1
|
Li XC, Gandara L, Ekelöf M, Richter K, Alexandrov T, Crocker J. Rapid response of fly populations to gene dosage across development and generations. Nat Commun 2024; 15:4551. [PMID: 38811562 PMCID: PMC11137061 DOI: 10.1038/s41467-024-48960-4] [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: 09/06/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Although the effects of genetic and environmental perturbations on multicellular organisms are rarely restricted to single phenotypic layers, our current understanding of how developmental programs react to these challenges remains limited. Here, we have examined the phenotypic consequences of disturbing the bicoid regulatory network in early Drosophila embryos. We generated flies with two extra copies of bicoid, which causes a posterior shift of the network's regulatory outputs and a decrease in fitness. We subjected these flies to EMS mutagenesis, followed by experimental evolution. After only 8-15 generations, experimental populations have normalized patterns of gene expression and increased survival. Using a phenomics approach, we find that populations were normalized through rapid increases in embryo size driven by maternal changes in metabolism and ovariole development. We extend our results to additional populations of flies, demonstrating predictability. Together, our results necessitate a broader view of regulatory network evolution at the systems level.
Collapse
Affiliation(s)
- Xueying C Li
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Lautaro Gandara
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Måns Ekelöf
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Theodore Alexandrov
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit between EMBL and Heidelberg University, Heidelberg, Germany
- BioInnovation Institute, Copenhagen, Denmark
| | - Justin Crocker
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| |
Collapse
|
2
|
Holloway DM, Saunders R, Wenzel CL. Size regulation of the lateral organ initiation zone and its role in determining cotyledon number in conifers. FRONTIERS IN PLANT SCIENCE 2023; 14:1166226. [PMID: 37265639 PMCID: PMC10230826 DOI: 10.3389/fpls.2023.1166226] [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: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 06/03/2023]
Abstract
Introduction Unlike monocots and dicots, many conifers, particularly Pinaceae, form three or more cotyledons. These are arranged in a whorl, or ring, at a particular distance from the embryo tip, with cotyledons evenly spaced within the ring. The number of cotyledons, nc, varies substantially within species, both in clonal cultures and in seed embryos. nc variability reflects embryo size variability, with larger diameter embryos having higher nc. Correcting for growth during embryo development, we extract values for the whorl radius at each nc. This radius, corresponding to the spatial pattern of cotyledon differentiation factors, varies over three-fold for the naturally observed range of nc. The current work focuses on factors in the patterning mechanism that could produce such a broad variability in whorl radius. Molecularly, work in Arabidopsis has shown that the initiation zone for leaf primordia occurs at a minimum between inhibitor zones of HD-ZIP III at the shoot apical meristem (SAM) tip and KANADI (KAN) encircling this farther from the tip. PIN1-auxin dynamics within this uninhibited ring form auxin maxima, specifying primordia initiation sites. A similar mechanism is indicated in conifer embryos by effects on cotyledon formation with overexpression of HD-ZIP III inhibitors and by interference with PIN1-auxin patterning. Methods We develop a mathematical model for HD-ZIP III/KAN spatial localization and use this to characterize the molecular regulation that could generate (a) the three-fold whorl radius variation (and associated nc variability) observed in conifer cotyledon development, and (b) the HD-ZIP III and KAN shifts induced experimentally in conifer embryos and in Arabidopsis. Results This quantitative framework indicates the sensitivity of mechanism components for positioning lateral organs closer to or farther from the tip. Positional shifting is most readily driven by changes to the extent of upstream (meristematic) patterning and changes in HD-ZIP III/KAN mutual inhibition, and less efficiently driven by changes in upstream dosage or the activation of HD-ZIP III. Sharper expression boundaries can also be more resistant to shifting than shallower expression boundaries. Discussion The strong variability seen in conifer nc (commonly from 2 to 10) may reflect a freer variation in regulatory interactions, whereas monocot (nc = 1) and dicot (nc = 2) development may require tighter control of such variation. These results provide direction for future quantitative experiments on the positional control of lateral organ initiation, and consequently on plant phyllotaxy and architecture.
Collapse
Affiliation(s)
- David M. Holloway
- Mathematics Department, British Columbia Institute of Technology, Burnaby, BC, Canada
| | - Rebecca Saunders
- Biotechnology Department, British Columbia Institute of Technology, Burnaby, BC, Canada
| | - Carol L. Wenzel
- Biotechnology Department, British Columbia Institute of Technology, Burnaby, BC, Canada
| |
Collapse
|
3
|
Xu R, Dai F, Wu H, Jiao R, He F, Ma J. Shaping the scaling characteristics of gap gene expression patterns in Drosophila. Heliyon 2023; 9:e13623. [PMID: 36879745 PMCID: PMC9984453 DOI: 10.1016/j.heliyon.2023.e13623] [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: 09/23/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
How patterns are formed to scale with tissue size remains an unresolved problem. Here we investigate embryonic patterns of gap gene expression along the anterior-posterior (AP) axis in Drosophila. We use embryos that greatly differ in length and, importantly, possess distinct length-scaling characteristics of the Bicoid (Bcd) gradient. We systematically analyze the dynamic movements of gap gene expression boundaries in relation to both embryo length and Bcd input as a function of time. We document the process through which such dynamic movements drive both an emergence of a global scaling landscape and evolution of boundary-specific scaling characteristics. We show that, despite initial differences in pattern scaling characteristics that mimic those of Bcd in the anterior, such characteristics of final patterns converge. Our study thus partitions the contributions of Bcd input and regulatory dynamics inherent to the AP patterning network in shaping embryonic pattern's scaling characteristics.
Collapse
Affiliation(s)
- Ruoqing Xu
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Fei Dai
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Honggang Wu
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 510182, China
- Key Laboratory of Interdisciplinary Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Renjie Jiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 510182, China
- Key Laboratory of Interdisciplinary Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng He
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Corresponding author. Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
| | - Jun Ma
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang, China
- Corresponding author. Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
| |
Collapse
|
4
|
Liu H, Li J, Chang X, He F, Ma J. Modeling Obesity-Associated Ovarian Dysfunction in Drosophila. Nutrients 2022; 14:nu14245365. [PMID: 36558524 PMCID: PMC9783805 DOI: 10.3390/nu14245365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
We perform quantitative studies to investigate the effect of high-calorie diet on Drosophila oogenesis. We use the central composite design (CCD) method to obtain quadratic regression models of body fat and fertility as a function of the concentrations of protein and sucrose, two major macronutrients in Drosophila diet, and treatment duration. Our results reveal complex interactions between sucrose and protein in impacting body fat and fertility when they are considered as an integrated physiological response. We verify the utility of our quantitative modeling approach by experimentally confirming the physiological responses-including increased body fat, reduced fertility, and ovarian insulin insensitivity-expected of a treatment condition identified by our modeling method. Under this treatment condition, we uncover a Drosophila oogenesis phenotype that exhibits an accumulation of immature oocytes and a halt in the production of mature oocytes, a phenotype that bears resemblance to key aspects of the human condition of polycystic ovary syndrome (PCOS). Our analysis of the dynamic progression of different aspects of diet-induced pathophysiology also suggests an order of the onset timing for obesity, ovarian dysfunction, and insulin resistance. Thus, our study documents the utility of quantitative modeling approaches toward understanding the biology of Drosophila female reproduction, in relation to diet-induced obesity and type II diabetes, serving as a potential disease model for human ovarian dysfunction.
Collapse
Affiliation(s)
- Huanju Liu
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou 310058, China
| | - Jiajun Li
- ZJU-UOE Institute, Zhejiang University School of Medicine, Haining 314400, China
| | - Xinyue Chang
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou 310058, China
| | - Feng He
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou 310058, China
- Correspondence: (F.H.); (J.M.)
| | - Jun Ma
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou 310058, China
- Women’s Reproductive Health Research Laboratory of Zhejiang Province, Hangzhou 310006, China
- Zhejiang University-University of Toronto Joint Institute of Genetics and Genome Medicine, Hangzhou 310058, China
- Correspondence: (F.H.); (J.M.)
| |
Collapse
|
5
|
Shen J, Liu F, Tang C. Scaling dictates the decoder structure. Sci Bull (Beijing) 2022; 67:1486-1495. [PMID: 36546192 DOI: 10.1016/j.scib.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/06/2022] [Accepted: 06/13/2022] [Indexed: 01/07/2023]
Abstract
Despite fluctuations in embryo size within a species, the spatial gene expression pattern and hence the embryonic structure can nonetheless maintain the correct proportion to the embryo size. This is known as the scaling phenomenon. For morphogen-induced patterning of gene expression, the positional information encoded in the local morphogen concentrations is decoded by the downstream genetic network (the decoder). In this paper, we show that the requirement of scaling sets severe constraints on the geometric structure of such a local decoder, which in turn enables deduction of mutants' behavior and extraction of regulation information without going into any molecular details. We demonstrate that the Drosophila gap gene system achieves scaling in the way consistent with our theory-the decoder geometry required by scaling correctly accounts for the observed gap gene expression pattern in nearly all maternal morphogen mutants. Furthermore, the regulation logic and the coding/decoding strategy of the gap gene system can also be revealed from the decoder geometry. Our work provides a general theoretical framework for a large class of problems where scaling output is achieved by non-scaling inputs and a local decoder, as well as a unified understanding of scaling, mutants' behavior, and gene regulation for the Drosophila gap gene system.
Collapse
Affiliation(s)
- Jingxiang Shen
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
6
|
The early Drosophila embryo as a model system for quantitative biology. Cells Dev 2021; 168:203722. [PMID: 34298230 DOI: 10.1016/j.cdev.2021.203722] [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: 03/05/2021] [Revised: 06/03/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022]
Abstract
With the rise of new tools, from controlled genetic manipulations and optogenetics to improved microscopy, it is now possible to make clear, quantitative and reproducible measurements of biological processes. The humble fruit fly Drosophila melanogaster, with its ease of genetic manipulation combined with excellent imaging accessibility, has become a major model system for performing quantitative in vivo measurements. Such measurements are driving a new wave of interest from physicists and engineers, who are developing a range of testable dynamic models of active systems to understand fundamental biological processes. The reproducibility of the early Drosophila embryo has been crucial for understanding how biological systems are robust to unavoidable noise during development. Insights from quantitative in vivo experiments in the Drosophila embryo are having an impact on our understanding of critical biological processes, such as how cells make decisions and how complex tissue shape emerges. Here, to highlight the power of using Drosophila embryogenesis for quantitative biology, I focus on three main areas: (1) formation and robustness of morphogen gradients; (2) how gene regulatory networks ensure precise boundary formation; and (3) how mechanical interactions drive packing and tissue folding. I further discuss how such data has driven advances in modelling.
Collapse
|
7
|
Abstract
Spatially distributed signaling molecules, known as morphogens, provide spatial information during development. A host of different morphogens have now been identified, from subcellular gradients through to morphogens that act across a whole embryo. These gradients form over a wide-range of timescales, from seconds to hours, and their time windows for interpretation are also highly variable; the processes of morphogen gradient formation and interpretation are highly dynamic. The morphogen Bicoid (Bcd), present in the early Drosophila embryo, is essential for setting up the future Drosophila body segments. Due to its accessibility for both genetic perturbations and imaging, this system has provided key insights into how precise patterning can occur within a highly dynamic system. Here, we review the temporal scales of Bcd gradient formation and interpretation. In particular, we discuss the quantitative evidence for different models of Bcd gradient formation, outline the time windows for Bcd interpretation, and describe how Bcd temporally adapts its own ability to be interpreted. The utilization of temporal information in morphogen readout may provide crucial inputs to ensure precise spatial patterning, particularly in rapidly developing systems.
Collapse
|
8
|
He F, Wu H, Cheung D, Ma J. Detection and Quantification of the Bicoid Concentration Gradient in Drosophila Embryos. Methods Mol Biol 2019; 1863:19-27. [PMID: 30324590 DOI: 10.1007/978-1-4939-8772-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
We describe methods for detecting and quantifying the concentration gradient of the morphogenetic protein Bicoid through fluorescent immunostaining in fixed Drosophila embryos. We introduce image-processing steps using MATLAB functions, and discuss how the measured signal intensities can be analyzed to extract quantitative information. The described procedures permit robust detection of the endogenous Bicoid concentration gradient at a cellular resolution.
Collapse
Affiliation(s)
- Feng He
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honggang Wu
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - David Cheung
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Jun Ma
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA.
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, OH, USA.
- Laboratory of Systems Developmental Biology, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| |
Collapse
|
9
|
|
10
|
Holloway DM, Rozada I, Bray JJH. Two-stage patterning dynamics in conifer cotyledon whorl morphogenesis. ANNALS OF BOTANY 2018; 121:525-534. [PMID: 29309524 PMCID: PMC5838814 DOI: 10.1093/aob/mcx185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/16/2017] [Indexed: 06/03/2023]
Abstract
Background and Aims Conifer embryos, unlike those of monocots or dicots, have variable numbers of cotyledons, even within the same species. Cotyledons form in a single whorl on a dome-shaped embryo. The closely spaced cotyledons are not found outside this ring, indicating a radial control on where they can form. Polar transport of the hormone auxin affects outgrowth of distinct cotyledons, but not the radial aspect of the whorl or the within-whorl spacing between cotyledons. A quantitative model of plant growth regulator patterning is needed to understand the dynamics of this complex morphogenetic process. Methods A two-stage reaction-diffusion model is developed for the spatial patterning of growth regulators on the embryo surface, with a radial pattern (P1) constraining the shorter-wavelength cotyledon pattern (P2) to a whorl. These patterns drive three-dimensional (3-D) morphogenesis by catalysing local surface growth. Key Results Growth driven by P2 generates single whorls across the experimentally observed range of two to 11 cotyledons, as well as the circularly symmetric response to auxin transport interference. These computations are the first corroboration of earlier theoretical proposals for hierarchical control of whorl formation. The model generates the linear relationship between cotyledon number and embryo diameter observed experimentally. This accounts for normal integer cotyledon number selection, as well as the less common cotyledon fusings and splittings observed experimentally. Flattening of the embryo during development may affect the upward outgrowth angle of the cotyledons. Conclusions Cotyledon morphogenesis is more complex geometrically in conifers than in angiosperms, involving 2-D patterning which deforms a surface in three dimensions. This work develops a quantitative framework for understanding the growth and patterning dynamics involved in conifer cotyledon development, and applies more generally to the morphogenesis of whorls with many primordia.
Collapse
Affiliation(s)
- David M Holloway
- Mathematics Department, British Columbia Institute of Technology, Burnaby, B.C., Canada
- Biology Department, University of Victoria, Victoria, B.C., Canada
| | - Ignacio Rozada
- Mathematics Department, British Columbia Institute of Technology, Burnaby, B.C., Canada
| | - Joshua J H Bray
- Biotechnology Program, British Columbia Institute of Technology, Burnaby, B.C., Canada
| |
Collapse
|
11
|
|
12
|
Abstract
Morphogen gradients provide positional information to underlying cells that translate the information into differential gene expression and eventually different cell fates. Scale invariance is the property where the gradients of the morphogen adjust proportionately to the size of the domain. Scale invariance of morphogen gradients or patterns of differentiation is a common phenomenon observed between individuals within the same species and between homologous tissues or structures in different species. To determine whether or not a pattern is scale invariant, others and we have developed definitions and measurements of gradient scaling. These include point-wise and global scaling errors as well as global scaling power. Furthermore, there are a number of mathematical conditions for scale invariance of advection-diffusion-reaction models that inform mechanisms of scaling. Herein we provide a deeper perspective on modeling and measurement of scale invariance of morphogen gradients.
Collapse
Affiliation(s)
- Yan Huang
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - David Umulis
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA.
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
13
|
Yang D, Lian T, Tu J, Gaur U, Mao X, Fan X, Li D, Li Y, Yang M. LncRNA mediated regulation of aging pathways in Drosophila melanogaster during dietary restriction. Aging (Albany NY) 2017; 8:2182-2203. [PMID: 27687893 PMCID: PMC5076457 DOI: 10.18632/aging.101062] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/12/2016] [Indexed: 12/25/2022]
Abstract
Dietary restriction (DR) extends lifespan in many species which is a well-known phenomenon. Long non-coding RNAs (lncRNAs) play an important role in regulation of cell senescence and important age-related signaling pathways. Here, we profiled the lncRNA and mRNA transcriptome of fruit flies at 7 day and 42 day during DR and fully-fed conditions, respectively. In general, 102 differentially expressed lncRNAs and 1406 differentially expressed coding genes were identified. Most informatively we found a large number of differentially expressed lncRNAs and their targets enriched in GO and KEGG analysis. We discovered some new aging related signaling pathways during DR, such as hippo signaling pathway-fly, phototransduction-fly and protein processing in endoplasmic reticulum etc. Novel lncRNAs XLOC_092363 and XLOC_166557 are found to be located in 10 kb upstream sequences of hairy and ems promoters, respectively. Furthermore, tissue specificity of some novel lncRNAs had been analyzed at 7 day of DR in fly head, gut and fat body. Also the silencing of lncRNA XLOC_076307 resulted in altered expression level of its targets including Gadd45 (involved in FoxO signaling pathway). Together, the results implicated many lncRNAs closely associated with dietary restriction, which could provide a resource for lncRNA in aging and age-related disease field.
Collapse
Affiliation(s)
- Deying Yang
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Ting Lian
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Jianbo Tu
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Uma Gaur
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Xueping Mao
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Xiaolan Fan
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Diyan Li
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Ying Li
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| | - Mingyao Yang
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
| |
Collapse
|
14
|
Simunovic M, Brivanlou AH. Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis. Development 2017; 144:976-985. [PMID: 28292844 PMCID: PMC5358114 DOI: 10.1242/dev.143529] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells have an intrinsic ability to self-assemble and self-organize into complex and functional tissues and organs. By taking advantage of this ability, embryoids, organoids and gastruloids have recently been generated in vitro, providing a unique opportunity to explore complex embryological events in a detailed and highly quantitative manner. Here, we examine how such approaches are being used to answer fundamental questions in embryology, such as how cells self-organize and assemble, how the embryo breaks symmetry, and what controls timing and size in development. We also highlight how further improvements to these exciting technologies, based on the development of quantitative platforms to precisely follow and measure subcellular and molecular events, are paving the way for a more complete understanding of the complex events that help build the human embryo.
Collapse
Affiliation(s)
- Mijo Simunovic
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Ali H Brivanlou
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| |
Collapse
|
15
|
Amourda C, Saunders TE. Gene expression boundary scaling and organ size regulation in the Drosophila embryo. Dev Growth Differ 2017; 59:21-32. [PMID: 28093727 DOI: 10.1111/dgd.12333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 12/21/2022]
Abstract
How the shape and size of tissues and organs is regulated during development is a major question in developmental biology. Such regulation relies upon both intrinsic cues (such as signaling networks) and extrinsic inputs (such as from neighboring tissues). Here, we focus on pattern formation and organ development during Drosophila embryogenesis. In particular, we outline the importance of both biochemical and mechanical tissue-tissue interactions in size regulation. We describe how the Drosophila embryo can potentially provide novel insights into how shape and size are regulated during development. We focus on gene expression boundary scaling in the early embryo and how size is regulated in three organs (hindgut, trachea, and ventral nerve cord) later in development, with particular focus on the role of tissue-tissue interactions. Overall, we demonstrate that Drosophila embryogenesis provides a suitable model system for studying spatial and temporal scaling and size control in vivo.
Collapse
Affiliation(s)
- Christopher Amourda
- Mechanobiology Institute, National University of Singapore, T-Lab, #10-01, 5A Engineering Drive 1, 117411, Singapore
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, T-Lab, #10-01, 5A Engineering Drive 1, 117411, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.,Institute Of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| |
Collapse
|
16
|
Ma J, He F, Xie G, Deng WM. Maternal AP determinants in the Drosophila oocyte and embryo. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:562-81. [PMID: 27253156 DOI: 10.1002/wdev.235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/24/2016] [Accepted: 03/13/2016] [Indexed: 12/12/2022]
Abstract
An animal embryo cannot initiate its journey of forming a new life on its own. It must rely on maternally provided resources and inputs to kick-start its developmental process. In Drosophila, the initial polarities of the embryo along both the anterior-posterior (AP) and dorsal-ventral (DV) axes are also specified by maternal determinants. Over the past several decades, genetic and molecular studies have identified and characterized such determinants, as well as the zygotic genetic regulatory networks that control patterning in the early embryo. Extensive studies of oogenesis have also led to a detailed knowledge of the cellular and molecular interactions that control the formation of a mature egg. Despite these efforts, oogenesis and embryogenesis have been studied largely as separate problems, except for qualitative aspects with regard to maternal regulation of the asymmetric localization of maternal determinants. Can oogenesis and embryogenesis be viewed from a unified perspective at a quantitative level, and can that improve our understanding of how robust embryonic patterning is achieved? Here, we discuss the basic knowledge of the regulatory mechanisms controlling oogenesis and embryonic patterning along the AP axis. We explore properties of the maternal Bicoid gradient in relation to embryo size in search for a unified framework for robust AP patterning. WIREs Dev Biol 2016, 5:562-581. doi: 10.1002/wdev.235 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Jun Ma
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, OH, USA.,Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Feng He
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| |
Collapse
|
17
|
Liu J, Xiao Y, Zhang T, Ma J. Time to move on: Modeling transcription dynamics during an embryonic transition away from maternal control. Fly (Austin) 2016; 10:101-7. [PMID: 27172244 DOI: 10.1080/19336934.2016.1188231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In a recent study, we investigated the regulation of hunchback (hb) transcription dynamics in Drosophila embryos. Our results suggest that shutdown of hb transcription at early nuclear cycle (nc) 14 is an event associated with the global changes taking place during the mid-blastula transition (MBT). Here we have developed a simple model of hb transcription dynamics during this transition time. With kinetic parameters estimated from our published experimental data, the model describes the dynamical processes of hb gene transcription and hb mRNA accumulation. With two steps, transcription onset upon exiting the previous mitosis followed by a sudden impact that blocks gene activation, the model recapitulates the observed dynamics of hb transcription during the nc14 interphase. The timing of gene inactivation is essential, as its alterations lead to changes in both hb transcription dynamics and hb mRNA levels. Our model provides a clear dynamical picture of hb transcription regulation as one of the many, actively regulated events concurrently taking place during the MBT.
Collapse
Affiliation(s)
- Junbo Liu
- a Division of Biomedical Informatics, Cincinnati Children's Research Foundation , Cincinnati , OH
| | - Yanyu Xiao
- b Department of Mathematical Sciences , University of Cincinnati , Cincinnati , OH
| | - Tongli Zhang
- c Department of Molecular and Cellular Physiology , University of Cincinnati College of Medicine , Cincinnati , OH
| | - Jun Ma
- a Division of Biomedical Informatics, Cincinnati Children's Research Foundation , Cincinnati , OH.,d Division of Developmental Biology, Cincinnati Children's Research Foundation , Cincinnati , OH
| |
Collapse
|
18
|
Temporal and spatial dynamics of scaling-specific features of a gene regulatory network in Drosophila. Nat Commun 2015; 6:10031. [PMID: 26644070 PMCID: PMC4686680 DOI: 10.1038/ncomms10031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 10/28/2015] [Indexed: 01/19/2023] Open
Abstract
A widely appreciated aspect of developmental robustness is pattern formation in proportion to size. But how such scaling features emerge dynamically remains poorly understood. Here we generate a data set of the expression profiles of six gap genes in Drosophila melanogaster embryos that differ significantly in size. Expression patterns exhibit size-dependent dynamics both spatially and temporally. We uncover a dynamic emergence of under-scaling in the posterior, accompanied by reduced expression levels of gap genes near the middle of large embryos. Simulation results show that a size-dependent Bicoid gradient input can lead to reduced Krüppel expression that can have long-range and dynamic effects on gap gene expression in the posterior. Thus, for emergence of scaled patterns, the entire embryo may be viewed as a single unified dynamic system where maternally derived size-dependent information interpreted locally can be propagated in space and time as governed by the dynamics of a gene regulatory network. How pattern formation is regulated relative to the size of an organism is unclear. Here, Wu et al. take data from gap gene expression in flies of different sizes together with simulations, identifying how scaling emerges dynamically and that local patterning influences global gene regulatory networks.
Collapse
|
19
|
Fried P, Iber D. Read-Out of Dynamic Morphogen Gradients on Growing Domains. PLoS One 2015; 10:e0143226. [PMID: 26599604 PMCID: PMC4657938 DOI: 10.1371/journal.pone.0143226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/05/2015] [Indexed: 01/12/2023] Open
Abstract
Quantitative data from the Drosophila wing imaginal disc reveals that the amplitude of the Decapentaplegic (Dpp) morphogen gradient increases continuously. It is an open question how cells can determine their relative position within a domain based on a continuously increasing gradient. Here we show that pre-steady state diffusion-based dispersal of morphogens results in a zone within the growing domain where the concentration remains constant over the patterning period. The position of the zone that is predicted based on quantitative data for the Dpp morphogen corresponds to where the Dpp-dependent gene expression boundaries of spalt (sal) and daughters against dpp (dad) emerge. The model also suggests that genes that are scaling and are expressed at lateral positions are either under the control of a different read-out mechanism or under the control of a different morphogen. The patterning mechanism explains the extraordinary robustness that is observed for variations in Dpp production, and offers an explanation for the dual role of Dpp in controlling patterning and growth. Pre-steady-state dynamics are pervasive in morphogen-controlled systems, thus making this a probable general mechanism for the scaled read-out of morphogen gradients in growing developmental systems.
Collapse
Affiliation(s)
- Patrick Fried
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
| |
Collapse
|
20
|
Liu J, Ma J. Modulation of temporal dynamics of gene transcription by activator potency in the Drosophila embryo. Development 2015; 142:3781-90. [PMID: 26395487 DOI: 10.1242/dev.126946] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/07/2015] [Indexed: 12/24/2022]
Abstract
The Drosophila embryo at the mid-blastula transition (MBT) concurrently experiences a receding first wave of zygotic transcription and the surge of a massive second wave. It is not well understood how genes in the first wave become turned off transcriptionally and how their precise timing may impact embryonic development. Here we perturb the timing of the shutdown of Bicoid (Bcd)-dependent hunchback (hb) transcription in the embryo through the use of a Bcd mutant that has heightened activating potency. A delayed shutdown specifically increases Bcd-activated hb levels, and this alters spatial characteristics of the patterning outcome and causes developmental defects. Our study thus documents a specific participation of maternal activator input strength in the timing of molecular events in precise accordance with MBT morphological progression.
Collapse
Affiliation(s)
- Junbo Liu
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Jun Ma
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA Division of Developmental Biology, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| |
Collapse
|
21
|
Probing the impact of temperature on molecular events in a developmental system. Sci Rep 2015; 5:13124. [PMID: 26286011 PMCID: PMC4541335 DOI: 10.1038/srep13124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/16/2015] [Indexed: 01/19/2023] Open
Abstract
A well-appreciated general feature of development is the ability to achieve a normal outcome despite the inevitable variability at molecular, genetic, or environmental levels. But it is not well understood how changes in a global factor such as temperature bring about specific challenges to a developmental system in molecular terms. Here we address this question using early Drosophila embryos where the maternal gradient Bicoid (Bcd) instructs anterior-patterning (AP) patterning. We show that temperature can impact the amplitude of the Bcd gradient in the embryo. To evaluate how molecular decisions are made at different temperatures, we quantify Bcd concentrations and the expression of its target gene hunchback (hb) in individual embryos. Our results suggest a relatively robust Bcd concentration threshold in inducing hb transcription within a temperature range. Our results also reveal a complex nature of the effects of temperature on the progressions of developmental and molecular events of the embryo. Our study thus advances the concept of developmental robustness by quantitatively elaborating specific features and challenges—imposed by changes in temperature—that an embryo must resolve.
Collapse
|