Plant stem cell organization and differentiation at single-cell resolution

Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem cell organizing center subtending these cells. In addition, we use trajectory inference to trace the gene expression changes that accompany cell differentiation. These data provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis.

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Plant stem-cell organization and differentiation at single-cell resolution

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2018788117 ◽

2020 ◽

Vol 117 (52) ◽

pp. 33689-33699

Author(s):

James W. Satterlee ◽

Josh Strable ◽

Michael J. Scanlon

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Cell Differentiation ◽

Single Cell ◽

Cell Fate ◽

Cell Function ◽

Ectopic Expression ◽

Cellular Level ◽

Organizing Center ◽

Cell Niche

Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.

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Spatial specificity of auxin responses coordinates wood formation

10.1101/142885 ◽

2017 ◽

Author(s):

Klaus Brackmann ◽

Virginie Jouannet ◽

Jiyan Qi ◽

Theresa Schlamp ◽

Karin Grünwald ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Spatial Organization ◽

Wood Formation ◽

Auxin Signaling ◽

Cambium Activity ◽

Plant Stem ◽

Cell Niche ◽

Spatial Specificity ◽

Signaling Components

AbstractSpatial organization of signaling events of the phytohormone auxin is fundamental for maintaining a dynamic transition from plant stem cells to differentiated descendants. The cambium, the stem cell niche mediating wood formation, fundamentally depends on auxin signaling but its exact role and spatial organization is obscure. Here, we show that, while auxin signaling levels increase in differentiating cambium descendants, a moderate level of signaling in cambial stem cells is essential for cambium activity. We identify the auxin-dependent transcription factor ARF5/MONOPTEROS to cell-autonomously restrict the number of stem cells by attenuating the activity of the stem cell promoting WOX4 gene. In contrast, ARF3 and ARF4 function as cambium activators in a redundant fashion from outside of WOX4-expressing cells. Our results reveal an influence of auxin signaling on distinct cambium features by specific signaling components and allow the conceptual integration of plant stem cell systems with distinct anatomies.

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Bi-compartmentalized stem cell organization of the corneal limbal niche

10.1101/2020.06.25.171462 ◽

2020 ◽

Author(s):

Olivia Farrelly ◽

Yoko Suzuki-Horiuchi ◽

Megan Brewster ◽

Paola Kuri ◽

Sixia Huang ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Stem Cell Niche ◽

Tissue Architecture ◽

Corneal Regeneration ◽

Cell Organization ◽

Cell Niche ◽

Slow Cycling ◽

And Function

AbstractStem cells exist in precise locations within tissues, yet how their organization supports tissue architecture and function is poorly understood. The limbus is the presumptive stem cell niche of the corneal epithelium. Here, we visualize the live limbus and track the activity of single stem cells in their native environment by 2-photon microscopy. We identify previously unknown niche compartments and show that long implicated slow-cycling cells form separate lineages in the outer limbus, with only local clonal dynamics. Instead, we find distinct stem cells in the pericorneal limbus to be required for corneal regeneration. Unbiased photolabeling captures their progeny exiting the niche, then moving centripetally in unison before undergoing terminal differentiation. This study demonstrates how a compartmentalized stem cell organization coordinates tissue regeneration.One Sentence SummaryIn vivo live imaging of the regenerating cornea reveals distinct stem cell activities in the limbal niche

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Cytonemes coordinate asymmetric signaling and organization in the Drosophila muscle progenitor niche

10.1101/2021.10.29.466429 ◽

2021 ◽

Author(s):

Akshay Patel ◽

Yicong Wu ◽

Xiaofei Han ◽

Yijun Su ◽

Tim K. Maugel ◽

...

Keyword(s):

Stem Cell ◽

Wing Disc ◽

Dependent Manner ◽

Fgf Signaling ◽

Cell Fates ◽

Fgf Receptor ◽

Drosophila Wing ◽

Epithelial Junctions ◽

Cell Organization ◽

Cell Niche

Asymmetric signaling and organization in the stem-cell niche determine stem-cell fates. We investigated the basis of asymmetric signaling and stem-cell organization using the Drosophila wing-disc that creates an adult muscle progenitor (AMP) niche. We uncovered that AMPs extend polarized cytonemes to contact the disc epithelial junctions and adhere themselves to the disc/niche. Niche-adhering cytonemes localize an FGF-receptor to selectively adhere to the FGF-producing disc and receive FGFs in a contact-dependent manner. Activation of FGF-signaling in AMPs, in turn, reinforces disc-specific cytoneme polarity/adhesion, which maintains their disc-proximal positions. The wing-disc produces two FGFs in distinct zones and restricts their signaling only through cytonemes. Consequently, although both FGFs use the same receptor, their cytoneme-mediated signaling asymmetrically distributes different muscle-specific AMPs into different FGF-producing niches. Loss of cytoneme-mediated adhesion and FGF-signaling promotes AMPs to lose niche occupancy, occupy a disc-distal position, and acquire morphological hallmarks of differentiation. Thus, cytonemes are essential for asymmetric signaling and niche-specific AMP organization.

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Characterization of the Limbal Epithelial Stem Cell Niche: Novel Imaging Techniques Permit In Vivo Observation and Targeted Biopsy of Limbal Epithelial Stem Cells

Stem Cells ◽

10.1634/stemcells.2006-0580 ◽

2007 ◽

Vol 25 (6) ◽

pp. 1402-1409 ◽

Cited By ~ 183

Author(s):

Alex J. Shortt ◽

Genevieve A. Secker ◽

Peter M. Munro ◽

Peng T. Khaw ◽

Stephen J. Tuft ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Stem Cell Niche ◽

Imaging Techniques ◽

Targeted Biopsy ◽

Epithelial Stem Cells ◽

Limbal Epithelial Stem Cells ◽

Cell Niche

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Characterization of an in vitro neural stem cell niche with educational component : Stem cells and society

10.32469/10355/6054 ◽

2008 ◽

Author(s):

Chris Pierret

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Neural Stem Cell ◽

Stem Cell Niche ◽

Neural Stem Cell Niche ◽

Cell Niche ◽

Educational Component

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A model of protein interactions for regulating plant stem cells

10.1101/237933 ◽

2017 ◽

Cited By ~ 1

Author(s):

Jérémy Gruel ◽

Julia Deichmann ◽

Benoit Landrein ◽

Thomas Hitchcock ◽

Henrik Jönsson

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Protein Interactions ◽

Stem Cell Niche ◽

Apical Meristem ◽

Stem Cell Marker ◽

Tissue Size ◽

Plant Stem ◽

Cell Niche ◽

Plant Stem Cells

AbstractThe plant shoot apical meristem holds a stem cell niche from which all aerial organs originate. Using a computational approach we show that a mixture of monomers and heterodimers of the transcription factors WUSCHEL and HAIRY MERISTEM is sufficient to pattern the stem cell niche, and predict that immobile heterodimers form a regulatory ‘pocket’ surrounding the stem cells. The model achieves to reproduce an array of perturbations, including mutants and tissue size modifications. We also show its ability to reproduce the recently observed dynamical shift of the stem cell niche during the development of an axillary meristem. The work integrates recent experimental results to answer the longstanding question of how the asymmetry of expression between the stem cell marker CLAVATA3 and its activator WUSCHEL is achieved, and recent findings of plasticity in the system.

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High resolution mouse subventricular zone stem cell niche transcriptome reveals features of lineage, anatomy, and aging

10.1101/2020.07.27.223602 ◽

2020 ◽

Author(s):

Xuanhua P. Xie ◽

Dan R. Laks ◽

Daochun Sun ◽

Asaf Poran ◽

Ashley M. Laughney ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Neural Stem Cells ◽

Single Cell ◽

Rna Sequencing ◽

Subventricular Zone ◽

Stem Cell Niche ◽

Advanced Age ◽

Single Cell Rna Sequencing ◽

Cell Niche

AbstractAdult neural stem cells (NSC) serve as a reservoir for brain plasticity and origin for certain gliomas. Lineage tracing and genomic approaches have portrayed complex underlying heterogeneity within the major anatomical location for NSC, the subventricular zone (SVZ). To gain a comprehensive profile of NSC heterogeneity, we utilized a well validated stem/progenitor specific reporter transgene in concert with single cell RNA sequencing to achieve unbiased analysis of SVZ cells from infancy to advanced age. The magnitude and high specificity of the resulting transcriptional data sets allow precise identification of the varied cell types embedded in the SVZ including specialized parenchymal cells (neurons, glia, microglia), and non-central nervous system cells (endothelial, immune). Initial mining of the data delineates four quiescent NSC and three progenitor cell subpopulations formed in a linear progression. Further evidence indicates that distinct stem and progenitor populations reside in different regions of the SVZ. As stem/progenitor populations progress from neonatal to advanced age, they acquire a deficiency in transition from quiescence to proliferation. Further data mining identifies stage specific biological processes, transcription factor networks, and cell surface markers for investigation of cellular identities, lineage relationships, and key regulatory pathways in adult NSC maintenance and neurogenesis.Significance StatementAdult neural stem cells (NSC) are closely related to multiple neurological disorders and brain tumors. Comprehensive investigation of their composition, lineage, and aging will provide new insights that may lead to enhanced patient treatment. This study applies a novel transgene to label and manipulate neural stem/progenitor cells, and monitor their evolution during aging. Together with high-throughput single cell RNA sequencing, we are able to analyze the subventricular zone (SVZ) cells from infancy to advanced age with unprecedented granularity. Diverse new cell states are identified in the stem cell niche, and an aging related NSC deficiency in transition from quiescence to proliferation is identified. The related biological features provide rich resources to inspect adult NSC maintenance and neurogenesis.

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