1
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Lukas P. Embryonic pattern of cartilaginous head development in the European toad, Bufo bufo. J Exp Zool B Mol Dev Evol 2023; 340:437-454. [PMID: 37358281 DOI: 10.1002/jez.b.23214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 04/17/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
The craniofacial skeleton of vertebrates is a major innovation of the whole clade. Its development and composition requires a precisely orchestrated sequence of chondrification events which lead to a fully functional skeleton. Sequential information on the precise timing and sequence of embryonic cartilaginous head development are available for a growing number of vertebrates. This enables a more and more comprehensive comparison of the evolutionary trends within and among different vertebrate clades. This comparison of sequential patterns of cartilage formation enables insights into the evolution of development of the cartilaginous head skeleton. The cartilaginous sequence of head formation of three basal anurans (Xenopus laevis, Bombina orientalis, Discoglossus scovazzi) was investigated so far. This study investigates the sequence and timing of larval cartilaginous development of the head skeleton from the appearance of mesenchymal Anlagen until the premetamorphic larvae in the neobatrachian species Bufo bufo. Clearing and staining, histology, and 3D reconstruction enabled the tracking of 75 cartilaginous structures and the illustration of the sequential changes of the skull as well as the identification of evolutionary trends of sequential cartilage formation in the anuran head. The anuran viscerocranium does not chondrify in the ancestral anterior to posterior direction and the neurocranial elements do not chondrify in posterior to anterior direction. Instead, the viscerocranial and neurocranial development is mosaic-like and differs greatly from the gnathostome sequence. Strict ancestral anterior to posterior developmental sequences can be observed within the branchial basket. Thus, this data is the basis for further comparative developmental studies of anuran skeletal development.
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Affiliation(s)
- Paul Lukas
- Institute of Zoology and Evolutionary Research, Friedrich-Schiller-University Jena, Jena, Germany
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2
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Gross JB, Berning D, Phelps A, Luc H. An analysis of lateralized neural crest marker expression across development in the Mexican tetra, Astyanax mexicanus. Front Cell Dev Biol 2023; 11:1074616. [PMID: 36875772 PMCID: PMC9975491 DOI: 10.3389/fcell.2023.1074616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
The biological basis of lateralized cranial aberrations can be rooted in early asymmetric patterning of developmental tissues. However, precisely how development impacts natural cranial asymmetries remains incompletely understood. Here, we examined embryonic patterning of the cranial neural crest at two phases of embryonic development in a natural animal system with two morphotypes: cave-dwelling and surface-dwelling fish. Surface fish are highly symmetric with respect to cranial form at adulthood, however adult cavefish harbor diverse cranial asymmetries. To examine if lateralized aberrations of the developing neural crest underpin these asymmetries, we used an automated technique to quantify the area and expression level of cranial neural crest markers on the left and right sides of the embryonic head. We examined the expression of marker genes encoding both structural proteins and transcription factors at two key stages of development: 36 hpf (∼mid-migration of the neural crest) and 72 hpf (∼early differentiation of neural crest derivatives). Interestingly, our results revealed asymmetric biases at both phases of development in both morphotypes, however consistent lateral biases were less common in surface fish as development progressed. Additionally, this work provides the information on neural crest development, based on whole-mount expression patterns of 19 genes, between stage-matched cave and surface morphs. Further, this study revealed 'asymmetric' noise as a likely normative component of early neural crest development in natural Astyanax fish. Mature cranial asymmetries in cave morphs may arise from persistence of asymmetric processes during development, or as a function of asymmetric processes occurring later in the life history.
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Affiliation(s)
- Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Daniel Berning
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Ayana Phelps
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Heidi Luc
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
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3
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Yang Z, Zhu H, Kong K, Wu X, Chen J, Li P, Jiang J, Zhao J, Cui B, Liu F. The dynamic transmission of positional information in stau- mutants during Drosophila embryogenesis. eLife 2020; 9:e54276. [PMID: 32511091 PMCID: PMC7332292 DOI: 10.7554/elife.54276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/06/2020] [Indexed: 01/04/2023] Open
Abstract
It has been suggested that Staufen (Stau) is key in controlling the variability of the posterior boundary of the Hb anterior domain (xHb). However, the mechanism that underlies this control is elusive. Here, we quantified the dynamic 3D expression of segmentation genes in Drosophila embryos. With improved control of measurement errors, we show that the xHb of stau- mutants reproducibly moves posteriorly by 10% of the embryo length (EL) to the wild type (WT) position in the nuclear cycle (nc) 14, and that its variability over short time windows is comparable to that of the WT. Moreover, for stau- mutants, the upstream Bicoid (Bcd) gradients show equivalent relative intensity noise to that of the WT in nc12-nc14, and the downstream Even-skipped (Eve) and cephalic furrow (CF) show the same positional errors as these factors in WT. Our results indicate that threshold-dependent activation and self-organized filtering are not mutually exclusive and could both be implemented in early Drosophila embryogenesis.
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Affiliation(s)
- Zhe Yang
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
- China National Center for Biotechnology DevelopmentBeijingChina
| | - Hongcun Zhu
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Kakit Kong
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Xiaoxuan Wu
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Jiayi Chen
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Peiyao Li
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Jialong Jiang
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Jinchao Zhao
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Bofei Cui
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
| | - Feng Liu
- State Key Laboratory of Nuclear Physics and Technology & Center for Quantitative Biology, Peking UniversityBeijingChina
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4
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Ding B, Patterson EL, Holalu SV, Li J, Johnson GA, Stanley LE, Greenlee AB, Peng F, Bradshaw HD, Blinov ML, Blackman BK, Yuan YW. Two MYB Proteins in a Self-Organizing Activator-Inhibitor System Produce Spotted Pigmentation Patterns. Curr Biol 2020; 30:802-814.e8. [PMID: 32155414 PMCID: PMC7156294 DOI: 10.1016/j.cub.2019.12.067] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 11/19/2022]
Abstract
Many organisms exhibit visually striking spotted or striped pigmentation patterns. Developmental models predict that such spatial patterns can form when a local autocatalytic feedback loop and a long-range inhibitory feedback loop interact. At its simplest, this self-organizing network only requires one self-activating activator that also activates a repressor, which inhibits the activator and diffuses to neighboring cells. However, the molecular activators and inhibitors fully fitting this versatile model remain elusive in pigmentation systems. Here, we characterize an R2R3-MYB activator and an R3-MYB repressor in monkeyflowers (Mimulus). Through experimental perturbation and mathematical modeling, we demonstrate that the properties of these two proteins correspond to an activator-inhibitor pair in a two-component, reaction-diffusion system, explaining the formation of dispersed anthocyanin spots in monkeyflower petals. Notably, disrupting this pattern impacts pollinator visitation. Thus, subtle changes in simple activator-inhibitor systems are likely essential contributors to the evolution of the remarkable diversity of pigmentation patterns in flowers.
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Affiliation(s)
- Baoqing Ding
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Erin L Patterson
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA; Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Srinidhi V Holalu
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA; Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Jingjian Li
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA; College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Grace A Johnson
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA
| | - Lauren E Stanley
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Anna B Greenlee
- Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Foen Peng
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195, USA
| | - H D Bradshaw
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195, USA
| | - Michael L Blinov
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall #3102, Berkeley, CA 94720, USA; Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA 22904, USA.
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, 67 North Eagleville Road, Storrs, CT 06269, USA.
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5
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Satterlee JW, Scanlon MJ. Coordination of Leaf Development Across Developmental Axes. Plants (Basel) 2019; 8:plants8100433. [PMID: 31652517 PMCID: PMC6843618 DOI: 10.3390/plants8100433] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023]
Abstract
Leaves are initiated as lateral outgrowths from shoot apical meristems throughout the vegetative life of the plant. To achieve proper developmental patterning, cell-type specification and growth must occur in an organized fashion along the proximodistal (base-to-tip), mediolateral (central-to-edge), and adaxial–abaxial (top-bottom) axes of the developing leaf. Early studies of mutants with defects in patterning along multiple leaf axes suggested that patterning must be coordinated across developmental axes. Decades later, we now recognize that a highly complex and interconnected transcriptional network of patterning genes and hormones underlies leaf development. Here, we review the molecular genetic mechanisms by which leaf development is coordinated across leaf axes. Such coordination likely plays an important role in ensuring the reproducible phenotypic outcomes of leaf morphogenesis.
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Affiliation(s)
- James W Satterlee
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Michael J Scanlon
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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6
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Farrar MJ, Kolkman KE, Fetcho JR. Features of the structure, development, and activity of the zebrafish noradrenergic system explored in new CRISPR transgenic lines. J Comp Neurol 2018; 526:2493-2508. [PMID: 30070695 DOI: 10.1002/cne.24508] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/24/2018] [Accepted: 07/29/2018] [Indexed: 11/11/2022]
Abstract
The noradrenergic (NA) system of vertebrates is implicated in learning, memory, arousal, and neuroinflammatory responses, but is difficult to access experimentally. Small and optically transparent, larval zebrafish offer the prospect of exploration of NA structure and function in an intact animal. We made multiple transgenic zebrafish lines using the CRISPR/Cas9 system to insert fluorescent reporters upstream of slc6a2, the norepinephrine transporter gene. These lines faithfully express reporters in NA cell populations, including the locus coeruleus (LC), which contains only about 14 total neurons. We used the lines in combination with two-photon microscopy to explore the structure and projections of the NA system in the context of the columnar organization of cell types in the zebrafish hindbrain. We found robust alignment of NA projections with glutamatergic neurotransmitter stripes in some hindbrain segments, suggesting orderly relations to neuronal cell types early in life. We also quantified neurite density in the rostral spinal cord in individual larvae with as much as 100% difference in the number of LC neurons, and found no correlation between neuronal number in the LC and projection density in the rostral spinal cord. Finally, using light sheet microscopy, we performed bilateral calcium imaging of the entire LC. We found that large-amplitude calcium responses were evident in all LC neurons and showed bilateral synchrony, whereas small-amplitude events were more likely to show interhemispheric asynchrony, supporting the potential for targeted LC neuromodulation. Our observations and new transgenic lines set the stage for a deeper understanding of the NA system.
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Affiliation(s)
- Matthew J Farrar
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York.,Department of Math, Physics and Statistics, Messiah College, Mechanicsburg, Pennsylvania
| | - Kristine E Kolkman
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York
| | - Joseph R Fetcho
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York
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7
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Dine E, Gil AA, Uribe G, Brangwynne CP, Toettcher JE. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst 2018; 6:655-663.e5. [PMID: 29859829 PMCID: PMC6023754 DOI: 10.1016/j.cels.2018.05.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/29/2018] [Accepted: 05/02/2018] [Indexed: 12/13/2022]
Abstract
Protein/RNA clusters arise frequently in spatially regulated biological processes, from the asymmetric distribution of P granules and PAR proteins in developing embryos to localized receptor oligomers in migratory cells. This co-occurrence suggests that protein clusters might possess intrinsic properties that make them a useful substrate for spatial regulation. Here, we demonstrate that protein droplets show a robust form of spatial memory, maintaining the spatial pattern of an inhibitor of droplet formation long after it has been removed. Despite this persistence, droplets can be highly dynamic, continuously exchanging monomers with the diffuse phase. We investigate the principles of biophysical spatial memory in three contexts: a computational model of phase separation; a novel optogenetic system where light can drive rapid, localized dissociation of liquid-like protein droplets; and membrane-localized signal transduction from clusters of receptor tyrosine kinases. Our results suggest that the persistent polarization underlying many cellular and developmental processes could arise through a simple biophysical process, without any additional biochemical feedback loops.
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Affiliation(s)
- Elliot Dine
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Agnieszka A Gil
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Giselle Uribe
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA.
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8
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Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC, Reyon D, Tsai SQ, Joung JK, Schier AF. Nodal patterning without Lefty inhibitory feedback is functional but fragile. eLife 2017; 6. [PMID: 29215332 PMCID: PMC5720593 DOI: 10.7554/elife.28785] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022] Open
Abstract
Developmental signaling pathways often activate their own inhibitors. Such inhibitory feedback has been suggested to restrict the spatial and temporal extent of signaling or mitigate signaling fluctuations, but these models are difficult to rigorously test. Here, we determine whether the ability of the mesendoderm inducer Nodal to activate its inhibitor Lefty is required for development. We find that zebrafish lefty mutants exhibit excess Nodal signaling and increased specification of mesendoderm, resulting in embryonic lethality. Strikingly, development can be fully restored without feedback: Lethal patterning defects in lefty mutants can be rescued by ectopic expression of lefty far from its normal expression domain or by spatially and temporally uniform exposure to a Nodal inhibitor drug. While drug-treated mutants are less tolerant of mild perturbations to Nodal signaling levels than wild type embryos, they can develop into healthy adults. These results indicate that patterning without inhibitory feedback is functional but fragile. During animal development, a single fertilized cell gives rise to different tissues and organs. This ‘patterning’ process depends on signaling molecules that instruct cells in different positions in the embryo to acquire different identities. To avoid mistakes during patterning, each cell must receive the correct amount of signal at the appropriate time. In a process called ‘inhibitory feedback’, a signaling molecule instructs cells to produce molecules that block its own signaling. Although inhibitory feedback is widely used during patterning in organisms ranging from sea urchins to mammals, its exact purpose is often not clear. In part this is because feedback is challenging to experimentally manipulate. Removing the inhibitor disrupts feedback, but also increases signaling. Since the effects of broken feedback and increased signaling are intertwined, any resulting developmental defects do not provide information about what feedback specifically does. In order to examine the role of feedback, it is therefore necessary to disconnect the production of the inhibitor from the signaling process. In developing embryos, a well-known signaling molecule called Nodal instructs cells to become specific types – for example, a heart or gut cell. Nodal also promotes the production of its inhibitor, Lefty. To understand how this feedback system works, Rogers, Lord et al. first removed Lefty from zebrafish embryos. These embryos had excessive levels of Nodal signaling, did not develop correctly, and could not survive. Bathing the embryos in a drug that inhibits Nodal reduced excess signaling and allowed them to develop successfully. In these drug-treated embryos, inhibitor production is disconnected from the signaling process, allowing the role of feedback to be examined. Drug-treated embryos were less able to tolerate fluctuations in Nodal signaling than normal zebrafish embryos, which could compensate for such disturbances by adjusting Lefty levels. Overall, it appears that inhibitory feedback in this patterning system is important to compensate for alterations in Nodal signaling, but is not essential for development. Understanding the role of inhibitory feedback will be useful for efforts to grow tissues and organs in the laboratory for clinical use. The results presented by Rogers, Lord et al. also suggest the possibility that drug treatments could be developed to help correct birth defects in the womb.
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Affiliation(s)
- Katherine W Rogers
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Nathan D Lord
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - James A Gagnon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Steven Zimmerman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Deniz C Aksel
- Program in Biophysics, Harvard Medical School, Boston, United States
| | - Deepak Reyon
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, United States.,Department of Pathology, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, United States
| | - Shengdar Q Tsai
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, United States.,Department of Pathology, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, United States
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, United States.,Department of Pathology, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, United States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Broad Institute of MIT and Harvard University, Cambridge, United States.,Center for Brain Science, Harvard University, Cambridge, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, United States.,Center for Systems Biology, Harvard University, Cambridge, United States
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9
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LeBon L, Lee TV, Sprinzak D, Jafar-Nejad H, Elowitz MB. Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states. eLife 2014; 3:e02950. [PMID: 25255098 PMCID: PMC4174579 DOI: 10.7554/elife.02950] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 08/31/2014] [Indexed: 12/31/2022] Open
Abstract
The Notch signaling pathway consists of multiple types of receptors and ligands, whose interactions can be tuned by Fringe glycosyltransferases. A major challenge is to determine how these components control the specificity and directionality of Notch signaling in developmental contexts. Here, we analyzed same-cell (cis) Notch-ligand interactions for Notch1, Dll1, and Jag1, and their dependence on Fringe protein expression in mammalian cells. We found that Dll1 and Jag1 can cis-inhibit Notch1, and Fringe proteins modulate these interactions in a way that parallels their effects on trans interactions. Fringe similarly modulated Notch-ligand cis interactions during Drosophila development. Based on these and previously identified interactions, we show how the design of the Notch signaling pathway leads to a restricted repertoire of signaling states that promote heterotypic signaling between distinct cell types, providing insight into the design principles of the Notch signaling system, and the specific developmental process of Drosophila dorsal-ventral boundary formation. DOI:http://dx.doi.org/10.7554/eLife.02950.001 In animals, cells use a process called Notch signaling to communicate with neighboring cells. During this process, a protein known as a DSL ligand from one cell binds to a protein called a Notch receptor on a neighboring cell. This triggers a series of events in the neighboring cell that change how the genes in this cell are expressed. Notch signaling is involved in many processes including the early growth of embryos, the formation of organs and limbs, and the maintenance of stem cells throughout adult life. Enzymes called Fringe enzymes can control Notch signaling by blocking or promoting the formation of the DSL ligand-Notch receptor pairs. It is also possible for a DSL ligand and a Notch receptor from the same cell to interact. This is thought to be important because it prevents an individual cell from sending and receiving Notch signals at the same time. There are several different DSL ligands, Notch receptors and Fringe enzymes, so it is difficult to determine which configurations of receptors, ligands and Fringe enzymes can enable Notch signals to be sent or received. To address this problem, LeBon et al. investigated how Fringe enzymes acted on several different DSL-Notch receptor pairs in mammalian cells, and also in fruit flies. They focused in particular on the interactions that occurred within the same cell, as the role of Fringe enzymes in this type of interaction has not been examined previously. The experiments revealed that Fringe proteins modify specific same-cell interactions in a way that enables a cell to receive one type of Notch signal from a neighboring cell and send a different type of Notch signal to another cell at the same time. More generally, these results show how an unconventional, ‘bottom-up’ approach can reveal the design principles of cell signaling systems, and suggest that it should now be possible to use these principles to try to understand which cell types send signals to which other cell types in many different contexts. DOI:http://dx.doi.org/10.7554/eLife.02950.002
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Affiliation(s)
- Lauren LeBon
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
| | - Tom V Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - David Sprinzak
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | | | - Michael B Elowitz
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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10
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Abstract
Computer simulations and quantitative imaging of Drosophila embryos have been used to recreate the dynamic activities of a complex transcriptional enhancer.
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Affiliation(s)
- Michael Levine
- is at the Center for Integrative Genomics, Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , United States
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11
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Ilsley GR, Fisher J, Apweiler R, DePace AH, Luscombe NM. Cellular resolution models for even skipped regulation in the entire Drosophila embryo. eLife 2013; 2:e00522. [PMID: 23930223 PMCID: PMC3736529 DOI: 10.7554/elife.00522] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 06/17/2013] [Indexed: 12/14/2022] Open
Abstract
Transcriptional control ensures genes are expressed in the right amounts at the correct times and locations. Understanding quantitatively how regulatory systems convert input signals to appropriate outputs remains a challenge. For the first time, we successfully model even skipped (eve) stripes 2 and 3+7 across the entire fly embryo at cellular resolution. A straightforward statistical relationship explains how transcription factor (TF) concentrations define eve's complex spatial expression, without the need for pairwise interactions or cross-regulatory dynamics. Simulating thousands of TF combinations, we recover known regulators and suggest new candidates. Finally, we accurately predict the intricate effects of perturbations including TF mutations and misexpression. Our approach imposes minimal assumptions about regulatory function; instead we infer underlying mechanisms from models that best fit the data, like the lack of TF-specific thresholds and the positional value of homotypic interactions. Our study provides a general and quantitative method for elucidating the regulation of diverse biological systems. DOI:http://dx.doi.org/10.7554/eLife.00522.001.
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Affiliation(s)
- Garth R Ilsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jasmin Fisher
- Microsoft Research Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Nicholas M Luscombe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
- London Research Institute, Cancer Research UK, London, United Kingdom
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12
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van Mourik S, van Dijk ADJ, Angenent GC, Merk RMH, Molenaar J. Integrating two patterning processes in the flower. Plant Signal Behav 2012; 7:682-684. [PMID: 22580700 PMCID: PMC3442867 DOI: 10.4161/psb.20017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Spatial organ arrangement plays an important role in flower development. The position and the identity of floral organs is influenced by various processes, in particular the expression of MADS-box transcription factors for identity and dynamics of the plant hormone auxin for positioning. We are currently integrating patterning processes of MADS and auxin into our computational models, based on interactions that are known from experiments, in order to get insight in how these define the floral body plan. The resulting computational model will help to explore hypothetical interactions between the MADS and auxin regulation networks in floral organ patterning.
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Affiliation(s)
- Simon van Mourik
- Biometris, Plant Sciences Group, Wageningen University and Research Center; Wageningen, The Netherlands.
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Jefferson WN, Padilla-Banks E, Phelps JY, Gerrish KE, Williams CJ. Permanent oviduct posteriorization after neonatal exposure to the phytoestrogen genistein. Environ Health Perspect 2011; 119:1575-1582. [PMID: 21810550 PMCID: PMC3226509 DOI: 10.1289/ehp.1104018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/02/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND Preimplantation embryo loss during oviduct transit has been observed in adult mice after a 5-day neonatal exposure to the phytoestrogen genistein (Gen; 50 mg/kg/day). OBJECTIVE We investigated the mechanisms underlying the contribution of the oviduct to infertility. METHODS Female mice were treated on postnatal days 1-5 with corn oil or Gen (50 mg/kg/day). We compared morphology, gene expression, and protein expression in different regions of the reproductive tracts of Gen-treated mice with those of control littermates at several time points. RESULTS Neonatal Gen treatment resulted in substantial changes in expression of genes that modulate neonatal oviduct morphogenesis, including Hoxa (homeobox A cluster), Wnt (wingless-related MMTV integration site), and hedgehog signaling genes. An estrogen receptor antagonist blocked these effects, indicating that they were induced by the estrogenic activity of Gen. Oviducts of adults treated neonatally with Gen had abnormal morphology and were stably "posteriorized," as indicated by altered Hoxa gene patterning during the time of treatment and dramatic, permanent up-regulation of homeobox genes (e.g., Pitx1, Six1) normally expressed only in the cervix and vagina. CONCLUSIONS Neonatal exposure to estrogenic environmental chemicals permanently disrupts oviduct morphogenesis and adult gene expression patterns, and these changes likely contribute to the infertility phenotype.
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Affiliation(s)
- Wendy N Jefferson
- Reproductive Medicine Group, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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