vector that transmits arboviruses including yellow fever, dengue, chikungunya, and Zika viruses to humans. The mosquito exhibits typical sexually dimorphic behaviors such as courtship, mating, host seeking, bloodfeeding, and oviposition. All these behaviors are mainly regulated by the brain; however, little is known about the function and neuron composition of the mosquito brain. In this study, we generated an initial atlas of the adult male and female brain of Ae. aegypti using 10xGenomics based single-nucleus RNA sequencing. RESULTS We identified 35 brain cell clusters in male and female brains, and 15 of those clusters were assigned to known cell types. Identified cell types include glia (astrocytes), Kenyon cells, (ventral) projection neurons, monoaminergic neurons, medulla neurons, and proximal medulla neurons. In addition, the cell type compositions of male and female brains were compared to each other showing that they were quantitatively distinct, as 17 out of 35 cell clusters varied significantly in their cell type proportions. Overall, the transcriptomes from each cell cluster looked very similar between the male and female brain as only up to 25 genes were differentially expressed in these clusters. The sex determination factor Nix was highly expressed in neurons and glia of the male brain, whereas doublesex (dsx) was expressed in all neuron and glia cell clusters of the male and female brain. CONCLUSIONS An initial cell atlas of the brain of the mosquito Ae. aegypti has been generated showing that the cellular compositions of the male and female brains of this hematophagous insect differ significantly from each other. Although some of the rare brain cell types have not been detected in our single biological replicate, this study provides an important basis for the further development of a complete brain cell atlas as well as a better understanding of the neurobiology of the brains of male and female mosquitoes and their sexually dimorphic behaviors.
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55
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Wang C, Huang W, Lu J, Chen H, Yu Z. TRPV1-Mediated Microglial Autophagy Attenuates Alzheimer’s Disease-Associated Pathology and Cognitive Decline. Front Pharmacol 2022; 12:763866. [PMID: 35115924 PMCID: PMC8804218 DOI: 10.3389/fphar.2021.763866] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/06/2021] [Indexed: 01/21/2023] Open
Abstract
Autophagy is a major regulator of the ageing process of the central nervous system and neurodegeneration. Autophagy dysfunction has been implicated in the pathogenesis of Alzheimer’s disease (AD). TRPV1 was reported to regulate autophagy to protect against foam cell formation and reduce the release of inflammatory factors in atherosclerosis. In this study, pharmacological activation of TRPV1 with the TRPV1 agonist capsaicin induced autophagy in a TRPV1-dependent manner in both primary microglia and BV2 cells. TRPV1-mediated autophagy regulated glycolysis and oxidative phosphorylation by controlling the expression of genes required for aerobic glycolysis and mitochondrial respiration in primary microglia. TRPV1 agonist capsaicin decreased amyloid and phosphorylated tau pathology and reversed memory deficits by promoting microglia activation, metabolism, and autophagy in 3xTg mice. These results indicate that TRPV1 was a potential therapeutic target for AD, which suggests that capsaicin should be further assessed as a possible treatment for AD.
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Affiliation(s)
- Chenfei Wang
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Huang
- Cardiology Department, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jia Lu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongzhuan Chen
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Zhihua Yu, ; Hongzhuan Chen,
| | - Zhihua Yu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Zhihua Yu, ; Hongzhuan Chen,
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56
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Closser M, Guo Y, Wang P, Patel T, Jang S, Hammelman J, De Nooij JC, Kopunova R, Mazzoni EO, Ruan Y, Gifford DK, Wichterle H. An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity. Neuron 2022; 110:70-85.e6. [PMID: 34727520 PMCID: PMC8738133 DOI: 10.1016/j.neuron.2021.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
Proper assembly and function of the nervous system requires the generation of a uniquely diverse population of neurons expressing a cell-type-specific combination of effector genes that collectively define neuronal morphology, connectivity, and function. How countless partially overlapping but cell-type-specific patterns of gene expression are controlled at the genomic level remains poorly understood. Here we show that neuronal genes are associated with highly complex gene regulatory systems composed of independent cell-type- and cell-stage-specific regulatory elements that reside in expanded non-coding genomic domains. Mapping enhancer-promoter interactions revealed that motor neuron enhancers are broadly distributed across the large chromatin domains. This distributed regulatory architecture is not a unique property of motor neurons but is employed throughout the nervous system. The number of regulatory elements increased dramatically during the transition from invertebrates to vertebrates, suggesting that acquisition of new enhancers might be a fundamental process underlying the evolutionary increase in cellular complexity.
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Affiliation(s)
- Michael Closser
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yuchun Guo
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Tulsi Patel
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sumin Jang
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jennifer Hammelman
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Joriene C De Nooij
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel Kopunova
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA.
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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57
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Yousefian S, Musillo MJ, Bageritz J. Analysis of Single-Cell Transcriptome Data in Drosophila. Methods Mol Biol 2022; 2540:93-111. [PMID: 35980574 DOI: 10.1007/978-1-0716-2541-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The fly Drosophila is a versatile model organism that has led to fascinating biological discoveries. In the past few years, Drosophila researchers have used single-cell RNA-sequencing (scRNA-seq) to gain insights into the cellular composition, and developmental processes of various tissues and organs. Given the success of single-cell technologies a variety of computational tools and software packages were developed to enable and facilitate the analysis of scRNA-seq data. In this book chapter we want to give guidance on analyzing droplet-based scRNA-seq data from Drosophila. We will initially describe the preprocessing commonly done for Drosophila, point out possible downstream analyses, and finally highlight computational methods developed using Drosophila scRNA-seq data.
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Affiliation(s)
- Schayan Yousefian
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Jelena Musillo
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany
| | - Josephine Bageritz
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany.
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58
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Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier KI, De Rop FV, González-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, De Waegeneer M, Christiaens V, Southall T, Aerts S. Decoding gene regulation in the fly brain. Nature 2022; 601:630-636. [PMID: 34987221 DOI: 10.1038/s41586-021-04262-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1-6, three-dimensional morphological classification7 and electron microscopy mapping of the connectome8,9 have revealed an immense diversity of neuronal and glial cell types that underlie an array of functional and behavioural traits in the fly. The identities of these cell types are controlled by gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. Here, to characterize GRNs at the cell-type level in the fly brain, we profiled the chromatin accessibility of 240,919 single cells spanning 9 developmental timepoints and integrated these data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which 70,000 are linked to developmental trajectories involving neurogenesis, reprogramming and maturation. For 40 cell types, uniquely accessible regions were associated with their expressed transcription factors and downstream target genes through a combination of motif discovery, network inference and deep learning, creating enhancer GRNs. The enhancer architectures revealed by DeepFlyBrain lead to a better understanding of neuronal regulatory diversity and can be used to design genetic driver lines for cell types at specific timepoints, facilitating their characterization and manipulation.
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Affiliation(s)
- Jasper Janssens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joy N Ismail
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London, UK
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Florian V De Rop
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marc Dionne
- Department of Life Sciences, Imperial College London, London, UK
| | - Krista Grimes
- Department of Life Sciences, Imperial College London, London, UK
| | - Xiao Jiang Quan
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Dafni Papasokrati
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tony Southall
- Department of Life Sciences, Imperial College London, London, UK
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Human Genetics, KU Leuven, Leuven, Belgium.
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59
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Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts. Nat Ecol Evol 2022; 6:63-76. [PMID: 34824389 PMCID: PMC10387363 DOI: 10.1038/s41559-021-01580-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 10/04/2021] [Indexed: 01/13/2023]
Abstract
Hundreds of cell types form the vertebrate brain but it is largely unknown how similar cellular repertoires are between or within species or how cell-type diversity evolves. To examine cell-type diversity across and within species, we performed single-cell RNA sequencing of ~130,000 hypothalamic cells from zebrafish (Danio rerio) and surface and cave morphs of Mexican tetra (Astyanax mexicanus). We found that over 75% of cell types were shared between zebrafish and Mexican tetra, which diverged from a common ancestor over 150 million years ago. Shared cell types displayed shifts in paralogue expression that were generated by subfunctionalization after genome duplication. Expression of terminal effector genes, such as neuropeptides, was more conserved than the expression of their associated transcriptional regulators. Species-specific cell types were enriched for the expression of species-specific genes and characterized by the neofunctionalization of expression patterns of members of recently expanded or contracted gene families. Comparisons between surface and cave morphs revealed differences in immune repertoires and transcriptional changes in neuropeptidergic cell types associated with genomic differences. The single-cell atlases presented here are a powerful resource to explore hypothalamic cell types and reveal how gene family evolution and shifts in paralogue expression contribute to cellular diversity.
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60
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Kind E, Longden KD, Nern A, Zhao A, Sancer G, Flynn MA, Laughland CW, Gezahegn B, Ludwig HDF, Thomson AG, Obrusnik T, Alarcón PG, Dionne H, Bock DD, Rubin GM, Reiser MB, Wernet MF. Synaptic targets of photoreceptors specialized to detect color and skylight polarization in Drosophila. eLife 2021; 10:e71858. [PMID: 34913436 PMCID: PMC8789284 DOI: 10.7554/elife.71858] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/15/2021] [Indexed: 11/18/2022] Open
Abstract
Color and polarization provide complementary information about the world and are detected by specialized photoreceptors. However, the downstream neural circuits that process these distinct modalities are incompletely understood in any animal. Using electron microscopy, we have systematically reconstructed the synaptic targets of the photoreceptors specialized to detect color and skylight polarization in Drosophila, and we have used light microscopy to confirm many of our findings. We identified known and novel downstream targets that are selective for different wavelengths or polarized light, and followed their projections to other areas in the optic lobes and the central brain. Our results revealed many synapses along the photoreceptor axons between brain regions, new pathways in the optic lobes, and spatially segregated projections to central brain regions. Strikingly, photoreceptors in the polarization-sensitive dorsal rim area target fewer cell types, and lack strong connections to the lobula, a neuropil involved in color processing. Our reconstruction identifies shared wiring and modality-specific specializations for color and polarization vision, and provides a comprehensive view of the first steps of the pathways processing color and polarized light inputs.
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Affiliation(s)
- Emil Kind
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Kit D Longden
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Aljoscha Nern
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Arthur Zhao
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Gizem Sancer
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Miriam A Flynn
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Connor W Laughland
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Bruck Gezahegn
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Henrique DF Ludwig
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Alex G Thomson
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Tessa Obrusnik
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Paula G Alarcón
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
| | - Heather Dionne
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Davi D Bock
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Michael B Reiser
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Mathias F Wernet
- Instititut für Biologie – Abteilung Neurobiologie, Fachbereich Biologie, Chemie & Pharmazie, Freie Universität BerlinBerlinGermany
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61
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Phansalkar R, Krieger J, Zhao M, Kolluru SS, Jones RC, Quake SR, Weissman I, Bernstein D, Winn VD, D'Amato G, Red-Horse K. Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development. eLife 2021; 10:70246. [PMID: 34910626 PMCID: PMC8673841 DOI: 10.7554/elife.70246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Most cell fate trajectories during development follow a diverging, tree-like branching pattern, but the opposite can occur when distinct progenitors contribute to the same cell type. During this convergent differentiation, it is unknown if cells ‘remember’ their origins transcriptionally or whether this influences cell behavior. Most coronary blood vessels of the heart develop from two different progenitor sources—the endocardium (Endo) and sinus venosus (SV)—but whether transcriptional or functional differences related to origin are retained is unknown. We addressed this by combining lineage tracing with single-cell RNA sequencing (scRNAseq) in embryonic and adult mouse hearts. Shortly after coronary development begins, capillary endothelial cells (ECs) transcriptionally segregated into two states that retained progenitor-specific gene expression. Later in development, when the coronary vasculature is well established but still remodeling, capillary ECs again segregated into two populations, but transcriptional differences were primarily related to tissue localization rather than lineage. Specifically, ECs in the heart septum expressed genes indicative of increased local hypoxia and decreased blood flow. Adult capillary ECs were more homogeneous with respect to both lineage and location. In agreement, SV- and Endo-derived ECs in adult hearts displayed similar responses to injury. Finally, scRNAseq of developing human coronary vessels indicated that the human heart followed similar principles. Thus, over the course of development, transcriptional heterogeneity in coronary ECs is first influenced by lineage, then by location, until heterogeneity declines in the homeostatic adult heart. These results highlight the plasticity of ECs during development, and the validity of the mouse as a model for human coronary development.
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Affiliation(s)
- Ragini Phansalkar
- Department of Genetics, Stanford University School of Medicine, Stanford, United States.,Department of Biology, Stanford University, Stanford, United States
| | | | - Mingming Zhao
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford University School of Medicine, Stanford, United States.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, United States
| | - Sai Saroja Kolluru
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, Stanford, United States
| | - Robert C Jones
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, United States
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, Stanford, United States
| | - Irving Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Daniel Bernstein
- Division of Pediatric Cardiology, Department of Pediatrics, Stanford University School of Medicine, Stanford, United States.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, United States
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, United States
| | - Gaetano D'Amato
- Department of Biology, Stanford University, Stanford, United States
| | - Kristy Red-Horse
- Department of Biology, Stanford University, Stanford, United States.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
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62
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Karki P, Carney TD, Maracci C, Yatsenko AS, Shcherbata HR, Rodnina MV. Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor. Nucleic Acids Res 2021; 50:6001-6019. [PMID: 34897510 PMCID: PMC9226519 DOI: 10.1093/nar/gkab1189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Translational readthrough (TR) occurs when the ribosome decodes a stop codon as a sense codon, resulting in two protein isoforms synthesized from the same mRNA. TR has been identified in several eukaryotic organisms; however, its biological significance and mechanism remain unclear. Here, we quantify TR of several candidate genes in Drosophila melanogaster and characterize the regulation of TR in the large Maf transcription factor Traffic jam (Tj). Using CRISPR/Cas9-generated mutant flies, we show that the TR-generated Tj isoform is expressed in a subset of neural cells of the central nervous system and is excluded from the somatic cells of gonads. Control of TR in Tj is critical for preservation of neuronal integrity and maintenance of reproductive health. The tissue-specific distribution of a release factor splice variant, eRF1H, plays a critical role in modulating differential TR of leaky stop codon contexts. Fine-tuning of gene regulatory functions of transcription factors by TR provides a potential mechanism for cell-specific regulation of gene expression.
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Affiliation(s)
- Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Travis D Carney
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Andriy S Yatsenko
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Halyna R Shcherbata
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
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63
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Tosches MA. From Cell Types to an Integrated Understanding of Brain Evolution: The Case of the Cerebral Cortex. Annu Rev Cell Dev Biol 2021; 37:495-517. [PMID: 34416113 DOI: 10.1146/annurev-cellbio-120319-112654] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the discovery of the incredible diversity of neurons, Cajal and coworkers laid the foundation of modern neuroscience. Neuron types are not only structural units of nervous systems but also evolutionary units, because their identities are encoded in the genome. With the advent of high-throughput cellular transcriptomics, neuronal identities can be characterized and compared systematically across species. The comparison of neurons in mammals, reptiles, and birds indicates that the mammalian cerebral cortex is a mosaic of deeply conserved and recently evolved neuron types. Using the cerebral cortex as a case study, this review illustrates how comparing neuron types across species is key to reconciling observations on neural development, neuroanatomy, circuit wiring, and physiology for an integrated understanding of brain evolution.
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64
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Li H. Single-cell RNA sequencing in Drosophila: Technologies and applications. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2021; 10:e396. [PMID: 32940008 PMCID: PMC7960577 DOI: 10.1002/wdev.396] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cell states and functions at the single-cell level. It has greatly revolutionized transcriptomic studies in many life science research fields, such as neurobiology, immunology, and developmental biology. With the fast development of both experimental platforms and bioinformatics approaches over the past decade, scRNA-seq is becoming economically feasible and experimentally practical for many biomedical laboratories. Drosophila has served as an excellent model organism for dissecting cellular and molecular mechanisms that underlie tissue development, adult cell function, disease, and aging. The recent application of scRNA-seq methods to Drosophila tissues has led to a number of exciting discoveries. In this review, I will provide a summary of recent scRNA-seq studies in Drosophila, focusing on technical approaches and biological applications. I will also discuss current challenges and future opportunities of making new discoveries using scRNA-seq in Drosophila. This article is categorized under: Technologies > Analysis of the Transcriptome.
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Affiliation(s)
- Hongjie Li
- Department of Biology, Stanford University, Stanford, California, USA
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65
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Sieriebriennikov B, Reinberg D, Desplan C. A molecular toolkit for superorganisms. Trends Genet 2021; 37:846-859. [PMID: 34116864 PMCID: PMC8355152 DOI: 10.1016/j.tig.2021.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022]
Abstract
Social insects, such as ants, bees, wasps, and termites, draw biologists' attention due to their distinctive lifestyles. As experimental systems, they provide unique opportunities to study organismal differentiation, division of labor, longevity, and the evolution of development. Ants are particularly attractive because several ant species can be propagated in the laboratory. However, the same lifestyle that makes social insects interesting also hampers the use of molecular genetic techniques. Here, we summarize the efforts of the ant research community to surmount these hurdles and obtain novel mechanistic insight into the biology of social insects. We review current approaches and propose novel ones involving genomics, transcriptomics, chromatin and DNA methylation profiling, RNA interference (RNAi), and genome editing in ants and discuss future experimental strategies.
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Affiliation(s)
- Bogdan Sieriebriennikov
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.
| | - Claude Desplan
- Department of Biology, New York University, New York, NY, USA.
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66
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Allen AM, B Sokolowski M. Expression of the foraging gene in adult Drosophila melanogaster. J Neurogenet 2021; 35:192-212. [PMID: 34382904 PMCID: PMC8846931 DOI: 10.1080/01677063.2021.1941946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The foraging gene in Drosophila melanogaster, which encodes a cGMP-dependent protein kinase, is a highly conserved, complex gene with multiple pleiotropic behavioral and physiological functions in both the larval and adult fly. Adult foraging expression is less well characterized than in the larva. We characterized foraging expression in the brain, gastric system, and reproductive systems using a T2A-Gal4 gene-trap allele. In the brain, foraging expression appears to be restricted to multiple sub-types of glia. This glial-specific cellular localization of foraging was supported by single-cell transcriptomic atlases of the adult brain. foraging is extensively expressed in most cell types in the gastric and reproductive systems. We then mapped multiple cis-regulatory elements responsible for parts of the observed expression patterns by a nested cloned promoter-Gal4 analysis. The mapped cis-regulatory elements were consistently modular when comparing the larval and adult expression patterns. These new data using the T2A-Gal4 gene-trap and cloned foraging promoter fusion GAL4's are discussed with respect to previous work using an anti-FOR antibody, which we show here to be non-specific. Future studies of foraging's function will consider roles for glial subtypes and peripheral tissues (gastric and reproductive systems) in foraging's pleiotropic behavioral and physiological effects.
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Affiliation(s)
- Aaron M Allen
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
| | - Marla B Sokolowski
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Canada
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67
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Simon F, Konstantinides N. Single-cell transcriptomics in the Drosophila visual system: Advances and perspectives on cell identity regulation, connectivity, and neuronal diversity evolution. Dev Biol 2021; 479:107-122. [PMID: 34375653 DOI: 10.1016/j.ydbio.2021.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/10/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022]
Abstract
The Drosophila visual system supports complex behaviors and shares many of its anatomical and molecular features with the vertebrate brain. Yet, it contains a much more manageable number of neurons and neuronal types. In addition to the extensive Drosophila genetic toolbox, this relative simplicity has allowed decades of work to yield a detailed account of its neuronal type diversity, morphology, connectivity and specification mechanisms. In the past three years, numerous studies have applied large scale single-cell transcriptomic approaches to the Drosophila visual system and have provided access to the complete gene expression profile of most neuronal types throughout development. This makes the fly visual system particularly well suited to perform detailed studies of the genetic mechanisms underlying the evolution and development of neuronal systems. Here, we highlight how these transcriptomic resources allow exploring long-standing biological questions under a new light. We first present the efforts made to characterize neuronal diversity in the Drosophila visual system and suggest ways to further improve this description. We then discuss current advances allowed by the single-cell datasets, and envisage how these datasets can be further leveraged to address fundamental questions regarding the regulation of neuronal identity, neuronal circuit development and the evolution of neuronal diversity.
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Affiliation(s)
- Félix Simon
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Nikolaos Konstantinides
- Department of Biology, New York University, New York, NY, 10003, USA; Institut Jacques Monod, Centre National de la Recherche Scientifique-UMR 7592, Université Paris Diderot, Paris, France.
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68
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Zeppilli S, Ackels T, Attey R, Klimpert N, Ritola KD, Boeing S, Crombach A, Schaefer AT, Fleischmann A. Molecular characterization of projection neuron subtypes in the mouse olfactory bulb. eLife 2021; 10:e65445. [PMID: 34292150 PMCID: PMC8352594 DOI: 10.7554/elife.65445] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Projection neurons (PNs) in the mammalian olfactory bulb (OB) receive input from the nose and project to diverse cortical and subcortical areas. Morphological and physiological studies have highlighted functional heterogeneity, yet no molecular markers have been described that delineate PN subtypes. Here, we used viral injections into olfactory cortex and fluorescent nucleus sorting to enrich PNs for high-throughput single nucleus and bulk RNA deep sequencing. Transcriptome analysis and RNA in situ hybridization identified distinct mitral and tufted cell populations with characteristic transcription factor network topology, cell adhesion, and excitability-related gene expression. Finally, we describe a new computational approach for integrating bulk and snRNA-seq data and provide evidence that different mitral cell populations preferentially project to different target regions. Together, we have identified potential molecular and gene regulatory mechanisms underlying PN diversity and provide new molecular entry points into studying the diverse functional roles of mitral and tufted cell subtypes.
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Affiliation(s)
- Sara Zeppilli
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, and CNRS UMR 7241 and INSERM U1050ParisFrance
| | - Tobias Ackels
- The Francis Crick Institute, Sensory Circuits and Neurotechnology LaboratoryLondonUnited Kingdom
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
| | - Robin Attey
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Kimberly D Ritola
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Stefan Boeing
- The Francis Crick Institute, Bioinformatics and BiostatisticsLondonUnited Kingdom
- The Francis Crick Institute, Scientific Computing - Digital Development TeamLondonUnited Kingdom
| | - Anton Crombach
- Inria Antenne Lyon La DouaVilleurbanneFrance
- Université de Lyon, INSA-Lyon, LIRIS, UMR 5205VilleurbanneFrance
| | - Andreas T Schaefer
- The Francis Crick Institute, Sensory Circuits and Neurotechnology LaboratoryLondonUnited Kingdom
- Department of Neuroscience, Physiology & Pharmacology, University College LondonLondonUnited Kingdom
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine, and the Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, and CNRS UMR 7241 and INSERM U1050ParisFrance
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69
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Profile of Claude Desplan. Proc Natl Acad Sci U S A 2021; 118:2110547118. [PMID: 34244438 DOI: 10.1073/pnas.2110547118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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70
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Neural specification, targeting, and circuit formation during visual system assembly. Proc Natl Acad Sci U S A 2021; 118:2101823118. [PMID: 34183440 DOI: 10.1073/pnas.2101823118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Like other sensory systems, the visual system is topographically organized: Its sensory neurons, the photoreceptors, and their targets maintain point-to-point correspondence in physical space, forming a retinotopic map. The iterative wiring of circuits in the visual system conveniently facilitates the study of its development. Over the past few decades, experiments in Drosophila have shed light on the principles that guide the specification and connectivity of visual system neurons. In this review, we describe the main findings unearthed by the study of the Drosophila visual system and compare them with similar events in mammals. We focus on how temporal and spatial patterning generates diverse cell types, how guidance molecules distribute the axons and dendrites of neurons within the correct target regions, how vertebrates and invertebrates generate their retinotopic map, and the molecules and mechanisms required for neuronal migration. We suggest that basic principles used to wire the fly visual system are broadly applicable to other systems and highlight its importance as a model to study nervous system development.
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71
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Stone OA, Zhou B, Red-Horse K, Stainier DYR. Endothelial ontogeny and the establishment of vascular heterogeneity. Bioessays 2021; 43:e2100036. [PMID: 34145927 DOI: 10.1002/bies.202100036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
The establishment of distinct cellular identities was pivotal during the evolution of Metazoa, enabling the emergence of an array of specialized tissues with different functions. In most animals including vertebrates, cell specialization occurs in response to a combination of intrinsic (e.g., cellular ontogeny) and extrinsic (e.g., local environment) factors that drive the acquisition of unique characteristics at the single-cell level. The first functional organ system to form in vertebrates is the cardiovascular system, which is lined by a network of endothelial cells whose organ-specific characteristics have long been recognized. Recent genetic analyses at the single-cell level have revealed that heterogeneity exists not only at the organ level but also between neighboring endothelial cells. Thus, how endothelial heterogeneity is established has become a key question in vascular biology. Drawing upon evidence from multiple organ systems, here we will discuss the role that lineage history may play in establishing endothelial heterogeneity.
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Affiliation(s)
- Oliver A Stone
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kristy Red-Horse
- Department of Biology, Stanford Cardiovascular Institute, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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72
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Nguyen TH, Vicidomini R, Choudhury SD, Coon SL, Iben J, Brody T, Serpe M. Single-Cell RNA Sequencing Analysis of the Drosophila Larval Ventral Cord. Curr Protoc 2021; 1:e38. [PMID: 33620770 DOI: 10.1002/cpz1.38] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Drosophila provides a powerful genetic system and an excellent model to study the development and function of the nervous system. The fly's small brain and complex behavior has been instrumental in mapping neuronal circuits and elucidating the neural basis of behavior. The fast pace of fly development and the wealth of genetic tools has enabled systematic studies on cell differentiation and fate specification, and has uncovered strategies for axon guidance and targeting. The accessibility of neuronal structures and the ability to edit and manipulate gene expression in selective cells and/or synaptic compartments has revealed mechanisms for synapse assembly and neuronal connectivity. Recent advances in single-cell RNA sequencing (scRNA-seq) have further enhanced our appreciation and understanding of neuronal diversity in a fly brain. However, due to the small size of the fly brain and its constituent cells, scRNA-seq methodologies require a few adaptations. Here, we describe a set of protocols optimized for scRNA-seq analysis of the Drosophila larval ventral nerve cord, starting from tissue dissection and cell dissociation to cDNA library preparation, sequencing, and data analysis. We apply this workflow to three separate samples and detail the technical challenges associated with successful application of scRNA-seq to studies on neuronal diversity. An accompanying article (Vicidomini, Nguyen, Choudhury, Brody, & Serpe, 2021) presents a custom multistage analysis pipeline that integrates modules contained in different R packages to ensure high-flexibility, high-quality RNA-seq data analysis. These protocols are developed for Drosophila larval ventral nerve cord, but could easily be adapted to other tissues and model organisms. © 2021 U.S. Government. Basic Protocol 1: Dissection of larval ventral nerve cords and preparation of single-cell suspensions Basic Protocol 2: Preparation and sequencing of single-cell transcriptome libraries Basic Protocol 3: Alignment of raw sequencing data to indexed genome and generation of count matrices.
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Affiliation(s)
- Tho Huu Nguyen
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Rosario Vicidomini
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Saumitra Dey Choudhury
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Steven L Coon
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - James Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Thomas Brody
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Mihaela Serpe
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
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73
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Douthit J, Hairston A, Lee G, Morrison CA, Holguera I, Treisman JE. R7 photoreceptor axon targeting depends on the relative levels of lost and found expression in R7 and its synaptic partners. eLife 2021; 10:65895. [PMID: 34003117 PMCID: PMC8205486 DOI: 10.7554/elife.65895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/17/2021] [Indexed: 01/17/2023] Open
Abstract
As neural circuits form, growing processes select the correct synaptic partners through interactions between cell surface proteins. The presence of such proteins on two neuronal processes may lead to either adhesion or repulsion; however, the consequences of mismatched expression have rarely been explored. Here, we show that the Drosophila CUB-LDL protein Lost and found (Loaf) is required in the UV-sensitive R7 photoreceptor for normal axon targeting only when Loaf is also present in its synaptic partners. Although targeting occurs normally in loaf mutant animals, removing loaf from photoreceptors or expressing it in their postsynaptic neurons Tm5a/b or Dm9 in a loaf mutant causes mistargeting of R7 axons. Loaf localizes primarily to intracellular vesicles including endosomes. We propose that Loaf regulates the trafficking or function of one or more cell surface proteins, and an excess of these proteins on the synaptic partners of R7 prevents the formation of stable connections.
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Affiliation(s)
- Jessica Douthit
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Ariel Hairston
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Gina Lee
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Carolyn A Morrison
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Isabel Holguera
- Department of Biology, New York University, New York, United States
| | - Jessica E Treisman
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
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74
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Pagni M, Haikala V, Oberhauser V, Meyer PB, Reiff DF, Schnaitmann C. Interaction of “chromatic” and “achromatic” circuits in Drosophila color opponent processing. Curr Biol 2021; 31:1687-1698.e4. [DOI: 10.1016/j.cub.2021.01.105] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023]
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75
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Sancer G, Wernet MF. The development and function of neuronal subtypes processing color and skylight polarization in the optic lobes of Drosophila melanogaster. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 61:101012. [PMID: 33618155 DOI: 10.1016/j.asd.2020.101012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/01/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
The retinal mosaics of many insects contain different ommatidial subtypes harboring photoreceptors that are both molecularly and morphologically specialized for comparing between different wavelengths versus detecting the orientation of skylight polarization. The neural circuits underlying these different inputs and the characterization of their specific cellular elements are the subject of intense research. Here we review recent progress on the description of both assembly and function of color and skylight polarization circuitry, by focusing on two cell types located in the distal portion of the medulla neuropil of the fruit fly Drosophila melanogaster's optic lobes, called Dm8 and Dm9. In the main part of the retina, Dm8 cells fall into two molecularly distinct subtypes whose center becomes specifically connected to either one of randomly distributed 'pale' or 'yellow' R7 photoreceptor fates during development. Only in the 'dorsal rim area' (DRA), both polarization-sensitive R7 and R8 photoreceptors are connected to different Dm8-like cell types, called Dm-DRA1 and Dm-DRA2, respectively. An additional layer of interommatidial integration is introduced by Dm9 cells, which receive input from multiple neighboring R7 and R8 cells, as well as providing feedback synapses back into these photoreceptors. As a result, the response properties of color-sensitive photoreceptor terminals are sculpted towards being both maximally decorrelated, as well as harboring several levels of opponency (both columnar as well as intercolumnar). In the DRA, individual Dm9 cells appear to mix both polarization and color signals, thereby potentially serving as the first level of integration of different celestial stimuli. The molecular mechanisms underlying the establishment of these synaptic connections are beginning to be revealed, by using a combination of live imaging, developmental genetic studies, and cell type-specific transcriptomics.
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Affiliation(s)
- Gizem Sancer
- Freie Universität Berlin, Fachbereich Biologie, Chemie und Pharmazie, Institut für Biologie - Neurobiologie, Königin-Luise Strasse 1-3, 14195 Berlin, Germany
| | - Mathias F Wernet
- Freie Universität Berlin, Fachbereich Biologie, Chemie und Pharmazie, Institut für Biologie - Neurobiologie, Königin-Luise Strasse 1-3, 14195 Berlin, Germany.
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76
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Rossi AM, Jafari S, Desplan C. Integrated Patterning Programs During Drosophila Development Generate the Diversity of Neurons and Control Their Mature Properties. Annu Rev Neurosci 2021; 44:153-172. [PMID: 33556251 DOI: 10.1146/annurev-neuro-102120-014813] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
During the approximately 5 days of Drosophila neurogenesis (late embryogenesis to the beginning of pupation), a limited number of neural stem cells produce approximately 200,000 neurons comprising hundreds of cell types. To build a functional nervous system, neuronal types need to be produced in the proper places, appropriate numbers, and correct times. We discuss how neural stem cells (neuroblasts) obtain so-called area codes for their positions in the nervous system (spatial patterning) and how they keep time to sequentially produce neurons with unique fates (temporal patterning). We focus on specific examples that demonstrate how a relatively simple patterning system (Notch) can be used reiteratively to generate different neuronal types. We also speculate on how different modes of temporal patterning that operate over short versus long time periods might be linked. We end by discussing how specification programs are integrated and lead to the terminal features of different neuronal types.
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Affiliation(s)
- Anthony M Rossi
- Department of Biology, New York University, New York, NY 10003, USA; .,Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shadi Jafari
- Department of Biology, New York University, New York, NY 10003, USA;
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA;
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77
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Armand EJ, Li J, Xie F, Luo C, Mukamel EA. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron 2021; 109:11-26. [PMID: 33412093 PMCID: PMC7808568 DOI: 10.1016/j.neuron.2020.12.010] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022]
Abstract
Single-cell sequencing technologies, including transcriptomic and epigenomic assays, are transforming our understanding of the cellular building blocks of neural circuits. By directly measuring multiple molecular signatures in thousands to millions of individual cells, single-cell sequencing methods can comprehensively characterize the diversity of brain cell types. These measurements uncover gene regulatory mechanisms that shape cellular identity and provide insight into developmental and evolutionary relationships between brain cell populations. Single-cell sequencing data can aid the design of tools for targeted functional studies of brain circuit components, linking molecular signatures with anatomy, connectivity, morphology, and physiology. Here, we discuss the fundamental principles of single-cell transcriptome and epigenome sequencing, integrative computational analysis of the data, and key applications in neuroscience.
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Affiliation(s)
- Ethan J Armand
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Fangming Xie
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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78
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Abstract
Large amounts of effort have been invested in trying to understand how a single genome is able to specify the identity of hundreds of cell types. Inspired by some aspects of Caenorhabditis elegans biology, we implemented an in silico evolutionary strategy to produce gene regulatory networks (GRNs) that drive cell-specific gene expression patterns, mimicking the process of terminal cell differentiation. Dynamics of the gene regulatory networks are governed by a thermodynamic model of gene expression, which uses DNA sequences and transcription factor degenerate position weight matrixes as input. In a version of the model, we included chromatin accessibility. Experimentally, it has been determined that cell-specific and broadly expressed genes are regulated differently. In our in silico evolved GRNs, broadly expressed genes are regulated very redundantly and the architecture of their cis-regulatory modules is different, in accordance to what has been found in C. elegans and also in other systems. Finally, we found differences in topological positions in GRNs between these two classes of genes, which help to explain why broadly expressed genes are so resilient to mutations. Overall, our results offer an explanatory hypothesis on why broadly expressed genes are regulated so redundantly compared to cell-specific genes, which can be extrapolated to phenomena such as ChIP-seq HOT regions.
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Affiliation(s)
- Carlos Mora-Martinez
- Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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79
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Zhang H, Wang H, Shen X, Jia X, Yu S, Qiu X, Wang Y, Du J, Yan J, He J. The landscape of regulatory genes in brain-wide neuronal phenotypes of a vertebrate brain. eLife 2021; 10:68224. [PMID: 34895465 PMCID: PMC8769648 DOI: 10.7554/elife.68224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 12/05/2021] [Indexed: 11/18/2022] Open
Abstract
Multidimensional landscapes of regulatory genes in neuronal phenotypes at whole-brain levels in the vertebrate remain elusive. We generated single-cell transcriptomes of ~67,000 region- and neurotransmitter/neuromodulator-identifiable cells from larval zebrafish brains. Hierarchical clustering based on effector gene profiles ('terminal features') distinguished major brain cell types. Sister clusters at hierarchical termini displayed similar terminal features. It was further verified by a population-level statistical method. Intriguingly, glutamatergic/GABAergic sister clusters mostly expressed distinct transcription factor (TF) profiles ('convergent pattern'), whereas neuromodulator-type sister clusters predominantly expressed the same TF profiles ('matched pattern'). Interestingly, glutamatergic/GABAergic clusters with similar TF profiles could also display different terminal features ('divergent pattern'). It led us to identify a library of RNA-binding proteins that differentially marked divergent pair clusters, suggesting the post-transcriptional regulation of neuron diversification. Thus, our findings reveal multidimensional landscapes of transcriptional and post-transcriptional regulators in whole-brain neuronal phenotypes in the zebrafish brain.
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Affiliation(s)
- Hui Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Xiaoyu Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Xinling Jia
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Shuguang Yu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Xiaoying Qiu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Yufan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Jiulin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina,School of Future Technology, University of Chinese Academy of SciencesBeijingChina
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina,School of Future Technology, University of Chinese Academy of SciencesBeijingChina
| | - Jie He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
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80
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Konstantinides N, Desplan C. Neuronal differentiation strategies: insights from single-cell sequencing and machine learning. Development 2020; 147:dev193631. [PMID: 33293292 PMCID: PMC7746664 DOI: 10.1242/dev.193631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Neuronal replacement therapies rely on the in vitro differentiation of specific cell types from embryonic or induced pluripotent stem cells, or on the direct reprogramming of differentiated adult cells via the expression of transcription factors or signaling molecules. The factors used to induce differentiation or reprogramming are often identified by informed guesses based on differential gene expression or known roles for these factors during development. Moreover, differentiation protocols usually result in partly differentiated cells or the production of a mix of cell types. In this Hypothesis article, we suggest that, to overcome these inefficiencies and improve neuronal differentiation protocols, we need to take into account the developmental history of the desired cell types. Specifically, we present a strategy that uses single-cell sequencing techniques combined with machine learning as a principled method to select a sequence of programming factors that are important not only in adult neurons but also during differentiation.
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Affiliation(s)
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA
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81
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Abstract
The formation of the human brain, which contains nearly 100 billion neurons making an average of 1000 connections each, represents an astonishing feat of self-organization. Despite impressive progress, our understanding of how neurons form the nervous system and enable function is very fragmentary, especially for the human brain. New technologies that produce large volumes of high-resolution measurements-big data-are now being brought to bear on this problem. Single-cell molecular profiling methods allow the exploration of neural diversity with increasing spatial and temporal resolution. Advances in human genetics are shedding light on the genetic architecture of neurodevelopmental disorders, and new approaches are revealing plausible neurobiological mechanisms underlying these conditions. Here, we review the opportunities and challenges of integrating large-scale genomics and genetics for the study of brain development.
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Affiliation(s)
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK. .,MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
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82
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Akin O, Zipursky SL. Activity regulates brain development in the fly. Curr Opin Genet Dev 2020; 65:8-13. [DOI: 10.1016/j.gde.2020.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/14/2020] [Indexed: 12/31/2022]
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83
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Neuronal diversity and convergence in a visual system developmental atlas. Nature 2020; 589:88-95. [PMID: 33149298 PMCID: PMC7790857 DOI: 10.1038/s41586-020-2879-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/27/2020] [Indexed: 01/01/2023]
Abstract
Deciphering how neuronal diversity is established and maintained requires a detailed knowledge of neuronal gene expression throughout development. In contrast to mammalian brains1,2, the large neuronal diversity of the Drosophila optic lobes3 and its connectome4–6 are almost completely characterized. However, a molecular characterization of this diversity, particularly during development, has been lacking. We present novel insights into brain development through a nearly exhaustive description of the transcriptomic diversity of the optic lobes. We acquired the transcriptome of 275,000 single-cells at adult and five pupal stages, and developed a machine learning framework to assign them to almost 200 cell-types at all timepoints. We discovered two large neuronal populations that wrap neuropils during development but die just before adulthood, as well as neuronal subtypes that partition dorsal and ventral visual circuits by differential Wnt signaling throughout development. Moreover, we showed that neurons of the same type but produced days apart synchronize their transcriptomes shortly after being produced. We also resolved during synaptogenesis neuronal subtypes that converge to indistinguishable transcriptomic profiles in adults while greatly differing in morphology and connectivity. Our datasets almost completely account for the known neuronal diversity of the optic lobes and serve as a paradigm to understand brain development across species.
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84
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Kurmangaliyev YZ, Yoo J, Valdes-Aleman J, Sanfilippo P, Zipursky SL. Transcriptional Programs of Circuit Assembly in the Drosophila Visual System. Neuron 2020; 108:1045-1057.e6. [PMID: 33125872 DOI: 10.1016/j.neuron.2020.10.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 10/03/2020] [Indexed: 12/19/2022]
Abstract
Precise patterns of synaptic connections between neurons are encoded in their genetic programs. Here, we use single-cell RNA sequencing to profile neuronal transcriptomes at multiple stages in the developing Drosophila visual system. We devise an efficient strategy for profiling neurons at multiple time points in a single pool, thereby minimizing batch effects and maximizing the reliability of time-course data. A transcriptional atlas spanning multiple stages is generated, including more than 150 distinct neuronal populations; of these, 88 are followed through synaptogenesis. This analysis reveals a common (pan-neuronal) program unfolding in highly coordinated fashion in all neurons, including genes encoding proteins comprising the core synaptic machinery and membrane excitability. This program is overlaid by cell-type-specific programs with diverse cell recognition molecules expressed in different combinations and at different times. We propose that a pan-neuronal program endows neurons with the competence to form synapses and that cell-type-specific programs control synaptic specificity.
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Affiliation(s)
- Yerbol Z Kurmangaliyev
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Juyoun Yoo
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Neuroscience Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Javier Valdes-Aleman
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Piero Sanfilippo
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - S Lawrence Zipursky
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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85
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Ogienko AA, Andreyeva EN, Omelina ES, Oshchepkova AL, Pindyurin AV. Molecular and cytological analysis of widely-used Gal4 driver lines for Drosophila neurobiology. BMC Genet 2020; 21:96. [PMID: 33092520 PMCID: PMC7583314 DOI: 10.1186/s12863-020-00895-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 11/13/2022] Open
Abstract
Background The Drosophila central nervous system (CNS) is a convenient model system for the study of the molecular mechanisms of conserved neurobiological processes. The manipulation of gene activity in specific cell types and subtypes of the Drosophila CNS is frequently achieved by employing the binary Gal4/UAS system. However, many Gal4 driver lines available from the Bloomington Drosophila Stock Center (BDSC) and commonly used in Drosophila neurobiology are still not well characterized. Among these are three lines with Gal4 driven by the elav promoter (BDSC #8760, #8765, and #458), one line with Gal4 driven by the repo promoter (BDSC #7415), and the 69B-Gal4 line (BDSC #1774). For most of these lines, the exact insertion sites of the transgenes and the detailed expression patterns of Gal4 are not known. This study is aimed at filling these gaps. Results We have mapped the genomic location of the Gal4-bearing P-elements carried by the BDSC lines #8760, #8765, #458, #7415, and #1774. In addition, for each of these lines, we have analyzed the Gal4-driven GFP expression pattern in the third instar larval CNS and eye-antennal imaginal discs. Localizations of the endogenous Elav and Repo proteins were used as markers of neuronal and glial cells, respectively. Conclusions We provide a mini-atlas of the spatial activity of Gal4 drivers that are widely used for the expression of UAS–target genes in the Drosophila CNS. The data will be helpful for planning experiments with these drivers and for the correct interpretation of the results.
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Affiliation(s)
- Anna A Ogienko
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Evgeniya S Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Anastasiya L Oshchepkova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
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86
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Fendl S, Vieira RM, Borst A. Conditional protein tagging methods reveal highly specific subcellular distribution of ion channels in motion-sensing neurons. eLife 2020; 9:62953. [PMID: 33079061 PMCID: PMC7655108 DOI: 10.7554/elife.62953] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/14/2020] [Indexed: 11/25/2022] Open
Abstract
Neurotransmitter receptors and ion channels shape the biophysical properties of neurons, from the sign of the response mediated by neurotransmitter receptors to the dynamics shaped by voltage-gated ion channels. Therefore, knowing the localizations and types of receptors and channels present in neurons is fundamental to our understanding of neural computation. Here, we developed two approaches to visualize the subcellular localization of specific proteins in Drosophila: The flippase-dependent expression of GFP-tagged receptor subunits in single neurons and ‘FlpTag’, a versatile new tool for the conditional labelling of endogenous proteins. Using these methods, we investigated the subcellular distribution of the receptors GluClα, Rdl, and Dα7 and the ion channels para and Ih in motion-sensing T4/T5 neurons of the Drosophila visual system. We discovered a strictly segregated subcellular distribution of these proteins and a sequential spatial arrangement of glutamate, acetylcholine, and GABA receptors along the dendrite that matched the previously reported EM-reconstructed synapse distributions.
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Affiliation(s)
- Sandra Fendl
- Max Planck Institute of Neurobiology, Martinsried, Germany.,Graduate School of Systemic Neurosciences, LMU Munich, Martinsried, Germany
| | | | - Alexander Borst
- Max Planck Institute of Neurobiology, Martinsried, Germany.,Graduate School of Systemic Neurosciences, LMU Munich, Martinsried, Germany
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87
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Li Y, Osuma A, Correa E, Okebalama MA, Dao P, Gaylord O, Aburas J, Islam P, Brown AE, Kratsios P. Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function. eLife 2020; 9:59464. [PMID: 33001031 PMCID: PMC7529460 DOI: 10.7554/elife.59464] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/20/2020] [Indexed: 02/06/2023] Open
Abstract
Terminal selectors are transcription factors (TFs) that establish during development and maintain throughout life post-mitotic neuronal identity. We previously showed that UNC-3/Ebf, the terminal selector of C. elegans cholinergic motor neurons (MNs), acts indirectly to prevent alternative neuronal identities (Feng et al., 2020). Here, we globally identify the direct targets of UNC-3. Unexpectedly, we find that the suite of UNC-3 targets in MNs is modified across different life stages, revealing ‘temporal modularity’ in terminal selector function. In all larval and adult stages examined, UNC-3 is required for continuous expression of various protein classes (e.g. receptors, transporters) critical for MN function. However, only in late larvae and adults, UNC-3 is required to maintain expression of MN-specific TFs. Minimal disruption of UNC-3’s temporal modularity via genome engineering affects locomotion. Another C. elegans terminal selector (UNC-30/Pitx) also exhibits temporal modularity, supporting the potential generality of this mechanism for the control of neuronal identity.
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Affiliation(s)
- Yinan Li
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Anthony Osuma
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Edgar Correa
- Department of Neurobiology, University of Chicago, Chicago, United States.,Cell and Molecular Biology Program, University of Chicago, Chicago, United States
| | | | - Pauline Dao
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Olivia Gaylord
- Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States
| | - Jihad Aburas
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Priota Islam
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - André Ex Brown
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States.,Cell and Molecular Biology Program, University of Chicago, Chicago, United States.,Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States.,The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, United States
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88
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Charest J, Daniele T, Wang J, Bykov A, Mandlbauer A, Asparuhova M, Röhsner J, Gutiérrez-Pérez P, Cochella L. Combinatorial Action of Temporally Segregated Transcription Factors. Dev Cell 2020; 55:483-499.e7. [PMID: 33002421 PMCID: PMC7704111 DOI: 10.1016/j.devcel.2020.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 09/01/2020] [Indexed: 01/05/2023]
Abstract
Combinatorial action of transcription factors (TFs) with partially overlapping expression is a widespread strategy to generate novel gene-expression patterns and, thus, cellular diversity. Known mechanisms underlying combinatorial activity require co-expression of TFs within the same cell. Here, we describe the mechanism by which two TFs that are never co-expressed generate a new, intersectional expression pattern in C. elegans embryos: lineage-specific priming of a gene by a transiently expressed TF generates a unique intersection with a second TF acting on the same gene four cell divisions later; the second TF is expressed in multiple cells but only activates transcription in those where priming occurred. Early induction of active transcription is necessary and sufficient to establish a competent state, maintained by broadly expressed regulators in the absence of the initial trigger. We uncover additional cells diversified through this mechanism. Our findings define a mechanism for combinatorial TF activity with important implications for generation of cell-type diversity. Lineage-specific priming enables asymmetric gene expression in L/R neuron pairs Transient, lineage-specific TFs prime a locus for later activation by a bilateral TF An early active transcriptional state is necessary and sufficient for priming Maintenance of asymmetric primed state occurs in a symmetric regulatory environment
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Affiliation(s)
- Julien Charest
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Thomas Daniele
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Aleksandr Bykov
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Ariane Mandlbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Mila Asparuhova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Josef Röhsner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Paula Gutiérrez-Pérez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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89
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Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome. Genome Res 2020; 30:1559-1569. [PMID: 32973040 PMCID: PMC7605248 DOI: 10.1101/gr.259200.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 09/22/2020] [Indexed: 12/15/2022]
Abstract
Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophila midbrain and found that transposon expression patterns are highly stereotyped. Every detected transposon is resident in at least one cellular gene with a matching expression pattern. Bulk RNA sequencing from fly heads of the same strain revealed that coexpression is a physical link in the form of abundant chimeric transposon-gene mRNAs. We identified 264 genes where transposons introduce cryptic splice sites into the nascent transcript and thereby significantly expand the neural transcript repertoire. Some genes exclusively produce chimeric mRNAs with transposon sequence; on average, 11.6% of the mRNAs produced from a given gene are chimeric. Conversely, most transposon-containing transcripts are chimeric, which suggests that somatic expression of these transposons is largely driven by cellular genes. We propose that chimeric mRNAs produced by alternative splicing into polymorphic transposons, rather than transposon mobilization, may contribute to functional differences between individual cells and animals.
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90
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Li G, Hidalgo A. Adult Neurogenesis in the Drosophila Brain: The Evidence and the Void. Int J Mol Sci 2020; 21:ijms21186653. [PMID: 32932867 PMCID: PMC7554932 DOI: 10.3390/ijms21186653] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 01/05/2023] Open
Abstract
Establishing the existence and extent of neurogenesis in the adult brain throughout the animals including humans, would transform our understanding of how the brain works, and how to tackle brain damage and disease. Obtaining convincing, indisputable experimental evidence has generally been challenging. Here, we revise the state of this question in the fruit-fly Drosophila. The developmental neuroblasts that make the central nervous system and brain are eliminated, either through apoptosis or cell cycle exit, before the adult fly ecloses. Despite this, there is growing evidence that cell proliferation can take place in the adult brain. This occurs preferentially at, but not restricted to, a critical period. Adult proliferating cells can give rise to both glial cells and neurons. Neuronal activity, injury and genetic manipulation in the adult can increase the incidence of both gliogenesis and neurogenesis, and cell number. Most likely, adult glio- and neuro-genesis promote structural brain plasticity and homeostasis. However, a definitive visualisation of mitosis in the adult brain is still lacking, and the elusive adult progenitor cells are yet to be identified. Resolving these voids is important for the fundamental understanding of any brain. Given its powerful genetics, Drosophila can expedite discovery into mammalian adult neurogenesis in the healthy and diseased brain.
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91
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Serotonergic modulation of visual neurons in Drosophila melanogaster. PLoS Genet 2020; 16:e1009003. [PMID: 32866139 PMCID: PMC7485980 DOI: 10.1371/journal.pgen.1009003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/11/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
Sensory systems rely on neuromodulators, such as serotonin, to provide flexibility for information processing as stimuli vary, such as light intensity throughout the day. Serotonergic neurons broadly innervate the optic ganglia of Drosophila melanogaster, a widely used model for studying vision. It remains unclear whether serotonin modulates the physiology of interneurons in the optic ganglia. To address this question, we first mapped the expression patterns of serotonin receptors in the visual system, focusing on a subset of cells with processes in the first optic ganglion, the lamina. Serotonin receptor expression was found in several types of columnar cells in the lamina including 5-HT2B in lamina monopolar cell L2, required for spatiotemporal luminance contrast, and both 5-HT1A and 5-HT1B in T1 cells, whose function is unknown. Subcellular mapping with GFP-tagged 5-HT2B and 5-HT1A constructs indicated that these receptors localize to layer M2 of the medulla, proximal to serotonergic boutons, suggesting that the medulla neuropil is the primary site of serotonergic regulation for these neurons. Exogenous serotonin increased basal intracellular calcium in L2 terminals in layer M2 and modestly decreased the duration of visually induced calcium transients in L2 neurons following repeated dark flashes, but otherwise did not alter the calcium transients. Flies without functional 5-HT2B failed to show an increase in basal calcium in response to serotonin. 5-HT2B mutants also failed to show a change in amplitude in their response to repeated light flashes but other calcium transient parameters were relatively unaffected. While we did not detect serotonin receptor expression in L1 neurons, they, like L2, underwent serotonin-induced changes in basal calcium, presumably via interactions with other cells. These data demonstrate that serotonin modulates the physiology of interneurons involved in early visual processing in Drosophila. Serotonergic neurons innervate the Drosophila melanogaster eye, but it was not known whether serotonin signaling could induce acute physiological responses in visual interneurons. We found serotonin receptors expressed in all neuropils of the optic lobe and identified specific neurons involved in visual information processing that express serotonin receptors. Activation of these receptors increased intracellular calcium in first order interneurons L1 and L2 and may enhance visually induced calcium transients in L2 neurons. These data support a role for the serotonergic neuromodulation of interneurons in the Drosophila visual system.
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92
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Sheng L, Shields EJ, Gospocic J, Glastad KM, Ratchasanmuang P, Berger SL, Raj A, Little S, Bonasio R. Social reprogramming in ants induces longevity-associated glia remodeling. SCIENCE ADVANCES 2020; 6:eaba9869. [PMID: 32875108 PMCID: PMC7438095 DOI: 10.1126/sciadv.aba9869] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/09/2020] [Indexed: 05/16/2023]
Abstract
In social insects, workers and queens arise from the same genome but display profound differences in behavior and longevity. In Harpegnathos saltator ants, adult workers can transition to a queen-like state called gamergate, which results in reprogramming of social behavior and life-span extension. Using single-cell RNA sequencing, we compared the distribution of neuronal and glial populations before and after the social transition. We found that the conversion of workers into gamergates resulted in the expansion of neuroprotective ensheathing glia. Brain injury assays revealed that activation of the damage response gene Mmp1 was weaker in old workers, where the relative frequency of ensheathing glia also declined. On the other hand, long-lived gamergates retained a larger fraction of ensheathing glia and the ability to mount a strong Mmp1 response to brain injury into old age. We also observed molecular and cellular changes suggestive of age-associated decline in ensheathing glia in Drosophila.
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Affiliation(s)
- Lihong Sheng
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emily J. Shields
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Janko Gospocic
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karl M. Glastad
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Puttachai Ratchasanmuang
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shelley L. Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Arjun Raj
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Shawn Little
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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93
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Naidu VG, Zhang Y, Lowe S, Ray A, Zhu H, Li X. Temporal progression of Drosophila medulla neuroblasts generates the transcription factor combination to control T1 neuron morphogenesis. Dev Biol 2020; 464:35-44. [PMID: 32442418 PMCID: PMC7377279 DOI: 10.1016/j.ydbio.2020.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022]
Abstract
Proper neural function depends on the correct specification of individual neural fates, controlled by combinations of neuronal transcription factors. Different neural types are sequentially generated by neural progenitors in a defined order, and this temporal patterning process can be controlled by Temporal Transcription Factors (TTFs) that form temporal cascades in neural progenitors. The Drosophila medulla, part of the visual processing center of the brain, contains more than 70 neural types generated by medulla neuroblasts which sequentially express several TTFs, including Homothorax (Hth), eyeless (Ey), Sloppy paired 1 and 2 (Slp), Dichaete (D) and Tailless (Tll). However, it is not clear how such a small number of TTFs could give rise to diverse combinations of neuronal transcription factors that specify a large number of medulla neuron types. Here we report how temporal patterning specifies one neural type, the T1 neuron. We show that the T1 neuron is the only medulla neuron type that expresses the combination of three transcription factors Ocelliless (Oc or Otd), Sox102F and Ets65A. Using CRISPR-Cas9 system, we show that each transcription factor is required for the correct morphogenesis of T1 neurons. Interestingly, Oc, Sox102F and Ets65A initiate expression in neurons beginning at different temporal stages and last in a few subsequent temporal stages. Oc expressing neurons are generated in the Ey, Slp and D stages; Sox102F expressing neurons are produced in the Slp and D stages; while Ets65A is expressed in subsets of medulla neurons born in the D and later stages. The TTF Ey, Slp or D is required to initiate the expression of Oc, Sox102F or Ets65A in neurons, respectively. Thus, the neurons expressing all three transcription factors are born in the D stage and become T1 neurons. In neurons where the three transcription factors do not overlap, each of the three transcription factors can act in combination with other neuronal transcription factors to specify different neural fates. We show that this way of expression regulation of neuronal transcription factors by temporal patterning can generate more possible combinations of transcription factors in neural progeny to diversify neural fates.
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Affiliation(s)
- Vamsikrishna G Naidu
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Yu Zhang
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Scott Lowe
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Alokananda Ray
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Hailun Zhu
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Xin Li
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA.
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94
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Mira H, Morante J. Neurogenesis From Embryo to Adult - Lessons From Flies and Mice. Front Cell Dev Biol 2020; 8:533. [PMID: 32695783 PMCID: PMC7339912 DOI: 10.3389/fcell.2020.00533] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
The human brain is composed of billions of cells, including neurons and glia, with an undetermined number of subtypes. During the embryonic and early postnatal stages, the vast majority of these cells are generated from neural progenitors and stem cells located in all regions of the neural tube. A smaller number of neurons will continue to be generated throughout our lives, in localized neurogenic zones, mainly confined at least in rodents to the subependymal zone of the lateral ventricles and the subgranular zone of the hippocampal dentate gyrus. During neurogenesis, a combination of extrinsic cues interacting with temporal and regional intrinsic programs are thought to be critical for increasing neuronal diversity, but their underlying mechanisms need further elucidation. In this review, we discuss the recent findings in Drosophila and mammals on the types of cell division and cell interactions used by neural progenitors and stem cells to sustain neurogenesis, and how they are influenced by glia.
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Affiliation(s)
- Helena Mira
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Javier Morante
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas y Universidad Miguel Hernandez, Alicante, Spain
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95
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Yuan D, Ji X, Hao S, Gestrich JY, Duan W, Wang X, Xiang Y, Yang J, Hu P, Xu M, Liu L, Wei H. Lamina feedback neurons regulate the bandpass property of the flicker-induced orientation response in Drosophila. J Neurochem 2020; 156:59-75. [PMID: 32383496 DOI: 10.1111/jnc.15036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/28/2022]
Abstract
Natural scenes contain complex visual cues with specific features, including color, motion, flicker, and position. It is critical to understand how different visual features are processed at the early stages of visual perception to elicit appropriate cellular responses, and even behavioral output. Here, we studied the visual orientation response induced by flickering stripes in a novel behavioral paradigm in Drosophila melanogaster. We found that free walking flies exhibited bandpass orientation response to flickering stripes of different frequencies. The most sensitive frequency spectrum was confined to low frequencies of 2-4 Hz. Through genetic silencing, we showed that lamina L1 and L2 neurons, which receive visual inputs from R1 to R6 neurons, were the main components in mediating flicker-induced orientation behavior. Moreover, specific blocking of different types of lamina feedback neurons Lawf1, Lawf2, C2, C3, and T1 modulated orientation responses to flickering stripes of particular frequencies, suggesting that bandpass orientation response was generated through cooperative modulation of lamina feedback neurons. Furthermore, we found that lamina feedback neurons Lawf1 were glutamatergic. Thermal activation of Lawf1 neurons could suppress neural activities in L1 and L2 neurons, which could be blocked by the glutamate-gated chloride channel inhibitor picrotoxin (PTX). In summary, lamina monopolar neurons L1 and L2 are the primary components in mediating flicker-induced orientation response. Meanwhile, lamina feedback neurons cooperatively modulate the orientation response in a frequency-dependent way, which might be achieved through modulating neural activities of L1 and L2 neurons.
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Affiliation(s)
- Deliang Yuan
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiaoxiao Ji
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Shun Hao
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Julia Yvonne Gestrich
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Wenlan Duan
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Xinwei Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Yuanhang Xiang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Jihua Yang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Pengbo Hu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
| | - Mengbo Xu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China
| | - Li Liu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China.,CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Hongying Wei
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, P. R. China
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96
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Estacio-Gómez A, Hassan A, Walmsley E, Le LW, Southall TD. Dynamic neurotransmitter specific transcription factor expression profiles during Drosophila development. Biol Open 2020; 9:9/5/bio052928. [PMID: 32493733 PMCID: PMC7286294 DOI: 10.1242/bio.052928] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The remarkable diversity of neurons in the nervous system is generated during development, when properties such as cell morphology, receptor profiles and neurotransmitter identities are specified. In order to gain a greater understanding of neurotransmitter specification we profiled the transcription state of cholinergic, GABAergic and glutamatergic neurons in vivo at three developmental time points. We identified 86 differentially expressed transcription factors that are uniquely enriched, or uniquely depleted, in a specific neurotransmitter type. Some transcription factors show a similar profile across development, others only show enrichment or depletion at specific developmental stages. Profiling of Acj6 (cholinergic enriched) and Ets65A (cholinergic depleted) binding sites in vivo reveals that they both directly bind the ChAT locus, in addition to a wide spectrum of other key neuronal differentiation genes. We also show that cholinergic enriched transcription factors are expressed in mostly non-overlapping populations in the adult brain, implying the absence of combinatorial regulation of neurotransmitter fate in this context. Furthermore, our data underlines that, similar to Caenorhabditis elegans, there are no simple transcription factor codes for neurotransmitter type specification. This article has an associated First Person interview with the first author of the paper. Summary: Transcriptome profiling of cholinergic, GABAergic and glutamatergic neurons in Drosophila identified multiple transcription factors as potential regulators of neurotransmitter fate.
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Affiliation(s)
- Alicia Estacio-Gómez
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Amira Hassan
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Emma Walmsley
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Lily Wong Le
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
| | - Tony D Southall
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London SW7 2AZ, UK
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97
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Modular Organization of Cis-regulatory Control Information of Neurotransmitter Pathway Genes in Caenorhabditis elegans. Genetics 2020; 215:665-681. [PMID: 32444379 DOI: 10.1534/genetics.120.303206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 11/18/2022] Open
Abstract
We explore here the cis-regulatory logic that dictates gene expression in specific cell types in the nervous system. We focus on a set of eight genes involved in the synthesis, transport, and breakdown of three neurotransmitter systems: acetylcholine (unc-17 /VAChT, cha-1 /ChAT, cho-1 /ChT, and ace-2 /AChE), glutamate (eat-4 /VGluT), and γ-aminobutyric acid (unc-25 /GAD, unc-46 /LAMP, and unc-47 /VGAT). These genes are specifically expressed in defined subsets of cells in the nervous system. Through transgenic reporter gene assays, we find that the cellular specificity of expression of all of these genes is controlled in a modular manner through distinct cis-regulatory elements, corroborating the previously inferred piecemeal nature of specification of neurotransmitter identity. This modularity provides the mechanistic basis for the phenomenon of "phenotypic convergence," in which distinct regulatory pathways can generate similar phenotypic outcomes (i.e., the acquisition of a specific neurotransmitter identity) in different neuron classes. We also identify cases of enhancer pleiotropy, in which the same cis-regulatory element is utilized to control gene expression in distinct neuron types. We engineered a cis-regulatory allele of the vesicular acetylcholine transporter, unc-17 /VAChT, to assess the functional contribution of a "shadowed" enhancer. We observed a selective loss of unc-17 /VAChT expression in one cholinergic pharyngeal pacemaker motor neuron class and a behavioral phenotype that matches microsurgical removal of this neuron. Our analysis illustrates the value of understanding cis-regulatory information to manipulate gene expression and control animal behavior.
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98
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Putative cell type discovery from single-cell gene expression data. Nat Methods 2020; 17:621-628. [DOI: 10.1038/s41592-020-0825-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 04/02/2020] [Indexed: 12/15/2022]
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99
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Hörmann N, Schilling T, Ali AH, Serbe E, Mayer C, Borst A, Pujol-Martí J. A combinatorial code of transcription factors specifies subtypes of visual motion-sensing neurons in Drosophila. Development 2020; 147:223179. [PMID: 32238425 PMCID: PMC7240302 DOI: 10.1242/dev.186296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/20/2020] [Indexed: 12/21/2022]
Abstract
Direction-selective T4/T5 neurons exist in four subtypes, each tuned to visual motion along one of the four cardinal directions. Along with their directional tuning, neurons of each T4/T5 subtype orient their dendrites and project their axons in a subtype-specific manner. Directional tuning, thus, appears strictly linked to morphology in T4/T5 neurons. How the four T4/T5 subtypes acquire their distinct morphologies during development remains largely unknown. Here, we investigated when and how the dendrites of the four T4/T5 subtypes acquire their specific orientations, and profiled the transcriptomes of all T4/T5 neurons during this process. This revealed a simple and stable combinatorial code of transcription factors defining the four T4/T5 subtypes during their development. Changing the combination of transcription factors of specific T4/T5 subtypes resulted in predictable and complete conversions of subtype-specific properties, i.e. dendrite orientation and matching axon projection pattern. Therefore, a combinatorial code of transcription factors coordinates the development of dendrite and axon morphologies to generate anatomical specializations that differentiate subtypes of T4/T5 motion-sensing neurons. Summary: Morphological and transcriptomic analyses allowed the identification of a combinatorial code of transcription factors that controls the development of subtype-specific morphologies in motion-detecting neurons of the Drosophila visual system.
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Affiliation(s)
- Nikolai Hörmann
- Department of Circuits - Computation - Models, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Tabea Schilling
- Department of Circuits - Computation - Models, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Aicha Haji Ali
- Department of Circuits - Computation - Models, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Etienne Serbe
- Department of Circuits - Computation - Models, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Christian Mayer
- Laboratory of Neurogenomics, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Alexander Borst
- Department of Circuits - Computation - Models, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Jesús Pujol-Martí
- Department of Circuits - Computation - Models, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
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100
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Allen AM, Neville MC, Birtles S, Croset V, Treiber CD, Waddell S, Goodwin SF. A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord. eLife 2020; 9:e54074. [PMID: 32314735 PMCID: PMC7173974 DOI: 10.7554/elife.54074] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 04/03/2020] [Indexed: 02/07/2023] Open
Abstract
The Drosophila ventral nerve cord (VNC) receives and processes descending signals from the brain to produce a variety of coordinated locomotor outputs. It also integrates sensory information from the periphery and sends ascending signals to the brain. We used single-cell transcriptomics to generate an unbiased classification of cellular diversity in the VNC of five-day old adult flies. We produced an atlas of 26,000 high-quality cells, representing more than 100 transcriptionally distinct cell types. The predominant gene signatures defining neuronal cell types reflect shared developmental histories based on the neuroblast from which cells were derived, as well as their birth order. The relative position of cells along the anterior-posterior axis could also be assigned using adult Hox gene expression. This single-cell transcriptional atlas of the adult fly VNC will be a valuable resource for future studies of neurodevelopment and behavior.
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Affiliation(s)
- Aaron M Allen
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Megan C Neville
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Sebastian Birtles
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Vincent Croset
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | | | - Scott Waddell
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Stephen F Goodwin
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
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