Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development

The Notch gene of Drosophila encodes a large transmembrane protein involved in cell-cell interactions and cell fate decisions in the Drosophila embryo. To determine if a gene homologous to Drosophila Notch plays a role in early mouse development, we screened a mouse embryo cDNA library with probes from the Xenopus Notch homolog, Xotch. A partial cDNA clone encoding the mouse Notch homolog, which we have termed Motch, was used to analyze expression of the Motch gene. Motch transcripts were detected in a wide variety of adult tissues, which included derivatives of all three germ layers. Differentiation of P19 embryonal carcinoma cells into neuronal cell types resulted in increased expression of Motch RNA. In the postimplantation mouse embryo Motch transcripts were first detected in mesoderm at 7.5 days post coitum (dpc). By 8.5 dpc, transcript levels were highest in presomitic mesoderm, mesenchyme and endothelial cells, while much lower levels were detected in neuroepithelium. In contrast, at 9.5 dpc, neuroepithelium was a major site of Motch expression. Transcripts were also abundant in cell types derived from neural crest. These data suggest that the Motch gene plays multiple roles in patterning and differentiation of the early postimplantation mouse embryo.

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Genetic dissection of Nodal and Bmp signalling requirements during primordial germ cell development

10.1101/464776 ◽

2018 ◽

Author(s):

Anna D. Senft ◽

Elizabeth K. Bikoff ◽

Elizabeth J. Robertson ◽

Ita Costello

Keyword(s):

Germ Cell ◽

Cell Fate ◽

Primordial Germ Cell ◽

Genetic Dissection ◽

Mouse Development ◽

Cell Fate Decisions ◽

Conditional Deletion ◽

Bmp Signalling ◽

And Migration ◽

Early Mouse

AbstractThe essential roles played by Nodal and Bmp signalling during early mouse development have been extensively documented. Here we used conditional deletion strategies to investigate functional contributions made by Nodal, Bmp and Smad downstream effectors during primordial germ cell (PGC) development. We demonstrate that Nodal and its target gene Eomes provide early instructions during formation of the PGC lineage. We discovered that Smad2 inactivation in the visceral endoderm results in increased numbers of PGCs due to an expansion of the PGC niche. Smad1 is required for specification, whereas in contrast Smad4 controls the maintenance and migration of PGCs. Importantly we found that beside Blimp1, down-regulated phosphoSmad159 levels also distinguishes PGCs from their somatic neighbours so that emerging PGCs become refractory to Bmp signalling that otherwise promotes mesodermal development in the posterior epiblast. Thus balanced Nodal/Bmp signalling cues regulate germ cell versus somatic cell fate decisions in the early posterior epiblast.

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Coordination between patterning and morphogenesis ensures robustness during mouse development

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0562 ◽

2020 ◽

Vol 375 (1809) ◽

pp. 20190562 ◽

Cited By ~ 1

Author(s):

Néstor Saiz ◽

Anna-Katerina Hadjantonakis

Keyword(s):

Cell Fate ◽

Cell Types ◽

Biological Noise ◽

Mouse Development ◽

Lineage Specification ◽

Cell Fate Decisions ◽

The Past ◽

Early Mouse ◽

The Right ◽

External Signals

The mammalian preimplantation embryo is a highly tractable, self-organizing developmental system in which three cell types are consistently specified without the need for maternal factors or external signals. Studies in the mouse over the past decades have greatly improved our understanding of the cues that trigger symmetry breaking in the embryo, the transcription factors that control lineage specification and commitment, and the mechanical forces that drive morphogenesis and inform cell fate decisions. These studies have also uncovered how these multiple inputs are integrated to allocate the right number of cells to each lineage despite inherent biological noise, and as a response to perturbations. In this review, we summarize our current understanding of how these processes are coordinated to ensure a robust and precise developmental outcome during early mouse development. This article is part of a discussion meeting issue ‘Contemporary morphogenesis'.

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Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

eLife ◽

10.7554/elife.09571 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 56

Author(s):

Jan J Zylicz ◽

Sabine Dietmann ◽

Ufuk Günesdogan ◽

Jamie A Hackett ◽

Delphine Cougot ◽

...

Keyword(s):

Cell Fate ◽

Regulatory Networks ◽

Histone H3 ◽

Epigenetic Mechanism ◽

Mouse Development ◽

Germline Development ◽

Chromatin Dynamics ◽

Cell Fate Decisions ◽

Active Enhancer ◽

Early Mouse

Early mouse development is accompanied by dynamic changes in chromatin modifications, including G9a-mediated histone H3 lysine 9 dimethylation (H3K9me2), which is essential for embryonic development. Here we show that genome-wide accumulation of H3K9me2 is crucial for postimplantation development, and coincides with redistribution of enhancer of zeste homolog 2 (EZH2)-dependent histone H3 lysine 27 trimethylation (H3K27me3). Loss of G9a or EZH2 results in upregulation of distinct gene sets involved in cell cycle regulation, germline development and embryogenesis. Notably, the H3K9me2 modification extends to active enhancer elements where it promotes developmentally-linked gene silencing and directly marks promoters and gene bodies. This epigenetic mechanism is important for priming gene regulatory networks for critical cell fate decisions in rapidly proliferating postimplantation epiblast cells.

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Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

Developmental Cell ◽

10.1016/j.devcel.2010.02.012 ◽

2010 ◽

Vol 18 (4) ◽

pp. 675-685 ◽

Cited By ~ 568

Author(s):

Guoji Guo ◽

Mikael Huss ◽

Guo Qing Tong ◽

Chaoyang Wang ◽

Li Li Sun ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Cell Fate ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Cell Fate Decisions ◽

Cell Gene Expression ◽

Cell Gene

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Mechanistic models of blood cell fate decisions in the era of single-cell data

Current Opinion in Systems Biology ◽

10.1016/j.coisb.2021.100355 ◽

2021 ◽

pp. 100355

Author(s):

Ingmar Glauche ◽

Carsten Marr

Keyword(s):

Blood Cell ◽

Single Cell ◽

Cell Fate ◽

Mechanistic Models ◽

Cell Fate Decisions ◽

Cell Data

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Basal stem cell fate specification is mediated by SMAD signaling in the developing human lung

10.1101/461103 ◽

2018 ◽

Cited By ~ 3

Author(s):

Alyssa J. Miller ◽

Qianhui Yu ◽

Michael Czerwinski ◽

Yu-Hwai Tsai ◽

Renee F. Conway ◽

...

Keyword(s):

Single Cell ◽

Progenitor Cells ◽

Cell Fate ◽

Basal Cell ◽

Human Lung ◽

Branching Morphogenesis ◽

Basal Cells ◽

Smad Signaling ◽

Cell Fate Decisions ◽

Cell Transition

AbstractBasal stem cells (basal cells), located in the bronchi and trachea of the human lung epithelium, play a critical role in normal airway homeostasis and repair, and have been implicated in the development of diseases such as cancer1-4. Additionally, basal-like cells contribute to alveolar regeneration and fibrosis following severe injury5-8. However, the developmental origin of basal cells in humans is unclear. Previous work has shown that specialized progenitor cells exist at the tips of epithelial tubes during lung branching morphogenesis, and in mice, give rise to all alveolar and airway lineages9,10. These ‘bud tip progenitor cells’ have also been described in the developing human lung11-13, but the mechanisms controlling bud tip differentiation into specific cell lineages, including basal cells, are unknown. Here, we interrogated the bud tip-to-basal cell transition using human tissue specimens, bud tip progenitor organoid cultures11, and single-cell transcriptomics. We used single-cell mRNA sequencing (scRNAseq) of developing human lung specimens from 15-21 weeks gestation to identify molecular signatures and cell states in the developing human airway epithelium. We then inferred differentiation trajectories during bud tip-to-airway differentiation, which revealed a previously undescribed transitional cell state (‘hub progenitors’) and implicated SMAD signaling as a regulator of the bud tip-to-basal cell transition. We used bud tip progenitor organoids to show that TGFT1 and BMP4 mediated SMAD signaling robustly induced the transition into functional basal-like cells, and these in vitro-derived basal cells exhibited clonal expansion, self-renewal and multilineage differentiation. This work provides a framework for deducing and validating key regulators of cell fate decisions using single cell transcriptomics and human organoid models. Further, the identification of SMAD signaling as a critical regulator of newly born basal cells in the lung may have implications for regenerative medicine, basal cell development in other organs, and understanding basal cell misregulation in disease.

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Genomic insights into chromatin reprogramming to totipotency in embryos

The Journal of Cell Biology ◽

10.1083/jcb.201807044 ◽

2018 ◽

Vol 218 (1) ◽

pp. 70-82 ◽

Cited By ~ 10

Author(s):

Sabrina Ladstätter ◽

Kikuë Tachibana

Keyword(s):

Cell Fate ◽

Regulatory Networks ◽

Chromatin Accessibility ◽

Early Embryo ◽

Epigenetic Reprogramming ◽

Mammalian Embryo ◽

Cell Fate Decisions ◽

A Cell ◽

Early Mouse ◽

Chromatin Reprogramming

The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.

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Abstract 39: Fate Of Renin Cell Progenitors In The Developing Kidney Vasculature

Hypertension ◽

10.1161/hyp.78.suppl_1.39 ◽

2021 ◽

Vol 78 (Suppl_1) ◽

Author(s):

Alexandre Martini ◽

Ariel R Gomez ◽

Maria Luisa Sequeira Lopez

Keyword(s):

Single Cell ◽

Cell Fate ◽

Fluorescent Protein ◽

Enrichment Analysis ◽

Cell Fate Decisions ◽

Mural Cells ◽

Developing Kidney ◽

Green Fluorescent ◽

Old Mice ◽

Accessible Chromatin

The unique spatial arregement of the kidney arterioles is an essential event for its development. However, the mechanisms that govern this process are still poorly understood. During nephrogenesis, a group of stromal cells expressing the Forkhead Box D1 ( FoxD1 ) transcription factor (TF) will give rise to the metanephric progenitors for the mural cells of the kidneys arteries and arterioles. We aim to identify the core TFs involved in the cell fate along the differentiaton pathways of the developing kidney vasculature. Therefore, we generated Foxd1-cre; mTmG mice, whose Foxd1 derivative cells are labeled with green fluorescent protein (GFP). GFP+ cells were isolated from 5 (P5) or 30 (P30) days old mice kidneys, and processed either for single-cell RNA-Seq (scRNA-Seq) or for single-cell Assay for Transposase-Accessible Chromatin (scATAC-Seq ). The top5 highly expressed TFs on scRNA-Seq at P5 are: Tcf21, Zeb2, Meis2, Cebpd and Nme3 (p_adjusted_value(padj)= 0, 3.8E-187, 3.9E-180, 4E-172, 4.1E-172 and 3.2E-154, respectively). They are involved in developmental processes and cell proliferation. At P30, the top5 highly expressed TFs are: Atf3, klf2, Fos, Nr4a2 and Junb (padj= 4.2E-294, 2.1E-200, 3.5E-182, 1.7E-52 and 0.2E-24, respectively). They are implicated with calcium-signaling pathway and inflammation. Additionally, scATAC-Seq identifies regions of accessible chromatin for pontential TFs binding, leading to changes in gene expression content and cell identity. At P30, scATAC-Seq showed differential accessible regions with subsequent putative motif enrichment analysis for the TF N4a2 (padj: 4E-297). This is in accordance with our scRNA-Seq results and might play a role in the Foxd1 progenitors cell fate decisions. Our results tracks the fate of the Foxd1+ cells during the kidney vasculature assembly and suggest a new transcription factors network that might play a role to orchestrate cell fate decisions during kidney vascular development.

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Hypersensitivity to DNA damage leads to increased apoptosis during early mouse development

Genes & Development ◽

10.1101/gad.14.16.2072 ◽

2000 ◽

Vol 14 (16) ◽

pp. 2072-2084

Author(s):

Babette S. Heyer ◽

Alasdair MacAuley ◽

Ole Behrendtsen ◽

Zena Werb

Keyword(s):

Dna Damage ◽

Cell Fate ◽

Genotoxic Stress ◽

Embryonic Cells ◽

Mouse Development ◽

Potential Cost ◽

Proliferation And Differentiation ◽

A Cell ◽

Early Mouse ◽

Surveillance Mechanism

Gastrulation in mice is associated with the start of extreme proliferation and differentiation. The potential cost to the embryo of a very rapid proliferation rate is a high production of damaged cells. We demonstrate a novel surveillance mechanism for the elimination of cells damaged by ionizing radiation during mouse gastrulation. During this restricted developmental window, the embryo becomes hypersensitive to DNA damage induced by low dose irradiation (<0.5 Gy) and undergoes apoptosis without cell cycle arrest. Intriguingly, embryonic cells, including germ cell progenitors, but not extraembryonic cells, become hypersensitive to genotoxic stress and undergo Atm- and p53-dependent apoptosis. Thus, hypersensitivity to apoptosis in the early mouse embryo is a cell fate-dependent mechanism to ensure genomic integrity during a period of extreme proliferation and differentiation.

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