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Turner CD, Ramos CM, Curran SP. Disrupting the SKN-1 homeostat: mechanistic insights and phenotypic outcomes. FRONTIERS IN AGING 2024; 5:1369740. [PMID: 38501033 PMCID: PMC10944932 DOI: 10.3389/fragi.2024.1369740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/15/2024] [Indexed: 03/20/2024]
Abstract
The mechanisms that govern maintenance of cellular homeostasis are crucial to the lifespan and healthspan of all living systems. As an organism ages, there is a gradual decline in cellular homeostasis that leads to senescence and death. As an organism lives into advanced age, the cells within will attempt to abate age-related decline by enhancing the activity of cellular stress pathways. The regulation of cellular stress responses by transcription factors SKN-1/Nrf2 is a well characterized pathway in which cellular stress, particularly xenobiotic stress, is abated by SKN-1/Nrf2-mediated transcriptional activation of the Phase II detoxification pathway. However, SKN-1/Nrf2 also regulates a multitude of other processes including development, pathogenic stress responses, proteostasis, and lipid metabolism. While this process is typically tightly regulated, constitutive activation of SKN-1/Nrf2 is detrimental to organismal health, this raises interesting questions surrounding the tradeoff between SKN-1/Nrf2 cryoprotection and cellular health and the ability of cells to deactivate stress response pathways post stress. Recent work has determined that transcriptional programs of SKN-1 can be redirected or suppressed to abate negative health outcomes of constitutive activation. Here we will detail the mechanisms by which SKN-1 is controlled, which are important for our understanding of SKN-1/Nrf2 cytoprotection across the lifespan.
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Affiliation(s)
- Chris D. Turner
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
| | - Carmen M. Ramos
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
- Dornsife College of Letters, Arts, and Sciences, Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States
| | - Sean P. Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
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2
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Demouchy F, Nicolle O, Michaux G, Pacquelet A. PAR-4/LKB1 prevents intestinal hyperplasia by restricting endoderm specification in Caenorhabditis elegans embryos. Development 2024; 151:dev202205. [PMID: 38078543 DOI: 10.1242/dev.202205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
The kinase PAR-4/LKB1 is a major regulator of intestinal homeostasis, which prevents polyposis in humans. Moreover, its ectopic activation is sufficient to induce polarization and formation of microvilli-like structures in intestinal cell lines. Here, we use Caenorhabditis elegans to examine the role of PAR-4 during intestinal development in vivo. We show that it is not required to establish enterocyte polarity and plays only a minor role in brush border formation. By contrast, par-4 mutants display severe deformations of the intestinal lumen as well as supernumerary intestinal cells, thereby revealing a previously unappreciated function of PAR-4 in preventing intestinal hyperplasia. The presence of supernumerary enterocytes in par-4 mutants is not due to excessive cell proliferation, but rather to the abnormal expression of the intestinal cell fate factors end-1 and elt-2 outside the E lineage. Notably, par-4 mutants also display reduced expression of end-1 and elt-2 inside the E lineage. Our work thereby unveils an essential and dual role of PAR-4, which both restricts intestinal specification to the E lineage and ensures its robust differentiation.
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Affiliation(s)
- Flora Demouchy
- University of Rennes, CNRS, IGDR (Institut de Génétique et de Développement de Rennes), UMR 6290, F-35000 Rennes, France
| | - Ophélie Nicolle
- University of Rennes, CNRS, IGDR (Institut de Génétique et de Développement de Rennes), UMR 6290, F-35000 Rennes, France
| | - Grégoire Michaux
- University of Rennes, CNRS, IGDR (Institut de Génétique et de Développement de Rennes), UMR 6290, F-35000 Rennes, France
| | - Anne Pacquelet
- University of Rennes, CNRS, IGDR (Institut de Génétique et de Développement de Rennes), UMR 6290, F-35000 Rennes, France
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Turner CD, Stuhr NL, Ramos CM, Van Camp BT, Curran SP. A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons. Proc Natl Acad Sci U S A 2023; 120:e2308565120. [PMID: 38113255 PMCID: PMC10756303 DOI: 10.1073/pnas.2308565120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/02/2023] [Indexed: 12/21/2023] Open
Abstract
Coordination of cellular responses to stress is essential for health across the lifespan. The transcription factor SKN-1 is an essential homeostat that mediates survival in stress-inducing environments and cellular dysfunction, but constitutive activation of SKN-1 drives premature aging thus revealing the importance of turning off cytoprotective pathways. Here, we identify how SKN-1 activation in two ciliated ASI neurons in Caenorhabditis elegans results in an increase in organismal transcriptional capacity that drives pleiotropic outcomes in peripheral tissues. An increase in the expression of established SKN-1 stress response and lipid metabolism gene classes of RNA in the ASI neurons, in addition to the increased expression of several classes of noncoding RNA, define a molecular signature of animals with constitutive SKN-1 activation and diminished healthspan. We reveal neddylation as a unique regulator of the SKN-1 homeostat that mediates SKN-1 abundance within intestinal cells. Moreover, RNAi-independent activity of the dicer-related DExD/H-box helicase, drh-1, in the intestine, can oppose the effects of aberrant SKN-1 transcriptional activation and delays age-dependent decline in health. Taken together, our results uncover a cell nonautonomous circuit to maintain organism-level homeostasis in response to excessive SKN-1 transcriptional activity in the sensory nervous system.
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Affiliation(s)
- Chris D. Turner
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Nicole L. Stuhr
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Carmen M. Ramos
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Bennett T. Van Camp
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Sean P. Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
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4
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Liu J, Murray JI. Mechanisms of lineage specification in Caenorhabditis elegans. Genetics 2023; 225:iyad174. [PMID: 37847877 DOI: 10.1093/genetics/iyad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
The studies of cell fate and lineage specification are fundamental to our understanding of the development of multicellular organisms. Caenorhabditis elegans has been one of the premiere systems for studying cell fate specification mechanisms at single cell resolution, due to its transparent nature, the invariant cell lineage, and fixed number of somatic cells. We discuss the general themes and regulatory mechanisms that have emerged from these studies, with a focus on somatic lineages and cell fates. We next review the key factors and pathways that regulate the specification of discrete cells and lineages during embryogenesis and postembryonic development; we focus on transcription factors and include numerous lineage diagrams that depict the expression of key factors that specify embryonic founder cells and postembryonic blast cells, and the diverse somatic cell fates they generate. We end by discussing some future perspectives in cell and lineage specification.
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Affiliation(s)
- Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Turner CD, Stuhr NL, Ramos CM, Van Camp BT, Curran SP. A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.01.560409. [PMID: 37873147 PMCID: PMC10592859 DOI: 10.1101/2023.10.01.560409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Coordination of cellular responses to stress are essential for health across the lifespan. The transcription factor SKN-1 is an essential homeostat that mediates survival in stress-inducing environments and cellular dysfunction, but constitutive activation of SKN-1 drives premature aging thus revealing the importance of turning off cytoprotective pathways. Here we identify how SKN-1 activation in two ciliated ASI neurons in C. elegans results in an increase in organismal transcriptional capacity that drives pleiotropic outcomes in peripheral tissues. An increase in the expression of established SKN-1 stress response and lipid metabolism gene classes of RNA in the ASI neurons, in addition to the increased expression of several classes of non-coding RNA, define a molecular signature of animals with constitutive SKN-1 activation and diminished healthspan. We reveal neddylation as a novel regulator of the SKN-1 homeostat that mediates SKN-1 abundance within intestinal cells. Moreover, RNAi-independent activity of the dicer-related DExD/H-box helicase, drh-1 , in the intestine, can oppose the e2ffects of aberrant SKN-1 transcriptional activation and delays age-dependent decline in health. Taken together, our results uncover a cell non-autonomous circuit to maintain organism-level homeostasis in response to excessive SKN-1 transcriptional activity in the sensory nervous system. SIGNIFICANCE STATEMENT Unlike activation, an understudied fundamental question across biological systems is how to deactivate a pathway, process, or enzyme after it has been turned on. The irony that the activation of a transcription factor that is meant to be protective can diminish health was first documented by us at the organismal level over a decade ago, but it has long been appreciated that chronic activation of the human ortholog of SKN-1, NRF2, could lead to chemo- and radiation resistance in cancer cells. A colloquial analogy to this biological idea is a sink faucet that has an on valve without a mechanism to shut the water off, which will cause the sink to overflow. Here, we define this off valve.
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Broitman-Maduro G, Maduro MF. Evolutionary Change in Gut Specification in Caenorhabditis Centers on the GATA Factor ELT-3 in an Example of Developmental System Drift. J Dev Biol 2023; 11:32. [PMID: 37489333 PMCID: PMC10366740 DOI: 10.3390/jdb11030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Cells in a developing animal embryo become specified by the activation of cell-type-specific gene regulatory networks. The network that specifies the gut in the nematode Caenorhabditis elegans has been the subject of study for more than two decades. In this network, the maternal factors SKN-1/Nrf and POP-1/TCF activate a zygotic GATA factor cascade consisting of the regulators MED-1,2 → END-1,3 → ELT-2,7, leading to the specification of the gut in early embryos. Paradoxically, the MED, END, and ELT-7 regulators are present only in species closely related to C. elegans, raising the question of how the gut can be specified without them. Recent work found that ELT-3, a GATA factor without an endodermal role in C. elegans, acts in a simpler ELT-3 → ELT-2 network to specify gut in more distant species. The simpler ELT-3 → ELT-2 network may thus represent an ancestral pathway. In this review, we describe the elucidation of the gut specification network in C. elegans and related species and propose a model by which the more complex network might have formed. Because the evolution of this network occurred without a change in phenotype, it is an example of the phenomenon of Developmental System Drift.
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Affiliation(s)
- Gina Broitman-Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Morris F Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
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7
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Broitman-Maduro G, Maduro MF. The long isoform of the C. elegans ELT-3 GATA factor can specify endoderm when overexpressed. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000748. [PMID: 36748041 PMCID: PMC9898813 DOI: 10.17912/micropub.biology.000748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023]
Abstract
The C. elegans elt-3 gene encodes a GATA transcription factor that is expressed in the hypodermis and has roles in hypodermal specification and regulation of collagen and stress response genes. The gene encodes short and long isoforms, ELT-3A and ELT-3B respectively, that differ upstream of their DNA-binding domains. Previous work showed that ELT-3A can specify hypodermal cell fates when forcibly overexpressed throughout early embryos. We recently showed that the ELT-3B orthologue from the distantly related species C. angaria can specify endodermal fates when forcibly overexpressed in C. elegans. Here, we show that C. elegans ELT-3B can also specify endoderm.
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Affiliation(s)
- Gina Broitman-Maduro
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA USA
| | - Morris F. Maduro
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA USA
,
Correspondence to: Morris F. Maduro (
)
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8
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Broitman-Maduro G, Sun S, Kikuchi T, Maduro MF. The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network. Development 2022; 149:277064. [PMID: 36196618 PMCID: PMC9720673 DOI: 10.1242/dev.200984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Endoderm specification in Caenorhabditis elegans occurs through a network in which maternally provided SKN-1/Nrf, with additional input from POP-1/TCF, activates the GATA factor cascade MED-1,2→END-1,3→ELT-2,7. Orthologues of the MED, END and ELT-7 factors are found only among nematodes closely related to C. elegans, raising the question of how gut is specified in their absence in more distant species in the genus. We find that the C. angaria, C. portoensis and C. monodelphis orthologues of the GATA factor gene elt-3 are expressed in the early E lineage, just before their elt-2 orthologues. In C. angaria, Can-pop-1(RNAi), Can-elt-3(RNAi) and a Can-elt-3 null mutation result in a penetrant ‘gutless’ phenotype. Can-pop-1 is necessary for Can-elt-3 activation, showing that it acts upstream. Forced early E lineage expression of Can-elt-3 in C. elegans can direct the expression of a Can-elt-2 transgene and rescue an elt-7 end-1 end-3; elt-2 quadruple mutant strain to viability. Our results demonstrate an ancestral mechanism for gut specification and differentiation in Caenorhabditis involving a simpler POP-1→ELT-3→ELT-2 gene network.
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Affiliation(s)
- Gina Broitman-Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Morris F. Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
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9
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Rumley JD, Preston EA, Cook D, Peng FL, Zacharias AL, Wu L, Jileaeva I, Murray JI. pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo. Dev Biol 2022; 489:34-46. [PMID: 35660370 PMCID: PMC9378603 DOI: 10.1016/j.ydbio.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/21/2022] [Accepted: 05/26/2022] [Indexed: 11/25/2022]
Abstract
Patterning of the anterior-posterior axis is fundamental to animal development. The Wnt pathway plays a major role in this process by activating the expression of posterior genes in animals from worms to humans. This observation raises the question of whether the Wnt pathway or other regulators control the expression of the many anterior-expressed genes. We found that the expression of five anterior-specific genes in Caenorhabditis elegans embryos depends on the Wnt pathway effectors pop-1/TCF and sys-1/β-catenin. We focused further on one of these anterior genes, ref-2/ZIC, a conserved transcription factor expressed in multiple anterior lineages. Live imaging of ref-2 mutant embryos identified defects in cell division timing and position in anterior lineages. Cis-regulatory dissection identified three ref-2 transcriptional enhancers, one of which is necessary and sufficient for anterior-specific expression. This enhancer is activated by the T-box transcription factors TBX-37 and TBX-38, and surprisingly, concatemerized TBX-37/38 binding sites are sufficient to drive anterior-biased expression alone, despite the broad expression of TBX-37 and TBX-38. Taken together, our results highlight the diverse mechanisms used to regulate anterior expression patterns in the embryo.
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Affiliation(s)
- Jonathan D Rumley
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elicia A Preston
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dylan Cook
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Felicia L Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amanda L Zacharias
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Lucy Wu
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ilona Jileaeva
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Ewe CK, Sommermann EM, Kenchel J, Flowers SE, Maduro MF, Joshi PM, Rothman JH. Feedforward regulatory logic controls the specification-to-differentiation transition and terminal cell fate during Caenorhabditis elegans endoderm development. Development 2022; 149:dev200337. [PMID: 35758255 PMCID: PMC10656426 DOI: 10.1242/dev.200337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/13/2022] [Indexed: 11/20/2023]
Abstract
The architecture of gene regulatory networks determines the specificity and fidelity of developmental outcomes. We report that the core regulatory circuitry for endoderm development in Caenorhabditis elegans operates through a transcriptional cascade consisting of six sequentially expressed GATA-type factors that act in a recursive series of interlocked feedforward modules. This structure results in sequential redundancy, in which removal of a single factor or multiple alternate factors in the cascade leads to a mild or no effect on gut development, whereas elimination of any two sequential factors invariably causes a strong phenotype. The phenotypic strength is successfully predicted with a computational model based on the timing and levels of transcriptional states. We found that one factor in the middle of the cascade, END-1, which straddles the distinct events of specification and differentiation, functions in both processes. Finally, we reveal roles for key GATA factors in establishing spatial regulatory state domains by repressing other fates, thereby defining boundaries in the digestive tract. Our findings provide a paradigm that could account for the genetic redundancy observed in many developmental regulatory systems.
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Affiliation(s)
- Chee Kiang Ewe
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Erica M. Sommermann
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Josh Kenchel
- Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Chemical and Biomolecular Engineering Department, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sagen E. Flowers
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Morris F. Maduro
- Molecular, Cell and Systems Biology Department, University of California Riverside, Riverside, CA 92521, USA
| | - Pradeep M. Joshi
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Joel H. Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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Phuangphong S, Tsunoda J, Wada H, Morino Y. Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage. EvoDevo 2021; 12:11. [PMID: 34663437 PMCID: PMC8524836 DOI: 10.1186/s13227-021-00181-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Background Despite the conserved pattern of the cell-fate map among spiralians, bivalves display several modified characteristics during their early development, including early specification of the D blastomere by the cytoplasmic content, as well as the distinctive fate of the 2d blastomere. However, it is unclear what changes in gene regulatory mechanisms led to such changes in cell specification patterns. Spiralian-TALE (SPILE) genes are a group of spiralian-specific transcription factors that play a role in specifying blastomere cell fates during early development in limpets. We hypothesised that the expansion of SPILE gene repertoires influenced the evolution of the specification pattern of blastomere cell fates. Results We performed a transcriptome analysis of early development in the purplish bifurcate mussel and identified 13 SPILE genes. Phylogenetic analysis of the SPILE gene in molluscs suggested that duplications of SPILE genes occurred in the bivalve lineage. We examined the expression patterns of the SPILE gene in mussels and found that some SPILE genes were expressed in quartet-specific patterns, as observed in limpets. Furthermore, we found that several SPILE genes that had undergone gene duplication were specifically expressed in the D quadrant, C and D quadrants or the 2d blastomere. These expression patterns were distinct from the expression patterns of SPILE in their limpet counterparts. Conclusions These results suggest that, in addition to their ancestral role in quartet specification, certain SPILE genes in mussels contribute to the specification of the C and D quadrants. We suggest that the expansion of SPILE genes in the bivalve lineage contributed to the evolution of a unique cell fate specification pattern in bivalves. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-021-00181-2.
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Affiliation(s)
- Supanat Phuangphong
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Jumpei Tsunoda
- College of Biological Sciences, School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis. Nat Methods 2021; 18:893-902. [PMID: 34312566 DOI: 10.1038/s41592-021-01216-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/17/2021] [Indexed: 12/27/2022]
Abstract
Complex biological processes such as embryogenesis require precise coordination of cell differentiation programs across both space and time. Using protein-fusion fluorescent reporters and four-dimensional live imaging, we present a protein expression atlas of transcription factors (TFs) mapped onto developmental cell lineages during Caenorhabditis elegans embryogenesis, at single-cell resolution. This atlas reveals a spatiotemporal combinatorial code of TF expression, and a cascade of lineage-specific, tissue-specific and time-specific TFs that specify developmental states. The atlas uncovers regulators of embryogenesis, including an unexpected role of a skin specifier in neurogenesis and the critical function of an uncharacterized TF in convergent muscle differentiation. At the systems level, the atlas provides an opportunity to model cell state-fate relationships, revealing a lineage-dependent state diversity within functionally related cells and a winding trajectory of developmental state progression. Collectively, this single-cell protein atlas represents a valuable resource for elucidating metazoan embryogenesis at the molecular and systems levels.
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Ewe CK, Alok G, Rothman JH. Stressful development: integrating endoderm development, stress, and longevity. Dev Biol 2020; 471:34-48. [PMID: 33307045 DOI: 10.1016/j.ydbio.2020.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
In addition to performing digestion and nutrient absorption, the intestine serves as one of the first barriers to the external environment, crucial for protecting the host from environmental toxins, pathogenic invaders, and other stress inducers. The gene regulatory network (GRN) governing embryonic development of the endoderm and subsequent differentiation and maintenance of the intestine has been well-documented in C. elegans. A key regulatory input that initiates activation of the embryonic GRN for endoderm and mesoderm in this animal is the maternally provided SKN-1 transcription factor, an ortholog of the vertebrate Nrf1 and 2, which, like C. elegans SKN-1, perform conserved regulatory roles in mediating a variety of stress responses across metazoan phylogeny. Other key regulatory factors in early gut development also participate in stress response as well as in innate immunity and aging and longevity. In this review, we discuss the intersection between genetic nodes that mediate endoderm/intestine differentiation and regulation of stress and homeostasis. We also consider how direct signaling from the intestine to the germline, in some cases involving SKN-1, facilitates heritable epigenetic changes, allowing transmission of adaptive stress responses across multiple generations. These connections between regulation of endoderm/intestine development and stress response mechanisms suggest that varying selective pressure exerted on the stress response pathways may influence the architecture of the endoderm GRN, thereby leading to genetic and epigenetic variation in early embryonic GRN regulatory events.
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Affiliation(s)
- Chee Kiang Ewe
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Geneva Alok
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Joel H Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
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14
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Eurmsirilerd E, Maduro MF. Evolution of Developmental GATA Factors in Nematodes. J Dev Biol 2020; 8:jdb8040027. [PMID: 33207804 PMCID: PMC7712238 DOI: 10.3390/jdb8040027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
GATA transcription factors are found in animals, plants, and fungi. In animals, they have important developmental roles in controlling specification of cell identities and executing tissue-specific differentiation. The Phylum Nematoda is a diverse group of vermiform animals that inhabit ecological niches all over the world. Both free-living and parasitic species are known, including those that cause human infectious disease. To date, GATA factors in nematodes have been studied almost exclusively in the model system C. elegans and its close relatives. In this study, we use newly available sequences to identify GATA factors across the nematode phylum. We find that most species have fewer than six GATA factors, but some species have 10 or more. Comparisons of gene and protein structure suggest that there were at most two GATA factors at the base of the phylum, which expanded by duplication and modification to result in a core set of four factors. The high degree of structural similarity with the corresponding orthologues in C. elegans suggests that the nematode GATA factors share similar functions in development.
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Affiliation(s)
- Ethan Eurmsirilerd
- Undergraduate Program in Biology, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA;
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Morris F. Maduro
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Correspondence:
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15
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Kostouros A, Koliarakis I, Natsis K, Spandidos DA, Tsatsakis A, Tsiaoussis J. Large intestine embryogenesis: Molecular pathways and related disorders (Review). Int J Mol Med 2020; 46:27-57. [PMID: 32319546 PMCID: PMC7255481 DOI: 10.3892/ijmm.2020.4583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
The large intestine, part of the gastrointestinal tract (GI), is composed of all three germ layers, namely the endoderm, the mesoderm and the ectoderm, forming the epithelium, the smooth muscle layers and the enteric nervous system, respectively. Since gastrulation, these layers develop simultaneously during embryogenesis, signaling to each other continuously until adult age. Two invaginations, the anterior intestinal portal (AIP) and the caudal/posterior intestinal portal (CIP), elongate and fuse, creating the primitive gut tube, which is then patterned along the antero‑posterior (AP) axis and the radial (RAD) axis in the context of left‑right (LR) asymmetry. These events lead to the formation of three distinct regions, the foregut, midgut and hindgut. All the above‑mentioned phenomena are under strict control from various molecular pathways, which are critical for the normal intestinal development and function. Specifically, the intestinal epithelium constitutes a constantly developing tissue, deriving from the progenitor stem cells at the bottom of the intestinal crypt. Epithelial differentiation strongly depends on the crosstalk with the adjacent mesoderm. Major molecular pathways that are implicated in the embryogenesis of the large intestine include the canonical and non‑canonical wingless‑related integration site (Wnt), bone morphogenetic protein (BMP), Notch and hedgehog systems. The aberrant regulation of these pathways inevitably leads to several intestinal malformation syndromes, such as atresia, stenosis, or agangliosis. Novel theories, involving the regulation and homeostasis of intestinal stem cells, suggest an embryological basis for the pathogenesis of colorectal cancer (CRC). Thus, the present review article summarizes the diverse roles of these molecular factors in intestinal embryogenesis and related disorders.
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Affiliation(s)
- Antonios Kostouros
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion
| | - Ioannis Koliarakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion
| | - Konstantinos Natsis
- Department of Anatomy and Surgical Anatomy, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki
| | | | - Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, 71409 Heraklion, Greece
| | - John Tsiaoussis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion
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16
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Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade in Caenorhabditis Endoderm Specification. G3-GENES GENOMES GENETICS 2020; 10:333-356. [PMID: 31740453 PMCID: PMC6945043 DOI: 10.1534/g3.119.400724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene regulatory networks and their evolution are important in the study of animal development. In the nematode, Caenorhabditis elegans, the endoderm (gut) is generated from a single embryonic precursor, E. Gut is specified by the maternal factor SKN-1, which activates the MED → END-1,3 → ELT-2,7 cascade of GATA transcription factors. In this work, genome sequences from over two dozen species within the Caenorhabditis genus are used to identify MED and END-1,3 orthologs. Predictions are validated by comparison of gene structure, protein conservation, and putative cis-regulatory sites. All three factors occur together, but only within the Elegans supergroup, suggesting they originated at its base. The MED factors are the most diverse and exhibit an unexpectedly extensive gene amplification. In contrast, the highly conserved END-1 orthologs are unique in nearly all species and share extended regions of conservation. The END-1,3 proteins share a region upstream of their zinc finger and an unusual amino-terminal poly-serine domain exhibiting high codon bias. Compared with END-1, the END-3 proteins are otherwise less conserved as a group and are typically found as paralogous duplicates. Hence, all three factors are under different evolutionary constraints. Promoter comparisons identify motifs that suggest the SKN-1, MED, and END factors function in a similar gut specification network across the Elegans supergroup that has been conserved for tens of millions of years. A model is proposed to account for the rapid origin of this essential kernel in the gut specification network, by the upstream intercalation of duplicate genes into a simpler ancestral network.
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17
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Rothman J, Jarriault S. Developmental Plasticity and Cellular Reprogramming in Caenorhabditis elegans. Genetics 2019; 213:723-757. [PMID: 31685551 PMCID: PMC6827377 DOI: 10.1534/genetics.119.302333] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022] Open
Abstract
While Caenorhabditis elegans was originally regarded as a model for investigating determinate developmental programs, landmark studies have subsequently shown that the largely invariant pattern of development in the animal does not reflect irreversibility in rigidly fixed cell fates. Rather, cells at all stages of development, in both the soma and germline, have been shown to be capable of changing their fates through mutation or forced expression of fate-determining factors, as well as during the normal course of development. In this chapter, we review the basis for natural and induced cellular plasticity in C. elegans We describe the events that progressively restrict cellular differentiation during embryogenesis, starting with the multipotency-to-commitment transition (MCT) and subsequently through postembryonic development of the animal, and consider the range of molecular processes, including transcriptional and translational control systems, that contribute to cellular plasticity. These findings in the worm are discussed in the context of both classical and recent studies of cellular plasticity in vertebrate systems.
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Affiliation(s)
- Joel Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93111, and
| | - Sophie Jarriault
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Department of Development and Stem Cells, CNRS UMR7104, Inserm U1258, Université de Strasbourg, 67404 Illkirch CU Strasbourg, France
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18
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Torres Cleuren YN, Ewe CK, Chipman KC, Mears ER, Wood CG, Al-Alami CEA, Alcorn MR, Turner TL, Joshi PM, Snell RG, Rothman JH. Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network. eLife 2019; 8:48220. [PMID: 31414984 PMCID: PMC6754231 DOI: 10.7554/elife.48220] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Innovations in metazoan development arise from evolutionary modification of gene regulatory networks (GRNs). We report widespread cryptic variation in the requirement for two key regulatory inputs, SKN-1/Nrf2 and MOM-2/Wnt, into the C. elegans endoderm GRN. While some natural isolates show a nearly absolute requirement for these two regulators, in others, most embryos differentiate endoderm in their absence. GWAS and analysis of recombinant inbred lines reveal multiple genetic regions underlying this broad phenotypic variation. We observe a reciprocal trend, in which genomic variants, or knockdown of endoderm regulatory genes, that result in a high SKN-1 requirement often show low MOM-2/Wnt requirement and vice-versa, suggesting that cryptic variation in the endoderm GRN may be tuned by opposing requirements for these two key regulatory inputs. These findings reveal that while the downstream components in the endoderm GRN are common across metazoan phylogeny, initiating regulatory inputs are remarkably plastic even within a single species.
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Affiliation(s)
- Yamila N Torres Cleuren
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chee Kiang Ewe
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Kyle C Chipman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Emily R Mears
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Cricket G Wood
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | | | - Melissa R Alcorn
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Thomas L Turner
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Pradeep M Joshi
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joel H Rothman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
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19
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The C. elegans intestine: organogenesis, digestion, and physiology. Cell Tissue Res 2019; 377:383-396. [DOI: 10.1007/s00441-019-03036-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/12/2019] [Indexed: 12/16/2022]
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20
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Furuta T, Joo HJ, Trimmer KA, Chen SY, Arur S. GSK-3 promotes S-phase entry and progression in C. elegans germline stem cells to maintain tissue output. Development 2018; 145:dev.161042. [PMID: 29695611 DOI: 10.1242/dev.161042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/17/2018] [Indexed: 12/26/2022]
Abstract
Adult C. elegans germline stem cells (GSCs) and mouse embryonic stem cells (mESCs) exhibit a non-canonical cell cycle structure with an abbreviated G1 phase and phase-independent expression of Cdk2 and cyclin E. Mechanisms that promote the abbreviated cell cycle remain unknown, as do the consequences of not maintaining an abbreviated cell cycle in these tissues. In GSCs, we discovered that loss of gsk-3 results in reduced GSC proliferation without changes in differentiation or responsiveness to GLP-1/Notch signaling. We find that DPL-1 transcriptional activity inhibits CDK-2 mRNA accumulation in GSCs, which leads to slower S-phase entry and progression. Inhibition of dpl-1 or transgenic expression of CDK-2 via a heterologous germline promoter rescues the S-phase entry and progression defects of the gsk-3 mutants, demonstrating that transcriptional regulation rather than post-translational control of CDK-2 establishes the abbreviated cell cycle structure in GSCs. This highlights an inhibitory cascade wherein GSK-3 inhibits DPL-1 and DPL-1 inhibits cdk-2 transcription. Constitutive GSK-3 activity through this cascade maintains an abbreviated cell cycle structure to permit the efficient proliferation of GSCs necessary for continuous tissue output.
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Affiliation(s)
- Tokiko Furuta
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyoe-Jin Joo
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth A Trimmer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Genes and Development Graduate Program, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Shin-Yu Chen
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Swathi Arur
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA .,Genes and Development Graduate Program, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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21
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Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 2018. [PMID: 29539636 PMCID: PMC5866720 DOI: 10.1038/nature25981] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring single cell gene expression are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain elusive. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single cell resolution. Using single cell combinatorial indexing assay for transposase accessible chromatin (sci-ATAC-seq)1, we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila embryos spanning three landmark embryonic stages: 2-4 hours (hrs) after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises ~6,000 multipotent cells; 6-8hrs (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified; and 10-12hrs (predominantly stage 13), when each of the embryo’s >20,000 cells are undergoing terminal differentiation. Our results reveal spatial heterogeneity in the usage of the regulatory genome prior to gastrulation, a feature that aligns with future cell fate, and nuclei can be temporally ordered along developmental trajectories. During mid-embryogenesis, tissue granularity emerges such that individual cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. The data reveal overlapping usage of regulatory elements between cells of the endoderm and non-myogenic mesoderm, suggesting a common developmental program reminiscent of the mesendoderm lineage in other species2–4. Altogether, we identify over 30,000 distal regulatory elements exhibiting tissue-specific accessibility. We validated the germ layer specificity of a subset of these predicted enhancers in transgenic embryos, achieving 90% accuracy. Overall, our results demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in the chromatin landscape during development, and to uncover the cis-regulatory programs of metazoan germ layers and cell types.
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Affiliation(s)
- Darren A Cusanovich
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James P Reddington
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Delasa Aghamirzaie
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Raquel Marco-Ferreres
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Hannah A Pliner
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Xiaojie Qiu
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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22
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Choi H, Broitman-Maduro G, Maduro MF. Partially compromised specification causes stochastic effects on gut development in C. elegans. Dev Biol 2017; 427:49-60. [PMID: 28502614 DOI: 10.1016/j.ydbio.2017.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/26/2017] [Accepted: 05/08/2017] [Indexed: 12/29/2022]
Abstract
The C. elegans gut descends from the E progenitor cell through a series of stereotyped cell divisions and morphogenetic events. Effects of perturbations of upstream cell specification on downstream organogenesis have not been extensively investigated. Here we have assembled an allelic series of strains that variably compromise specification of E by perturbing the activation of the gut-specifying end-1 and end-3 genes. Using a marker that allows identification of all E descendants regardless of fate, superimposed with markers that identify cells that have adopted a gut fate, we have examined the fate of E lineage descendants among hundreds of embryos. We find that when specification is partially compromised, the E lineage undergoes hyperplasia accompanied by stochastic and variable specification of gut fate among the E descendants. As anticipated by prior work, the activation of the gut differentiation factor elt-2 becomes delayed in these strains, although ultimate protein levels of a translational ELT-2::GFP reporter resemble those of the wild type. By comparing these effects among the various specification mutants, we find that the stronger the defect in specification (i.e. the fewer number of embryos specifying gut), the stronger the defects in the E lineage and delay in activation of elt-2. Despite the changes in the E lineage in these strains, we find that supernumerary E descendants that adopt a gut fate are accommodated into a relatively normal-looking intestine. Hence, upstream perturbation of specification dramatically affects the E lineage, but as long as sufficient descendants adopt a gut fate, organogenesis overcomes these effects to form a relatively normal intestine.
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Affiliation(s)
- Hailey Choi
- Department of Biology, University of California, Riverside, CA 92521, United States; Graduate program in Cell, Molecular and Developmental Biology, University of California, Riverside, CA 92521, United States
| | - Gina Broitman-Maduro
- Department of Biology, University of California, Riverside, CA 92521, United States
| | - Morris F Maduro
- Department of Biology, University of California, Riverside, CA 92521, United States.
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23
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Robertson SM, Medina J, Oldenbroek M, Lin R. Reciprocal signaling by Wnt and Notch specifies a muscle precursor in the C. elegans embryo. Development 2017; 144:419-429. [PMID: 28049659 DOI: 10.1242/dev.145391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022]
Abstract
The MS blastomere produces one-third of the body wall muscles (BWMs) in the C. elegans embryo. MS-derived BWMs require two distinct cell-cell interactions, the first inhibitory and the second, two cell cycles later, required to overcome this inhibition. The inductive interaction is not required if the inhibitory signal is absent. Although the Notch receptor GLP-1 was implicated in both interactions, the molecular nature of the two signals was unknown. We now show that zygotically expressed MOM-2 (Wnt) is responsible for both interactions. Both the inhibitory and the activating interactions require precise spatiotemporal expression of zygotic MOM-2, which is dependent upon two distinct Notch signals. In a Notch mutant defective only in the inductive interaction, MS-derived BWMs can be restored by preventing zygotic MOM-2 expression, which removes the inhibitory signal. Our results suggest that the inhibitory interaction ensures the differential lineage specification of MS and its sister blastomere, whereas the inductive interaction promotes the expression of muscle-specifying genes by modulating TCF and β-catenin levels. These results highlight the complexity of cell fate specification by cell-cell interactions in a rapidly dividing embryo.
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Affiliation(s)
- Scott M Robertson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jessica Medina
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marieke Oldenbroek
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rueyling Lin
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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24
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Maduro MF. Gut development in C. elegans. Semin Cell Dev Biol 2017; 66:3-11. [PMID: 28065852 DOI: 10.1016/j.semcdb.2017.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/28/2016] [Accepted: 01/03/2017] [Indexed: 12/13/2022]
Abstract
The midgut (intestine) of the nematode, C. elegans, is a tube consisting of 20 cells that arises from a single embryonic precursor. Owing to its comparatively simple anatomy and the advantages inherent to the C. elegans system, the gut has been used as a model for organogenesis for more than 25 years. In this review, the salient features of C. elegans gut development are described from the E progenitor through to the 20-cell intestine. The core gene regulatory network that drives specification of the gut, and other genes with roles in organogenesis, lumen morphogenesis and the cell cycle, are also described. Questions for future work are posed.
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Affiliation(s)
- Morris F Maduro
- Biology Department, University of California, Riverside, CA 92521, United States.
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25
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Pushpa K, Kumar GA, Subramaniam K. Translational Control of Germ Cell Decisions. Results Probl Cell Differ 2017; 59:175-200. [PMID: 28247049 DOI: 10.1007/978-3-319-44820-6_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Germline poses unique challenges to gene expression control at the transcriptional level. While the embryonic germline maintains a global hold on new mRNA transcription, the female adult germline produces transcripts that are not translated into proteins until embryogenesis of subsequent generation. As a consequence, translational control plays a central role in governing various germ cell decisions including the formation of primordial germ cells, self-renewal/differentiation decisions in the adult germline, onset of gametogenesis and oocyte maturation. Mechanistically, several common themes such as asymmetric localization of mRNAs, conserved RNA-binding proteins that control translation by 3' UTR binding, translational activation by the cytoplasmic elongation of the polyA tail and the assembly of mRNA-protein complexes called mRNPs have emerged from the studies on Caenorhabditis elegans, Xenopus and Drosophila. How mRNPs assemble, what influences their dynamics, and how a particular 3' UTR-binding protein turns on the translation of certain mRNAs while turning off other mRNAs at the same time and space are key challenges for future work.
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Affiliation(s)
- Kumari Pushpa
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Ganga Anil Kumar
- Indian Institute of Technology-Kanpur, Kanpur, India.,Indian Institute of Technology-Madras, Chennai, India
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26
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Abstract
The nematode Caenorhabditis elegans is a simple metazoan animal that is widely used as a model to understand the genetic control of development. The completely sequenced C. elegans genome contains 22 T-box genes, and they encode factors that show remarkable diversity in sequence, DNA-binding specificity, and function. Only three of the C. elegans T-box factors can be grouped into the conserved subfamilies found in other organisms, while the remaining factors are significantly diverged and unlike those in most other animals. While some of the C. elegans factors can bind canonical T-box binding elements, others bind and regulate target gene expression through distinct sequences. The nine genetically characterized T-box factors have varied functions in development and morphogenesis of muscle, hypodermal tissues, and neurons, as well as in early blastomere fate specification, cell migration, apoptosis, and sex determination, but the functions of most of the C. elegans T-box factors have not yet been extensively characterized. Like T-box factors in other animals, interaction with a Groucho-family corepressor and posttranslational SUMOylation have been shown to affect C. elegans T-box factor activity, and it is likely that additional mechanisms affecting T-box factor activity will be discovered using the effective genetic approaches in this organism.
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27
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Loboda A, Damulewicz M, Pyza E, Jozkowicz A, Dulak J. Role of Nrf2/HO-1 system in development, oxidative stress response and diseases: an evolutionarily conserved mechanism. Cell Mol Life Sci 2016; 73:3221-47. [PMID: 27100828 PMCID: PMC4967105 DOI: 10.1007/s00018-016-2223-0] [Citation(s) in RCA: 1619] [Impact Index Per Article: 202.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 12/12/2022]
Abstract
The multifunctional regulator nuclear factor erythroid 2-related factor (Nrf2) is considered not only as a cytoprotective factor regulating the expression of genes coding for anti-oxidant, anti-inflammatory and detoxifying proteins, but it is also a powerful modulator of species longevity. The vertebrate Nrf2 belongs to Cap 'n' Collar (Cnc) bZIP family of transcription factors and shares a high homology with SKN-1 from Caenorhabditis elegans or CncC found in Drosophila melanogaster. The major characteristics of Nrf2 are to some extent mimicked by Nrf2-dependent genes and their proteins including heme oxygenase-1 (HO-1), which besides removing toxic heme, produces biliverdin, iron ions and carbon monoxide. HO-1 and their products exert beneficial effects through the protection against oxidative injury, regulation of apoptosis, modulation of inflammation as well as contribution to angiogenesis. On the other hand, the disturbances in the proper HO-1 level are associated with the pathogenesis of some age-dependent disorders, including neurodegeneration, cancer or macular degeneration. This review summarizes our knowledge about Nrf2 and HO-1 across different phyla suggesting their conservative role as stress-protective and anti-aging factors.
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Affiliation(s)
- Agnieszka Loboda
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Milena Damulewicz
- Department of Cell Biology and Imaging, Faculty of Biology and Earth Sciences, Jagiellonian University, Krakow, Poland
| | - Elzbieta Pyza
- Department of Cell Biology and Imaging, Faculty of Biology and Earth Sciences, Jagiellonian University, Krakow, Poland
| | - Alicja Jozkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Jozef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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28
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Tintori SC, Osborne Nishimura E, Golden P, Lieb JD, Goldstein B. A Transcriptional Lineage of the Early C. elegans Embryo. Dev Cell 2016; 38:430-44. [PMID: 27554860 PMCID: PMC4999266 DOI: 10.1016/j.devcel.2016.07.025] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/19/2016] [Accepted: 07/27/2016] [Indexed: 12/30/2022]
Abstract
During embryonic development, cells must establish fates, morphologies, and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell's fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify genome-wide mRNA abundance in each cell of the Caenorhabditis elegans embryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify genes that were previously unappreciated as being critical for development. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fate of each cell, describes at a cellular resolution the mRNA landscape that guides development.
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Affiliation(s)
- Sophia C Tintori
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erin Osborne Nishimura
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Patrick Golden
- School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason D Lieb
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Hudson C, Sirour C, Yasuo H. Co-expression of Foxa.a, Foxd and Fgf9/16/20 defines a transient mesendoderm regulatory state in ascidian embryos. eLife 2016; 5. [PMID: 27351101 PMCID: PMC4945153 DOI: 10.7554/elife.14692] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/24/2016] [Indexed: 12/12/2022] Open
Abstract
In many bilaterian embryos, nuclear β-catenin (nβ-catenin) promotes mesendoderm over ectoderm lineages. Although this is likely to represent an evolutionary ancient developmental process, the regulatory architecture of nβ-catenin-induced mesendoderm remains elusive in the majority of animals. Here, we show that, in ascidian embryos, three nβ-catenin transcriptional targets, Foxa.a, Foxd and Fgf9/16/20, are each required for the correct initiation of both the mesoderm and endoderm gene regulatory networks. Conversely, these three factors are sufficient, in combination, to produce a mesendoderm ground state that can be further programmed into mesoderm or endoderm lineages. Importantly, we show that the combinatorial activity of these three factors is sufficient to reprogramme developing ectoderm cells to mesendoderm. We conclude that in ascidian embryos, the transient mesendoderm regulatory state is defined by co-expression of Foxa.a, Foxd and Fgf9/16/20. DOI:http://dx.doi.org/10.7554/eLife.14692.001
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Affiliation(s)
- Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, Villefranche-sur-Mer, France
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, Villefranche-sur-Mer, France
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30
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Wong MK, Guan D, Ng KHC, Ho VWS, An X, Li R, Ren X, Zhao Z. Timing of Tissue-specific Cell Division Requires a Differential Onset of Zygotic Transcription during Metazoan Embryogenesis. J Biol Chem 2016; 291:12501-12513. [PMID: 27056332 DOI: 10.1074/jbc.m115.705426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 12/20/2022] Open
Abstract
Metazoan development demands not only precise cell fate differentiation but also accurate timing of cell division to ensure proper development. How cell divisions are temporally coordinated during development is poorly understood. Caenorhabditis elegans embryogenesis provides an excellent opportunity to study this coordination due to its invariant development and widespread division asynchronies. One of the most pronounced asynchronies is a significant delay of cell division in two endoderm progenitor cells, Ea and Ep, hereafter referred to as E2, relative to its cousins that mainly develop into mesoderm organs and tissues. To unravel the genetic control over the endoderm-specific E2 division timing, a total of 822 essential and conserved genes were knocked down using RNAi followed by quantification of cell cycle lengths using in toto imaging of C. elegans embryogenesis and automated lineage. Intriguingly, knockdown of numerous genes encoding the components of general transcription pathway or its regulatory factors leads to a significant reduction in the E2 cell cycle length but an increase in cell cycle length of the remaining cells, indicating a differential requirement of transcription for division timing between the two. Analysis of lineage-specific RNA-seq data demonstrates an earlier onset of transcription in endoderm than in other germ layers, the timing of which coincides with the birth of E2, supporting the notion that the endoderm-specific delay in E2 division timing demands robust zygotic transcription. The reduction in E2 cell cycle length is frequently associated with cell migration defect and gastrulation failure. The results suggest that a tissue-specific transcriptional activation is required to coordinate fate differentiation, division timing, and cell migration to ensure proper development.
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Affiliation(s)
- Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Daogang Guan
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Kaoru Hon Chun Ng
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Xiaomeng An
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
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31
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Du L, Tracy S, Rifkin SA. Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. Dev Biol 2016; 412:160-170. [PMID: 26896592 PMCID: PMC4814310 DOI: 10.1016/j.ydbio.2016.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
Cis-regulatory elements (CREs) are crucial links in developmental gene regulatory networks, but in many cases, it can be difficult to discern whether similar CREs are functionally equivalent. We found that despite similar conservation and binding capability to upstream activators, different GATA cis-regulatory motifs within the promoter of the C. elegans endoderm regulator elt-2 play distinctive roles in activating and modulating gene expression throughout development. We fused wild-type and mutant versions of the elt-2 promoter to a gfp reporter and inserted these constructs as single copies into the C. elegans genome. We then counted early embryonic gfp transcripts using single-molecule RNA FISH (smFISH) and quantified gut GFP fluorescence. We determined that a single primary dominant GATA motif located 527bp upstream of the elt-2 start codon was necessary for both embryonic activation and later maintenance of transcription, while nearby secondary GATA motifs played largely subtle roles in modulating postembryonic levels of elt-2. Mutation of the primary activating site increased low-level spatiotemporally ectopic stochastic transcription, indicating that this site acts repressively in non-endoderm cells. Our results reveal that CREs with similar GATA factor binding affinities in close proximity can play very divergent context-dependent roles in regulating the expression of a developmentally critical gene in vivo.
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Affiliation(s)
- Lawrence Du
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Sharon Tracy
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Scott A Rifkin
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States.
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32
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Zacharias AL, Murray JI. Combinatorial decoding of the invariant C. elegans embryonic lineage in space and time. Genesis 2016; 54:182-97. [PMID: 26915329 PMCID: PMC4840027 DOI: 10.1002/dvg.22928] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/19/2022]
Abstract
Understanding how a single cell, the zygote, can divide and differentiate to produce the diverse animal cell types is a central goal of developmental biology research. The model organism Caenorhabditis elegans provides a system that enables a truly comprehensive understanding of this process across all cells. Its invariant cell lineage makes it possible to identify all of the cells in each individual and compare them across organisms. Recently developed methods automate the process of cell identification, allowing high-throughput gene expression characterization and phenotyping at single cell resolution. In this Review, we summarize the sequences of events that pattern the lineage including establishment of founder cell identity, the signaling pathways that diversify embryonic fate, and the regulators involved in patterning within these founder lineages before cells adopt their terminal fates. We focus on insights that have emerged from automated approaches to lineage tracking, including insights into mechanisms of robustness, context-specific regulation of gene expression, and temporal coordination of differentiation. We suggest a model by which lineage history produces a combinatorial code of transcription factors that act, often redundantly, to ensure terminal fate.
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Affiliation(s)
- Amanda L. Zacharias
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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33
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Mann FG, Van Nostrand EL, Friedland AE, Liu X, Kim SK. Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans. PLoS Genet 2016; 12:e1005956. [PMID: 27070429 PMCID: PMC4829211 DOI: 10.1371/journal.pgen.1005956] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 03/04/2016] [Indexed: 02/07/2023] Open
Abstract
To understand the molecular processes underlying aging, we screened modENCODE ChIP-seq data to identify transcription factors that bind to age-regulated genes in C. elegans. The most significant hit was the GATA transcription factor encoded by elt-2, which is responsible for inducing expression of intestinal genes during embryogenesis. Expression of ELT-2 decreases during aging, beginning in middle age. We identified genes regulated by ELT-2 in the intestine during embryogenesis, and then showed that these developmental genes markedly decrease in expression as worms grow old. Overexpression of elt-2 extends lifespan and slows the rate of gene expression changes that occur during normal aging. Thus, our results identify the developmental regulator ELT-2 as a major driver of normal aging in C. elegans.
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Affiliation(s)
- Frederick G Mann
- Departments of Genetics and Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Ari E Friedland
- Editas Medicine, Cambridge, Massachusetts, United States of America
| | - Xiao Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Stuart K Kim
- Departments of Genetics and Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
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34
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Jang J, Wang Y, Lalli MA, Guzman E, Godshalk SE, Zhou H, Kosik KS. Primary Cilium-Autophagy-Nrf2 (PAN) Axis Activation Commits Human Embryonic Stem Cells to a Neuroectoderm Fate. Cell 2016; 165:410-20. [PMID: 27020754 DOI: 10.1016/j.cell.2016.02.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 11/16/2015] [Accepted: 02/06/2016] [Indexed: 12/20/2022]
Abstract
Under defined differentiation conditions, human embryonic stem cells (hESCs) can be directed toward a mesendoderm (ME) or neuroectoderm (NE) fate, the first decision during hESC differentiation. Coupled with lineage-specific G1 lengthening, a divergent ciliation pattern emerged within the first 24 hr of induced lineage specification, and these changes heralded a neuroectoderm decision before any neural precursor markers were expressed. By day 2, increased ciliation in NE precursors induced autophagy that resulted in the inactivation of Nrf2 and thereby relieved transcriptional activation of OCT4 and NANOG. Nrf2 binds directly to upstream regions of these pluripotency genes to promote their expression and repress NE derivation. Nrf2 suppression was sufficient to rescue poorly neurogenic iPSC lines. Only after these events had been initiated did neural precursor markers get expressed at day 4. Thus, we have identified a primary cilium-autophagy-Nrf2 (PAN) control axis coupled to cell-cycle progression that directs hESCs toward NE.
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Affiliation(s)
- Jiwon Jang
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Yidi Wang
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Matthew A Lalli
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elmer Guzman
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Sirie E Godshalk
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Hongjun Zhou
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Kenneth S Kosik
- Department of Molecular Cellular Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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35
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Abstract
In this issue of Developmental Cell, Elewa et al. (2015) show that combinatorial action of RNA binding proteins modulates poly(A) tail length of maternal mRNAs, leading to asymmetric expression of a cell fate determinant in early C. elegans embryos. Genome-wide profiling suggests this mechanism may be widely used to establish cell identities.
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Affiliation(s)
- Pradeep M Joshi
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Joel H Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
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36
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Maduro MF. Developmental robustness in the Caenorhabditis elegans embryo. Mol Reprod Dev 2015; 82:918-31. [PMID: 26382067 DOI: 10.1002/mrd.22582] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/03/2015] [Indexed: 12/25/2022]
Abstract
Developmental robustness is the ability of an embryo to develop normally despite many sources of variation, from differences in the environment to stochastic cell-to-cell differences in gene expression. The nematode Caenorhabditis elegans exhibits an additional level of robustness: Unlike most other animals, the embryonic pattern of cell divisions is nearly identical from animal to animal. The endoderm (gut) lineage is an ideal model for studying such robustness as the juvenile gut has a simple anatomy, consisting of 20 cells that are derived from a single cell, E, and the gene regulatory network that controls E specification shares features with developmental regulatory networks in many other systems, including genetic redundancy, parallel pathways, and feed-forward loops. Early studies were initially concerned with identifying the genes in the network, whereas recent work has focused on understanding how the endoderm produces a robust developmental output in the face of many sources of variation. Genetic control exists at three levels of endoderm development: Progenitor specification, cell divisions within the developing gut, and maintenance of gut differentiation. Recent findings show that specification genes regulate all three of these aspects of gut development, and that mutant embryos can experience a "partial" specification state in which some, but not all, E descendants adopt a gut fate. Ongoing studies using newer quantitative and genome-wide methods promise further insights into how developmental gene-regulatory networks buffer variation.
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Affiliation(s)
- Morris F Maduro
- Department of Biology, University of California, Riverside, California
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37
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Viotti M, Foley AC, Hadjantonakis AK. Gutsy moves in mice: cellular and molecular dynamics of endoderm morphogenesis. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0547. [PMID: 25349455 DOI: 10.1098/rstb.2013.0547] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite the importance of the gut and its accessory organs, our understanding of early endoderm development is still incomplete. Traditionally, endoderm has been difficult to study because of its small size and relative fragility. However, recent advances in live cell imaging technologies have dramatically expanded our understanding of this tissue, adding a new appreciation for the complex molecular and morphogenetic processes that mediate gut formation. Several spatially and molecularly distinct subpopulations have been shown to exist within the endoderm before the onset of gastrulation. Here, we review findings that have uncovered complex cell movements within the endodermal layer, before and during gastrulation, leading to the conclusion that cells from primitive endoderm contribute descendants directly to gut.
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Affiliation(s)
- Manuel Viotti
- Genentech Incorporated, South San Francisco, CA 94080, USA
| | - Ann C Foley
- Department of Bioengineering, Clemson University, Charleston, SC 29425, USA
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Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC. POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA. Dev Cell 2015; 34:108-18. [PMID: 26096734 DOI: 10.1016/j.devcel.2015.05.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/17/2015] [Accepted: 05/27/2015] [Indexed: 12/01/2022]
Abstract
The regulation of mRNA translation is of fundamental importance in biological mechanisms ranging from embryonic axis specification to the formation of long-term memory. POS-1 is one of several CCCH zinc-finger RNA-binding proteins that regulate cell fate specification during C. elegans embryogenesis. Paradoxically, pos-1 mutants exhibit striking defects in endo-mesoderm development but have wild-type distributions of SKN-1, a key determinant of endo-mesoderm fates. RNAi screens for pos-1 suppressors identified genes encoding the cytoplasmic poly(A)-polymerase homolog GLD-2, the Bicaudal-C homolog GLD-3, and the protein NEG-1. We show that NEG-1 localizes in anterior nuclei, where it negatively regulates endo-mesoderm fates. In posterior cells, POS-1 binds the neg-1 3' UTR to oppose GLD-2 and GLD-3 activities that promote NEG-1 expression and cytoplasmic lengthening of the neg-1 mRNA poly(A) tail. Our findings uncover an intricate series of post-transcriptional regulatory interactions that, together, achieve precise spatial expression of endo-mesoderm fates in C. elegans embryos.
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Affiliation(s)
- Ahmed Elewa
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Masaki Shirayama
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul F Harrison
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria 3800, Australia; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - David R Powell
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria 3800, Australia; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3053, Australia
| | - Zhuo Du
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Christopher D Chute
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Life Science and Bioengineering Center, Gateway Park, 60 Prescott Street, Worcester, MA 01605, USA
| | - Hannah Woolf
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dongni Yi
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Takao Ishidate
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Life Science and Bioengineering Center, Gateway Park, 60 Prescott Street, Worcester, MA 01605, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- Program in Molecular Medicine, RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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MED GATA factors promote robust development of the C. elegans endoderm. Dev Biol 2015; 404:66-79. [PMID: 25959238 DOI: 10.1016/j.ydbio.2015.04.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 12/25/2022]
Abstract
The MED-1,2 GATA factors contribute to specification of E, the progenitor of the Caenorhabditis elegans endoderm, through the genes end-1 and end-3, and in parallel with the maternal factors SKN-1, POP-1 and PAL-1. END-1,3 activate elt-2 and elt-7 to initiate a program of intestinal development, which is maintained by positive autoregulation. Here, we advance the understanding of MED-1,2 in E specification. We find that expression of end-1 and end-3 is greatly reduced in med-1,2(-) embryos. We generated strains in which MED sites have been mutated in end-1 and end-3. Without MED input, gut specification relies primarily on POP-1 and PAL-1. 25% of embryos fail to make intestine, while those that do display abnormal numbers of gut cells due to a delayed and stochastic acquisition of intestine fate. Surviving adults exhibit phenotypes consistent with a primary defect in the intestine. Our results establish that MED-1,2 provide robustness to endoderm specification through end-1 and end-3, and reveal that gut differentiation may be more directly linked to specification than previously appreciated. The results argue against an "all-or-none" description of cell specification, and suggest that activation of tissue-specific master regulators, even when expression of these is maintained by positive autoregulation, does not guarantee proper function of differentiated cells.
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40
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41
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Passamaneck YJ, Hejnol A, Martindale MQ. Mesodermal gene expression during the embryonic and larval development of the articulate brachiopod Terebratalia transversa. EvoDevo 2015; 6:10. [PMID: 25897375 PMCID: PMC4404124 DOI: 10.1186/s13227-015-0004-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
Background Brachiopods undergo radial cleavage, which is distinct from the stereotyped development of closely related spiralian taxa. The mesoderm has been inferred to derive from the archenteron walls following gastrulation, and the primary mesoderm derivative in the larva is a complex musculature. To investigate the specification and differentiation of the mesoderm in the articulate brachiopod Terebratalia transversa, we have identified orthologs of genes involved in mesoderm development in other taxa and investigated their spatial and temporal expression during the embryonic and larval development of T. transversa. Results Orthologs of 17 developmental regulatory genes with roles in the development of the mesoderm in other bilaterian animals were found to be expressed in the developing mesoderm of T. transversa. Five genes, Tt.twist, Tt.GATA456, Tt.dachshund, Tt.mPrx, and Tt.NK1, were found to have expression throughout the archenteron wall at the radial gastrula stage, shortly after the initiation of gastrulation. Three additional genes, Tt.Pax1/9, Tt.MyoD, and Tt.Six1/2, showed expression at this stage in only a portion of the archenteron wall. Tt.eya, Tt.FoxC, Tt.FoxF, Tt.Mox, Tt.paraxis, Tt.Limpet, and Tt.Mef2 all showed initial mesodermal expression during later gastrula or early larval stages. At the late larval stage, Tt.dachshund, Tt.Limpet, and Tt.Mef2 showed expression in nearly all mesoderm cells, while all other genes were localized to specific regions of the mesoderm. Tt.FoxD and Tt.noggin both showed expression in the ventral mesoderm at the larval stages, with gastrula expression patterns in the archenteron roof and blastopore lip, respectively. Conclusions Expression analyses support conserved roles for developmental regulators in the specification and differentiation of the mesoderm during the development of T. transversa. Expression of multiple mesodermal factors in the archenteron wall during gastrulation supports previous morphological observations that this region gives rise to larval mesoderm. Localized expression domains during gastrulation and larval development evidence early regionalization of the mesoderm and provide a basis for hypotheses regarding the molecular regulation underlying the complex system of musculature observed in the larva. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0004-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yale J Passamaneck
- Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813 USA ; The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate, 55, 5008 Bergen, Norway
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080 USA
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β-Catenin-related protein WRM-1 is a multifunctional regulatory subunit of the LIT-1 MAPK complex. Proc Natl Acad Sci U S A 2014; 112:E137-46. [PMID: 25548171 DOI: 10.1073/pnas.1416339112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Vertebrate β-catenin has two functions, as a structural component of the adherens junction in cell adhesion and as the T-cell factor (TCF) transcriptional coactivator in canonical Wnt (wingless-related integration site) signaling. These two functions are split between three of the four β-catenin-related proteins present in the round worm Caenorhabditis elegans. The fourth β-catenin-related protein, WRM-1, exhibits neither of these functions. Instead, WRM-1 binds the MAPK loss of intestine 1 (LIT-1), and these two proteins have been shown to be essential for the transcription of Wnt target genes by phosphorylating and regulating the nuclear level of the sole worm TCF protein. We showed previously that WRM-1 binds to worm TCF and functions as the substrate-binding subunit for LIT-1. In this study, we show that phosphorylation of T220 in the activation loop is essential for LIT-1 kinase activity in vivo and in vitro. T220 can be phosphorylated either through LIT-1 autophosphorylation or directly by the upstream MAP3K MOM-4. Our data support a model in which WRM-1, which can undergo homotypic interaction, binds LIT-1 and thereby generates a kinase complex in which LIT-1 molecules are situated in a conformation enabling autophosphorylation as well as promoting phosphorylation of the T220 residue by MOM-4. In addition, we show that WRM-1 is essential for the translocation of the LIT-1 kinase complex to the nucleus, the site of its TCF substrate. To our knowledge, this is the first report of a MAP3K directly activating a MAPK by phosphorylation within the activation loop. This study should help uncover novel and as yet underappreciated functions of vertebrate β-catenin.
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Du Z, He F, Yu Z, Bowerman B, Bao Z. E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis. Dev Biol 2014; 398:267-79. [PMID: 25523393 DOI: 10.1016/j.ydbio.2014.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 01/22/2023]
Abstract
Regulated choice between cell fate maintenance and differentiation provides decision points in development to progress toward more restricted cell fates or to maintain the current one. Caenorhabditis elegans embryogenesis follows an invariant cell lineage where cell fate is generally more restricted upon each cell division. EMS is a progenitor cell in the four-cell embryo that gives rise to the endomesoderm. We recently found that when ubiquitin-mediated protein degradation is compromised, the anterior daughter of EMS, namely MS, reiterates the EMS fate. This observation demonstrates an essential function of ubiquitin-mediated protein degradation in driving the progression of EMS-to-MS differentiation. Here we report a genome-wide screen of the ubiquitin pathway and extensive lineage analyses. The results suggest a broad role of E3 ligases in driving differentiation progression. First, we identified three substrate-binding proteins for two Cullin-RING ubiquitin ligase (CRL) E3 complexes that promote the progression from the EMS fate to MS, namely LIN-23/β-TrCP and FBXB-3 for the CRL1/SCF complex and ZYG-11/ZYG-11B for the CRL2 complex. Genetic analyses suggest these E3 ligases function through a multifunctional protein OMA-1 and the endomesoderm lineage specifier SKN-1 to drive differentiation. Second, we found that depletion of components of the CRL1/SCF complex induces fate reiteration in all major founder cell lineages. These data suggest that regulated choice between self-renewal and differentiation is widespread during C. elegans embryogenesis as in organisms with regulative development, and ubiquitin-mediated protein degradation drives the choice towards differentiation. Finally, bioinformatic analysis of time series gene expression data showed that expression of E3 genes is transiently enriched during time windows of developmental stage transitions. Transcription factors show similar enrichment, but not other classes of regulatory genes. Based on these findings we propose that ubiquitin-mediated protein degradation, like many transcription factors, function broadly as regulators driving developmental progression during embryogenesis in C. elegans.
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Affiliation(s)
- Zhuo Du
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave. New York, NY 10065, United States
| | - Fei He
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave. New York, NY 10065, United States
| | - Zidong Yu
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave. New York, NY 10065, United States; School of Energy and Power Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212003, China
| | - Bruce Bowerman
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, United States
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave. New York, NY 10065, United States.
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Molecular conservation of metazoan gut formation: evidence from expression of endomesoderm genes in Capitella teleta (Annelida). EvoDevo 2014; 5:39. [PMID: 25908956 PMCID: PMC4407770 DOI: 10.1186/2041-9139-5-39] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 09/17/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Metazoan digestive systems develop from derivatives of ectoderm, endoderm and mesoderm, and vary in the relative contribution of each germ layer across taxa and between gut regions. In a small number of well-studied model systems, gene regulatory networks specify endoderm and mesoderm of the gut within a bipotential germ layer precursor, the endomesoderm. Few studies have examined expression of endomesoderm genes outside of those models, and thus, it is unknown whether molecular specification of gut formation is broadly conserved. In this study, we utilize a sequenced genome and comprehensive fate map to correlate the expression patterns of six transcription factors with embryonic germ layers and gut subregions during early development in Capitella teleta. RESULTS The genome of C. teleta contains the five core genes of the sea urchin endomesoderm specification network. Here, we extend a previous study and characterize expression patterns of three network orthologs and three additional genes by in situ hybridization during cleavage and gastrulation stages and during formation of distinct gut subregions. In cleavage stage embryos, Ct-otx, Ct-blimp1, Ct-bra and Ct-nkx2.1a are expressed in all four macromeres, the endoderm precursors. Ct-otx, Ct-blimp1, and Ct-nkx2.1a are also expressed in presumptive endoderm of gastrulae and later during midgut development. Additional gut-specific expression patterns include Ct-otx, Ct-bra, Ct-foxAB and Ct-gsc in oral ectoderm; Ct-otx, Ct-blimp1, Ct-bra and Ct-nkx2.1a in the foregut; and both Ct-bra and Ct-nkx2.1a in the hindgut. CONCLUSIONS Identification of core sea urchin endomesoderm genes in C. teleta indicates they are present in all three bilaterian superclades. Expression of Ct-otx, Ct-blimp1 and Ct-bra, combined with previously published Ct-foxA and Ct-gataB1 patterns, provide the most comprehensive comparison of these five orthologs from a single species within Spiralia. Each ortholog is likely involved in endoderm specification and midgut development, and several may be essential for establishment of the oral ectoderm, foregut and hindgut, including specification of ectodermal and mesodermal contributions. When the five core genes are compared across the Metazoa, their conserved expression patterns suggest that 'gut gene' networks evolved to specify distinct digestive system subregions, regardless of species-specific differences in gut architecture or germ layer contributions within each subregion.
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Xu C, Su Z. Identification of genes driving lineage divergence from single-cell gene expression data in C. elegans. Dev Biol 2014; 393:236-244. [PMID: 25050933 DOI: 10.1016/j.ydbio.2014.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 07/09/2014] [Accepted: 07/11/2014] [Indexed: 11/25/2022]
Abstract
The nematode Caenorhabditis elegans (C. elegans) is an ideal model organism to study the cell fate specification mechanisms during embryogenesis. It is generally believed that cell fate specification in C. elegans is mainly mediated by lineage-based mechanisms, where the specification paths are driven forward by a succession of asymmetric cell divisions. However, little is known about how each binary decision is made by gene regulatory programs. In this study, we endeavor to obtain a global understanding of cell lineage/fate divergence processes during the early embryogenesis of C. elegans. We reanalyzed the EPIC data set, which traced the expression level of reporter genes at single-cell resolution on a nearly continuous time scale up to the 350-cell stage in C. elegans embryos. We examined the expression patterns for a total of 131 genes from 287 embryos with high quality image recordings, among which 86 genes have replicate embryos. Our results reveal that during early embryogenesis, divergence between sister lineages could be largely explained by a few genes. We predicted genes driving lineage divergence and explored their expression patterns in sister lineages. Moreover, we found that divisions leading to fate divergence are associated with a large number of genes being differentially expressed between sister lineages. Interestingly, we found that the developmental paths of lineages could be differentiated by a small set of genes. Therefore, our results support the notion that the cell fate patterns in C. elegans are achieved through stepwise binary decisions punctuated by cell divisions. Our predicted genes driving lineage divergence provide good starting points for future detailed characterization of their roles in the embryogenesis in this important model organism.
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Affiliation(s)
- Chen Xu
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 351 Bioinformatics Building, 9201 University City Blvd, Charlotte, NC 28223, USA.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 351 Bioinformatics Building, 9201 University City Blvd, Charlotte, NC 28223, USA.
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Robertson SM, Medina J, Lin R. Uncoupling different characteristics of the C. elegans E lineage from differentiation of intestinal markers. PLoS One 2014; 9:e106309. [PMID: 25181289 PMCID: PMC4152275 DOI: 10.1371/journal.pone.0106309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/04/2014] [Indexed: 11/29/2022] Open
Abstract
In the 4-cell C. elegans embryo, a signal from P2 to its anterior sister, EMS, specifies the posterior daughter of EMS, E, as the sole founder cell for intestine. The P2-to-EMS signal restricts high level zygotic expression of the redundant GATA transcription factors, END-1 and END-3, to only the E lineage. Expression of END-1 or END-3 in early blastomeres is sufficient to drive intestinal differentiation. We show here that a number of E lineage characteristics, which are also regulated through P2-EMS signaling, can be uncoupled from intestine development, and each with a different sensitivity to specific perturbations of the P2-EMS signal. For example, we show that the extended cell cycle in Ea and Ep depends on the P2-induced high level expression of the cell cycle regulator, WEE-1.1, in E. A mutation in wee-1.1 results in shortened Ea and Ep cell cycles, but has no effect upon intestinal differentiation or embryogenesis. Furthermore, it has been shown previously that the total number of E lineage cell divisions is regulated by a mechanism dependent upon E being specified as the intestinal founder cell. We now show, however, that cell division counting can be uncoupled from intestine differentiation in the E lineage. Many mutations in P2-EMS signal genes exhibit nonfully-penetrant defects in intestinal differentiation. When embryos with those mutations generate intestinal cells, they often make too many intestinal cells. In addition, at the level of individual embryos, expression of end-1 and end-3, and another very early E-specific zygotic gene, sdz-23, exhibit stochastic and discordant defects in P2-EMS signaling mutants. We show here that sdz-23 is expressed close to wildtype levels in embryos deleted of both end-1 and end-3. sdz-23 does not appear to function in intestine development, raising the intriguing possibility that the P2-EMS interaction has downstream molecular consequences within the E lineage independent of end-1/3 and intestinal development.
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Affiliation(s)
- Scott M. Robertson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
| | - Jessica Medina
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Rueyling Lin
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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Du Z, Santella A, He F, Tiongson M, Bao Z. De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis. Cell 2014; 156:359-72. [PMID: 24439388 PMCID: PMC3998820 DOI: 10.1016/j.cell.2013.11.046] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/25/2013] [Accepted: 11/11/2013] [Indexed: 12/21/2022]
Abstract
Elucidation of complex phenotypes for mechanistic insights presents a significant challenge in systems biology. We report a strategy to automatically infer mechanistic models of cell fate differentiation based on live-imaging data. We use cell lineage tracing and combinations of tissue-specific marker expression to assay progenitor cell fate and detect fate changes upon genetic perturbation. Based on the cellular phenotypes, we further construct a model for how fate differentiation progresses in progenitor cells and predict cell-specific gene modules and cell-to-cell signaling events that regulate the series of fate choices. We validate our approach in C. elegans embryogenesis by perturbing 20 genes in over 300 embryos. The result not only recapitulates current knowledge but also provides insights into gene function and regulated fate choice, including an unexpected self-renewal. Our study provides a powerful approach for automated and quantitative interpretation of complex in vivo information.
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Affiliation(s)
- Zhuo Du
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Fei He
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Michael Tiongson
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.
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Ruf V, Holzem C, Peyman T, Walz G, Blackwell TK, Neumann-Haefelin E. TORC2 signaling antagonizes SKN-1 to induce C. elegans mesendodermal embryonic development. Dev Biol 2013; 384:214-27. [PMID: 23973804 DOI: 10.1016/j.ydbio.2013.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 01/18/2023]
Abstract
The evolutionarily conserved target of rapamycin (TOR) kinase controls fundamental metabolic processes to support cell and tissue growth. TOR functions within the context of two distinct complexes, TORC1 and TORC2. TORC2, with its specific component Rictor, has been recently implicated in aging and regulation of growth and metabolism. Here, we identify rict-1/Rictor as a regulator of embryonic development in C. elegans. The transcription factor skn-1 establishes development of the mesendoderm in embryos, and is required for cellular homeostasis and longevity in adults. Loss of maternal skn-1 function leads to mis-specification of the mesendodermal precursor and failure to form intestine and pharynx. We found that genetic inactivation of rict-1 suppressed skn-1-associated lethality by restoring mesendodermal specification in skn-1 deficient embryos. Inactivation of other TORC2 but not TORC1 components also partially rescued skn-1 embryonic lethality. The SGK-1 kinase mediated these functions downstream of rict-1/TORC2, as a sgk-1 gain-of-function mutant suppressed the rict-1 mutant phenotype. These data indicate that TORC2 and SGK-1 antagonize SKN-1 during embryonic development.
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Affiliation(s)
- Vanessa Ruf
- Department of Medicine, Renal Division, University Hospital Freiburg, D-79106 Freiburg, Germany
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Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. ACTA ACUST UNITED AC 2013:1-34. [PMID: 23801596 DOI: 10.1895/wormbook.1.45.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.
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Affiliation(s)
- Valerie Reinke
- Department of Genetics, Yale University, New Haven, CT 06520, USA.
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