scholarly journals Notch signaling is a critical initiator of roof plate formation as revealed by the use of RNA profiling of the dorsal neural tube

2020 ◽  
Author(s):  
Shai Ofek ◽  
Sophie Wiszniak ◽  
Sarah Kagan ◽  
Markus Tondl ◽  
Quenten Schwarz ◽  
...  
Keyword(s):  
Notch Signaling ◽  
Neural Tube ◽  
Transcriptome Analysis ◽  
Cell Types ◽  
Molecular Heterogeneity ◽  
Specific Cell ◽  
Rna Profiling ◽  
Dorsal Neural Tube ◽  
Roof Plate ◽  
Plate Formation

AbstractThe factors underlying establishment of the definitive roof plate (RP) and its segregation from neural crest (NC) and interneurons are unknown. We performed transcriptome analysis at trunk levels of quail embryos comparing the dorsal neural tube at premigratory NC and RP stages. This unraveled molecular heterogeneity between NC and RP stages, and within the RP itself. By implementing these genes, we asked whether Notch signaling is involved in RP development. First, we observed that Notch is active at the RP-interneuron interface. Furthermore, gain and loss of Notch function in quail and mouse embryos, respectively, revealed no effect on early NC behavior. Constitutive Notch activation caused a local downregulation of RP markers with a concomitant development of dI1 interneurons, as well as an ectopic upregulation of RP markers in the interneuron domain. Reciprocally, in mice lacking Notch activity both the RP and dI1 interneurons failed to form and this was associated with expansion of the dI2 population. Collectively, our results offer a new resource for defining specific cell types, and provide evidence that Notch is required to establish the definitive RP, and to determine the choice between RP and interneuron fates, but not the segregation of RP from NC.Summary statementA new set of genes involved in Notch-dependent roof plate formation is unraveled by transcriptome analysis.

scholarly journals Notch signaling is a critical initiator of roof plate formation as revealed by the use of RNA profiling of the dorsal neural tube

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Shai Ofek ◽  
Sophie Wiszniak ◽  
Sarah Kagan ◽  
Markus Tondl ◽  
Quenten Schwarz ◽  
...  
Keyword(s):  
Nervous System ◽  
Notch Signaling ◽  
Neural Tube ◽  
Cell Types ◽  
Molecular Heterogeneity ◽  
Specific Cell ◽  
Rna Profiling ◽  
Dorsal Neural Tube ◽  
Roof Plate ◽  
The Central Nervous System

AbstractBackgroundThe dorsal domain of the neural tube is an excellent model to investigate the generation of complexity during embryonic development. It is a highly dynamic and multifaceted region being first transiently populated by prospective neural crest (NC) cells that sequentially emigrate to generate most of the peripheral nervous system. Subsequently, it becomes the definitive roof plate (RP) of the central nervous system. The RP, in turn, constitutes a patterning center for dorsal interneuron development. The factors underlying establishment of the definitive RP and its segregation from NC and dorsal interneurons are currently unknown.ResultsWe performed a transcriptome analysis at trunk levels of quail embryos comparing the dorsal neural tube at premigratory NC and RP stages. This unraveled molecular heterogeneity between NC and RP stages, and within the RP itself. By implementing these genes, we asked whether Notch signaling is involved in RP development. First, we observed that Notch is active at the RP-interneuron interface. Furthermore, gain and loss of Notch function in quail and mouse embryos, respectively, revealed no effect on early NC behavior. Constitutive Notch activation caused a local downregulation of RP markers with a concomitant development of dI1 interneurons, as well as an ectopic upregulation of RP markers in the interneuron domain. Reciprocally, in mice lacking Notch activity, both the RP and dI1 interneurons failed to form and this was associated with expansion of the dI2 population.ConclusionsCollectively, our results offer a new resource for defining specific cell types, and provide evidence that Notch is required to establish the definitive RP, and to determine the choice between RP and interneuron fates, but not the segregation of RP from NC.

scholarly journals From Neural Crest to Definitive Roof Plate: The Dynamic Behavior of the Dorsal Neural Tube

2021 ◽  
Vol 22 (8) ◽  
pp. 3911
Author(s):  
Dina Rekler ◽  
Chaya Kalcheim
Keyword(s):  
Neural Crest ◽  
Neural Tube ◽  
Epithelial To Mesenchymal Transition ◽  
Cell Types ◽  
Mesenchymal Transition ◽  
Dorsal Neural Tube ◽  
Roof Plate ◽  
Organizing Center ◽  
The Central Nervous System ◽  
And Migration

Research on the development of the dorsal neural tube is particularly challenging. In this highly dynamic domain, a temporal transition occurs between early neural crest progenitors that undergo an epithelial-to-mesenchymal transition and exit the neural primordium, and the subsequent roof plate, a resident epithelial group of cells that constitutes the dorsal midline of the central nervous system. Among other functions, the roof plate behaves as an organizing center for the generation of dorsal interneurons. Despite extensive knowledge of the formation, emigration and migration of neural crest progenitors, little is known about the mechanisms leading to the end of neural crest production and the transition into a roof plate stage. Are these two mutually dependent or autonomously regulated processes? Is the generation of roof plate and dorsal interneurons induced by neural tube-derived factors throughout both crest and roof plate stages, respectively, or are there differences in signaling properties and responsiveness as a function of time? In this review, we discuss distinctive characteristics of each population and possible mechanisms leading to the shift between the above cell types.

scholarly journals Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation

2019 ◽  
Author(s):  
Ryoji Amamoto ◽  
Mauricio D. Garcia ◽  
Emma R. West ◽  
Jiho Choi ◽  
Sylvain W. Lapan ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Cell Types ◽  
Cell Populations ◽  
Specific Cell ◽  
Rna Profiling ◽  
Complementary Method ◽  
Dissociated Cells ◽  
Multiple Cell ◽  
Heterogeneous Tissue

ABSTRACTRecent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labelled using fluorescent in situ hybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as the Drosophila midgut. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism.

scholarly journals FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system

2019 ◽  
Author(s):  
Ryoji Amamoto ◽  
Emanuela Zuccaro ◽  
Nathan C Curry ◽  
Sonia Khurana ◽  
Hsu-Hsin Chen ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Rna Sequencing ◽  
Human Tissue ◽  
Transcriptional Profiling ◽  
Cell Types ◽  
Specific Cell ◽  
Human Central Nervous System ◽  
Tissue Samples ◽  
Rna Profiling

Abstract Thousands of frozen, archived tissue samples from the human central nervous system (CNS) are currently available in brain banks. As recent developments in RNA sequencing technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that an understanding of this diversity would greatly benefit from deeper transcriptional analyses. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples that have been stored long-term. Here, we developed FIN-Seq (Frozen Immunolabeled Nuclei Sequencing), a method that accomplishes these goals. FIN-Seq uses immunohistochemical isolation of nuclei of specific cell types from frozen human tissue, followed by bulk RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.

scholarly journals Dynamics of BMP and Hes1/Hairy1 signaling in the dorsal neural tube underlies the transition from neural crest to definitive roof plate

BMC Biology ◽  
2016 ◽  
Vol 14 (1) ◽  
Author(s):  
Erez Nitzan ◽  
Oshri Avraham ◽  
Nitza Kahane ◽  
Shai Ofek ◽  
Deepak Kumar ◽  
...  
Keyword(s):  
Neural Crest ◽  
Neural Tube ◽  
Dorsal Neural Tube ◽  
Roof Plate

scholarly journals BMP4 patterns Smad activity and generates stereotyped cell fate organisation in spinal organoids

2019 ◽  
Author(s):  
Nathalie Duval ◽  
Célia Vaslin ◽  
Tiago Barata ◽  
Stéphane Nédélec ◽  
Vanessa Ribes
Keyword(s):  
Cell Fate ◽  
Bone Morphogenetic Proteins ◽  
Neural Tube ◽  
Spatial Organization ◽  
Time Windows ◽  
Spatial Dynamics ◽  
Spatial Arrangement ◽  
Cell Types ◽  
Dorsal Neural Tube ◽  
Bmp Signalling

AbstractBone Morphogenetic Proteins (BMP) are secreted regulators of cell fate in several developing tissues. In the embryonic spinal cord, they control the emergence of the neural crest, roof plate and distinct subsets of dorsal interneurons. Although a gradient of BMP activity has been proposed to determine cell type identity in vivo, whether this is sufficient for pattern formation in vitro is unclear. Here, we demonstrate that exposure to BMP4 initiates distinct spatial dynamics of BMP signalling within the self-emerging epithelia of both mouse and human pluripotent stem cells derived spinal organoids. The pattern of BMP signalling results in the stereotyped spatial arrangement of dorsal neural tube cell types and concentration, timing and duration of BMP4 exposure modulate these patterns. Moreover, differences in the duration of competence time-windows between mouse and human account for the species specific tempo of neural differentiation. Together the study describes efficient methods to generate patterned subsets of dorsal interneurons in spinal organoids and supports the conclusion that graded BMP activity orchestrates the spatial organization of the dorsal neural tube cellular diversity in mouse and human.

scholarly journals Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Ryoji Amamoto ◽  
Mauricio D Garcia ◽  
Emma R West ◽  
Jiho Choi ◽  
Sylvain W Lapan ◽  
...  
Keyword(s):  
Transcriptional Profiling ◽  
Cell Types ◽  
Cell Populations ◽  
Specific Cell ◽  
Rna Profiling ◽  
Complementary Method ◽  
Dissociated Cells ◽  
Multiple Cell ◽  
Heterogeneous Tissue

Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labeled using fluorescent in situ hybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as from Drosophila midguts. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism.

scholarly journals Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum

2021 ◽  
Author(s):  
Annalie Martin ◽  
Anne Babbitt ◽  
Allison G Pickens ◽  
Brett E Pickett ◽  
Jonathon T Hill ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Optic Tectum ◽  
Cell Types ◽  
Cell Populations ◽  
Molecular Heterogeneity ◽  
Specific Cell ◽  
Larval Zebrafish ◽  
Enhancer Trap Line ◽  
Single Cell Rna Sequencing

The optic tectum (OT) is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus, the OT is responsible for the reception and integration of stimuli, followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades, less is known concerning specific cell types, microcircuitry, and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however, a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single-cell RNA-sequencing (scRNA-seq) to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Et(cfos:Gal4;UAS:Kaede). We sequenced 13,320 cells, a 4X cellular coverage, and identified 25 putative OT cell populations. Within those cells, we identified several mature and developing neuronal populations, as well as non-neuronal cell types including oligodendrocytes, microglia, and radial glia. Although most mature neurons demonstrate GABAergic activity, several glutamatergic populations are present, as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes, and computed RNA velocity to infer current and future transcriptional cell states. Finally, we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion, the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge, this is the first time scRNA-seq has been applied to explore the OT alone and in depth.

scholarly journals The roof plate boundary is a bi-directional organiser of dorsal neural tube and choroid plexus development

Development ◽  
2012 ◽  
Vol 139 (22) ◽  
pp. 4261-4270 ◽  
Author(s):  
E. R. Broom ◽  
J. D. Gilthorpe ◽  
T. Butts ◽  
F. Campo-Paysaa ◽  
R. J. T. Wingate
Keyword(s):  
Choroid Plexus ◽  
Neural Tube ◽  
Plate Boundary ◽  
Dorsal Neural Tube ◽  
Roof Plate

scholarly journals Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types

2015 ◽  
pp. bhv273 ◽  
Author(s):  
Pilar Gil-Ibañez ◽  
Francisco García-García ◽  
Joaquín Dopazo ◽  
Juan Bernal ◽  
Beatriz Morte
Keyword(s):  
Transcriptome Analysis ◽  
Cell Types ◽  
Specific Cell ◽  
Global Transcriptome
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