scholarly journals Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons

Development ◽  
2019 ◽  
Vol 146 (17) ◽  
pp. dev178103 ◽  
Author(s):  
Quentin Lo Giudice ◽  
Marion Leleu ◽  
Gioele La Manno ◽  
Pierre J. Fabre
Keyword(s):  
Axon Guidance ◽  
Single Cell ◽  
Cell Fate ◽  
Cell Fate Specification ◽  
Retinal Neurons ◽  
Fate Specification

scholarly journals Transcriptional logic of cell fate specification and axon guidance in early born retinal neurons revealed by single-cell mRNA profiling

2018 ◽  
Author(s):  
Quentin Lo Giudice ◽  
Marion Leleu ◽  
Pierre J. Fabre
Keyword(s):  
Axon Guidance ◽  
Cell Fate ◽  
Ganglion Cells ◽  
Amacrine Cells ◽  
Retinal Ganglion ◽  
Cell Fate Specification ◽  
Retinal Neurons ◽  
Fate Specification ◽  
Guidance Cues ◽  
Insight Into

ABSTRACTRetinal ganglion cells (RGC), together with cone photoreceptors, horizontal cells (HC) and amacrine cells (AC), are the first classes of neurons produced in the retina. Here we have profiled 5348 single retinal cells and provided a comprehensive transcriptomic atlas showing the broad diversity of the developing retina at the time when the four early-born cells are being produced. Our results show the transcriptional sequences that establish the hierarchical ordering of early cell fate specification in the retina. RGC maturation follows six waves of gene expression, giving new insight into the regulatory logic of RGC differentiation. Early-generated RGCs transcribe an increasing amount of guidance cues for young peripheral RGC axons that express the matching receptors. Finally, spatial signatures in sub-populations of RGCs allowed to define novel molecular markers that are spatially restricted during the development of the retina. Altogether this study is a valuable resource that identifies new players in mouse retinal development, shedding light on transcription factors sequence and guidance cues dynamics in space and time.

scholarly journals Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Serrano-Ron ◽  
Javier Cabrera ◽  
Pablo Perez-Garcia ◽  
Miguel A. Moreno-Risueno
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Gene Regulatory Networks ◽  
Root Development ◽  
Regulatory Networks ◽  
Primary Root ◽  
Cell Fate Specification ◽  
Rna Seq ◽  
Fate Specification ◽  
Gene Regulatory

Over the last decades, research on postembryonic root development has been facilitated by “omics” technologies. Among these technologies, microarrays first, and RNA sequencing (RNA-seq) later, have provided transcriptional information on the underlying molecular processes establishing the basis of System Biology studies in roots. Cell fate specification and development have been widely studied in the primary root, which involved the identification of many cell type transcriptomes and the reconstruction of gene regulatory networks (GRN). The study of lateral root (LR) development has not been an exception. However, the molecular mechanisms regulating cell fate specification during LR formation remain largely unexplored. Recently, single-cell RNA-seq (scRNA-seq) studies have addressed the specification of tissues from stem cells in the primary root. scRNA-seq studies are anticipated to be a useful approach to decipher cell fate specification and patterning during LR formation. In this review, we address the different scRNA-seq strategies used both in plants and animals and how we could take advantage of scRNA-seq to unravel new regulatory mechanisms and reconstruct GRN. In addition, we discuss how to integrate scRNA-seq results with previous RNA-seq datasets and GRN. We also address relevant findings obtained through single-cell based studies and how LR developmental studies could be facilitated by scRNA-seq approaches and subsequent GRN inference. The use of single-cell approaches to investigate LR formation could help to decipher fundamental biological mechanisms such as cell memory, synchronization, polarization, or pluripotency.

Single cell transplantation reveals interspecific cell communication in Drosophila chimeras

Development ◽  
1990 ◽  
Vol 109 (4) ◽  
pp. 821-832 ◽  
Author(s):  
T. Becker ◽  
G.M. Technau
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Cell Size ◽  
Cell Fate ◽  
Cell Communication ◽  
Host Tissue ◽  
Cell Fate Specification ◽  
Fate Specification ◽  
Common Strategy ◽  
Invertebrate Development

Cell-cell communication is not only a common strategy for cell fate specification in vertebrates, but plays important roles in invertebrate development as well. We report here on experiments testing the compatibility of mechanisms specifying cell fate among six different Drosophila species. Following interspecific transplantation, the development of single ectodermal cells was traced in order to test their abilities to proliferate and differentiate in a heterologous environment. Despite considerable differences in cell size and length of cell cycle among some of the species, the transplants gave rise to fully differentiated clones that were integrated into the host tissue. Clones comprised cells of epidermal and/or neural histotypes, indicating that mechanisms mediating the epidermal/neural dichotomy in the ectoderm are conserved between the species. Cells of the neural lineages differentiated into neurones, glia, or both. Moreover, heterologous neurones sent out axons that followed major pathways along nerves and within the neuropile, demonstrating their ability to recognize positional cues in the heterologous CNS of the host.

scholarly journals Single-cell epigenomics reveals mechanisms of human cortical development

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 205-213
Author(s):  
Ryan S. Ziffra ◽  
Chang N. Kim ◽  
Jayden M. Ross ◽  
Amy Wilfert ◽  
Tychele N. Turner ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Cortical Development ◽  
Chromatin Accessibility ◽  
Chromatin State ◽  
Open Chromatin ◽  
Cell Fate Specification ◽  
Cell Type ◽  
Fate Specification ◽  
Cell Type Specific

AbstractDuring mammalian development, differences in chromatin state coincide with cellular differentiation and reflect changes in the gene regulatory landscape1. In the developing brain, cell fate specification and topographic identity are important for defining cell identity2 and confer selective vulnerabilities to neurodevelopmental disorders3. Here, to identify cell-type-specific chromatin accessibility patterns in the developing human brain, we used a single-cell assay for transposase accessibility by sequencing (scATAC-seq) in primary tissue samples from the human forebrain. We applied unbiased analyses to identify genomic loci that undergo extensive cell-type- and brain-region-specific changes in accessibility during neurogenesis, and an integrative analysis to predict cell-type-specific candidate regulatory elements. We found that cerebral organoids recapitulate most putative cell-type-specific enhancer accessibility patterns but lack many cell-type-specific open chromatin regions that are found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed unexpected diversity among neural progenitor cells in the cerebral cortex and implicated retinoic acid signalling in the specification of neuronal lineage identity in the prefrontal cortex. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

Sox proteins: regulators of cell fate specification and differentiation

Development ◽  
2013 ◽  
Vol 140 (20) ◽  
pp. 4129-4144 ◽  
Author(s):  
Y. Kamachi ◽  
H. Kondoh
Keyword(s):  
Cell Fate ◽  
Cell Fate Specification ◽  
Fate Specification ◽  
Sox Proteins

scholarly journals Differential requirement for Gli2 and Gli3 in ventral neural cell fate specification

2003 ◽  
Vol 259 (1) ◽  
pp. 150-161 ◽  
Author(s):  
Jun Motoyama ◽  
Ljiljana Milenkovic ◽  
Mizuho Iwama ◽  
Yayoi Shikata ◽  
Matthew P. Scott ◽  
...  
Keyword(s):  
Cell Fate ◽  
Neural Cell ◽  
Cell Fate Specification ◽  
Fate Specification ◽  
Neural Cell Fate
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