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Article ; Online: The bHLH-PAS gene

Cook, Steven J / Vidal, Berta / Hobert, Oliver

microPublication biology

2021 Volume 2021

Abstract: Single neuron-specific drivers are important tools for visualizing neuron anatomy, manipulating neuron activity and gene rescue experiments. We report here that genomic regions upstream of ... ...

Abstract	Single neuron-specific drivers are important tools for visualizing neuron anatomy, manipulating neuron activity and gene rescue experiments. We report here that genomic regions upstream of the
Language	English
Publishing date	2021-09-28
Publishing country	United States
Document type	Journal Article
ISSN	2578-9430
ISSN (online)	2578-9430
DOI	10.17912/micropub.biology.000467
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Article ; Online: The enteric nervous system of the

Vidal, Berta / Gulez, Burcu / Cao, Wen Xi / Leyva-Díaz, Eduardo / Reilly, Molly B / Tekieli, Tessa / Hobert, Oliver

eLife

2022 Volume 11

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 ...

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
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Enteric Nervous System/embryology ; Enteric Nervous System/growth & development ; Gene Expression Regulation, Developmental/genetics ; Genes, Homeobox ; Homeodomain Proteins/metabolism ; Pharynx ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	CEH-34 protein, C elegans ; Caenorhabditis elegans Proteins ; Homeodomain Proteins ; Transcription Factors
Language	English
Publishing date	2022-03-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.76003
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Article: EAG responses increase of Spodoptera littoralis antennae after a single pheromone pulse.

Quero, Carmen / Vidal, Berta / Guerrero, Angel

Natural product communications

2014 Volume 9, Issue 8, Page(s) 1099–1101

Abstract: Increased behavioral sensitivity to the pheromone after brief exposure of the whole insect to the sex pheromone has been documented in antennal lobe neurons of Spodoptera littoralis. We investigated whether a brief stimulus of the major component of the ... ...

Abstract	Increased behavioral sensitivity to the pheromone after brief exposure of the whole insect to the sex pheromone has been documented in antennal lobe neurons of Spodoptera littoralis. We investigated whether a brief stimulus of the major component of the pheromone on naïve antenna separated from the head increased the electroantennographic responses after successive stimulations at different times. The response increase was clear 30 min after the first stimulation, and this effect lasted at least 60 min, the average life time of the antenna. Our results suggest that the olfactory receptor neurons, and not only the neurons in the antennal lobe, may be involved in the increased antennal response after a single pheromone pulse.
MeSH term(s)	Animals ; Arthropod Antennae/drug effects ; Arthropod Antennae/physiology ; Electrophysiology ; Female ; Male ; Olfactory Receptor Neurons/drug effects ; Olfactory Receptor Neurons/physiology ; Sex Attractants/pharmacology ; Spodoptera/drug effects ; Spodoptera/physiology
Chemical Substances	Sex Attractants
Language	English
Publishing date	2014-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1934-578X
ISSN	1934-578X
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Article ; Online: An atlas of Caenorhabditis elegans chemoreceptor expression.

Vidal, Berta / Aghayeva, Ulkar / Sun, Haosheng / Wang, Chen / Glenwinkel, Lori / Bayer, Emily A / Hobert, Oliver

PLoS biology

2018 Volume 16, Issue 1, Page(s) e2004218

Abstract: One goal of modern day neuroscience is the establishment of molecular maps that assign unique features to individual neuron types. Such maps provide important starting points for neuron classification, for functional analysis, and for developmental ... ...

Abstract	One goal of modern day neuroscience is the establishment of molecular maps that assign unique features to individual neuron types. Such maps provide important starting points for neuron classification, for functional analysis, and for developmental studies aimed at defining the molecular mechanisms of neuron identity acquisition and neuron identity diversification. In this resource paper, we describe a nervous system-wide map of the potential expression sites of 244 members of the largest gene family in the C. elegans genome, rhodopsin-like (class A) G-protein-coupled receptor (GPCR) chemoreceptors, using classic gfp reporter gene technology. We cover representatives of all sequence families of chemoreceptor GPCRs, some of which were previously entirely uncharacterized. Most reporters are expressed in a very restricted number of cells, often just in single cells. We assign GPCR reporter expression to all but two of the 37 sensory neuron classes of the sex-shared, core nervous system. Some sensory neurons express a very small number of receptors, while others, particularly nociceptive neurons, coexpress several dozen GPCR reporter genes. GPCR reporters are also expressed in a wide range of inter- and motorneurons, as well as non-neuronal cells, suggesting that GPCRs may constitute receptors not just for environmental signals, but also for internal cues. We observe only one notable, frequent association of coexpression patterns, namely in one nociceptive amphid (ASH) and two nociceptive phasmid sensory neurons (PHA, PHB). We identified GPCRs with sexually dimorphic expression and several GPCR reporters that are expressed in a left/right asymmetric manner. We identified a substantial degree of GPCR expression plasticity; particularly in the context of the environmentally-induced dauer diapause stage when one third of all tested GPCRs alter the cellular specificity of their expression within and outside the nervous system. Intriguingly, in a number of cases, the dauer-specific alterations of GPCR reporter expression in specific neuron classes are maintained during postdauer life and in some case new patterns are induced post-dauer, demonstrating that GPCR gene expression may serve as traits of life history. Taken together, our resource provides an entry point for functional studies and also offers a host of molecular markers for studying molecular patterning and plasticity of the nervous system.
MeSH term(s)	Animals ; Body Patterning/genetics ; Body Patterning/physiology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Chemoreceptor Cells/physiology ; Chromosome Mapping/methods ; Gene Expression Regulation, Developmental/genetics ; Genes, Reporter ; Phenotype ; Sensory Receptor Cells/physiology ; Transcriptome/genetics
Chemical Substances	Caenorhabditis elegans Proteins
Language	English
Publishing date	2018-01-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.2004218
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Article ; Online: Modular Organization of

Serrano-Saiz, Esther / Gulez, Burcu / Pereira, Laura / Gendrel, Marie / Kerk, Sze Yen / Vidal, Berta / Feng, Weidong / Wang, Chen / Kratsios, Paschalis / Rand, James B / Hobert, Oliver

Genetics

2020 Volume 215, Issue 3, Page(s) 665–681

Abstract: We explore here ... ...

Abstract	We explore here the
MeSH term(s)	Animals ; Caenorhabditis elegans ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Genetic Pleiotropy ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Neurons/classification ; Neurons/metabolism ; Neurotransmitter Agents/genetics ; Neurotransmitter Agents/metabolism ; Regulatory Sequences, Nucleic Acid ; Vesicular Acetylcholine Transport Proteins/genetics ; Vesicular Acetylcholine Transport Proteins/metabolism ; Vesicular Glutamate Transport Proteins/genetics ; Vesicular Glutamate Transport Proteins/metabolism ; Vesicular Inhibitory Amino Acid Transport Proteins/genetics ; Vesicular Inhibitory Amino Acid Transport Proteins/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; Eat-4 protein, C elegans ; Membrane Transport Proteins ; Neurotransmitter Agents ; Unc-17 protein, C elegans ; Vesicular Acetylcholine Transport Proteins ; Vesicular Glutamate Transport Proteins ; Vesicular Inhibitory Amino Acid Transport Proteins ; choline transporter ; unc-46 protein, C elegans ; unc-47 protein, C elegans
Language	English
Publishing date	2020-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.120.303206
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Article ; Online: Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification.

Reilly, Molly B / Tekieli, Tessa / Cros, Cyril / Aguilar, G Robert / Lao, James / Toker, Itai Antoine / Vidal, Berta / Leyva-Díaz, Eduardo / Bhattacharya, Abhishek / Cook, Steven J / Smith, Jayson J / Kovacevic, Ismar / Gulez, Burcu / Fernandez, Robert W / Bradford, Elisabeth F / Ramadan, Yasmin H / Kratsios, Paschalis / Bao, Zhirong / Hobert, Oliver

PLoS genetics

2022 Volume 18, Issue 9, Page(s) e1010372

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 ... ...

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.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Cell Differentiation/genetics ; DNA-Binding Proteins/genetics ; Employment ; Gene Expression Regulation, Developmental ; Genes, Homeobox/genetics ; Neurons/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; DNA-Binding Proteins ; Transcription Factors
Language	English
Publishing date	2022-09-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1010372
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Article ; Online: C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types.

Vidal, Berta / Santella, Anthony / Serrano-Saiz, Esther / Bao, Zhirong / Chuang, Chiou-Fen / Hobert, Oliver

Development (Cambridge, England)

2015 Volume 142, Issue 14, Page(s) 2464–2477

Abstract: Neurogenesis involves deeply conserved patterning molecules, such as the proneural basic helix-loop-helix transcription factors. Sox proteins and specifically members of the SoxB and SoxC groups are another class of conserved transcription factors with ... ...

Abstract	Neurogenesis involves deeply conserved patterning molecules, such as the proneural basic helix-loop-helix transcription factors. Sox proteins and specifically members of the SoxB and SoxC groups are another class of conserved transcription factors with an important role in neuronal fate commitment and differentiation in various species. In this study, we examine the expression of all five Sox genes of the nematode C. elegans and analyze the effect of null mutant alleles of all members of the SoxB and SoxC groups on nervous system development. Surprisingly, we find that, unlike in other systems, neither of the two C. elegans SoxB genes sox-2 (SoxB1) and sox-3 (SoxB2), nor the sole C. elegans SoxC gene sem-2, is broadly expressed throughout the embryonic or adult nervous system and that all three genes are mostly dispensable for embryonic neurogenesis. Instead, sox-2 is required to maintain the developmental potential of blast cells that are generated in the embryo but divide only postembryonically to give rise to differentiated neuronal cell types. Moreover, sox-2 and sox-3 have selective roles in the terminal differentiation of specific neuronal cell types. Our findings suggest that the common themes of SoxB gene function across phylogeny lie in specifying developmental potential and, later on, in selectively controlling terminal differentiation programs of specific neuron types, but not in broadly controlling neurogenesis.
MeSH term(s)	Alleles ; Animals ; Basic Helix-Loop-Helix Transcription Factors/physiology ; Caenorhabditis elegans/embryology ; Caenorhabditis elegans Proteins/physiology ; Cell Differentiation ; Cell Lineage ; Gene Expression Regulation, Developmental ; Male ; Motor Neurons/metabolism ; Mutation ; Nervous System/embryology ; Neurogenesis/physiology ; Neurons/cytology ; SOXB1 Transcription Factors/physiology ; SOXC Transcription Factors/physiology ; Signal Transduction ; Transgenes
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors ; Caenorhabditis elegans Proteins ; SOXB1 Transcription Factors ; SOXC Transcription Factors
Language	English
Publishing date	2015-07-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.125740
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Article ; Online: Postmitotic diversification of olfactory neuron types is mediated by differential activities of the HMG-box transcription factor SOX-2.

Alqadah, Amel / Hsieh, Yi-Wen / Vidal, Berta / Chang, Chieh / Hobert, Oliver / Chuang, Chiou-Fen

The EMBO journal

2015 Volume 34, Issue 20, Page(s) 2574–2589

Abstract: Diversification of neuron classes is essential for functions of the olfactory system, but the underlying mechanisms that generate individual olfactory neuron types are only beginning to be understood. Here we describe a role of the highly conserved HMG- ... ...

Abstract	Diversification of neuron classes is essential for functions of the olfactory system, but the underlying mechanisms that generate individual olfactory neuron types are only beginning to be understood. Here we describe a role of the highly conserved HMG-box transcription factor SOX-2 in postmitotic specification and alternative differentiation of the Caenorhabditis elegans AWC and AWB olfactory neurons. We show that SOX-2 partners with different transcription factors to diversify postmitotic olfactory cell types. SOX-2 functions cooperatively with the OTX/OTD transcription factor CEH-36 to specify an AWC "ground state," and functions with the LIM homeodomain factor LIM-4 to suppress this ground state and drive an AWB identity instead. Our findings provide novel insights into combinatorial codes that drive terminal differentiation programs in the nervous system and reveal a biological function of the deeply conserved Sox2 protein that goes beyond its well-known role in stem cell biology.
MeSH term(s)	Animals ; Base Sequence ; COS Cells ; Caenorhabditis elegans/growth & development ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Cell Differentiation/physiology ; Cercopithecus aethiops ; Chromosome Mapping ; Electrophoretic Mobility Shift Assay ; Genome/genetics ; Homeodomain Proteins/metabolism ; LIM-Homeodomain Proteins/metabolism ; Luciferases ; Molecular Sequence Data ; Olfactory Receptor Neurons/cytology ; Olfactory Receptor Neurons/physiology ; Plasmids/genetics ; SOXB1 Transcription Factors/metabolism ; Sequence Analysis, DNA ; Transcription Factors/metabolism ; Transfection
Chemical Substances	Caenorhabditis elegans Proteins ; Homeodomain Proteins ; LIM-Homeodomain Proteins ; Lim-4 protein, C elegans ; SOXB1 Transcription Factors ; Transcription Factors ; ceh-36 protein, C elegans ; Luciferases (EC 1.13.12.-)
Language	English
Publishing date	2015-10-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.201592188
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Article: Molecular topography of an entire nervous system

Cell. 2021 Aug. 05, v. 184, no. 16

2021

Abstract: We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by ... ...

Abstract	We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses distinct codes of ∼23 neuropeptide genes and ∼36 neuropeptide receptors, delineating a complex and expansive “wireless” signaling network. To demonstrate the utility of this comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression and (2) reveal adhesion proteins with potential roles in process placement and synaptic specificity. Our expression data are available at https://cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity, and function throughout the C. elegans nervous system.
Keywords	Internet ; adhesion ; gene expression ; genes ; neurons ; neuropeptides ; topography
Language	English
Dates of publication	2021-0805
Size	p. 4329-4347.e23.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.06.023
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Article ; Online: Molecular topography of an entire nervous system.

Cell

2021 Volume 184, Issue 16, Page(s) 4329–4347.e23

Abstract	We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses distinct codes of ∼23 neuropeptide genes and ∼36 neuropeptide receptors, delineating a complex and expansive "wireless" signaling network. To demonstrate the utility of this comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression and (2) reveal adhesion proteins with potential roles in process placement and synaptic specificity. Our expression data are available at https://cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity, and function throughout the C. elegans nervous system.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Fluorescent Dyes/metabolism ; Gene Expression Regulation, Developmental ; Genes, Reporter ; Larva/metabolism ; Nervous System/metabolism ; Neurons/metabolism ; Neuropeptides/genetics ; Neuropeptides/metabolism ; Nucleotide Motifs/genetics ; RNA-Seq ; Regulatory Sequences, Nucleic Acid/genetics ; Signal Transduction/genetics ; Transcription Factors/metabolism ; Transcription, Genetic
Chemical Substances	Caenorhabditis elegans Proteins ; Fluorescent Dyes ; Neuropeptides ; Transcription Factors
Language	English
Publishing date	2021-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.06.023
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