A Transcriptional Lineage of the Early<i>C. elegans</i>Embryo

Tintori, Sophia C.; Nishimura, Erin Osborne; Golden, Patrick; Lieb, Jason D.; Goldstein, Bob

doi:10.1101/047746

Cited by 17 publications

(29 citation statements)

References 59 publications

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“…Between this study, our previous study of the L2 stage (2), and earlier studies of the 1 to 16-cell stage embryos (37,38), a large portion of the early C. elegans life-cycle has now been profiled by single cell transcriptomics. However, more datasets will be needed to complete missing stages, including other larval stages and the adult soma and germline.…”

Section: Discussionmentioning

confidence: 94%

A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution

Packer

Zhu

Huynh

et al. 2019

Preprint

108

234

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C. elegans is an animal with few cells, but a striking diversity of cell types. Here, we characterize the molecular basis for their specification by profiling the transcriptomes of 84,625 single embryonic cells. We identify 284 terminal and pre-terminal cell types, mapping most single cell transcriptomes to their exact position in C. elegans' invariant lineage. We use these annotations to perform the first quantitative analysis of the relationship between lineage and the transcriptome for a whole organism. We find that a strong lineage-transcriptome correlation in the early embryo breaks down in the final two cell divisions as cells adopt their terminal fates and that most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state. Users can explore our data with a graphical application "VisCello". Main text:To understand how cell fates are specified during development, it is essential to know the temporal sequence of gene expression in cells during their trajectories from uncommitted precursors to differentiated terminal cell types. Gene expression patterns near branch points in these trajectories can help identify candidate regulators of cell fate decisions (1). Single cell RNA sequencing (sc-RNA-seq) has made it possible to obtain comprehensive measurements of Fig 3. Developmental trajectories of ciliated neurons. (A) UMAP of ciliated neurons and precursors.Colors correspond to cell identity. Text labels indicate terminal cells. Numbers 1-13 indicate parents of 1 ADE-ADA, 2 CEP-URX 3 IL1 4 OLL 5 OLQ 6 ASJ-AUA 7 ASE 8 ASI 9 ASK 10 ADF-AWB 11 ASG-AWA 12 ADL 13 AFD-RMD. 3-5, 7-9, and 12 are listed as parents of only one cell type as the sister cells die. Numbers 14-17 indicate grandparents of 14 IL1 (= IL2 parent) 15 OLQ-URY 16, 17 ASE-ASJ-AUA. 18 indicates a progenitor cluster that includes the AWC-SAAVx and BAG-SMDVx parents, which were identified in a separate UMAP (Fig. S12C). This latter analysis also tentatively identified a few cells near the base of the ASH trajectory as the ASH-RIB parent. Late stage AUA cells cluster with non-ciliated neurons and are not included in this UMAP but are included in the heatmap in panel D. The tiny cluster of cells labeled with an asterisk (*) is putatively AWC-ON based on srt-28 expression. (B) UMAP plot colored by embryo time (colors matched to Fig. 1A) and gene expression (red indicates >0 reads for the listed gene). mcm-7 is gene associated with the cell cycle. unc-130 is known to be expressed in the ASG-AWA neuroblast but neither terminal cell (40) (C) Cartoon illustrating the lineage of the ASE, ASJ, and AUA neurons. (D) Heatmap showing patterns of differential transcription factor expression associated with branches in the ASE-ASJ-AUA lineage. Expression values are log-transformed, then centered and scaled by standard deviation for each row (gene).

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Section: Discussionmentioning

confidence: 94%

A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution

Packer

Zhu

Huynh

et al. 2019

Preprint

108

234

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“…Due to unequal segregation of cell-fate determinant [36] and multiple cell-cell signaling such as Wnt signaling from P2 to EMS [18] and the first Notch signaling from P2 to ABp [38][39] , cells in the early stage usually possess unique identity not only for for their spatial behavior but also for their distinguishable internal transcriptional profiling [40] . Consequently, for "eutely" C.…”

Section: Robust Progression Of Morphogenesis Induced By Division Evenmentioning

confidence: 99%

System-Level Quantification and Phenotyping of Early Embryonic Morphogenesis ofCaenorhabditis elegans

Guan

Wong

et al. 2019

Preprint

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Cell lineage consists of cell division timing, cell migration and cell fate, and is highly conserved during development of nematode species. An outstanding question is how differentiated cells are genetically and physically regulated in order to migrate to their precise destination among individuals. Here, we first generated a reference embryo using time-lapse 3 dimensional images of 222 wild-type C. elegans embryos at about 1.5-minute interval. This was achieved by automatic tracing and quantitative analysis of cellular phenotypes from 4-to 24-cell stage, including cell cycle duration, division orientation and migration trajectory. We next characterized cell division timing and cell kinematic state, which suggests that eight groups of cells can be clustered based on invariant and distinct division sequence. Cells may still be moving while others start to divide, indicating strong robustness against motional noise in developing embryo. We then devised a system-level phenotyping method for detecting mutant defect in global growth rate, cell cycle duration, division orientation and cell arrangement. A total of 758 genes were selected for perturbation by RNA interference followed by automatic phenotyping, which suggests a cryptic genetic architecture coordinating early morphogenesis spatially and temporally. The high-quality wild-type reference supports a conceptual close-packing model for cell arrangement during 4-to 8-cell stage, implying fundamental mechanical laws regulating the topological structure of early C. elegans embryo. Also, we observed a series of remarkable morphogenesis phenomena such as induced defect or recovery from defect in mutant embryo. To facilitate use of this quantification system, we built a software named STAR 1.0 for visualizing the wild-type reference and mutant phenotype. It also allows automatic phenotyping of new mutant embryo. Taken together, we not only provide a statistical wild-type reference with defined variability, but also shed light on both genetic and physical mechanisms coordinating early embryonic morphogenesis of C. elegans. The statistical reference permits a sensitive approach for mutant phenotype analysis, with which we phenotype a total of 1818 mutant embryos by depletion of 758 genes. Figure 1. Establishment of wild-type morphogenesis reference with spatio-temporal properties at single-cell level. A. A pipeline consisting of data acquisition, quality control, data processing and data integration. B. Time-lapse 3D in vivo imaging, embryo reconstruction and automatic cell-position tracing on a C. elegans embryoexpressing GFP in nucleus (green) and PH(PLC1d1) in membrane (red). The whole duration lasted from 4-to 350-cell stage ; the membrane marker here is only for illustration purpose, as most of the data in this work was not obtained from this strain ; 2-cell, 4-cell and 8-cell stages are presented (Supplementary Material 2). C. Cell-lineage tree up to 51-cell stage with tissue-differentiation information [1,21] and cell grouping based on invariant division ordering...

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“…As genome activity changes, so does histone stability; transcriptionally silent regions have more histone stability (Kireeva et al, 2002). In C. elegans embryos, transcription is activated in varying lineages at differing times (Tintori, Osborne Nishimura, Golden, Lieb, & Goldstein, 2016), thus it could be possible to detect these changes by probing histone population dynamics. We have found that gross histone dynamics are canonical (follow that reported in other model systems) in C. elegans with very little variation in differing lineages.…”

Section: Discussionmentioning

confidence: 99%

Embryo timelapses can be compiled and quantified to understand canonical histone dynamics across multiple cell cycles

Smith

Maddox

2018

Cytoskeleton

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In the last decade, computational processing of big datasets has facilitated the analyses of unprecedented quantities of biological data. Thus, automation and big data analysis have been revolutionary in detecting and quantifying subtle phenotypes in cell biological contexts. Analyzing similar quantities of data in larger and more complicated biological systems such as developing embryos has been more challenging due to experimental limitations on both ensemble data collection and analysis. These challenges include photosensitivity of living samples and of the fluorescently tagged proteins under study, collectively limiting the number of images that can be acquired in a single timelapse series. Here we present a streamlined workflow to quantify dynamics of fluorescently labeled proteins over the course of several cell cycles in early embryos, taking advantage of the stereotypical nature of early development that is inherent for many organisms. We benchmark this pipeline studying a fluorescently labeled histone during early embryonic development of the nematode Caenorhabditis elegans. Our strategy allowed us to overcome biological and experimental variation among our timelapse series and quantify nuclear accumulation rate, chromatin incorporation, and turnover/stability of canonical histones. We find that histone proteins are broadly stable in early C. elegans development. Thus, changes in genome regulation occurring in early development do not manifest in gross changes in histone metabolism. Our method enabling characterization of cumulative protein dynamics over several cell cycles of developmental time with high temporal resolution can be applied to expand our understanding of diverse cellular and developmental processes.

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A Transcriptional Lineage of the EarlyC. elegansEmbryo

Cited by 17 publications

References 59 publications

A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution

A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution

System-Level Quantification and Phenotyping of Early Embryonic Morphogenesis ofCaenorhabditis elegans

Embryo timelapses can be compiled and quantified to understand canonical histone dynamics across multiple cell cycles

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