scholarly journals A single-cell transcriptome atlas of the adult muscle precursors uncovers early events in fiber-type divergence in Drosophila

2019 ◽  
Author(s):  
Maria Paula Zappia ◽  
Lucia de Castro ◽  
Majd M. Ariss ◽  
Abul B.M.M.K. Islam ◽  
Maxim V Frolov
Keyword(s):  
Single Cell ◽  
Muscle Development ◽  
Fiber Type ◽  
Wing Disc ◽  
Adult Muscle ◽  
Direct Flight ◽  
A Cell ◽  
Flight Muscles ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

SummaryIn Drosophila, the wing disc-associated adult muscle precursors (AMPs) give rise to the fibrillar indirect flight muscles (IFM) and the tubular direct flight muscles (DFM). To understand early transcriptional events underlying this muscle diversification, we performed single cell RNA-sequencing experiments and built a cell atlas of AMPs associated with third instar larval wing disc. Our analysis identified distinct transcriptional signatures for IFM and DFM precursors that underlie the molecular basis of their divergence. The atlas further revealed various states of differentiation of AMPs, thus illustrating previously unappreciated spatial and temporal heterogeneity among them. We identified and validated novel markers for both IFM and DFM precursors at various states of differentiation by immunofluorescence and genetic tracing experiments. Finally, we performed a systematic genetic screen using a panel of markers from the reference cell atlas as an entry point and found a novel gene, Ama, which is functionally important in muscle development. Thus, our work provides a framework of leveraging scRNA-seq for gene discovery and therefore, this strategy can be applied to other scRNA-seq datasets.

scholarly journals Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions

2020 ◽  
Author(s):  
Nicholas J. Everetts ◽  
Melanie I. Worley ◽  
Riku Yasutomi ◽  
Nir Yosef ◽  
Iswar K. Hariharan
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Wing Disc ◽  
Transcriptional Program ◽  
Time Points ◽  
Drosophila Wing ◽  
Global View ◽  
Direct Flight ◽  
A Cell ◽  
Flight Muscles

AbstractIn both vertebrates and invertebrates, generating a functional appendage requires interactions between ectoderm-derived epithelia and mesoderm-derived cells. To investigate such interactions, we used single-cell transcriptomics to generate a cell atlas of the Drosophila wing disc at two time points during development. Using these data, we investigate gene expression using a multi-layered model of the wing disc and catalogued ligand-receptor pairs that could mediate signaling between epithelial cells and adult muscle precursors (AMPs). We found that localized expression of the FGF ligands, Thisbe and Pyramus, in the disc epithelium regulates the number and location of the AMPs. In addition, Hedgehog ligand from the epithelium activates a specific transcriptional program within adjacent AMP cells, which is critical for proper formation of a subset of the direct flight muscles. More generally, our annotated atlas provides a global view of potential cell-cell interactions between subpopulations of epithelial and myogenic cells.

scholarly journals Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Nicholas J Everetts ◽  
Melanie I Worley ◽  
Riku Yasutomi ◽  
Nir Yosef ◽  
Iswar K Hariharan
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Developmental Time ◽  
Wing Disc ◽  
Fibroblast Growth ◽  
Transcriptional Program ◽  
Time Points ◽  
Drosophila Wing ◽  
Direct Flight ◽  
Flight Muscles

In both vertebrates and invertebrates, generating a functional appendage requires interactions between ectoderm-derived epithelia and mesoderm-derived cells. To investigate such interactions, we used single-cell transcriptomics to generate a temporal cell atlas of theDrosophilawing disc from two developmental time points. Using these data, we visualized gene expression using a multilayered model of the wing disc and cataloged ligand–receptor pairs that could mediate signaling between epithelial cells and adult muscle precursors (AMPs). We found that localized expression of the fibroblast growth factor ligands, Thisbe and Pyramus, in the disc epithelium regulates the number and location of the AMPs. In addition, Hedgehog ligand from the epithelium activates a specific transcriptional program within adjacent AMP cells, defined by AMP-specific targetsNeurotactinandmidline, that is critical for proper formation of direct flight muscles. More generally, our annotated temporal cell atlas provides an organ-wide view of potential cell–cell interactions between epithelial and myogenic cells.

scholarly journals Single-cell transcriptome analyses recapitulate the cellular and developmental responses to abiotic stresses in rice

2020 ◽  
Author(s):  
Yu Wang ◽  
Qing Huan ◽  
Xiao Chu ◽  
Ke Li ◽  
Wenfeng Qian
Keyword(s):  
Single Cell ◽  
Abiotic Stresses ◽  
Developmental Trajectories ◽  
Cell Types ◽  
Data Resource ◽  
A Cell ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Developmental Responses ◽  
Computational Analyses

ABSTRACTThe metabolism and reproduction of plants depend on the division of labors among cells. However, cells with various functions are often studied as a bulk where their specificities were diluted. Here, we apply single-cell RNA sequencing to the aerial part of rice seedlings growing in various environments. We capture the transcriptomes of thousands of cells, identify all major cell types, and reconstruct their developmental trajectories. We find that abiotic stresses not only affect gene expression in a cell-type-specific manner but also have impacts on the physical size of cells and the composition of cell populations. We validate some of these conclusions with microscopy and provide developmental mechanisms with computational analyses. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas in rice and an illustration of exploiting such resource to drive discoveries in plant biology.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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