1
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Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024; 187:3461-3495. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
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Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
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2
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Smolin N, Dombrovski M, Hina BW, Moreno-Sanchez A, Gossart R, Carmona CR, Rehan A, Hussein RH, Mirshahidi P, Ausborn J, Kurmangaliyev YZ, von Reyn CR. Neuronal identity control at the resolution of a single transcription factor isoform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598883. [PMID: 38915533 PMCID: PMC11195191 DOI: 10.1101/2024.06.14.598883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The brain exhibits remarkable neuronal diversity which is critical for its functional integrity. From the sheer number of cell types emerging from extensive transcriptional, morphological, and connectome datasets, the question arises of how the brain is capable of generating so many unique identities. 'Terminal selectors' are transcription factors hypothesized to determine the final identity characteristics in post-mitotic cells. Which transcription factors function as terminal selectors and the level of control they exert over different terminal characteristics are not well defined. Here, we establish a novel role for the transcription factor broad as a terminal selector in Drosophila melanogaster. We capitalize on existing large sequencing and connectomics datasets and employ a comprehensive characterization of terminal characteristics including Perturb-seq and whole-cell electrophysiology. We find a single isoform broad-z4 serves as the switch between the identity of two visual projection neurons LPLC1 and LPLC2. Broad-z4 is natively expressed in LPLC1, and is capable of transforming the transcriptome, morphology, and functional connectivity of LPLC2 cells into LPLC1 cells when perturbed. Our comprehensive work establishes a single isoform as the smallest unit underlying an identity switch, which may serve as a conserved strategy replicated across developmental programs.
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Affiliation(s)
- Natalie Smolin
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA
| | - Mark Dombrovski
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Bryce W. Hina
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA
| | - Anthony Moreno-Sanchez
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA
| | - Ryan Gossart
- Brandeis University, Department of Biology, Waltham, MA
| | | | - Aadil Rehan
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Roni H. Hussein
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Parmis Mirshahidi
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Jessica Ausborn
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA
| | | | - Catherine R. von Reyn
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA
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3
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Haque R, Kurien SP, Setty H, Salzberg Y, Stelzer G, Litvak E, Gingold H, Rechavi O, Oren-Suissa M. Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans. Nat Commun 2024; 15:4273. [PMID: 38769103 PMCID: PMC11106331 DOI: 10.1038/s41467-024-48369-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Sex-specific traits and behaviors emerge during development by the acquisition of unique properties in the nervous system of each sex. However, the genetic events responsible for introducing these sex-specific features remain poorly understood. In this study, we create a comprehensive gene expression atlas of pure populations of hermaphrodites and males of the nematode Caenorhabditis elegans across development. We discover numerous differentially expressed genes, including neuronal gene families like transcription factors, neuropeptides, and G protein-coupled receptors. We identify INS-39, an insulin-like peptide, as a prominent male-biased gene expressed specifically in ciliated sensory neurons. We show that INS-39 serves as an early-stage male marker, facilitating the effective isolation of males in high-throughput experiments. Through complex and sex-specific regulation, ins-39 plays pleiotropic sexually dimorphic roles in various behaviors, while also playing a shared, dimorphic role in early life stress. This study offers a comparative sexual and developmental gene expression database for C. elegans. Furthermore, it highlights conserved genes that may underlie the sexually dimorphic manifestation of different human diseases.
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Affiliation(s)
- Rizwanul Haque
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Sonu Peedikayil Kurien
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Hagar Setty
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Salzberg
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Stelzer
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Einav Litvak
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Meital Oren-Suissa
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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4
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Destain H, Prahlad M, Kratsios P. Maintenance of neuronal identity in C. elegans and beyond: Lessons from transcription and chromatin factors. Semin Cell Dev Biol 2024; 154:35-47. [PMID: 37438210 PMCID: PMC10592372 DOI: 10.1016/j.semcdb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023]
Abstract
Neurons are remarkably long-lived, non-dividing cells that must maintain their functional features (e.g., electrical properties, chemical signaling) for extended periods of time - decades in humans. How neurons accomplish this incredible feat is poorly understood. Here, we review recent advances, primarily in the nematode C. elegans, that have enhanced our understanding of the molecular mechanisms that enable post-mitotic neurons to maintain their functionality across different life stages. We begin with "terminal selectors" - transcription factors necessary for the establishment and maintenance of neuronal identity. We highlight new findings on five terminal selectors (CHE-1 [Glass], UNC-3 [Collier/Ebf1-4], LIN-39 [Scr/Dfd/Hox4-5], UNC-86 [Acj6/Brn3a-c], AST-1 [Etv1/ER81]) from different transcription factor families (ZNF, COE, HOX, POU, ETS). We compare the functions of these factors in specific neuron types of C. elegans with the actions of their orthologs in other invertebrate (D. melanogaster) and vertebrate (M. musculus) systems, highlighting remarkable functional conservation. Finally, we reflect on recent findings implicating chromatin-modifying proteins, such as histone methyltransferases and Polycomb proteins, in the control of neuronal terminal identity. Altogether, these new studies on transcription factors and chromatin modifiers not only shed light on the fundamental problem of neuronal identity maintenance, but also outline mechanistic principles of gene regulation that may operate in other long-lived, post-mitotic cell types.
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Affiliation(s)
- Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Manasa Prahlad
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA.
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5
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Li Y, Chen S, Liu W, Zhao D, Gao Y, Hu S, Liu H, Li Y, Qu L, Liu X. A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans. Nat Commun 2024; 15:358. [PMID: 38195740 PMCID: PMC10776613 DOI: 10.1038/s41467-023-42677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/18/2023] [Indexed: 01/11/2024] Open
Abstract
Invariant cell lineage in C. elegans enables spatiotemporal resolution of transcriptional regulatory mechanisms controlling the fate of each cell. Here, we develop RAPCAT (Robust-point-matching- And Piecewise-affine-based Cell Annotation Tool) to automate cell identity assignment in three-dimensional image stacks of L1 larvae and profile reporter expression of 620 transcription factors in every cell. Transcription factor profile-based clustering analysis defines 80 cell types distinct from conventional phenotypic cell types and identifies three general phenotypic modalities related to these classifications. First, transcription factors are broadly downregulated in quiescent stage Hermaphrodite Specific Neurons, suggesting stage- and cell type-specific variation in transcriptome size. Second, transcription factor expression is more closely associated with morphology than other phenotypic modalities in different pre- and post-differentiation developmental stages. Finally, embryonic cell lineages can be associated with specific transcription factor expression patterns and functions that persist throughout postembryonic life. This study presents a comprehensive transcription factor atlas for investigation of intra-cell type heterogeneity.
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Affiliation(s)
- Yongbin Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Siyu Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Weihong Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Intelligent Perception Lab, Hanwang Technology Co., Ltd, Beijing, 100193, China
| | - Di Zhao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Institute of Sport, Exercise & Health, Tianjin University of Sport, Tianjin, 300381, China
| | - Yimeng Gao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shipeng Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Hanyu Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuanyuan Li
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, 230039, China
| | - Lei Qu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, 230039, China
| | - Xiao Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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6
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Xu C, Ramos TB, Rogers EM, Reiser MB, Doe CQ. Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity. eLife 2024; 12:RP90133. [PMID: 38180023 PMCID: PMC10942767 DOI: 10.7554/elife.90133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
How our brain generates diverse neuron types that assemble into precise neural circuits remains unclear. Using Drosophila lamina neuron types (L1-L5), we show that the primary homeodomain transcription factor (HDTF) brain-specific homeobox (Bsh) is initiated in progenitors and maintained in L4/L5 neurons to adulthood. Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates while repressing the HDTF Zfh1 to prevent ectopic L1/L3 fates (control: L1-L5; Bsh-knockdown: L1-L3), thereby generating lamina neuronal diversity for normal visual sensitivity. Subsequently, in L4 neurons, Bsh and Ap function in a feed-forward loop to activate the synapse recognition molecule DIP-β, thereby bridging neuronal fate decision to synaptic connectivity. Expression of a Bsh:Dam, specifically in L4, reveals Bsh binding to the DIP-β locus and additional candidate L4 functional identity genes. We propose that HDTFs function hierarchically to coordinate neuronal molecular identity, circuit formation, and function. Hierarchical HDTFs may represent a conserved mechanism for linking neuronal diversity to circuit assembly and function.
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Affiliation(s)
- Chundi Xu
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Tyler B Ramos
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Edward M Rogers
- Janelia Research Campus, Howard Hughes Medical Institute, Helix DriveAshburnUnited States
| | - Michael B Reiser
- Janelia Research Campus, Howard Hughes Medical Institute, Helix DriveAshburnUnited States
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
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7
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Smith JJ, Kratsios P. Hox gene functions in the C. elegans nervous system: From early patterning to maintenance of neuronal identity. Semin Cell Dev Biol 2024; 152-153:58-69. [PMID: 36496326 PMCID: PMC10244487 DOI: 10.1016/j.semcdb.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The nervous system emerges from a series of genetic programs that generate a remarkable array of neuronal cell types. Each cell type must acquire a distinct anatomical position, morphology, and function, enabling the generation of specialized circuits that drive animal behavior. How are these diverse cell types and circuits patterned along the anterior-posterior (A-P) axis of the animal body? Hox genes encode transcription factors that regulate cell fate and patterning events along the A-P axis of the nervous system. While most of our understanding of Hox-mediated control of neuronal development stems from studies in segmented animals like flies, mice, and zebrafish, important new themes are emerging from work in a non-segmented animal: the nematode Caenorhabditis elegans. Studies in C. elegans support the idea that Hox genes are needed continuously and across different life stages in the nervous system; they are not only required in dividing progenitor cells, but also in post-mitotic neurons during development and adult life. In C. elegans embryos and young larvae, Hox genes control progenitor cell specification, cell survival, and neuronal migration, consistent with their neural patterning roles in other animals. In late larvae and adults, C. elegans Hox genes control neuron type-specific identity features critical for neuronal function, thereby extending the Hox functional repertoire beyond early patterning. Here, we provide a comprehensive review of Hox studies in the C. elegans nervous system. To relate to readers outside the C. elegans community, we highlight conserved roles of Hox genes in patterning the nervous system of invertebrate and vertebrate animals. We end by calling attention to new functions in adult post-mitotic neurons for these paradigmatic regulators of cell fate.
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Affiliation(s)
- Jayson J Smith
- Department of Neurobiology, University of Chicago, 947 East 58th Street, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, 947 East 58th Street, Chicago, IL 60637, USA.
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, 947 East 58th Street, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, 947 East 58th Street, Chicago, IL 60637, USA.
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8
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Moroz LL, Romanova DY. Homologous vs. homocratic neurons: revisiting complex evolutionary trajectories. Front Cell Dev Biol 2023; 11:1336093. [PMID: 38178869 PMCID: PMC10764524 DOI: 10.3389/fcell.2023.1336093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Affiliation(s)
- Leonid L. Moroz
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, United States
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United States
| | - Daria Y. Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
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9
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Liu J, Murray JI. Mechanisms of lineage specification in Caenorhabditis elegans. Genetics 2023; 225:iyad174. [PMID: 37847877 DOI: 10.1093/genetics/iyad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
The studies of cell fate and lineage specification are fundamental to our understanding of the development of multicellular organisms. Caenorhabditis elegans has been one of the premiere systems for studying cell fate specification mechanisms at single cell resolution, due to its transparent nature, the invariant cell lineage, and fixed number of somatic cells. We discuss the general themes and regulatory mechanisms that have emerged from these studies, with a focus on somatic lineages and cell fates. We next review the key factors and pathways that regulate the specification of discrete cells and lineages during embryogenesis and postembryonic development; we focus on transcription factors and include numerous lineage diagrams that depict the expression of key factors that specify embryonic founder cells and postembryonic blast cells, and the diverse somatic cell fates they generate. We end by discussing some future perspectives in cell and lineage specification.
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Affiliation(s)
- Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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10
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Munguba H, Nikouei K, Hochgerner H, Oberst P, Kouznetsova A, Ryge J, Muñoz-Manchado AB, Close J, Batista-Brito R, Linnarsson S, Hjerling-Leffler J. Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration. Neuron 2023; 111:3590-3603.e5. [PMID: 37625400 DOI: 10.1016/j.neuron.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/08/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
Although cardinal cortical interneuron identity is established upon cell-cycle exit, it remains unclear whether specific interneuron subtypes are pre-established, and if so, how their identity is maintained prior to circuit integration. We conditionally removed Sox6 (Sox6-cKO) in migrating somatostatin (Sst+) interneurons and assessed the effects on their mature identity. In adolescent mice, five of eight molecular Sst+ subtypes were nearly absent in the Sox6-cKO cortex without a reduction in cell number. Sox6-cKO cells displayed electrophysiological maturity and expressed genes enriched within the broad class of Sst+ interneurons. Furthermore, we could infer subtype identity prior to cortical integration (embryonic day 18.5), suggesting that the loss in subtype was due to disrupted subtype maintenance. Conversely, Sox6 removal at postnatal day 7 did not disrupt marker expression in the mature cortex. Therefore, Sox6 is necessary during migration for maintenance of Sst+ subtype identity, indicating that subtype maintenance requires active transcriptional programs.
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Affiliation(s)
- Hermany Munguba
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kasra Nikouei
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hannah Hochgerner
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Polina Oberst
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alexandra Kouznetsova
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Ryge
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ana Belén Muñoz-Manchado
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Departamento de Anatomía Patológica, Biología Celular, Histología, Historia de la Ciencia, Medicina Legal y Forense y Toxicología, Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Universidad de Cádiz, Cádiz, Spain
| | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Renata Batista-Brito
- Einstein College of Medicine, Dominick Purpura Department of Neuroscience, 1300 Morris Park Ave, The Bronx, NY 10461, USA; Einstein College of Medicine, Department of Psychiatry and Behavioral Sciences, 1300 Morris Park Ave, The Bronx, NY 10461, USA; Einstein College of Medicine, Department of Genetics, 1300 Morris Park Ave, The Bronx, NY 10461, USA
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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11
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Godoy LF, Hochbaum D. Transcriptional and spatiotemporal regulation of the dauer program. Transcription 2023; 14:27-48. [PMID: 36951297 PMCID: PMC10353326 DOI: 10.1080/21541264.2023.2190295] [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] [Received: 10/31/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/24/2023] Open
Abstract
Caenorhabditis elegans can enter a diapause stage called "dauer" when it senses that the environment is not suitable for development. This implies a detour from the typical developmental trajectory and requires a tight control of the developmental clock and a massive tissue remodeling. In the last decades, core components of the signaling pathways that govern the dauer development decision have been identified, but the tissues where they function for the acquisition of dauer-specific traits are still under intense study. Growing evidence demonstrates that these pathways engage in complex cross-talk and feedback loops. In this review, we summarize the current knowledge regarding the transcriptional regulation of the dauer program and the relevant tissues for its achievement. A better understanding of this process will provide insight on how developmental plasticity is achieved and how development decisions are under a robust regulation to ensure an all-or-nothing response. Furthermore, this developmental decision can also serve as a simplified model for relevant developmental disorders.Abbreviations: AID Auxin Induced Degron DA dafachronic acid Daf-c dauer formation constitutive Daf-d dauer formation defective DTC Distal Tip Cells ECM modified extracellular matrix GPCRs G protein-coupled receptors IIS insulin/IGF-1 signaling ILPs insulin-like peptides LBD Ligand Binding Domain PDL4 Post Dauer L4 TGF-β transforming growth factor beta WT wild-type.
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Affiliation(s)
- Luciana F Godoy
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD) Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Daniel Hochbaum
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD) Universidad Maimónides, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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12
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Lamanna F, Hervas-Sotomayor F, Oel AP, Jandzik D, Sobrido-Cameán D, Santos-Durán GN, Martik ML, Stundl J, Green SA, Brüning T, Mößinger K, Schmidt J, Schneider C, Sepp M, Murat F, Smith JJ, Bronner ME, Rodicio MC, Barreiro-Iglesias A, Medeiros DM, Arendt D, Kaessmann H. A lamprey neural cell type atlas illuminates the origins of the vertebrate brain. Nat Ecol Evol 2023; 7:1714-1728. [PMID: 37710042 PMCID: PMC10555824 DOI: 10.1038/s41559-023-02170-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The vertebrate brain emerged more than ~500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey-a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits-based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of cell types, tissue structures and gene expression programs of the ancestral vertebrate brain. However, our analyses also revealed key tissues and cell types that arose later in evolution. For example, the ancestral brain was probably devoid of cerebellar cell types and oligodendrocytes (myelinating cells); our data suggest that the latter emerged from astrocyte-like evolutionary precursors in the jawed vertebrate lineage. Altogether, our work illuminates the cellular and molecular architecture of the ancestral vertebrate brain and provides a foundation for exploring its diversification during evolution.
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Affiliation(s)
- Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | | | - A Phillip Oel
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
- Department of Zoology, Comenius University, Bratislava, Slovakia
| | - Daniel Sobrido-Cameán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gabriel N Santos-Durán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Megan L Martik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jan Stundl
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen A Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - María Celina Rodicio
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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13
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Temporal control of neuronal wiring. Semin Cell Dev Biol 2023; 142:81-90. [PMID: 35644877 DOI: 10.1016/j.semcdb.2022.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/22/2022]
Abstract
Wiring an animal brain is a complex process involving a staggering number of cell-types born at different times and locations in the developing brain. Incorporation of these cells into precise circuits with high fidelity is critical for animal survival and behavior. Assembly of neuronal circuits is heavily dependent upon proper timing of wiring programs, requiring neurons to express specific sets of genes (sometimes transiently) at the right time in development. While cell-type specificity of genetic programs regulating wiring has been studied in detail, mechanisms regulating proper timing and coordination of these programs across cell-types are only just beginning to emerge. In this review, we discuss some temporal regulators of wiring programs and how their activity is controlled over time and space. A common feature emerges from these temporal regulators - they are induced by cell-extrinsic cues and control transcription factors capable of regulating a highly cell-type specific set of target genes. Target specificity in these contexts comes from cell-type specific transcription factors. We propose that the spatiotemporal specificity of wiring programs is controlled by the combinatorial activity of temporal programs and cell-type specific transcription factors. Going forward, a better understanding of temporal regulators will be key to understanding the mechanisms underlying brain wiring, and will be critical for the development of in vitro models like brain organoids.
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14
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Sen SQ. Generating neural diversity through spatial and temporal patterning. Semin Cell Dev Biol 2023; 142:54-66. [PMID: 35738966 DOI: 10.1016/j.semcdb.2022.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/19/2022]
Abstract
The nervous system consists of a vast diversity of neurons and glia that are accurately assembled into functional circuits. What are the mechanisms that generate these diverse cell types? During development, an epithelial sheet with neurogenic potential is initially regionalised into spatially restricted domains of gene expression. From this, pools of neural stem cells (NSCs) with distinct molecular profiles and the potential to generate different neuron types, are specified. These NSCs then divide asymmetrically to self-renew and generate post-mitotic neurons or glia. As NSCs age, they experience transitions in gene expression, which further allows them to generate different neurons or glia over time. Versions of this general template of spatial and temporal patterning operate during the development of different parts of different nervous systems. Here, I cover our current knowledge of Drosophila brain and optic lobe development as well as the development of the vertebrate cortex and spinal cord within the framework of this above template. I highlight where our knowledge is lacking, where mechanisms beyond these might operate, and how the emergence of new technologies might help address unanswered questions.
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Affiliation(s)
- Sonia Q Sen
- Tata Institute for Genetics and Society, UAS-GKVK Campus, Bellary Road, Bangalore, India.
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15
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Primack AS, Cazet JF, Little HM, Mühlbauer S, Cox BD, David CN, Farrell JA, Juliano CE. Differentiation trajectories of the Hydra nervous system reveal transcriptional regulators of neuronal fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.531610. [PMID: 36993575 PMCID: PMC10055148 DOI: 10.1101/2023.03.15.531610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The small freshwater cnidarian polyp Hydra vulgaris uses adult stem cells (interstitial stem cells) to continually replace neurons throughout its life. This feature, combined with the ability to image the entire nervous system (Badhiwala et al., 2021; Dupre & Yuste, 2017) and availability of gene knockdown techniques (Juliano, Reich, et al., 2014; Lohmann et al., 1999; Vogg et al., 2022), makes Hydra a tractable model for studying nervous system development and regeneration at the whole-organism level. In this study, we use single-cell RNA sequencing and trajectory inference to provide a comprehensive molecular description of the adult nervous system. This includes the most detailed transcriptional characterization of the adult Hydra nervous system to date. We identified eleven unique neuron subtypes together with the transcriptional changes that occur as the interstitial stem cells differentiate into each subtype. Towards the goal of building gene regulatory networks to describe Hydra neuron differentiation, we identified 48 transcription factors expressed specifically in the Hydra nervous system, including many that are conserved regulators of neurogenesis in bilaterians. We also performed ATAC-seq on sorted neurons to uncover previously unidentified putative regulatory regions near neuron-specific genes. Finally, we provide evidence to support the existence of transdifferentiation between mature neuron subtypes and we identify previously unknown transition states in these pathways. All together, we provide a comprehensive transcriptional description of an entire adult nervous system, including differentiation and transdifferentiation pathways, which provides a significant advance towards understanding mechanisms that underlie nervous system regeneration.
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Affiliation(s)
- Abby S Primack
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Hannah Morris Little
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Susanne Mühlbauer
- Department of Plant Biochemistry, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Ben D Cox
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Charles N David
- Department of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20814, USA
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
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16
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Cell context-dependent CFI-1/ARID3 functions control neuronal terminal differentiation. Cell Rep 2023; 42:112220. [PMID: 36897776 PMCID: PMC10124151 DOI: 10.1016/j.celrep.2023.112220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 12/21/2022] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
AT-rich interaction domain 3 (ARID3) transcription factors are expressed in the nervous system, but their mechanisms of action are largely unknown. Here, we provide, in vivo, a genome-wide binding map for CFI-1, the sole C. elegans ARID3 ortholog. We identify 6,396 protein-coding genes as putative direct targets of CFI-1, most of which encode neuronal terminal differentiation markers. In head sensory neurons, CFI-1 directly activates multiple terminal differentiation genes, thereby acting as a terminal selector. In motor neurons, however, CFI-1 acts as a direct repressor, continuously antagonizing three transcriptional activators. By focusing on the glr-4/GRIK4 glutamate receptor locus, we identify proximal CFI-1 binding sites and histone methyltransferase activity as necessary for glr-4 repression. Rescue assays reveal functional redundancy between core and extended DNA-binding ARID domains and a strict requirement for REKLES, the ARID3 oligomerization domain. Altogether, this study uncovers cell-context-dependent mechanisms through which a single ARID3 protein controls the terminal differentiation of distinct neuron types.
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17
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Heo W, Hwang H, Kim J, Oh SH, Yu Y, Lee JH, Kim K. The CCAAT-box transcription factor, NF-Y complex, mediates the specification of the IL1 neurons in C. elegans. BMB Rep 2023; 56:153-159. [PMID: 36330709 PMCID: PMC10068339 DOI: 10.5483/bmbrep.2022-0146] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 09/16/2023] Open
Abstract
Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between transacting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cisregulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes. [BMB Reports 2023; 56(3): 153-159].
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Affiliation(s)
- Woojung Heo
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | | | - Jimin Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Seung Hee Oh
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Youngseok Yu
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
| | - Jae-Hyung Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Kyuhyung Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
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18
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Heo W, Hwang H, Kim J, Oh SH, Yu Y, Lee JH, Kim K. The CCAAT-box transcription factor, NF-Y complex, mediates the specification of the IL1 neurons in C. elegans. BMB Rep 2023; 56:153-159. [PMID: 36330709 PMCID: PMC10068339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 03/29/2023] Open
Abstract
Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between transacting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cisregulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes. [BMB Reports 2023; 56(3): 153-159].
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Affiliation(s)
- Woojung Heo
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | | | - Jimin Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Seung Hee Oh
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Youngseok Yu
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
| | - Jae-Hyung Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Kyuhyung Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
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19
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Shrestha BR, Wu L, Goodrich LV. Runx1 controls auditory sensory neuron diversity in mice. Dev Cell 2023; 58:306-319.e5. [PMID: 36800995 PMCID: PMC10202259 DOI: 10.1016/j.devcel.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/28/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023]
Abstract
Sound stimulus is encoded in mice by three molecularly and physiologically diverse subtypes of sensory neurons, called Ia, Ib, and Ic spiral ganglion neurons (SGNs). Here, we show that the transcription factor Runx1 controls SGN subtype composition in the murine cochlea. Runx1 is enriched in Ib/Ic precursors by late embryogenesis. Upon the loss of Runx1 from embryonic SGNs, more SGNs take on Ia rather than Ib or Ic identities. This conversion was more complete for genes linked to neuronal function than to connectivity. Accordingly, synapses in the Ib/Ic location acquired Ia properties. Suprathreshold SGN responses to sound were enhanced in Runx1CKO mice, confirming the expansion of neurons with Ia-like functional properties. Runx1 deletion after birth also redirected Ib/Ic SGNs toward Ia identity, indicating that SGN identities are plastic postnatally. Altogether, these findings show that diverse neuronal identities essential for normal auditory stimulus coding arise hierarchically and remain malleable during postnatal development.
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Affiliation(s)
- Brikha R Shrestha
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA; Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA.
| | - Lorna Wu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lisa V Goodrich
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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20
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Masoudi N, Schnabel R, Yemini E, Leyva-Díaz E, Hobert O. Cell-specific effects of the sole C. elegans Daughterless/E protein homolog, HLH-2, on nervous system development. Development 2023; 150:286219. [PMID: 36595352 PMCID: PMC10108603 DOI: 10.1242/dev.201366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 01/04/2023]
Abstract
Are there common mechanisms of neurogenesis used throughout an entire nervous system? We explored to what extent canonical proneural class I/II bHLH complexes are responsible for neurogenesis throughout the entire Caenorhabditis elegans nervous system. Distinct, lineage-specific proneural class II bHLH factors are generally thought to operate via interaction with a common, class I bHLH subunit, encoded by Daughterless in flies, the E proteins in vertebrates and HLH-2 in C. elegans. To eliminate function of all proneuronal class I/II bHLH complexes, we therefore genetically removed maternal and zygotic hlh-2 gene activity. We observed broad effects on neurogenesis, but still detected normal neurogenesis in many distinct neuron-producing lineages of the central and peripheral nervous system. Moreover, we found that hlh-2 selectively affects some aspects of neuron differentiation while leaving others unaffected. Although our studies confirm the function of proneuronal class I/II bHLH complexes in many different lineages throughout a nervous system, we conclude that their function is not universal, but rather restricted by lineage, cell type and components of differentiation programs affected.
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Affiliation(s)
- Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA.,University of Massachusetts, Department of Neurobiology, Worcester, MA 1605-2324, USA
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
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21
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Özel MN, Gibbs CS, Holguera I, Soliman M, Bonneau R, Desplan C. Coordinated control of neuronal differentiation and wiring by sustained transcription factors. Science 2022; 378:eadd1884. [PMID: 36480601 DOI: 10.1126/science.add1884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The large diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of on average 10 continuously expressed transcription factors. We show that targeted modifications of this terminal selector code induce predictable conversions of neuronal fates that appear morphologically and transcriptionally complete. Cis-regulatory analysis of open chromatin links one of these genes to an upstream patterning factor that specifies neuronal fates in stem cells. Experimentally validated network models describe the synergistic regulation of downstream effectors by terminal selectors and ecdysone signaling during brain wiring. Our results provide a generalizable framework of how specific fates are implemented in postmitotic neurons.
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Affiliation(s)
| | - Claudia Skok Gibbs
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Isabel Holguera
- Department of Biology, New York University, New York, NY 10003, USA
| | - Mennah Soliman
- Department of Biology, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA.,Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA.,New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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22
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The premetazoan ancestry of the synaptic toolkit and appearance of first neurons. Essays Biochem 2022; 66:781-795. [PMID: 36205407 DOI: 10.1042/ebc20220042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 12/13/2022]
Abstract
Neurons, especially when coupled with muscles, allow animals to interact with and navigate through their environment in ways unique to life on earth. Found in all major animal lineages except sponges and placozoans, nervous systems range widely in organization and complexity, with neurons possibly representing the most diverse cell-type. This diversity has led to much debate over the evolutionary origin of neurons as well as synapses, which allow for the directed transmission of information. The broad phylogenetic distribution of neurons and presence of many of the defining components outside of animals suggests an early origin of this cell type, potentially in the time between the first animal and the last common ancestor of extant animals. Here, we highlight the occurrence and function of key aspects of neurons outside of animals as well as recent findings from non-bilaterian animals in order to make predictions about when and how the first neuron(s) arose during animal evolution and their relationship to those found in extant lineages. With advancing technologies in single cell transcriptomics and proteomics as well as expanding functional techniques in non-bilaterian animals and the close relatives of animals, it is an exciting time to begin unraveling the complex evolutionary history of this fascinating animal cell type.
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23
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Shi X, Zhuang Y, Chen Z, Xu M, Kuang J, Sun XL, Gao L, Kuang X, Zhang H, Li W, Wong SZH, Liu C, Liu L, Jiang D, Pei D, Lin Y, Wu QF. Hierarchical deployment of Tbx3 dictates the identity of hypothalamic KNDy neurons to control puberty onset. SCIENCE ADVANCES 2022; 8:eabq2987. [PMID: 36383654 PMCID: PMC9668310 DOI: 10.1126/sciadv.abq2987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/23/2022] [Indexed: 05/17/2023]
Abstract
The neuroendocrine system consists of a heterogeneous collection of neuropeptidergic neurons in the brain, among which hypothalamic KNDy neurons represent an indispensable cell subtype controlling puberty onset. Although neural progenitors and neuronal precursors along the cell lineage hierarchy adopt a cascade diversification strategy to generate hypothalamic neuronal heterogeneity, the cellular logic operating within the lineage to specify a subtype of neuroendocrine neurons remains unclear. As human genetic studies have recently established a link between TBX3 mutations and delayed puberty onset, we systematically studied Tbx3-derived neuronal lineage and Tbx3-dependent neuronal specification and found that Tbx3 hierarchically established and maintained the identity of KNDy neurons for triggering puberty. Apart from the well-established lineage-dependent fate determination, we uncovered rules of interlineage interaction and intralineage retention operating through neuronal differentiation in the absence of Tbx3. Moreover, we revealed that human TBX3 mutations disturbed the phase separation of encoded proteins and impaired transcriptional regulation of key neuropeptides, providing a pathological mechanism underlying TBX3-associated puberty disorders.
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Affiliation(s)
- Xiang Shi
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yanrong Zhuang
- IDG/McGovern Institute for Brain Research, Tsinghua–Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhenhua Chen
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Mingrui Xu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Junqi Kuang
- University of Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xue-Lian Sun
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lisen Gao
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Kuang
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huairen Zhang
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Li
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Samuel Zheng Hao Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chuanyu Liu
- BGI-ShenZhen, Shenzhen 518103, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Longqi Liu
- BGI-ShenZhen, Shenzhen 518103, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Danhua Jiang
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yi Lin
- IDG/McGovern Institute for Brain Research, Tsinghua–Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Corresponding author. (Q.-F.W.); (Y.L.)
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese Institute for Brain Research, Beijing 102206, China
- Beijing Children’s Hospital, Capital Medical University, Beijing 100045, China
- Corresponding author. (Q.-F.W.); (Y.L.)
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24
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Feng W, Destain H, Smith JJ, Kratsios P. Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism. Nat Commun 2022; 13:6097. [PMID: 36243871 PMCID: PMC9569373 DOI: 10.1038/s41467-022-33781-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Hox transcription factors play fundamental roles during early patterning, but they are also expressed continuously, from embryonic stages through adulthood, in the nervous system. However, the functional significance of their sustained expression remains unclear. In C. elegans motor neurons (MNs), we find that LIN-39 (Scr/Dfd/Hox4-5) is continuously required during post-embryonic life to maintain neurotransmitter identity, a core element of neuronal function. LIN-39 acts directly to co-regulate genes that define cholinergic identity (e.g., unc-17/VAChT, cho-1/ChT). We further show that LIN-39, MAB-5 (Antp/Hox6-8) and the transcription factor UNC-3 (Collier/Ebf) operate in a positive feedforward loop to ensure continuous and robust expression of cholinergic identity genes. Finally, we identify a two-component design principle for homeostatic control of Hox gene expression in adult MNs: Hox transcriptional autoregulation is counterbalanced by negative UNC-3 feedback. These findings uncover a noncanonical role for Hox proteins during post-embryonic life, critically broadening their functional repertoire from early patterning to the control of neurotransmitter identity.
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Affiliation(s)
- Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jayson J Smith
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA.
- University of Chicago Neuroscience Institute, Chicago, IL, USA.
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA.
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25
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Fernández‐Nogales M, López‐Cascales MT, Murcia‐Belmonte V, Escalante A, Fernández‐Albert J, Muñoz‐Viana R, Barco A, Herrera E. Multiomic Analysis of Neurons with Divergent Projection Patterns Identifies Novel Regulators of Axon Pathfinding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200615. [PMID: 35988153 PMCID: PMC9561852 DOI: 10.1002/advs.202200615] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Axon pathfinding is a key step in neural circuits formation. However, the transcriptional mechanisms regulating its progression remain poorly understood. The binary decision of crossing or avoiding the midline taken by some neuronal axons during development represents a robust model to investigate the mechanisms that control the selection of axonal trajectories. Here, to identify novel regulators of axon guidance, this work compares the transcriptome and chromatin occupancy profiles of two neuronal subpopulations, ipsilateral (iRGC) and contralateral retinal ganglion cells (cRGC), with similar functions but divergent axon trajectories. These analyses retrieved a number of genes encoding for proteins not previously implicated in axon pathfinding. In vivo functional experiments confirm the implication of some of these candidates in axonal navigation. Among the candidate genes, γ-synuclein is identified as essential for inducing midline crossing. Footprint and luciferase assays demonstrate that this small-sized protein is regulated by the transcription factor (TF) Pou4f1 in cRGCs. It is also shown that Lhx2/9 are specifically expressed in iRGCs and control a program that partially overlaps with that regulated by Zic2, previously described as essential for iRGC specification. Overall, the analyses identify dozens of new molecules potentially involved in axon guidance and reveal the regulatory logic behind the selection of axonal trajectories.
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Affiliation(s)
- Marta Fernández‐Nogales
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
| | - Maria Teresa López‐Cascales
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
| | - Verónica Murcia‐Belmonte
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
| | - Augusto Escalante
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
| | - Jordi Fernández‐Albert
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
| | - Rafael Muñoz‐Viana
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
| | - Angel Barco
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
| | - Eloísa Herrera
- Instituto de Neurociencias (Consejo Superior de Investigaciones Científicas ‐Universidad Miguel Hernández de Elche, CSIC‐UMH)San Juan de AlicanteAv. Santiago Ramón y Cajal s/nAlicante03550Spain
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26
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Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification. PLoS Genet 2022; 18:e1010372. [PMID: 36178933 PMCID: PMC9524666 DOI: 10.1371/journal.pgen.1010372] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans, each individual neuron class is defined by the expression of unique combinations of homeobox genes, prompting the question of whether each neuron class indeed requires a homeobox gene for its proper identity specification. We present here progress in addressing this question by extending previous mutant analysis of homeobox gene family members and describing multiple examples of homeobox gene function in different parts of the C. elegans nervous system. To probe homeobox function, we make use of a number of reporter gene tools, including a novel multicolor reporter transgene, NeuroPAL, which permits simultaneous monitoring of the execution of multiple differentiation programs throughout the entire nervous system. Using these tools, we add to the previous characterization of homeobox gene function by identifying neuronal differentiation defects for 14 homeobox genes in 24 distinct neuron classes that are mostly unrelated by location, function and lineage history. 12 of these 24 neuron classes had no homeobox gene function ascribed to them before, while in the other 12 neuron classes, we extend the combinatorial code of transcription factors required for specifying terminal differentiation programs. Furthermore, we demonstrate that in a particular lineage, homeotic identity transformations occur upon loss of a homeobox gene and we show that these transformations are the result of changes in homeobox codes. Combining the present with past analyses, 113 of the 118 neuron classes of C. elegans are now known to require a homeobox gene for proper execution of terminal differentiation programs. Such broad deployment indicates that homeobox function in neuronal identity specification may be an ancestral feature of animal nervous systems.
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27
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Song S, Creus Muncunill J, Galicia Aguirre C, Tshilenge KT, Hamilton BW, Gerencser AA, Benlhabib H, Cirnaru MD, Leid M, Mooney SD, Ellerby LM, Ehrlich ME. Postnatal Conditional Deletion of Bcl11b in Striatal Projection Neurons Mimics the Transcriptional Signature of Huntington's Disease. Biomedicines 2022; 10:2377. [PMID: 36289639 PMCID: PMC9598565 DOI: 10.3390/biomedicines10102377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The dysregulation of striatal gene expression and function is linked to multiple diseases, including Huntington's disease (HD), Parkinson's disease, X-linked dystonia-parkinsonism (XDP), addiction, autism, and schizophrenia. Striatal medium spiny neurons (MSNs) make up 90% of the neurons in the striatum and are critical to motor control. The transcription factor, Bcl11b (also known as Ctip2), is required for striatal development, but the function of Bcl11b in adult MSNs in vivo has not been investigated. We conditionally deleted Bcl11b specifically in postnatal MSNs and performed a transcriptomic and behavioral analysis on these mice. Multiple enrichment analyses showed that the D9-Cre-Bcl11btm1.1Leid transcriptional profile was similar to the HD gene expression in mouse and human data sets. A Gene Ontology enrichment analysis linked D9-Cre-Bcl11btm1.1Leid to calcium, synapse organization, specifically including the dopaminergic synapse, protein dephosphorylation, and HDAC-signaling, commonly dysregulated pathways in HD. D9-Cre-Bcl11btm1.1Leid mice had decreased DARPP-32/Ppp1r1b in MSNs and behavioral deficits, demonstrating the dysregulation of a subtype of the dopamine D2 receptor expressing MSNs. Finally, in human HD isogenic MSNs, the mislocalization of BCL11B into nuclear aggregates points to a mechanism for BCL11B loss of function in HD. Our results suggest that BCL11B is important for the function and maintenance of mature MSNs and Bcl11b loss of function drives, in part, the transcriptomic and functional changes in HD.
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Affiliation(s)
- Sicheng Song
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jordi Creus Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Galicia Aguirre
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | | | - B. Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Houda Benlhabib
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Maria-Daniela Cirnaru
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mark Leid
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Lisa M. Ellerby
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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28
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Doyle JJ. Cell types as species: Exploring a metaphor. FRONTIERS IN PLANT SCIENCE 2022; 13:868565. [PMID: 36072310 PMCID: PMC9444152 DOI: 10.3389/fpls.2022.868565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/29/2022] [Indexed: 06/05/2023]
Abstract
The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.
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29
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Post-transcriptional regulation of transcription factor codes in immature neurons drives neuronal diversity. Cell Rep 2022; 39:110992. [PMID: 35767953 PMCID: PMC9479746 DOI: 10.1016/j.celrep.2022.110992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/15/2022] [Accepted: 06/01/2022] [Indexed: 12/31/2022] Open
Abstract
How the vast array of neuronal diversity is generated remains an unsolved problem. Here, we investigate how 29 morphologically distinct leg motoneurons are generated from a single stem cell in Drosophila. We identify 19 transcription factor (TF) codes expressed in immature motoneurons just before their morphological differentiation. Using genetic manipulations and a computational tool, we demonstrate that the TF codes are progressively established in immature motoneurons according to their birth order. Comparing RNA and protein expression patterns of multiple TFs reveals that post-transcriptional regulation plays an essential role in shaping these TF codes. Two RNA-binding proteins, Imp and Syp, expressed in opposing gradients in immature motoneurons, control the translation of multiple TFs. The varying sensitivity of TF mRNAs to the opposing gradients of Imp and Syp in immature motoneurons decrypts these gradients into distinct TF codes, establishing the connectome between motoneuron axons and their target muscles.
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30
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Hauser D, Behr K, Konno K, Schreiner D, Schmidt A, Watanabe M, Bischofberger J, Scheiffele P. Targeted proteoform mapping uncovers specific Neurexin-3 variants required for dendritic inhibition. Neuron 2022; 110:2094-2109.e10. [PMID: 35550065 PMCID: PMC9275415 DOI: 10.1016/j.neuron.2022.04.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/05/2022] [Accepted: 04/15/2022] [Indexed: 12/21/2022]
Abstract
The diversification of cell adhesion molecules by alternative splicing is proposed to underlie molecular codes for neuronal wiring. Transcriptomic approaches mapped detailed cell-type-specific mRNA splicing programs. However, it has been hard to probe the synapse-specific localization and function of the resulting protein splice isoforms, or “proteoforms,” in vivo. We here apply a proteoform-centric workflow in mice to test the synapse-specific functions of the splice isoforms of the synaptic adhesion molecule Neurexin-3 (NRXN3). We uncover a major proteoform, NRXN3 AS5, that is highly expressed in GABAergic interneurons and at dendrite-targeting GABAergic terminals. NRXN3 AS5 abundance significantly diverges from Nrxn3 mRNA distribution and is gated by translation-repressive elements. Nrxn3 AS5 isoform deletion results in a selective impairment of dendrite-targeting interneuron synapses in the dentate gyrus without affecting somatic inhibition or glutamatergic perforant-path synapses. This work establishes cell- and synapse-specific functions of a specific neurexin proteoform and highlights the importance of alternative splicing regulation for synapse specification. Translational regulation guides alternative Neurexin proteoform expression NRXN3 AS5 proteoforms are concentrated at dendrite-targeting interneuron synapses A proteome-centric workflow uncovers NRXN3 AS5 interactors in vivo Loss of NRXN3 AS5 leads to selective impairments in dendritic inhibition
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Affiliation(s)
- David Hauser
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Katharina Behr
- Department of Biomedicine, University of Basel, Pestalozzistrasse 20, 4056 Basel, Switzerland
| | - Kohtarou Konno
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Dietmar Schreiner
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Josef Bischofberger
- Department of Biomedicine, University of Basel, Pestalozzistrasse 20, 4056 Basel, Switzerland
| | - Peter Scheiffele
- Biozentrum of the University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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31
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Ahn S, Yang H, Son S, Lee HS, Park D, Yim H, Choi HJ, Swoboda P, Lee J. The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Rep 2022; 39:110661. [PMID: 35417689 DOI: 10.1016/j.celrep.2022.110661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Cilia are important for the interaction with environments and the proper function of tissues. While the basic structure of cilia is well conserved, ciliated cells have various functions. To understand the distinctive identities of ciliated cells, the identification of cell-specific proteins and its regulation is essential. Here, we report the mechanism that confers a specific identity on IL2 neurons in Caenorhabditis elegans, neurons important for the dauer larva-specific nictation behavior. We show that DAF-19M, an isoform of the sole C. elegans RFX transcription factor DAF-19, heads a regulatory subroutine, regulating target genes through an X-box motif variant under the control of terminal selector proteins UNC-86 and CFI-1 in IL2 neurons. Considering the conservation of DAF-19M module in IL2 neurons for nictation and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature "recognizing the environment."
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Affiliation(s)
- Soungyub Ahn
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Sangwon Son
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyun Sik Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dongjun Park
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
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32
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Vidal B, Gulez B, Cao WX, Leyva-Diaz E, Reilly MB, Tekieli T, Hobert O. The enteric nervous system of the C. elegans pharynx is specified by the Sine oculis-like homeobox gene ceh-34. eLife 2022; 11:76003. [PMID: 35324425 PMCID: PMC8989417 DOI: 10.7554/elife.76003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/23/2022] [Indexed: 11/29/2022] Open
Abstract
Overarching themes in the terminal differentiation of the enteric nervous system, an autonomously acting unit of animal nervous systems, have so far eluded discovery. We describe here the overall regulatory logic of enteric nervous system differentiation of the nematode Caenorhabditis elegans that resides within the foregut (pharynx) of the worm. A C. elegans homolog of the Drosophila Sine oculis homeobox gene, ceh-34, is expressed in all 14 classes of interconnected pharyngeal neurons from their birth throughout their life time, but in no other neuron type of the entire animal. Constitutive and temporally controlled ceh-34 removal shows that ceh-34 is required to initiate and maintain the neuron type-specific terminal differentiation program of all pharyngeal neuron classes, including their circuit assembly. Through additional genetic loss of function analysis, we show that within each pharyngeal neuron class, ceh-34 cooperates with different homeodomain transcription factors to individuate distinct pharyngeal neuron classes. Our analysis underscores the critical role of homeobox genes in neuronal identity specification and links them to the control of neuronal circuit assembly of the enteric nervous system. Together with the pharyngeal nervous system simplicity as well as its specification by a Sine oculis homolog, our findings invite speculations about the early evolution of nervous systems.
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Affiliation(s)
- Berta Vidal
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Burcu Gulez
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Wen Xi Cao
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Eduardo Leyva-Diaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Tessa Tekieli
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
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33
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Catela C, Chen Y, Weng Y, Wen K, Kratsios P. Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity. eLife 2022; 11:70766. [PMID: 35315772 PMCID: PMC8940177 DOI: 10.7554/elife.70766] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/12/2022] [Indexed: 12/30/2022] Open
Abstract
Spinal motor neurons (MNs) constitute cellular substrates for several movement disorders. Although their early development has received much attention, how spinal MNs become and remain terminally differentiated is poorly understood. Here, we determined the transcriptome of mouse MNs located at the brachial domain of the spinal cord at embryonic and postnatal stages. We identified novel transcription factors (TFs) and terminal differentiation genes (e.g. ion channels, neurotransmitter receptors, adhesion molecules) with continuous expression in MNs. Interestingly, genes encoding homeodomain TFs (e.g. HOX, LIM), previously implicated in early MN development, continue to be expressed postnatally, suggesting later functions. To test this idea, we inactivated Hoxc8 at successive stages of mouse MN development and observed motor deficits. Our in vivo findings suggest that Hoxc8 is not only required to establish, but also maintain expression of several MN terminal differentiation markers. Data from in vitro generated MNs indicate Hoxc8 acts directly and is sufficient to induce expression of terminal differentiation genes. Our findings dovetail recent observations in Caenorhabditis elegans MNs, pointing toward an evolutionarily conserved role for Hox in neuronal terminal differentiation.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Yifei Weng
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Kailong Wen
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
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34
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Rapti G. Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration. Front Neurosci 2022; 15:787753. [PMID: 35321480 PMCID: PMC8934944 DOI: 10.3389/fnins.2021.787753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Nervous system cells, the building blocks of circuits, have been studied with ever-progressing resolution, yet neural circuits appear still resistant to schemes of reductionist classification. Due to their sheer numbers, complexity and diversity, their systematic study requires concrete classifications that can serve reduced dimensionality, reproducibility, and information integration. Conventional hierarchical schemes transformed through the history of neuroscience by prioritizing criteria of morphology, (electro)physiological activity, molecular content, and circuit function, influenced by prevailing methodologies of the time. Since the molecular biology revolution and the recent advents in transcriptomics, molecular profiling gains ground toward the classification of neurons and glial cell types. Yet, transcriptomics entails technical challenges and more importantly uncovers unforeseen spatiotemporal heterogeneity, in complex and simpler nervous systems. Cells change states dynamically in space and time, in response to stimuli or throughout their developmental trajectory. Mapping cell type and state heterogeneity uncovers uncharted terrains in neurons and especially in glial cell biology, that remains understudied in many aspects. Examining neurons and glial cells from the perspectives of molecular neuroscience, physiology, development and evolution highlights the advantage of multifaceted classification schemes. Among the amalgam of models contributing to neuroscience research, Caenorhabditis elegans combines nervous system anatomy, lineage, connectivity and molecular content, all mapped at single-cell resolution, and can provide valuable insights for the workflow and challenges of the multimodal integration of cell type features. This review reflects on concepts and practices of neuron and glial cells classification and how research, in C. elegans and beyond, guides nervous system experimentation through integrated multidimensional schemes. It highlights underlying principles, emerging themes, and open frontiers in the study of nervous system development, regulatory logic and evolution. It proposes unified platforms to allow integrated annotation of large-scale datasets, gene-function studies, published or unpublished findings and community feedback. Neuroscience is moving fast toward interdisciplinary, high-throughput approaches for combined mapping of the morphology, physiology, connectivity, molecular function, and the integration of information in multifaceted schemes. A closer look in mapped neural circuits and understudied terrains offers insights for the best implementation of these approaches.
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35
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Leyva-Díaz E, Hobert O. Robust regulatory architecture of pan-neuronal gene expression. Curr Biol 2022; 32:1715-1727.e8. [PMID: 35259341 PMCID: PMC9050922 DOI: 10.1016/j.cub.2022.02.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 12/17/2022]
Abstract
Pan-neuronally expressed genes, such as genes involved in the synaptic vesicle cycle or in neuropeptide maturation, are critical for proper function of all neurons, but the transcriptional control mechanisms that direct such genes to all neurons of a nervous system remain poorly understood. We show here that six members of the CUT family of homeobox genes control pan-neuronal identity specification in Caenorhabditis elegans. Single CUT mutants show barely any effects on pan-neuronal gene expression or global nervous system function, but such effects become apparent and progressively worsen upon removal of additional CUT family members, indicating a critical role of gene dosage. Overexpression of each individual CUT gene rescued the phenotype of compound mutants, corroborating that gene dosage, rather than the activity of specific members of the gene family, is critical for CUT gene family function. Genome-wide binding profiles, as well as mutation of CUT homeodomain binding sites by CRISPR/Cas9 genome engineering show that CUT genes directly control the expression of pan-neuronal features. Moreover, CUT genes act in conjunction with neuron-type-specific transcription factors to control pan-neuronal gene expression. Our study, therefore, provides a previously missing key insight into how neuronal gene expression programs are specified and reveals a highly buffered and robust mechanism that controls the most critical functional features of all neuronal cell types.
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A global timing mechanism regulates cell-type-specific wiring programmes. Nature 2022; 603:112-118. [PMID: 35197627 DOI: 10.1038/s41586-022-04418-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/10/2022] [Indexed: 01/04/2023]
Abstract
The assembly of neural circuits is dependent on precise spatiotemporal expression of cell recognition molecules1-5. Factors controlling cell type specificity have been identified6-8, but how timing is determined remains unknown. Here we describe induction of a cascade of transcription factors by a steroid hormone (ecdysone) in all fly visual system neurons spanning target recognition and synaptogenesis. We demonstrate through single-cell sequencing that the ecdysone pathway regulates the expression of a common set of targets required for synaptic maturation and cell-type-specific targets enriched for cell-surface proteins regulating wiring specificity. Transcription factors in the cascade regulate the expression of the same wiring genes in complex ways, including activation in one cell type and repression in another. We show that disruption of the ecdysone pathway generates specific defects in dendritic and axonal processes and synaptic connectivity, with the order of transcription factor expression correlating with sequential steps in wiring. We also identify shared targets of a cell-type-specific transcription factor and the ecdysone pathway that regulate specificity. We propose that neurons integrate a global temporal transcriptional module with cell-type-specific transcription factors to generate different cell-type-specific patterns of cell recognition molecules regulating wiring.
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Saul J, Hirose T, Horvitz HR. The transcriptional corepressor CTBP-1 acts with the SOX family transcription factor EGL-13 to maintain AIA interneuron cell identity in Caenorhabditis elegans. eLife 2022; 11:74557. [PMID: 35119366 PMCID: PMC8816384 DOI: 10.7554/elife.74557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Abstract
Cell identity is characterized by a distinct combination of gene expression, cell morphology, and cellular function established as progenitor cells divide and differentiate. Following establishment, cell identities can be unstable and require active and continuous maintenance throughout the remaining life of a cell. Mechanisms underlying the maintenance of cell identities are incompletely understood. Here, we show that the gene ctbp-1, which encodes the transcriptional corepressor C-terminal binding protein-1 (CTBP-1), is essential for the maintenance of the identities of the two AIA interneurons in the nematode Caenorhabditis elegans. ctbp-1 is not required for the establishment of the AIA cell fate but rather functions cell-autonomously and can act in later larval stage and adult worms to maintain proper AIA gene expression, morphology and function. From a screen for suppressors of the ctbp-1 mutant phenotype, we identified the gene egl-13, which encodes a SOX family transcription factor. We found that egl-13 regulates AIA function and aspects of AIA gene expression, but not AIA morphology. We conclude that the CTBP-1 protein maintains AIA cell identity in part by utilizing EGL-13 to repress transcriptional activity in the AIAs. More generally, we propose that transcriptional corepressors like CTBP-1 might be critical factors in the maintenance of cell identities, harnessing the DNA-binding specificity of transcription factors like EGL-13 to selectively regulate gene expression in a cell-specific manner.
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Affiliation(s)
- Josh Saul
- Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, United States
| | - Takashi Hirose
- Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, United States
| | - H Robert Horvitz
- Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, United States
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38
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Hori S, Mitani S. The transcription factor unc-130/FOXD3/4 contributes to the biphasic calcium response required to optimize avoidance behavior. Sci Rep 2022; 12:1907. [PMID: 35115609 PMCID: PMC8814005 DOI: 10.1038/s41598-022-05942-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/13/2022] [Indexed: 11/12/2022] Open
Abstract
The central neural network optimizes avoidance behavior depending on the nociceptive stimulation intensity and is essential for survival. How the property of hub neurons that enables the selection of behaviors is genetically defined is not well understood. We show that the transcription factor unc-130, a human FOXD3/4 ortholog, is required to optimize avoidance behavior depending on stimulus strength in Caenorhabditis elegans. unc-130 is necessary for both ON responses (calcium decreases) and OFF responses (calcium increases) in AIBs, central neurons of avoidance optimization. Ablation of predicted upstream inhibitory neurons reduces the frequency of turn behavior, suggesting that optimization needs both calcium responses. At the molecular level, unc-130 upregulates the expression of at least three genes: nca-2, a homolog of the vertebrate cation leak channel NALCN; glr-1, an AMPA-type glutamate receptor; and eat-4, a hypothetical L-glutamate transmembrane transporter in the central neurons of optimization. unc-130 shows more limited regulation in optimizing behavior than an atonal homolog lin-32, and unc-130 and lin-32 appear to act in parallel molecular pathways. Our findings suggest that unc-130 is required for the establishment of some AIB identities to optimize avoidance behavior.
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Affiliation(s)
- Sayaka Hori
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, 162-8666, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, 162-8666, Japan.
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39
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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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40
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Traets JJ, van der Burght SN, Rademakers S, Jansen G, van Zon JS. Mechanism of life-long maintenance of neuron identity despite molecular fluctuations. eLife 2021; 10:66955. [PMID: 34908528 PMCID: PMC8735970 DOI: 10.7554/elife.66955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
Cell fate is maintained over long timescales, yet molecular fluctuations can lead to spontaneous loss of this differentiated state. Our simulations identified a possible mechanism that explains life-long maintenance of ASE neuron fate in Caenorhabditis elegans by the terminal selector transcription factor CHE-1. Here, fluctuations in CHE-1 level are buffered by the reservoir of CHE-1 bound at its target promoters, which ensures continued che-1 expression by preferentially binding the che-1 promoter. We provide experimental evidence for this mechanism by showing that che-1 expression was resilient to induced transient CHE-1 depletion, while both expression of CHE-1 targets and ASE function were lost. We identified a 130 bp che-1 promoter fragment responsible for this resilience, with deletion of a homeodomain binding site in this fragment causing stochastic loss of ASE identity long after its determination. Because network architectures that support this mechanism are highly conserved in cell differentiation, it may explain stable cell fate maintenance in many systems.
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Affiliation(s)
| | | | | | - Gert Jansen
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands
| | - Jeroen S van Zon
- Quantitative Developmental Biology, AMOLF, Amsterdam, Netherlands
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41
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Evolutionary assembly of cooperating cell types in an animal chemical defense system. Cell 2021; 184:6138-6156.e28. [PMID: 34890552 DOI: 10.1016/j.cell.2021.11.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/29/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022]
Abstract
How the functions of multicellular organs emerge from the underlying evolution of cell types is poorly understood. We deconstructed evolution of an organ novelty: a rove beetle gland that secretes a defensive cocktail. We show how gland function arose via assembly of two cell types that manufacture distinct compounds. One cell type, comprising a chemical reservoir within the abdomen, produces alkane and ester compounds. We demonstrate that this cell type is a hybrid of cuticle cells and ancient pheromone and adipocyte-like cells, executing its function via a mosaic of enzymes from each parental cell type. The second cell type synthesizes benzoquinones using a chimera of conserved cellular energy and cuticle formation pathways. We show that evolution of each cell type was shaped by coevolution between the two cell types, yielding a potent secretion that confers adaptive value. Our findings illustrate how cooperation between cell types arises, generating new, organ-level behaviors.
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42
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Temporal transitions in the post-mitotic nervous system of Caenorhabditis elegans. Nature 2021; 600:93-99. [PMID: 34759317 PMCID: PMC8785361 DOI: 10.1038/s41586-021-04071-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 09/29/2021] [Indexed: 01/03/2023]
Abstract
In most animals, the majority of the nervous system is generated and assembled into neuronal circuits during embryonic development1. However, during juvenile stages, nervous systems still undergo extensive anatomical and functional changes to eventually form a fully mature nervous system by the adult stage2,3. The molecular changes in post-mitotic neurons across post-embryonic development and the genetic programs that control these temporal transitions are not well understood4,5. Here, using the model system Caenorhabditis elegans, we comprehensively characterized the distinct functional states (locomotor behaviour) and the corresponding distinct molecular states (transcriptome) of the post-mitotic nervous system across temporal transitions during post-embryonic development. We observed pervasive, neuron-type-specific changes in gene expression, many of which are controlled by the developmental upregulation of the conserved heterochronic microRNA LIN-4 and the subsequent promotion of a mature neuronal transcriptional program through the repression of its target, the transcription factor lin-14. The functional relevance of these molecular transitions are exemplified by a temporally regulated target gene of the LIN-14 transcription factor, nlp-45, a neuropeptide-encoding gene, which we find is required for several distinct temporal transitions in exploratory activity during post-embryonic development. Our study provides insights into regulatory strategies that control neuron-type-specific gene batteries to modulate distinct behavioural states across temporal, sexual and environmental dimensions of post-embryonic development.
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Cirnaru MD, Song S, Tshilenge KT, Corwin C, Mleczko J, Galicia Aguirre C, Benlhabib H, Bendl J, Apontes P, Fullard J, Creus-Muncunill J, Reyahi A, Nik AM, Carlsson P, Roussos P, Mooney SD, Ellerby LM, Ehrlich ME. Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation. eLife 2021; 10:e65979. [PMID: 34609283 PMCID: PMC8492065 DOI: 10.7554/elife.65979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Many diseases are linked to dysregulation of the striatum. Striatal function depends on neuronal compartmentation into striosomes and matrix. Striatal projection neurons are GABAergic medium spiny neurons (MSNs), subtyped by selective expression of receptors, neuropeptides, and other gene families. Neurogenesis of the striosome and matrix occurs in separate waves, but the factors regulating compartmentation and neuronal differentiation are largely unidentified. We performed RNA- and ATAC-seq on sorted striosome and matrix cells at postnatal day 3, using the Nr4a1-EGFP striosome reporter mouse. Focusing on the striosome, we validated the localization and/or role of Irx1, Foxf2, Olig2, and Stat1/2 in the developing striosome and the in vivo enhancer function of a striosome-specific open chromatin region 4.4 Kb downstream of Olig2. These data provide novel tools to dissect and manipulate the networks regulating MSN compartmentation and differentiation, including in human iPSC-derived striatal neurons for disease modeling and drug discovery.
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Affiliation(s)
- Maria-Daniela Cirnaru
- Department of Neurology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Sicheng Song
- Department of Biomedical Informatics and Medical Education, University of WashingtonSeattleUnited States
| | | | - Chuhyon Corwin
- Department of Neurology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Justyna Mleczko
- Department of Neurology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | | | - Houda Benlhabib
- Department of Biomedical Informatics and Medical Education, University of WashingtonSeattleUnited States
| | - Jaroslav Bendl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Pasha Apontes
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - John Fullard
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Jordi Creus-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Azadeh Reyahi
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Ali M Nik
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Peter Carlsson
- Department of Chemistry and Molecular Biology, University of GothenburgGothenburgSweden
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Mental Illness Research, Education, and Clinical Center (VISN 2 South)BronxUnited States
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of WashingtonSeattleUnited States
| | | | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
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44
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Hsieh YW, Xiong R, Chuang CF. Synergistic roles of homeodomain proteins UNC-62 homothorax and MLS-2 HMX/NKX in the specification of olfactory neurons in Caenorhabditis elegans. Genetics 2021; 219:6350488. [PMID: 34849889 DOI: 10.1093/genetics/iyab133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
General identity of the Caenorhabditis elegans AWC olfactory neuron pair is specified by the OTX/OTD transcription factor CEH-36 and the HMG-box transcription factor SOX-2, followed by asymmetrical differentiation of the pair into two distinct subtypes, default AWCOFF and induced AWCON, through a stochastic signaling event. The HMX/NKX transcription factor MLS-2 regulates the expression of ceh-36 to specify general AWC identity. However, general AWC identity is lost in only one of the two AWC cells in the majority of mls-2 null mutants displaying defective general AWC identity, suggesting that additional transcription factors have a partially overlapping role with MLS-2 in the specification of general AWC identity. Here, we identify a role of unc-62, encoding a homothorax/Meis/TALE homeodomain protein, in the specification of general AWC identity. As in mls-2 null mutants, unc-62 null mutants showed an incomplete penetrance in loss of general AWC identity. However, unc-62; mls-2 double mutants display a nearly complete penetrance of identity loss in both AWC cells. Thus, unc-62 and mls-2 have a partially overlapping function in the specification of general AWC identity. Furthermore, our genetic results suggest that mls-2 and unc-62 act cell autonomously in promoting the AWCON subtype. Together, our findings reveal the sequential roles of the unc-62 and mls-2 pair in AWC development, specification of general AWC identity in early embryogenesis, and asymmetric differentiation of AWC subtypes in late embryogenesis.
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Affiliation(s)
- Yi-Wen Hsieh
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Rui Xiong
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Chiou-Fen Chuang
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA.,Graduate Program in Neuroscience, University of Illinois at Chicago, IL 60607, USA
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45
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Tekieli T, Yemini E, Nejatbakhsh A, Wang C, Varol E, Fernandez RW, Masoudi N, Paninski L, Hobert O. Visualizing the organization and differentiation of the male-specific nervous system of C. elegans. Development 2021; 148:271902. [PMID: 34415309 DOI: 10.1242/dev.199687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/16/2021] [Indexed: 01/08/2023]
Abstract
Sex differences in the brain are prevalent throughout the animal kingdom and particularly well appreciated in the nematode Caenorhabditis elegans, where male animals contain a little-studied set of 93 male-specific neurons. To make these neurons amenable for future study, we describe here how a multicolor reporter transgene, NeuroPAL, is capable of visualizing the distinct identities of all male-specific neurons. We used NeuroPAL to visualize and characterize a number of features of the male-specific nervous system. We provide several proofs of concept for using NeuroPAL to identify the sites of expression of gfp-tagged reporter genes and for cellular fate analysis by analyzing the effect of removal of several developmental patterning genes on neuronal identity acquisition. We use NeuroPAL and its intrinsic cohort of more than 40 distinct differentiation markers to show that, even though male-specific neurons are generated throughout all four larval stages, they execute their terminal differentiation program in a coordinated manner in the fourth larval stage. This coordinated wave of differentiation, which we call 'just-in-time' differentiation, couples neuronal maturation programs with the appearance of sexual organs.
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Affiliation(s)
- Tessa Tekieli
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Amin Nejatbakhsh
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Chen Wang
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Erdem Varol
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Robert W Fernandez
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Neda Masoudi
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Liam Paninski
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
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46
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Hobert O. Homeobox genes and the specification of neuronal identity. Nat Rev Neurosci 2021; 22:627-636. [PMID: 34446866 DOI: 10.1038/s41583-021-00497-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2021] [Indexed: 12/27/2022]
Abstract
The enormous diversity of cell types that characterizes any animal nervous system is defined by neuron-type-specific gene batteries that endow cells with distinct anatomical and functional properties. To understand how such cellular diversity is genetically specified, one needs to understand the gene regulatory programmes that control the expression of cell-type-specific gene batteries. The small nervous system of the nematode Caenorhabditis elegans has been comprehensively mapped at the cellular and molecular levels, which has enabled extensive, nervous system-wide explorations into whether there are common underlying mechanisms that specify neuronal cell-type diversity. One principle that emerged from these studies is that transcription factors termed 'terminal selectors' coordinate the expression of individual members of neuron-type-specific gene batteries, thereby assigning unique identities to individual neuron types. Systematic mutant analyses and recent nervous system-wide expression analyses have revealed that one transcription factor family, the homeobox gene family, is broadly used throughout the entire C. elegans nervous system to specify neuronal identity as terminal selectors. I propose that the preponderance of homeobox genes in neuronal identity control is a reflection of an evolutionary trajectory in which an ancestral neuron type was specified by one or more ancestral homeobox genes, and that this functional linkage then duplicated and diversified to generate distinct cell types in an evolving nervous system.
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Affiliation(s)
- Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY, USA.
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47
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Rapti G. A perspective on C. elegans neurodevelopment: from early visionaries to a booming neuroscience research. J Neurogenet 2021; 34:259-272. [PMID: 33446023 DOI: 10.1080/01677063.2020.1837799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The formation of the nervous system and its striking complexity is a remarkable feat of development. C. elegans served as a unique model to dissect the molecular events in neurodevelopment, from its early visionaries to the current booming neuroscience community. Soon after being introduced as a model, C. elegans was mapped at the level of genes, cells, and synapses, providing the first metazoan with a complete cell lineage, sequenced genome, and connectome. Here, I summarize mechanisms underlying C. elegans neurodevelopment, from the generation and diversification of neural components to their navigation and connectivity. I point out recent noteworthy findings in the fields of glia biology, sex dimorphism and plasticity in neurodevelopment, highlighting how current research connects back to the pioneering studies by Brenner, Sulston and colleagues. Multifaceted investigations in model organisms, connecting genes to cell function and behavior, expand our mechanistic understanding of neurodevelopment while allowing us to formulate emerging questions for future discoveries.
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Affiliation(s)
- Georgia Rapti
- European Molecular Biology Laboratory, Unit of Developmental Biology, Heidelberg, Germany
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48
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Glenwinkel L, Taylor SR, Langebeck-Jensen K, Pereira L, Reilly MB, Basavaraju M, Rafi I, Yemini E, Pocock R, Sestan N, Hammarlund M, Miller DM, Hobert O. In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system. eLife 2021; 10:e64906. [PMID: 34165430 PMCID: PMC8225391 DOI: 10.7554/elife.64906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The generation of the enormous diversity of neuronal cell types in a differentiating nervous system entails the activation of neuron type-specific gene batteries. To examine the regulatory logic that controls the expression of neuron type-specific gene batteries, we interrogate single cell expression profiles of all 118 neuron classes of the Caenorhabditis elegans nervous system for the presence of DNA binding motifs of 136 neuronally expressed C. elegans transcription factors. Using a phylogenetic footprinting pipeline, we identify cis-regulatory motif enrichments among neuron class-specific gene batteries and we identify cognate transcription factors for 117 of the 118 neuron classes. In addition to predicting novel regulators of neuronal identities, our nervous system-wide analysis at single cell resolution supports the hypothesis that many transcription factors directly co-regulate the cohort of effector genes that define a neuron type, thereby corroborating the concept of so-called terminal selectors of neuronal identity. Our analysis provides a blueprint for how individual components of an entire nervous system are genetically specified.
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Affiliation(s)
- Lori Glenwinkel
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | | | - Laura Pereira
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Manasa Basavaraju
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Roger Pocock
- Biotech Research and Innovation Centre, University of CopenhagenCopenhagenDenmark
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash UniversityMelbourneAustralia
| | - Nenad Sestan
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Marc Hammarlund
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
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49
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Masoudi N, Yemini E, Schnabel R, Hobert O. Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans. Development 2021; 148:dev199224. [PMID: 34100067 PMCID: PMC8217713 DOI: 10.1242/dev.199224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/29/2021] [Indexed: 11/20/2022]
Abstract
Cells of the same type can be generated by distinct cellular lineages that originate in different parts of the developing embryo ('lineage convergence'). Several Caenorhabditis elegans neuron classes composed of left/right or radially symmetric class members display such lineage convergence. We show here that the C. elegans Atonal homolog lin-32 is differentially expressed in neuronal lineages that give rise to left/right or radially symmetric class members. Loss of lin-32 results in the selective loss of the expression of pan-neuronal markers and terminal selector-type transcription factors that confer neuron class-specific features. Another basic helix-loop-helix (bHLH) gene, the Achaete-Scute homolog hlh-14, is expressed in a mirror image pattern relative to lin-32 and is required to induce neuronal identity and terminal selector expression on the contralateral side of the animal. These findings demonstrate that distinct lineage histories converge via different bHLH factors at the level of induction of terminal selector identity determinants, which thus serve as integrators of distinct lineage histories. We also describe neuron-to-neuron identity transformations in lin-32 mutants, which we propose to also be the result of misregulation of terminal selector gene expression.
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Affiliation(s)
- Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
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50
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Causeret F, Moreau MX, Pierani A, Blanquie O. The multiple facets of Cajal-Retzius neurons. Development 2021; 148:268379. [PMID: 34047341 DOI: 10.1242/dev.199409] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Cajal-Retzius neurons (CRs) are among the first-born neurons in the developing cortex of reptiles, birds and mammals, including humans. The peculiarity of CRs lies in the fact they are initially embedded into the immature neuronal network before being almost completely eliminated by cell death at the end of cortical development. CRs are best known for controlling the migration of glutamatergic neurons and the formation of cortical layers through the secretion of the glycoprotein reelin. However, they have been shown to play numerous additional key roles at many steps of cortical development, spanning from patterning and sizing functional areas to synaptogenesis. The use of genetic lineage tracing has allowed the discovery of their multiple ontogenetic origins, migratory routes, expression of molecular markers and death dynamics. Nowadays, single-cell technologies enable us to appreciate the molecular heterogeneity of CRs with an unprecedented resolution. In this Review, we discuss the morphological, electrophysiological, molecular and genetic criteria allowing the identification of CRs. We further expose the various sources, migration trajectories, developmental functions and death dynamics of CRs. Finally, we demonstrate how the analysis of public transcriptomic datasets allows extraction of the molecular signature of CRs throughout their transient life and consider their heterogeneity within and across species.
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Affiliation(s)
- Frédéric Causeret
- Université de Paris, Imagine Institute, Team Genetics and Development of the Cerebral Cortex, F-75015 Paris, France.,Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, F-75014 Paris, France
| | - Matthieu X Moreau
- Université de Paris, Imagine Institute, Team Genetics and Development of the Cerebral Cortex, F-75015 Paris, France.,Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, F-75014 Paris, France
| | - Alessandra Pierani
- Université de Paris, Imagine Institute, Team Genetics and Development of the Cerebral Cortex, F-75015 Paris, France.,Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, F-75014 Paris, France.,Groupe Hospitalier Universitaire Paris Psychiatrie et Neurosciences, F-75014 Paris, France
| | - Oriane Blanquie
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University Mainz, D-55128 Mainz, Germany
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