scholarly journals Molecular recording of mammalian embryogenesis

2018 ◽  
Author(s):  
Michelle M. Chan ◽  
Zachary D. Smith ◽  
Stefanie Grosswendt ◽  
Helene Kretzmer ◽  
Thomas Norman ◽  
...  
Keyword(s):  
Cell Fate ◽  
Cell Types ◽  
Mouse Cell ◽  
Mammalian Development ◽  
Fate Map ◽  
Developmental Relationships ◽  
Other Information ◽  
Asymmetric Partitioning ◽  
Endodermal Cells ◽  
Multicellular Organisms

Understanding the emergence of complex multicellular organisms from single totipotent cells, or ontogenesis, represents a foundational question in biology. The study of mammalian development is particularly challenging due to the difficulty of monitoring embryos in utero, the variability of progenitor field sizes, and the indeterminate relationship between the generation of uncommitted progenitors and their progression to subsequent stages. Here, we present a flexible, high information, multi-channel molecular recorder with a single cell (sc) readout and apply it as an evolving lineage tracer to define a mouse cell fate map from fertilization through gastrulation. By combining lineage information with scRNA-seq profiles, we recapitulate canonical developmental relationships between different tissue types and reveal an unexpected transcriptional convergence of endodermal cells from extra-embryonic and embryonic origins, illustrating how lineage information complements scRNA-seq to define cell types. Finally, we apply our cell fate map to estimate the number of embryonic progenitor cells and the degree of asymmetric partitioning within the pluripotent epiblast during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems to facilitate a quantitative framework for describing developmental processes.

scholarly journals Regulatory network characterization in development: challenges and opportunities

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1477
Author(s):  
Guangdun Peng ◽  
Jing-Dong J. Han
Keyword(s):  
Stem Cell ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Stem Cell Differentiation ◽  
Cell Types ◽  
Mammalian Development ◽  
Distinct Cell ◽  
Challenges And Opportunities ◽  
Cell Processes ◽  
Early Mammalian Development

Embryonic development and stem cell differentiation, during which coordinated cell fate specification takes place in a spatial and temporal context, serve as a paradigm for studying the orderly assembly of gene regulatory networks (GRNs) and the fundamental mechanism of GRNs in driving lineage determination. However, knowledge of reliable GRN annotation for dynamic development regulation, particularly for unveiling the complex temporal and spatial architecture of tissue stem cells, remains inadequate. With the advent of single-cell RNA sequencing technology, elucidating GRNs in development and stem cell processes poses both new challenges and unprecedented opportunities. This review takes a snapshot of some of this work and its implication in the regulative nature of early mammalian development and specification of the distinct cell types during embryogenesis.

scholarly journals WhichTF is dominant in your open chromatin data?

2019 ◽  
Author(s):  
Yosuke Tanigawa ◽  
Ethan S. Dyer ◽  
Gill Bejerano
Keyword(s):  
Cell Fate ◽  
Molecular Mechanisms ◽  
Computational Prediction ◽  
Cell Types ◽  
Mouse Cell ◽  
Careful Consideration ◽  
Computational Method ◽  
Open Chromatin ◽  
Differential Analysis ◽  
Putative Gene

AbstractWe present WhichTF, a novel computational method to identify dominant transcription factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF integrates high-confidence genome-wide computational prediction of TF binding sites based on evolutionary sequence conservation, putative gene-regulatory models, and ontology-based gene annotations. Applying WhichTF, we find that the identified dominant TFs have been implicated as functionally important in well-studied cell types, such as NF-κB family members in lymphocytes and GATA factors in cardiac tissue. To distinguish the transcriptional regulatory landscape in closely related samples, we devise a differential analysis framework and demonstrate its utility in lymphocyte, mesoderm developmental, and disease cells. We also find TFs known for stress response in multiple samples, suggesting routine experimental caveats that warrant careful consideration. WhichTF yields biological insight into known and novel molecular mechanisms of TF-mediated transcriptional regulation in diverse contexts, including human and mouse cell types, cell fate trajectories, and disease-associated tissues.

scholarly journals Endodermal differentiation is reconstructed by coordination of two parallel signaling systems derived from the stele in roots

2017 ◽  
Author(s):  
Pengxue Li ◽  
Qiaozhi Yu ◽  
Chunmiao Xu ◽  
Xu Gu ◽  
Shilian Qi ◽  
...  
Keyword(s):  
Cell Division ◽  
Cell Fate ◽  
Asymmetric Cell Division ◽  
Cell Types ◽  
Plant Roots ◽  
Synthetic Approach ◽  
Fate Map ◽  
Signaling Systems ◽  
Apoplastic Barrier ◽  
Casparian Strips

AbstractThe plant roots represent the exquisitely controlled cell fate map in which different cell types undergo a complete status transition from stem cell division and initial fate specification, to the terminal differentiation. The endodermis is initially specified in meristem but further differentiates to form Casparian strips (CSs), the apoplastic barrier in the mature zone for the selective transport between stele and outer tissues, and thus is regarded as plant inner skin. In the Arabidopsis thaliana root the transcription factors SHORTROOT (SHR) regulate asymmetric cell division in cortical initials to separate endodermal and cortex cell layer. In this paper, we utilized synthetic approach to examine the reconstruction of fully functional Casparian strips in plant roots. Our results revealed that SHR serves as a master regulator of a hierarchical signaling cascade that, combined with stele-derived small peptides, is sufficient to rebuild the functional CS in non-endodermal cells. This is a demonstration of the deployment of two parallel signaling systems, in which both apoplastic and symplastic communication were employed, for coordinately specifying the endodermal cell fate.

Stem cells and lineage development in the mammalian blastocyst

2007 ◽  
Vol 19 (1) ◽  
pp. 111 ◽  
Author(s):  
Janet Rossant
Keyword(s):  
Stem Cells ◽  
Cell Fate ◽  
Es Cells ◽  
Mammalian Species ◽  
Embryonic Stem ◽  
Cell Types ◽  
Mouse Cell ◽  
Embryonic Cell ◽  
Primitive Endoderm ◽  
Key Factors

The mammalian blastocyst is the source of the most pluripotent stem cells known: embryonic stem (ES) cells. However, ES cells are not totipotent; in mouse chimeras, they do not contribute to extra-embryonic cell types of the trophectoderm (TE) and primitive endoderm (PrE) lineages. Understanding the genetic pathways that control pluripotency v. extra-embryonic lineage restriction is key to understanding not only normal embryonic development, but also how to reprogramme adult cells to pluripotency. The trophectoderm and primitive endoderm lineages also provide the first signals that drive patterned differentiation of the pluripotent epiblast cells of the embryo. My laboratory has produced permanent mouse cell lines from both the TE and the PrE, termed trophoblast stem (TS) and eXtra-embryonic ENdoderm (XEN) cells. We have used these cells to explore the genetic and molecular hierarchy of lineage restriction and identify the key factors that distinguish the ES cell v. the TS or XEN cell fate. The major molecular pathways of lineage commitment defined in mouse embryos and stem cells are probably conserved across mammalian species, but more comparative studies of lineage development in embryos of non-rodent mammals will likely yield interesting differences in terms of timing and details.

scholarly journals DNA writing at a single genomic site enables lineage tracing and analog recording in mammalian cells

2019 ◽  
Author(s):  
Theresa B. Loveless ◽  
Joseph H. Grotts ◽  
Mason W. Schechter ◽  
Elmira Forouzmand ◽  
Courtney K. Carlson ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Lineage Tracing ◽  
Mammalian Development ◽  
Other Information ◽  
Full Picture ◽  
New Type ◽  
Multicellular Organisms ◽  
Non Destructive ◽  
Conceptual Advance

SummaryThe study of intricate cellular and developmental processes in the context of complex multicellular organisms is difficult because it can require the non-destructive observation of thousands, millions, or even billions of cells deep within an animal. To address this difficulty, several groups have recently reported CRISPR-based DNA recorders that convert transient cellular experiences and processes into changes in the genome, which can then be read by sequencing in high-throughput. However, existing DNA recorders act primarily by erasing DNA: they use the random accumulation of CRISPR-induced deletions to record information. This is problematic because in the limit of progressive deletion, no record remains. Here, we present a new type of DNA recorder that acts primarily by writing new DNA. Our system, called CHYRON (Cell HistorY Recording by Ordered iNsertion), inserts random nucleotides at a single locus in temporal order in vivo and can be applied as an evolving lineage tracer as well as a recorder of user-selected cellular stimuli. As a lineage tracer, CHYRON allowed us to perfectly reconstruct the population lineage relationships among 16 groups of human cells descended from four starting groups that were subject to a series of splitting steps. In this experiment, CHYRON progressively wrote and retained base insertions in 20% percent of cells where the average amount written was 8.4 bp (~14.5 bits), reflecting high information content and density. As a stimulus recorder, we showed that when the CHYRON machinery was placed under the control of a stress-responsive promoter, the frequency and length of writing reflected the dose and duration of the stress. We believe CHYRON represents a conceptual advance in DNA recording technologies where writing rather than erasing becomes the primary mode of information accumulation. With further engineering of CHYRON’s components to increase writing efficiency, CHYRON should lead to single-cell-resolution recording of lineage and other information through long periods of time in complex animals or tumors, advancing the pursuit of a full picture of mammalian development.

scholarly journals Single cell RNA-seq identifies developing corneal cell fates in the human cornea organoid

2021 ◽  
Author(s):  
George Maiti ◽  
Maithe Rocha Monteiro de Barros ◽  
Nan Hu ◽  
Mona Roshan ◽  
Karl J Wahlin ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Three Dimensional ◽  
Cell Types ◽  
Human Cornea ◽  
Equal Proportion ◽  
Fate Map ◽  
Cell Fates ◽  
Developmental States ◽  
Induced Pluripotent

The cornea is a protective and refractive barrier in the eye crucial for vision. Understanding the human cornea in health, disease and cell-based treatments can be greatly advanced with cornea organoids developed in culture from induced pluripotent stem cells. While a limited number of studies have investigated the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly. Here we elucidated the transcriptomic cell fate map of 4 month-old human cornea organoids and the central cornea from three donors. The organoids harbor cell clusters representing corneal epithelium, stroma and endothelium with sub populations that capture signatures of early developmental states. Unlike the adult cornea where the largest cell population is stromal, the organoids develop almost equal proportion of the three major cell types. These corneal organoids offer a three-dimensional platform to model corneal diseases and integrated responses of the different cell types to treatments.

scholarly journals Conservation and Divergence of YODA MAPKKK Function in Regulation of Grass Epidermal Patterning

2018 ◽  
Author(s):  
Emily Abrash ◽  
M Ximena Anleu Gil ◽  
Juliana L Matos ◽  
Dominique C Bergmann
Keyword(s):  
Cell Fate ◽  
Cell Types ◽  
Lineage Tracing ◽  
Cell Fates ◽  
Kinase Gene ◽  
Asymmetric Cell Divisions ◽  
Cell Divisions ◽  
Asymmetric Divisions ◽  
Species Specific ◽  
Multicellular Organisms

AbstractAll multicellular organisms must properly pattern cell types to generate functional tissues and organs. The organized and predictable cell lineages of the Brachypodium leaf enabled us to characterize the role of the MAPK kinase kinase gene BdYODA1 in regulating asymmetric cell divisions. We find that YODA genes promote normal stomatal spacing patterns in both Arabidopsis and Brachypodium, despite species-specific differences in those patterns. Using lineage tracing and cell fate markers, we show that, unexpectedly, patterning defects in bdyoda1 mutants do not arise from faulty physical asymmetry in cell divisions but rather from improper enforcement of alternative cellular fates after division. These cross-species comparisons allow us to refine our interpretations of MAPK activities during plant asymmetric cell divisions.Summary StatementAnalysis of Brachypodium leaf epidermis development reveals that the MAPKKK, BdYODA1, regulates asymmetric divisions by enforcing resultant cell fates rather than driving initial physical asymmetries.

scholarly journals The genetic basis for the evolution of soma: mechanistic evidence for the co-option of a stress-induced gene into a developmental master regulator

2020 ◽  
Vol 287 (1940) ◽  
pp. 20201414
Author(s):  
Stephan G. König ◽  
Aurora M. Nedelcu
Keyword(s):  
Cell Fate ◽  
Stress Responses ◽  
Regulatory Gene ◽  
Somatic Cells ◽  
Cell Types ◽  
Volvox Carteri ◽  
Developmentally Regulated ◽  
Evolutionary Origins ◽  
Increased Sensitivity ◽  
Multicellular Organisms

In multicellular organisms with specialized cells, the most significant distinction among cell types is between reproductive (germ) cells and non-reproductive/somatic cells (soma). Although soma contributed to the marked increase in complexity of many multicellular lineages, little is known about its evolutionary origins. We have previously suggested that the evolution of genes responsible for the differentiation of somatic cells involved the co-option of life history trade-off genes that in unicellular organisms enhanced survival at a cost to immediate reproduction. In the multicellular green alga, Volvox carteri , cell fate is established early in development by the differential expression of a master regulatory gene known as regA . A closely related RegA -Like Sequence ( RLS1 ) is present in its single-celled relative, Chlamydomonas reinhardtii . RLS1 is expressed in response to stress, and we proposed that an environmentally induced RLS1 -like gene was co-opted into a developmental pathway in the lineage leading to V. carteri . However, the exact evolutionary scenario responsible for the postulated co-option event remains to be determined. Here, we show that in addition to being developmentally regulated, regA can also be induced by environmental cues, indicating that regA has maintained its ancestral regulation. We also found that the absence of a functional RegA protein confers increased sensitivity to stress, consistent with RegA having a direct or indirect role in stress responses. Overall, this study (i) provides mechanistic evidence for the co-option of an environmentally induced gene into a major developmental regulator, (ii) supports the view that major morphological innovations can evolve via regulatory changes and (iii) argues for the role of stress in the evolution of multicellular complexity.

scholarly journals To Be, or Notch to Be: Mediating Cell Fate from Embryogenesis to Lymphopoiesis

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 849
Author(s):  
Han Leng Ng ◽  
Elizabeth Quail ◽  
Mark N. Cruickshank ◽  
Daniela Ulgiati
Keyword(s):  
Notch Signaling ◽  
Cell Fate ◽  
Cell Types ◽  
Lymphoid Cells ◽  
Target Cells ◽  
Mammalian Development ◽  
Development And Differentiation ◽  
Cellular Development ◽  
Wing Morphogenesis

Notch signaling forms an evolutionarily conserved juxtacrine pathway crucial for cellular development. Initially identified in Drosophila wing morphogenesis, Notch signaling has since been demonstrated to play pivotal roles in governing mammalian cellular development in a large variety of cell types. Indeed, abolishing Notch constituents in mouse models result in embryonic lethality, demonstrating that Notch signaling is critical for development and differentiation. In this review, we focus on the crucial role of Notch signaling in governing embryogenesis and differentiation of multiple progenitor cell types. Using hematopoiesis as a diverse cellular model, we highlight the role of Notch in regulating the cell fate of common lymphoid progenitors. Additionally, the influence of Notch through microenvironment interplay with lymphoid cells and how dysregulation influences disease processes is explored. Furthermore, bi-directional and lateral Notch signaling between ligand expressing source cells and target cells are investigated, indicating potentially novel therapeutic options for treatment of Notch-mediated diseases. Finally, we discuss the role of cis‑inhibition in regulating Notch signaling in mammalian development.

scholarly journals Transitions in cell potency during early mouse development are driven by Notch

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Sergio Menchero ◽  
Isabel Rollan ◽  
Antonio Lopez-Izquierdo ◽  
Maria Jose Andreu ◽  
Julio Sainz de Aja ◽  
...  
Keyword(s):  
Cell Fate ◽  
Cell Types ◽  
Mammalian Development ◽  
Mouse Development ◽  
Cell Stage ◽  
Notch Signalling Pathway ◽  
Gradual Loss ◽  
Early Mouse

The Notch signalling pathway plays fundamental roles in diverse developmental processes in metazoans, where it is important in driving cell fate and directing differentiation of various cell types. However, we still have limited knowledge about the role of Notch in early preimplantation stages of mammalian development, or how it interacts with other signalling pathways active at these stages such as Hippo. By using genetic and pharmacological tools in vivo, together with image analysis of single embryos and pluripotent cell culture, we have found that Notch is active from the 4-cell stage. Transcriptomic analysis in single morula identified novel Notch targets, such as early naïve pluripotency markers or transcriptional repressors such as TLE4. Our results reveal a previously undescribed role for Notch in driving transitions during the gradual loss of potency that takes place in the early mouse embryo prior to the first lineage decisions.

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