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Schnider ST, Vigano MA, Affolter M, Aguilar G. Functionalized Protein Binders in Developmental Biology. Annu Rev Cell Dev Biol 2024; 40:119-142. [PMID: 39038471 DOI: 10.1146/annurev-cellbio-112122-025214] [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: 07/24/2024]
Abstract
Developmental biology has greatly profited from genetic and reverse genetic approaches to indirectly studying protein function. More recently, nanobodies and other protein binders derived from different synthetic scaffolds have been used to directly dissect protein function. Protein binders have been fused to functional domains, such as to lead to protein degradation, relocalization, visualization, or posttranslational modification of the target protein upon binding. The use of such functionalized protein binders has allowed the study of the proteome during development in an unprecedented manner. In the coming years, the advent of the computational design of protein binders, together with further advances in scaffold engineering and synthetic biology, will fuel the development of novel protein binder-based technologies. Studying the proteome with increased precision will contribute to a better understanding of the immense molecular complexities hidden in each step along the way to generate form and function during development.
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Affiliation(s)
| | | | | | - Gustavo Aguilar
- Current affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Biozentrum, Universität Basel, Basel, Switzerland;
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2
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Miao Y, Pourquié O. Cellular and molecular control of vertebrate somitogenesis. Nat Rev Mol Cell Biol 2024; 25:517-533. [PMID: 38418851 DOI: 10.1038/s41580-024-00709-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
Segmentation is a fundamental feature of the vertebrate body plan. This metameric organization is first implemented by somitogenesis in the early embryo, when paired epithelial blocks called somites are rhythmically formed to flank the neural tube. Recent advances in in vitro models have offered new opportunities to elucidate the mechanisms that underlie somitogenesis. Notably, models derived from human pluripotent stem cells introduced an efficient proxy for studying this process during human development. In this Review, we summarize the current understanding of somitogenesis gained from both in vivo studies and in vitro studies. We deconstruct the spatiotemporal dynamics of somitogenesis into four distinct modules: dynamic events in the presomitic mesoderm, segmental determination, somite anteroposterior polarity patterning, and epithelial morphogenesis. We first focus on the segmentation clock, as well as signalling and metabolic gradients along the tissue, before discussing the clock and wavefront and other models that account for segmental determination. We then detail the molecular and cellular mechanisms of anteroposterior polarity patterning and somite epithelialization.
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Affiliation(s)
- Yuchuan Miao
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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3
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Lodewijk GA, de Geus M, Guimarães RLFP, Jacobs FMJ. Emergence of the ZNF675 Gene During Primate Evolution-Influenced Human Neurodevelopment Through Changing HES1 Autoregulation. J Comp Neurol 2024; 532:e25648. [PMID: 38958676 DOI: 10.1002/cne.25648] [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: 12/31/2023] [Revised: 04/27/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
In this study, we investigated recurrent copy number variations (CNVs) in the 19p12 locus, which are associated with neurodevelopmental disorders. The two genes in this locus, ZNF675 and ZNF681, arose via gene duplication in primates, and their presence in several pathological CNVs in the human population suggests that either or both of these genes are required for normal human brain development. ZNF675 and ZNF681 are members of the Krüppel-associated box zinc finger (KZNF) protein family, a class of transcriptional repressors important for epigenetic silencing of specific genomic regions. About 170 primate-specific KZNFs are present in the human genome. Although KZNFs are primarily associated with repressing retrotransposon-derived DNA, evidence is emerging that they can be co-opted for other gene regulatory processes. We show that genetic deletion of ZNF675 causes developmental defects in cortical organoids, and our data suggest that part of the observed neurodevelopmental phenotype is mediated by a gene regulatory role of ZNF675 on the promoter of the neurodevelopmental gene Hes family BHLH transcription factor 1 (HES1). We also find evidence for the recently evolved regulation of genes involved in neurological disorders, microcephalin 1 and sestrin 3. We show that ZNF675 interferes with HES1 auto-inhibition, a process essential for the maintenance of neural progenitors. As a striking example of how some KZNFs have integrated into preexisting gene expression networks, these findings suggest the emergence of ZNF675 has caused a change in the balance of HES1 autoregulation. The association of ZNF675 CNV with human developmental disorders and ZNF675-mediated regulation of neurodevelopmental genes suggests that it evolved into an important factor for human brain development.
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Affiliation(s)
- Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthijs de Geus
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Rita L F P Guimarães
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, Evolutionary Neurogenomics, University of Amsterdam, Amsterdam, The Netherlands
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4
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Ham L, Coomer MA, Öcal K, Grima R, Stumpf MPH. A stochastic vs deterministic perspective on the timing of cellular events. Nat Commun 2024; 15:5286. [PMID: 38902228 PMCID: PMC11190182 DOI: 10.1038/s41467-024-49624-z] [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: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Cells are the fundamental units of life, and like all life forms, they change over time. Changes in cell state are driven by molecular processes; of these many are initiated when molecule numbers reach and exceed specific thresholds, a characteristic that can be described as "digital cellular logic". Here we show how molecular and cellular noise profoundly influence the time to cross a critical threshold-the first-passage time-and map out scenarios in which stochastic dynamics result in shorter or longer average first-passage times compared to noise-less dynamics. We illustrate the dependence of the mean first-passage time on noise for a set of exemplar models of gene expression, auto-regulatory feedback control, and enzyme-mediated catalysis. Our theory provides intuitive insight into the origin of these effects and underscores two important insights: (i) deterministic predictions for cellular event timing can be highly inaccurate when molecule numbers are within the range known for many cells; (ii) molecular noise can significantly shift mean first-passage times, particularly within auto-regulatory genetic feedback circuits.
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Affiliation(s)
- Lucy Ham
- School of BioSciences, University of Melbourne, Parkville, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, Australia
| | - Megan A Coomer
- School of BioSciences, University of Melbourne, Parkville, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, Australia
| | - Kaan Öcal
- School of Informatics, University of Edinburgh, Edinburgh, UK
- School of BioSciences, University of Melbourne, Parkville, Australia
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Michael P H Stumpf
- School of BioSciences, University of Melbourne, Parkville, Australia.
- School of Mathematics and Statistics, University of Melbourne, Parkville, Australia.
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5
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Taylor A, Prasad A, Mueller RL. Amphibian Segmentation Clock Models Suggest How Large Genome and Cell Sizes Slow Developmental Rate. Integr Org Biol 2024; 6:obae021. [PMID: 39006893 PMCID: PMC11245677 DOI: 10.1093/iob/obae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/20/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Evolutionary increases in genome size, cell volume, and nuclear volume have been observed across the tree of life, with positive correlations documented between all three traits. Developmental tempo slows as genomes, nuclei, and cells increase in size, yet the driving mechanisms are poorly understood. To bridge this gap, we use a mathematical model of the somitogenesis clock to link slowed developmental tempo with changes in intra-cellular gene expression kinetics induced by increasing genome size and nuclear volume. We adapt a well-known somitogenesis clock model to two model amphibian species that vary 10-fold in genome size: Xenopus laevis (3.1 Gb) and Ambystoma mexicanum (32 Gb). Based on simulations and backed by analytical derivations, we identify parameter changes originating from increased genome and nuclear size that slow gene expression kinetics. We simulate biological scenarios for which these parameter changes mathematically recapitulate slowed gene expression in A. mexicanum relative to X. laevis, and we consider scenarios for which additional alterations in gene product stability and chromatin packing are necessary. Results suggest that slowed degradation rates as well as changes induced by increasing nuclear volume and intron length, which remain relatively unexplored, are significant drivers of slowed developmental tempo.
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Affiliation(s)
- A Taylor
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - A Prasad
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - R Lockridge Mueller
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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6
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Barton A, Sesin P, Diambra L. Simplifications and approximations in a single-gene circuit modeling. Sci Rep 2024; 14:12498. [PMID: 38822072 PMCID: PMC11143231 DOI: 10.1038/s41598-024-63265-8] [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] [Received: 01/30/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024] Open
Abstract
The absence of detailed knowledge about regulatory interactions makes the use of phenomenological assumptions mandatory in cell biology modeling. Furthermore, the challenges associated with the analysis of these models compel the implementation of mathematical approximations. However, the constraints these methods introduce to biological interpretation are sometimes neglected. Consequently, understanding these restrictions is a very important task for systems biology modeling. In this article, we examine the impact of such simplifications, taking the case of a single-gene autoinhibitory circuit; however, our conclusions are not limited solely to this instance. We demonstrate that models grounded in the same biological assumptions but described at varying levels of detail can lead to different outcomes, that is, different and contradictory phenotypes or behaviors. Indeed, incorporating specific molecular processes like translation and elongation into the model can introduce instabilities and oscillations not seen when these processes are assumed to be instantaneous. Furthermore, incorporating a detailed description of promoter dynamics, usually described by a phenomenological regulatory function, can lead to instability, depending on the cooperative binding mechanism that is acting. Consequently, although the use of a regulating function facilitates model analysis, it may mask relevant aspects of the system's behavior. In particular, we observe that the two cooperative binding mechanisms, both compatible with the same sigmoidal function, can lead to different phenotypes, such as transcriptional oscillations with different oscillation frequencies.
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Affiliation(s)
- Alejandro Barton
- Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Pablo Sesin
- Departamento de Física Teórica, GAIDI, Comisión Nacional de Energía Atómica, 1429, Buenos Aires, Argentina
| | - Luis Diambra
- Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, La Plata, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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7
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Doostdar P, Hawley J, Chopra K, Marinopoulou E, Lea R, Arashvand K, Biga V, Papalopulu N, Soto X. Cell coupling compensates for changes in single-cell Her6 dynamics and provides phenotypic robustness. Development 2024; 151:dev202640. [PMID: 38682303 PMCID: PMC11190438 DOI: 10.1242/dev.202640] [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: 12/20/2023] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
This paper investigates the effect of altering the protein expression dynamics of the bHLH transcription factor Her6 at the single-cell level in the embryonic zebrafish telencephalon. Using a homozygote endogenous Her6:Venus reporter and 4D single-cell tracking, we show that Her6 oscillates in neural telencephalic progenitors and that the fusion of protein destabilisation (PEST) domain alters its expression dynamics, causing most cells to downregulate Her6 prematurely. However, counterintuitively, oscillatory cells increase, with some expressing Her6 at high levels, resulting in increased heterogeneity of Her6 expression in the population. These tissue-level changes appear to be an emergent property of coupling between single-cells, as revealed by experimentally disrupting Notch signalling and by computationally modelling alterations in Her6 protein stability. Despite the profound differences in the single-cell Her6 dynamics, the size of the telencephalon is only transiently altered and differentiation markers do not exhibit significant differences early on; however, a small increase is observed at later developmental stages. Our study suggests that cell coupling provides a compensation strategy, whereby an almost normal phenotype is maintained even though single-cell gene expression dynamics are abnormal, granting phenotypic robustness.
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Affiliation(s)
- Parnian Doostdar
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health,The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Joshua Hawley
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health,The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Kunal Chopra
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health,The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Elli Marinopoulou
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health,The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Robert Lea
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health,The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Kiana Arashvand
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Veronica Biga
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health,The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Nancy Papalopulu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health,The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Ximena Soto
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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8
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Chandel AS, Keseroglu K, Özbudak EM. Oscillatory control of embryonic development. Development 2024; 151:dev202191. [PMID: 38727565 PMCID: PMC11128281 DOI: 10.1242/dev.202191] [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] [Indexed: 05/28/2024]
Abstract
Proper embryonic development depends on the timely progression of a genetic program. One of the key mechanisms for achieving precise control of developmental timing is to use gene expression oscillations. In this Review, we examine how gene expression oscillations encode temporal information during vertebrate embryonic development by discussing the gene expression oscillations occurring during somitogenesis, neurogenesis, myogenesis and pancreas development. These oscillations play important but varied physiological functions in different contexts. Oscillations control the period of somite formation during somitogenesis, whereas they regulate the proliferation-to-differentiation switch of stem cells and progenitor cells during neurogenesis, myogenesis and pancreas development. We describe the similarities and differences of the expression pattern in space (i.e. whether oscillations are synchronous or asynchronous across neighboring cells) and in time (i.e. different time scales) of mammalian Hes/zebrafish Her genes and their targets in different tissues. We further summarize experimental evidence for the functional role of their oscillations. Finally, we discuss the outstanding questions for future research.
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Affiliation(s)
- Angad Singh Chandel
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Kemal Keseroglu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ertuğrul M. Özbudak
- 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 45229, USA
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9
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Mulas C. Control of cell state transitions by post-transcriptional regulation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230050. [PMID: 38432322 PMCID: PMC10909504 DOI: 10.1098/rstb.2023.0050] [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] [Received: 07/17/2023] [Accepted: 12/19/2023] [Indexed: 03/05/2024] Open
Abstract
Cell state transitions are prevalent in biology, playing a fundamental role in development, homeostasis and repair. Dysregulation of cell state transitions can lead to or occur in a wide range of diseases. In this letter, I explore and highlight the role of post-transcriptional regulatory mechanisms in determining the dynamics of cell state transitions. I propose that regulation of protein levels after transcription provides an under-appreciated regulatory route to obtain fast and sharp transitions between distinct cell states. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Carla Mulas
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, CB21 6GP, UK
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10
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Lázaro J, Sochacki J, Ebisuya M. The stem cell zoo for comparative studies of developmental tempo. Curr Opin Genet Dev 2024; 84:102149. [PMID: 38199063 PMCID: PMC10882223 DOI: 10.1016/j.gde.2023.102149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024]
Abstract
The rate of development is highly variable across animal species. However, the mechanisms regulating developmental tempo have remained elusive due to difficulties in performing direct interspecies comparisons. Here, we discuss how pluripotent stem cell-based models of development can be used to investigate cell- and tissue-autonomous temporal processes. These systems enable quantitative comparisons of different animal species under similar experimental conditions. Moreover, the constantly growing stem cell zoo collection allows the extension of developmental studies to a great number of unconventional species. We argue that the stem cell zoo constitutes a powerful platform to perform comparative studies of developmental tempo, as well as to study other forms of biological time control such as species-specific lifespan, heart rate, and circadian clocks.
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Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany. https://twitter.com/@JorgeLazaroF
| | - Jaroslaw Sochacki
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany.
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11
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Ramesh PS, Chu LF. Species-specific roles of the Notch ligands, receptors, and targets orchestrating the signaling landscape of the segmentation clock. Front Cell Dev Biol 2024; 11:1327227. [PMID: 38348091 PMCID: PMC10859470 DOI: 10.3389/fcell.2023.1327227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 02/15/2024] Open
Abstract
Somitogenesis is a hallmark feature of all vertebrates and some invertebrate species that involves the periodic formation of block-like structures called somites. Somites are transient embryonic segments that eventually establish the entire vertebral column. A highly conserved molecular oscillator called the segmentation clock underlies this periodic event and the pace of this clock regulates the pace of somite formation. Although conserved signaling pathways govern the clock in most vertebrates, the mechanisms underlying the species-specific divergence in various clock characteristics remain elusive. For example, the segmentation clock in classical model species such as zebrafish, chick, and mouse embryos tick with a periodicity of ∼30, ∼90, and ∼120 min respectively. This enables them to form the species-specific number of vertebrae during their overall timespan of somitogenesis. Here, we perform a systematic review of the species-specific features of the segmentation clock with a keen focus on mouse embryos. We perform this review using three different perspectives: Notch-responsive clock genes, ligand-receptor dynamics, and synchronization between neighboring oscillators. We further review reports that use non-classical model organisms and in vitro model systems that complement our current understanding of the segmentation clock. Our review highlights the importance of comparative developmental biology to further our understanding of this essential developmental process.
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Affiliation(s)
- Pranav S. Ramesh
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Calgary, AB, Canada
| | - Li-Fang Chu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Calgary, AB, Canada
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12
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McDaniel C, Simsek MF, Chandel AS, Özbudak EM. Spatiotemporal control of pattern formation during somitogenesis. SCIENCE ADVANCES 2024; 10:eadk8937. [PMID: 38277458 PMCID: PMC10816718 DOI: 10.1126/sciadv.adk8937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Spatiotemporal patterns widely occur in biological, chemical, and physical systems. Particularly, embryonic development displays a diverse gamut of repetitive patterns established in many tissues and organs. Branching treelike structures in lungs, kidneys, livers, pancreases, and mammary glands as well as digits and bones in appendages, teeth, and palates are just a few examples. A fascinating instance of repetitive patterning is the sequential segmentation of the primary body axis, which is conserved in all vertebrates and many arthropods and annelids. In these species, the body axis elongates at the posterior end of the embryo containing an unsegmented tissue. Meanwhile, segments sequentially bud off from the anterior end of the unsegmented tissue, laying down an exquisite repetitive pattern and creating a segmented body plan. In vertebrates, the paraxial mesoderm is sequentially divided into somites. In this review, we will discuss the most prominent models, the most puzzling experimental data, and outstanding questions in vertebrate somite segmentation.
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Affiliation(s)
- Cassandra McDaniel
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - M. Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Angad Singh Chandel
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ertuğrul M. Özbudak
- 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 45229, USA
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13
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Abstract
Organismal development requires the reproducible unfolding of an ordered sequence of discrete steps (cell fate determination, migration, tissue folding, etc.) in both time and space. Here, we review the mechanisms that grant temporal specificity to developmental steps, including molecular clocks and timers. Individual timing mechanisms must be coordinated with each other to maintain the overall developmental sequence. However, phenotypic novelties can also arise through the modification of temporal patterns over the course of evolution. Two main types of variation in temporal patterning characterize interspecies differences in developmental time: allochrony, where the overall developmental sequence is either accelerated or slowed down while maintaining the relative duration of individual steps, and heterochrony, where the duration of specific developmental steps is altered relative to the rest. New advances in in vitro modeling of mammalian development using stem cells have recently enabled the revival of mechanistic studies of allochrony and heterochrony. In both cases, differences in the rate of basic cellular functions such as splicing, translation, protein degradation, and metabolism seem to underlie differences in developmental time. In the coming years, these studies should identify the genetic differences that drive divergence in developmental time between species.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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14
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Simsek MF, Özbudak EM. A design logic for sequential segmentation across organisms. FEBS J 2023; 290:5086-5093. [PMID: 37422856 PMCID: PMC10774455 DOI: 10.1111/febs.16899] [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: 04/19/2023] [Revised: 05/24/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Multitudes of organisms display metameric compartmentalization of their body plan. Segmentation of these compartments happens sequentially in diverse phyla. In several sequentially segmenting species, periodically active molecular clocks and signaling gradients have been found. The clocks are proposed to control the timing of segmentation, while the gradients are proposed to instruct the positions of segment boundaries. However, the identity of the clock and gradient molecules differs across species. Furthermore, sequential segmentation of a basal chordate, Amphioxus, continues at late stages when the small tail bud cell population cannot establish long-range signaling gradients. Thus, it remains to be explained how a conserved morphological trait (i.e., sequential segmentation) is achieved by using different molecules or molecules with different spatial profiles. Here, we first focus on sequential segmentation of somites in vertebrate embryos and then draw parallels with other species. Thereafter, we propose a candidate design principle that has the potential to answer this puzzling question.
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Affiliation(s)
- M Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Ertuğrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, OH, USA
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15
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Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, Petkov S, Behr R, Trivedi V, Matsuda M, Ebisuya M. A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals. Cell Stem Cell 2023; 30:938-949.e7. [PMID: 37343565 PMCID: PMC10321541 DOI: 10.1016/j.stem.2023.05.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Differential speeds in biochemical reactions have been proposed to be responsible for the differences in developmental tempo between mice and humans. However, the underlying mechanism controlling the species-specific kinetics remains to be determined. Using in vitro differentiation of pluripotent stem cells, we recapitulated the segmentation clocks of diverse mammalian species varying in body weight and taxa: marmoset, rabbit, cattle, and rhinoceros. Together with mouse and human, the segmentation clock periods of the six species did not scale with the animal body weight, but with the embryogenesis length. The biochemical kinetics of the core clock gene HES7 displayed clear scaling with the species-specific segmentation clock period. However, the cellular metabolic rates did not show an evident correlation. Instead, genes involving biochemical reactions showed an expression pattern that scales with the segmentation clock period. Altogether, our stem cell zoo uncovered general scaling laws governing species-specific developmental tempo.
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Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Maria Costanzo
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marina Sanaki-Matsumiya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Masafumi Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Katsuhiko Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Sebastian Diecke
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | | | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Stoyan Petkov
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Vikas Trivedi
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Mitsuhiro Matsuda
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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16
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Roth G, Misailidis G, Pappa M, Ferralli J, Tsiairis CD. Unidirectional and phase-gated signaling synchronizes murine presomitic mesoderm cells. Dev Cell 2023:S1534-5807(23)00155-7. [PMID: 37098349 DOI: 10.1016/j.devcel.2023.04.002] [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: 03/17/2022] [Revised: 01/06/2023] [Accepted: 04/01/2023] [Indexed: 04/27/2023]
Abstract
Oscillator systems achieve synchronization when oscillators are coupled. The presomitic mesoderm is a system of cellular oscillators, where coordinated genetic activity is necessary for proper periodic generation of somites. While Notch signaling is required for the synchronization of these cells, it is unclear what information the cells exchange and how they react to this information to align their oscillatory pace with that of their neighbors. Combining mathematical modeling and experimental data, we found that interaction between murine presomitic mesoderm cells is controlled by a phase-gated and unidirectional coupling mechanism and results in deceleration of their oscillation pace upon Notch signaling. This mechanism predicts that isolated populations of well-mixed cells synchronize, revealing a stereotypical synchronization in the mouse PSM and contradicting expectations from previously applied theoretical approaches. Collectively, our theoretical and experimental findings reveal the underlying coupling mechanisms of the presomitic mesoderm cells and provide a framework to quantitatively characterize their synchronization.
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Affiliation(s)
- Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Georgios Misailidis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Maria Pappa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Jacqueline Ferralli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Charisios D Tsiairis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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17
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Kent MR, Calderon D, Silvius KM, Kucinski JP, LaVigne CA, Cannon MV, Kendall GC. Zebrafish her3 knockout impacts developmental and cancer-related gene signatures. Dev Biol 2023; 496:1-14. [PMID: 36696714 PMCID: PMC10054701 DOI: 10.1016/j.ydbio.2023.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/24/2023]
Abstract
HES3 is a basic helix-loop-helix transcription factor that regulates neural stem cell renewal during development. HES3 overexpression is predictive of reduced overall survival in patients with fusion-positive rhabdomyosarcoma, a pediatric cancer that resembles immature and undifferentiated skeletal muscle. However, the mechanisms of HES3 cooperation in fusion-positive rhabdomyosarcoma are unclear and are likely related to her3/HES3's role in neurogenesis. To investigate HES3's function during development, we generated a zebrafish CRISPR/Cas9 null mutation of her3, the zebrafish ortholog of HES3. Loss of her3 is not embryonic lethal and adults exhibit expected Mendelian ratios. Embryonic her3 zebrafish mutants exhibit dysregulated neurog1 expression, a her3 target gene, and the mutant her3 fails to bind the neurog1 promoter sequence. Further, her3 mutants are significantly smaller than wildtype and a subset present with lens defects as adults. Transcriptomic analysis of her3 mutant embryos indicates that genes involved in organ development, such as pctp and grinab, are significantly downregulated. Further, differentially expressed genes in her3 null mutant embryos are enriched for Hox and Sox10 motifs. Several cancer-related gene pathways are impacted, including the inhibition of matrix metalloproteinases. Altogether, this new model is a powerful system to study her3/HES3-mediated neural development and its misappropriation in cancer contexts.
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Affiliation(s)
- Matthew R Kent
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Delia Calderon
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA; Molecular, Cellular, and Developmental Biology Ph.D. Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Katherine M Silvius
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Jack P Kucinski
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA; Molecular, Cellular, and Developmental Biology Ph.D. Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Collette A LaVigne
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Matthew V Cannon
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Genevieve C Kendall
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA; Molecular, Cellular, and Developmental Biology Ph.D. Program, The Ohio State University, Columbus, OH, 43210, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.
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18
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Kageyama R, Isomura A, Shimojo H. Biological Significance of the Coupling Delay in Synchronized Oscillations. Physiology (Bethesda) 2023; 38:0. [PMID: 36256636 DOI: 10.1152/physiol.00023.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The significance of the coupling delay, which is the time required for interactions between coupled oscillators, in various oscillatory dynamics has been investigated mathematically for more than three decades, but its biological significance has been revealed only recently. In the segmentation clock, which regulates the periodic formation of somites in embryos, Hes7 expression oscillates synchronously between neighboring presomitic mesoderm (PSM) cells, and this synchronized oscillation is controlled by Notch signaling-mediated coupling between PSM cells. Recent studies have shown that inappropriate coupling delays dampen and desynchronize Hes7 oscillations, as simulated mathematically, leading to the severe fusion of somites and somite-derived tissues such as the vertebrae and ribs. These results indicate the biological significance of the coupling delay in synchronized Hes7 oscillations in the segmentation clock. The recent development of an in vitro PSM-like system will facilitate the detailed analysis of the coupling delay in synchronized oscillations.
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Affiliation(s)
- Ryoichiro Kageyama
- RIKEN Center for Brain Science, Wako, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Kyoto University Graduate School of Medicine, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Akihiro Isomura
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Hiromi Shimojo
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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19
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Blatnik MC, Gallagher TL, Amacher SL. Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1751. [PMID: 35851751 PMCID: PMC9840655 DOI: 10.1002/wrna.1751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 01/31/2023]
Abstract
Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.
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Affiliation(s)
- Monica C. Blatnik
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Thomas L. Gallagher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Sharon L. Amacher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
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20
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Carraco G, Martins-Jesus AP, Andrade RP. The vertebrate Embryo Clock: Common players dancing to a different beat. Front Cell Dev Biol 2022; 10:944016. [PMID: 36036002 PMCID: PMC9403190 DOI: 10.3389/fcell.2022.944016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
Vertebrate embryo somitogenesis is the earliest morphological manifestation of the characteristic patterned structure of the adult axial skeleton. Pairs of somites flanking the neural tube are formed periodically during early development, and the molecular mechanisms in temporal control of this early patterning event have been thoroughly studied. The discovery of a molecular Embryo Clock (EC) underlying the periodicity of somite formation shed light on the importance of gene expression dynamics for pattern formation. The EC is now known to be present in all vertebrate organisms studied and this mechanism was also described in limb development and stem cell differentiation. An outstanding question, however, remains unanswered: what sets the different EC paces observed in different organisms and tissues? This review aims to summarize the available knowledge regarding the pace of the EC, its regulation and experimental manipulation and to expose new questions that might help shed light on what is still to unveil.
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Affiliation(s)
- Gil Carraco
- ABC-RI, Algarve Biomedical Center Research Institute, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | | | - Raquel P. Andrade
- ABC-RI, Algarve Biomedical Center Research Institute, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, Lisbon, Portugal
- *Correspondence: Raquel P. Andrade,
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21
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Falk HJ, Tomita T, Mönke G, McDole K, Aulehla A. Imaging the onset of oscillatory signaling dynamics during mouse embryo gastrulation. Development 2022; 149:275659. [PMID: 35686648 PMCID: PMC9340547 DOI: 10.1242/dev.200083] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/25/2022] [Indexed: 01/24/2023]
Abstract
A fundamental requirement for embryonic development is the coordination of signaling activities in space and time. A notable example in vertebrate embryos is found during somitogenesis, where gene expression oscillations linked to the segmentation clock are synchronized across cells in the presomitic mesoderm (PSM) and result in tissue-level wave patterns. To examine their onset during mouse embryo development, we studied the dynamics of the segmentation clock gene Lfng during gastrulation. To this end, we established an imaging setup using selective plane illumination microscopy (SPIM) that enables culture and simultaneous imaging of up to four embryos (‘SPIM- for-4’). Using SPIM-for-4, combined with genetically encoded signaling reporters, we detected the onset of Lfng oscillations within newly formed mesoderm at presomite stages. Functionally, we found that initial synchrony and the first ∼6-8 oscillation cycles occurred even when Notch signaling was impaired, revealing similarities to previous findings made in zebrafish embryos. Finally, we show that a spatial period gradient is present at the onset of oscillatory activity, providing a potential mechanism accounting for our observation that wave patterns build up gradually over the first oscillation cycles. Summary: A versatile light-sheet imaging setup enabling simultaneous live imaging of multiple mouse embryos for 48 h, an approach that offers insight into the onset of oscillatory signaling dynamics and the segmentation clock.
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Affiliation(s)
- Henning J Falk
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Takehito Tomita
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gregor Mönke
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Katie McDole
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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22
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Abstract
Tight spatiotemporal control of cellular behavior and cell fate decisions is paramount to the formation of multicellular organisms during embryonic development. Intercellular communication via signaling pathways mediates this control. Interestingly, these signaling pathways are not static, but dynamic and change in activity over time. Signaling oscillations as a specific type of dynamics are found in various signaling pathways and model systems. Functions of oscillations include the regulation of periodic events or the transmission of information by encoding signals in the dynamic properties of a signaling pathway. For instance, signaling oscillations in neural or pancreatic progenitor cells modulate their proliferation and differentiation. Oscillations between neighboring cells can also be synchronized, leading to the emergence of waves traveling through the tissue. Such population-wide signaling oscillations regulate for example the consecutive segmentation of vertebrate embryos, a process called somitogenesis. Here, we outline our current understanding of signaling oscillations in embryonic development, how signaling oscillations are generated, how they are studied and how they contribute to the regulation of embryonic development.
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23
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Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nat Genet 2022; 54:328-341. [PMID: 35288709 PMCID: PMC8920898 DOI: 10.1038/s41588-022-01018-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells expressing a panoply of molecular programs. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here, we set out to integrate several single-cell RNA-sequencing (scRNA-seq) datasets that collectively span mouse gastrulation and organogenesis, supplemented with new profiling of ~150,000 nuclei from approximately embryonic day 8.5 (E8.5) embryos staged in one-somite increments. Overall, we define cell states at each of 19 successive stages spanning E3.5 to E13.5 and heuristically connect them to their pseudoancestors and pseudodescendants. Although constructed through automated procedures, the resulting directed acyclic graph (TOME (trajectories of mammalian embryogenesis)) is largely consistent with our contemporary understanding of mammalian development. We leverage TOME to systematically nominate transcription factors (TFs) as candidate regulators of each cell type's specification, as well as 'cell-type homologs' across vertebrate evolution.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Junyue Cao
- The Rockefeller University, New York, NY, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Christine M Disteche
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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24
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Essay the (unusual) heuristic value of Hox gene clusters; a matter of time? Dev Biol 2022; 484:75-87. [PMID: 35182536 DOI: 10.1016/j.ydbio.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022]
Abstract
Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.
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25
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Sanaki-Matsumiya M, Kageyama R. Time-Lapse Bioluminescence Imaging of Hes7 Expression In Vitro and Ex Vivo. Methods Mol Biol 2022; 2525:321-332. [PMID: 35836080 DOI: 10.1007/978-1-0716-2473-9_25] [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: 06/15/2023]
Abstract
Somites are formed sequentially by the segmentation of the anterior parts of the presomitic mesoderm (PSM), and such periodical somite formation is crucial to ensure the proper vertebrae. In the mouse embryo, Hes7, a segmentation clock gene, controls this periodic event with new somites forming every 2 h. Hes7 oscillations are synchronized between neighboring PSM cells and propagate from the posterior to the anterior PSM in the form of traveling waves. However, the exact mechanisms that generate these oscillatory dynamics and control synchronization are still unclear. Given that the half-life of Hes7 is too short to be monitored with most fluorescent proteins, time-lapse bioluminescence imaging (BLI) is a suitable tool to monitor the chronological Hes7 expression dynamics. In this chapter, we introduce a ubiquitinated luciferase reporter which enables the visualization of Hes7 expression dynamics with high temporal and spatial resolution in living cells and tissues.
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Affiliation(s)
- Marina Sanaki-Matsumiya
- European Molecular Biology Laboratory (EMBL), Barcelona, Spain.
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.
- RIKEN Center for Brain Science, Wako, Japan.
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26
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Signalling dynamics in embryonic development. Biochem J 2021; 478:4045-4070. [PMID: 34871368 PMCID: PMC8718268 DOI: 10.1042/bcj20210043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023]
Abstract
In multicellular organisms, cellular behaviour is tightly regulated to allow proper embryonic development and maintenance of adult tissue. A critical component in this control is the communication between cells via signalling pathways, as errors in intercellular communication can induce developmental defects or diseases such as cancer. It has become clear over the last years that signalling is not static but varies in activity over time. Feedback mechanisms present in every signalling pathway lead to diverse dynamic phenotypes, such as transient activation, signal ramping or oscillations, occurring in a cell type- and stage-dependent manner. In cells, such dynamics can exert various functions that allow organisms to develop in a robust and reproducible way. Here, we focus on Erk, Wnt and Notch signalling pathways, which are dynamic in several tissue types and organisms, including the periodic segmentation of vertebrate embryos, and are often dysregulated in cancer. We will discuss how biochemical processes influence their dynamics and how these impact on cellular behaviour within multicellular systems.
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27
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Differential phase register of Hes1 oscillations with mitoses underlies cell-cycle heterogeneity in ER + breast cancer cells. Proc Natl Acad Sci U S A 2021; 118:2113527118. [PMID: 34725165 PMCID: PMC8609326 DOI: 10.1073/pnas.2113527118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/08/2021] [Indexed: 12/14/2022] Open
Abstract
Tumors exhibit heterogeneities that are not due to mutations, including cancer stem cells with different potencies. We show that the cancer stem-cell state predisposed to dormancy in vivo has a highly variable and long cell cycle. Using single-cell live imaging for the transcriptional repressor Hes1 (a key molecule in cancer), we show a type of circadian-like oscillatory expression of Hes1 in all cells in the population. The most potent cancer stem cells tend to divide around the trough of the Hes1 oscillatory wave, a feature predictive of a long cell cycle. A concept proposed here is that the position of cell division with respect to the Hes1 wave is predictive of its prospective cell-cycle length and cancer cellular substate. Here, we study the dynamical expression of endogenously labeled Hes1, a transcriptional repressor implicated in controlling cell proliferation, to understand how cell-cycle length heterogeneity is generated in estrogen receptor (ER)+ breast cancer cells. We find that Hes1 shows oscillatory expression with ∼25 h periodicity and during each cell cycle has a variable peak in G1, a trough around G1–S transition, and a less variable second peak in G2/M. Compared to other subpopulations, the cell cycle in CD44HighCD24Low cancer stem cells is longest and most variable. Most cells divide around the peak of the Hes1 expression wave, but preceding mitoses in slow dividing CD44HighCD24Low cells appear phase-shifted, resulting in a late-onset Hes1 peak in G1. The position, duration, and shape of this peak, rather than the Hes1 expression levels, are good predictors of cell-cycle length. Diminishing Hes1 oscillations by enforcing sustained expression slows down the cell cycle, impairs proliferation, abolishes the dynamic expression of p21, and increases the percentage of CD44HighCD24Low cells. Reciprocally, blocking the cell cycle causes an elongation of Hes1 periodicity, suggesting a bidirectional interaction of the Hes1 oscillator and the cell cycle. We propose that Hes1 oscillations are functionally important for the efficient progression of the cell cycle and that the position of mitosis in relation to the Hes1 wave underlies cell-cycle length heterogeneity in cancer cell subpopulations.
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28
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Abstract
Arthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include: (i) the mechanistic origins of spatial organization within the segment addition zone (SAZ); (ii) the mechanistic origins of segment polarization; (iii) the mechanistic origins of axial variation; and (iv) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an 'oscillator', a 'switch' and up to three 'timers', successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarizing oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.
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Affiliation(s)
- Erik Clark
- Department of Systems Biology, Harvard Medical School, 210 Longwood Ave, Boston, MA 02115, USA
- Trinity College Cambridge, University of Cambridge, Trinity Street, Cambridge CB2 1TQ, UK
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29
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Uriu K, Liao BK, Oates AC, Morelli LG. From local resynchronization to global pattern recovery in the zebrafish segmentation clock. eLife 2021; 10:61358. [PMID: 33587039 PMCID: PMC7984840 DOI: 10.7554/elife.61358] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/27/2021] [Indexed: 01/26/2023] Open
Abstract
Integrity of rhythmic spatial gene expression patterns in the vertebrate segmentation clock requires local synchronization between neighboring cells by Delta-Notch signaling and its inhibition causes defective segment boundaries. Whether deformation of the oscillating tissue complements local synchronization during patterning and segment formation is not understood. We combine theory and experiment to investigate this question in the zebrafish segmentation clock. We remove a Notch inhibitor, allowing resynchronization, and analyze embryonic segment recovery. We observe unexpected intermingling of normal and defective segments, and capture this with a new model combining coupled oscillators and tissue mechanics. Intermingled segments are explained in the theory by advection of persistent phase vortices of oscillators. Experimentally observed changes in recovery patterns are predicted in the theory by temporal changes in tissue length and cell advection pattern. Thus, segmental pattern recovery occurs at two length and time scales: rapid local synchronization between neighboring cells, and the slower transport of the resulting patterns across the tissue through morphogenesis.
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Affiliation(s)
- Koichiro Uriu
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Bo-Kai Liao
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan.,Department of Cell and Developmental Biology, University College London, Gower Street, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrew C Oates
- Department of Cell and Developmental Biology, University College London, Gower Street, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Institute of Bioengineering, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Luis G Morelli
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Polo Científico Tecnológico, Buenos Aires, Argentina.,Departamento de Física, FCEyN UBA, Ciudad Universitaria, Buenos Aires, Argentina.,Max Planck Institute for Molecular Physiology, Department of Systemic Cell Biology, Dortmund, Germany
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30
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Nóbrega A, Maia-Fernandes AC, Andrade RP. Altered Cogs of the Clock: Insights into the Embryonic Etiology of Spondylocostal Dysostosis. J Dev Biol 2021; 9:5. [PMID: 33572886 PMCID: PMC7930992 DOI: 10.3390/jdb9010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 01/23/2023] Open
Abstract
Spondylocostal dysostosis (SCDO) is a rare heritable congenital condition, characterized by multiple severe malformations of the vertebrae and ribs. Great advances were made in the last decades at the clinical level, by identifying the genetic mutations underlying the different forms of the disease. These were matched by extraordinary findings in the Developmental Biology field, which elucidated the cellular and molecular mechanisms involved in embryo body segmentation into the precursors of the axial skeleton. Of particular relevance was the discovery of the somitogenesis molecular clock that controls the progression of somite boundary formation over time. An overview of these concepts is presented, including the evidence obtained from animal models on the embryonic origins of the mutant-dependent disease. Evidence of an environmental contribution to the severity of the disease is discussed. Finally, a brief reference is made to emerging in vitro models of human somitogenesis which are being employed to model the molecular and cellular events occurring in SCDO. These represent great promise for understanding this and other human diseases and for the development of more efficient therapeutic approaches.
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Affiliation(s)
- Ana Nóbrega
- CBMR, Centre for Biomedical Research, Universidade do Algarve, 8005-139 Faro, Portugal; (A.N.); (A.C.M.-F.)
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Ana C. Maia-Fernandes
- CBMR, Centre for Biomedical Research, Universidade do Algarve, 8005-139 Faro, Portugal; (A.N.); (A.C.M.-F.)
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Raquel P. Andrade
- CBMR, Centre for Biomedical Research, Universidade do Algarve, 8005-139 Faro, Portugal; (A.N.); (A.C.M.-F.)
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- ABC-RI, Algarve Biomedical Center Research Institute, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
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31
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Matsuda M, Hayashi H, Garcia-Ojalvo J, Yoshioka-Kobayashi K, Kageyama R, Yamanaka Y, Ikeya M, Toguchida J, Alev C, Ebisuya M. Species-specific segmentation clock periods are due to differential biochemical reaction speeds. Science 2020; 369:1450-1455. [PMID: 32943519 DOI: 10.1126/science.aba7668] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Although mechanisms of embryonic development are similar between mice and humans, the time scale is generally slower in humans. To investigate these interspecies differences in development, we recapitulate murine and human segmentation clocks that display 2- to 3-hour and 5- to 6-hour oscillation periods, respectively. Our interspecies genome-swapping analyses indicate that the period difference is not due to sequence differences in the HES7 locus, the core gene of the segmentation clock. Instead, we demonstrate that multiple biochemical reactions of HES7, including the degradation and expression delays, are slower in human cells than they are in mouse cells. With the measured biochemical parameters, our mathematical model accounts for the two- to threefold period difference between the species. We propose that cell-autonomous differences in biochemical reaction speeds underlie temporal differences in development between species.
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Affiliation(s)
- Mitsuhiro Matsuda
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047 Kobe, Japan.,European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Hanako Hayashi
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047 Kobe, Japan
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Kumiko Yoshioka-Kobayashi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, 606-8507 Kyoto, Japan
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, 606-8507 Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, 606-8501 Kyoto, Japan
| | - Yoshihiro Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, 606-8507 Kyoto, Japan.,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, 606-8501 Kyoto, Japan
| | - Makoto Ikeya
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, 606-8507 Kyoto, Japan
| | - Junya Toguchida
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, 606-8507 Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, 606-8507 Kyoto, Japan
| | - Cantas Alev
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, 606-8507 Kyoto, Japan.,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, 606-8501 Kyoto, Japan
| | - Miki Ebisuya
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047 Kobe, Japan. .,European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
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32
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Likhoshvai VA, Golubyatnikov VP, Khlebodarova TM. Limit cycles in models of circular gene networks regulated by negative feedback loops. BMC Bioinformatics 2020; 21:255. [PMID: 32921311 PMCID: PMC7488683 DOI: 10.1186/s12859-020-03598-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal reception and its implementation, provide natural conditions for complicated dynamic regimes in these systems. The delay phenomenon at the intracellular level is a consequence of the matrix principle of data transmission, implemented through the rather complex processes of transcription and translation.However, the rules of the influence of system structure on system dynamics are not clearly understood. Knowledge of these rules is particularly important for construction of synthetic gene networks with predetermined properties. RESULTS We study dynamical properties of models of simplest circular gene networks regulated by negative feedback mechanisms. We have shown existence and stability of oscillating trajectories (cycles) in these models. Two algorithms of construction and localization of these cycles have been proposed. For one of these models, we have solved an inverse problem of parameters identification. CONCLUSIONS The modeling results demonstrate that non-stationary dynamics in the models of circular gene networks with negative feedback loops is achieved by a high degree of non-linearity of the mechanism of the autorepressor influence on its own expression, by the presence of regulatory signal delay, the value of which must exceed a certain critical value, and transcription/translation should be initiated from a sufficiently strong promoter/Shine-Dalgarno site. We believe that the identified patterns are key elements of the oscillating construction design.
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Affiliation(s)
- Vitaly A Likhoshvai
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch RAS, Novosibirsk, Russia
| | - Vladimir P Golubyatnikov
- Laboratory of Inverse Problems of Mathematical Physics, Sobolev Institute of Mathematics Siberian Branch RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | - Tamara M Khlebodarova
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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33
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Kim D, Choe HK, Kim K. Ultradian Rhythms in the Hypothalamic Arcuate Nucleus Kisspeptin Neurons and Developmental Processes. Mol Cells 2020; 43:600-606. [PMID: 32489185 PMCID: PMC7398798 DOI: 10.14348/molcells.2020.0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/22/2020] [Accepted: 05/11/2020] [Indexed: 11/27/2022] Open
Abstract
Numerous physiological processes in nature have multiple oscillations within 24 h, that is, ultradian rhythms. Compared to the circadian rhythm, which has a period of approximately one day, these short oscillations range from seconds to hours, and the mechanisms underlying ultradian rhythms remain largely unknown. This review aims to explore and emphasize the implications of ultradian rhythms and their underlying regulations. Reproduction and developmental processes show ultradian rhythms, and these physiological systems can be regulated by short biological rhythms. Specifically, we recently uncovered synchronized calcium oscillations in the organotypic culture of hypothalamic arcuate nucleus (ARN) kisspeptin neurons that regulate reproduction. Synchronized calcium oscillations were dependent on voltage-gated ion channel-mediated action potentials and were repressed by chemogenetic inhibition, suggesting that the network within the ARN and between the kisspeptin population mediates the oscillation. This minireview describes that ultradian rhythms are a general theme that underlies biological features, with special reference to calcium oscillations in the hypothalamic ARN from a developmental perspective. We expect that more attention to these oscillations might provide insight into physiological or developmental mechanisms, since many oscillatory features in nature still remain to be explored.
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Affiliation(s)
- Doyeon Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Kyungjin Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
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34
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Oates AC. Waiting on the Fringe: cell autonomy and signaling delays in segmentation clocks. Curr Opin Genet Dev 2020; 63:61-70. [PMID: 32505051 DOI: 10.1016/j.gde.2020.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022]
Abstract
The rhythmic and sequential segmentation of the vertebrate body axis into somites during embryogenesis is governed by a multicellular, oscillatory patterning system called the segmentation clock. Despite many overt similarities between vertebrates, differences in genetic and dynamic regulation have been reported, raising intriguing questions about the evolution and conservation of this fundamental patterning process. Recent studies have brought insights into two important and related issues: (1) whether individual cells of segmentation clocks are autonomous oscillators or require cell-cell communication for their rhythm; and (2) the role of delays in the cell-cell communication that synchronizes the population of genetic oscillators. Although molecular details differ between species, conservation may exist at the level of the dynamics, hinting at rules for evolutionary trajectories in the system.
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Affiliation(s)
- Andrew C Oates
- Institute of Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédéral de Lausanne (EPFL), CH-1015, Switzerland.
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35
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Venzin OF, Oates AC. What are you synching about? Emerging complexity of Notch signaling in the segmentation clock. Dev Biol 2020; 460:40-54. [DOI: 10.1016/j.ydbio.2019.06.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 10/26/2022]
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36
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Naoki H, Matsui T. Somite boundary determination in normal and clock-less vertebrate embryos. Dev Growth Differ 2020; 62:177-187. [PMID: 32108939 DOI: 10.1111/dgd.12655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/31/2020] [Accepted: 02/01/2020] [Indexed: 12/21/2022]
Abstract
Vertebrate segments called somites are generated by periodic segmentation of the presomitic mesoderm (PSM). In the most accepted theoretical model for somite segmentation, the clock and wavefront (CW) model, a clock that ticks to determine particular timings and a wavefront that moves posteriorly are presented in the PSM, and somite positions are determined when the clock meets the posteriorly moving wavefront somewhere in the PSM. Over the last two decades, it has been revealed that the molecular mechanism of the clock and wavefront in vertebrates is based on clock genes including Hes family transcription factors and Notch effectors that oscillate within the PSM to determine particular timings and fibroblast growth factor (FGF) gradients, acting as the posteriorly moving wavefront to determine the position of somite segmentation. A clock-less condition in the CW model was predicted to form no somites; however, irregularly sized somites were still formed in mice and zebrafish, suggesting that this was one of the limitations of the CW model. Recently, we performed interdisciplinary research of experimental and theoretical biological studies and revealed the mechanisms of somite boundary determination in normal and clock-less conditions by characterization of the FGF/extracellular signal-regulated kinase (ERK) activity dynamics. Since features of the molecular clock have already been described in-depth in several reviews, we summarized recent findings regarding the role of FGF/ERK signaling in somite boundary formation and described our current understanding of how FGF/ERK signaling contributes to somitogenesis in normal and clock-less conditions in this review.
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Affiliation(s)
- Honda Naoki
- Laboratory of Theoretical Biology, Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
| | - Takaaki Matsui
- Gene Regulation Research, Division of Biological Science, Nara Institute of Science and Technology, Takayama, Nara, Japan
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37
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Ochi S, Imaizumi Y, Shimojo H, Miyachi H, Kageyama R. Oscillatory expression of Hes1 regulates cell proliferation and neuronal differentiation in the embryonic brain. Development 2020; 147:dev182204. [PMID: 32094111 DOI: 10.1242/dev.182204] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/01/2020] [Indexed: 03/01/2024]
Abstract
The expression of the transcriptional repressor Hes1 oscillates in many cell types, including neural progenitor cells (NPCs), but the significance of Hes1 oscillations in development is not fully understood. To examine the effect of altered oscillatory dynamics of Hes1, we generated two types of Hes1 knock-in mice, a shortened (type-1) and an elongated (type-2) Hes1 gene, and examined their phenotypes focusing on neural development. Although both mutations affected Hes1 oscillations, the type-1 mutation dampened Hes1 oscillations more severely, resulting in much lower amplitudes. The average levels of Hes1 expression in type-1 mutant NPCs were also lower than in wild-type NPCs but similar to or slightly higher than those in Hes1 heterozygous mutant mice, which exhibit no apparent defects. Whereas type-2 mutant mice were apparently normal, type-1 mutant mice displayed smaller brains than wild-type mice and upregulated proneural gene expression. Furthermore, proliferation of NPCs decreased and cell death increased in type-1 mutant embryos. When Hes3 and Hes5 were additionally deleted, neuronal differentiation was also accelerated, leading to microcephaly. Thus, robust Hes1 oscillations are required for maintenance and proliferation of NPCs and the normal timing of neurogenesis, thereby regulating brain morphogenesis.
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Affiliation(s)
- Shohei Ochi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan
- Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Yui Imaizumi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiromi Shimojo
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hitoshi Miyachi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin-Kawahara, Sakyo-ku, Kyoto 606-8507, Japan
- Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
- Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8507, Japan
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38
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Coupling delay controls synchronized oscillation in the segmentation clock. Nature 2020; 580:119-123. [PMID: 31915376 DOI: 10.1038/s41586-019-1882-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/05/2019] [Indexed: 11/08/2022]
Abstract
Individual cellular activities fluctuate but are constantly coordinated at the population level via cell-cell coupling. A notable example is the somite segmentation clock, in which the expression of clock genes (such as Hes7) oscillates in synchrony between the cells that comprise the presomitic mesoderm (PSM)1,2. This synchronization depends on the Notch signalling pathway; inhibiting this pathway desynchronizes oscillations, leading to somite fusion3-7. However, how Notch signalling regulates the synchronicity of HES7 oscillations is unknown. Here we establish a live-imaging system using a new fluorescent reporter (Achilles), which we fuse with HES7 to monitor synchronous oscillations in HES7 expression in the mouse PSM at a single-cell resolution. Wild-type cells can rapidly correct for phase fluctuations in HES7 oscillations, whereas the absence of the Notch modulator gene lunatic fringe (Lfng) leads to a loss of synchrony between PSM cells. Furthermore, HES7 oscillations are severely dampened in individual cells of Lfng-null PSM. However, when Lfng-null PSM cells were completely dissociated, the amplitude and periodicity of HES7 oscillations were almost normal, which suggests that LFNG is involved mostly in cell-cell coupling. Mixed cultures of control and Lfng-null PSM cells, and an optogenetic Notch signalling reporter assay, revealed that LFNG delays the signal-sending process of intercellular Notch signalling transmission. These results-together with mathematical modelling-raised the possibility that Lfng-null PSM cells shorten the coupling delay, thereby approaching a condition known as the oscillation or amplitude death of coupled oscillators8. Indeed, a small compound that lengthens the coupling delay partially rescues the amplitude and synchrony of HES7 oscillations in Lfng-null PSM cells. Our study reveals a delay control mechanism of the oscillatory networks involved in somite segmentation, and indicates that intercellular coupling with the correct delay is essential for synchronized oscillation.
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39
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Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J. Lighting up the central dogma for predictive developmental biology. Curr Top Dev Biol 2019; 137:1-35. [PMID: 32143740 DOI: 10.1016/bs.ctdb.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the last 30years have witnessed the mapping of the wiring diagrams of the gene regulatory networks that dictate cell fate and animal body plans, specific understanding building on such network diagrams that shows how DNA regulatory regions control gene expression lags far behind. These networks have yet to yield the predictive power necessary to, for example, calculate how the concentration dynamics of input transcription factors and DNA regulatory sequence prescribes output patterns of gene expression that, in turn, determine body plans themselves. Here, we argue that reaching a predictive understanding of developmental decision-making calls for an interplay between theory and experiment aimed at revealing how the regulation of the processes of the central dogma dictate network connections and how network topology guides cells toward their ultimate developmental fate. To make this possible, it is crucial to break free from the snapshot-based understanding of embryonic development facilitated by fixed-tissue approaches and embrace new technologies that capture the dynamics of developmental decision-making at the single cell level, in living embryos.
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Affiliation(s)
- Hernan G Garcia
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States; Department of Physics, University of California at Berkeley, Berkeley, CA, United States; Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States; Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, United States.
| | - Augusto Berrocal
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States
| | - Gabriella Martini
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, United States
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40
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Couturier L, Mazouni K, Corson F, Schweisguth F. Regulation of Notch output dynamics via specific E(spl)-HLH factors during bristle patterning in Drosophila. Nat Commun 2019; 10:3486. [PMID: 31375669 PMCID: PMC6677740 DOI: 10.1038/s41467-019-11477-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
The stereotyped arrangement of sensory bristles on the adult fly thorax arises from a self-organized process, in which inhibitory Notch signaling both delimits proneural stripes and singles out sensory organ precursor cells (SOPs). A dynamic balance between proneural factors and Enhancer of split-HLH (E(spl)-HLH) Notch targets underlies patterning, but how this is regulated is unclear. Here, were identify two classes of E(spl)-HLH factors, whose expression both precedes and delimits proneural activity, and is dependent on proneural activity and required for proper SOP spacing within the stripes, respectively. These two classes are partially redundant, since a member of the second class, that is normally cross-repressed by members of the first class, can functionally compensate for their absence. The regulation of specific E(spl)-HLH genes by proneural factors amplifies the response to Notch as SOPs are being selected, contributing to patterning dynamics in the notum, and likely operates in other developmental contexts. The patterning of sensory bristles on the dorsal thorax of flies is regulated by two transcription factor families but the dynamics of this regulation is unclear. Here, the authors visualize seven E(spl)-HLH proteins, showing their regulated expression promotes mutual inhibition by Notch during notum patterning.
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Affiliation(s)
- Lydie Couturier
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,CNRS, UMR3738, 75015, Paris, France
| | - Khalil Mazouni
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,CNRS, UMR3738, 75015, Paris, France
| | - Francis Corson
- Laboratoire de Physique de l'Ecole Normale Supérieure, CNRS, Sorbonne Université, Université Paris Diderot, 75005, Paris, France
| | - François Schweisguth
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France. .,CNRS, UMR3738, 75015, Paris, France.
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41
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Goh GH, Maloney SK, Mark PJ, Blache D. Episodic Ultradian Events-Ultradian Rhythms. BIOLOGY 2019; 8:E15. [PMID: 30875767 PMCID: PMC6466064 DOI: 10.3390/biology8010015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/24/2019] [Accepted: 03/09/2019] [Indexed: 11/16/2022]
Abstract
In the fast lane of chronobiology, ultradian events are short-term rhythms that have been observed since the beginning of modern biology and were quantified about a century ago. They are ubiquitous in all biological systems and found in all organisms, from unicellular organisms to mammals, and from single cells to complex biological functions in multicellular animals. Since these events are aperiodic and last for a few minutes to a few hours, they are better classified as episodic ultradian events (EUEs). Their origin is unclear. However, they could have a molecular basis and could be controlled by hormonal inputs-in vertebrates, they originate from the activity of the central nervous system. EUEs are receiving increasing attention but their aperiodic nature requires specific sampling and analytic tools. While longer scale rhythms are adaptations to predictable changes in the environment, in theory, EUEs could contribute to adaptation by preparing organisms and biological functions for unpredictability.
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Affiliation(s)
- Grace H Goh
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Shane K Maloney
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Peter J Mark
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Dominique Blache
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
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Naoki H, Akiyama R, Sari DWK, Ishii S, Bessho Y, Matsui T. Noise-resistant developmental reproducibility in vertebrate somite formation. PLoS Comput Biol 2019; 15:e1006579. [PMID: 30716091 PMCID: PMC6361423 DOI: 10.1371/journal.pcbi.1006579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/04/2018] [Indexed: 01/17/2023] Open
Abstract
The reproducibility of embryonic development is remarkable, although molecular processes are intrinsically stochastic at the single-cell level. How the multicellular system resists the inevitable noise to acquire developmental reproducibility constitutes a fundamental question in developmental biology. Toward this end, we focused on vertebrate somitogenesis as a representative system, because somites are repeatedly reproduced within a single embryo whereas such reproducibility is lost in segmentation clock gene-deficient embryos. However, the effect of noise on developmental reproducibility has not been fully investigated, because of the technical difficulty in manipulating the noise intensity in experiments. In this study, we developed a computational model of ERK-mediated somitogenesis, in which bistable ERK activity is regulated by an FGF gradient, cell-cell communication, and the segmentation clock, subject to the intrinsic noise. The model simulation generated our previous in vivo observation that the ERK activity was distributed in a step-like gradient in the presomitic mesoderm, and its boundary was posteriorly shifted by the clock in a stepwise manner, leading to regular somite formation. Here, we showed that this somite regularity was robustly maintained against the noise. Removing the clock from the model predicted that the stepwise shift of the ERK activity occurs at irregular timing with irregular distance owing to the noise, resulting in somite size variation. This model prediction was recently confirmed by live imaging of ERK activity in zebrafish embryos. Through theoretical analysis, we presented a mechanism by which the clock reduces the inherent somite irregularity observed in clock-deficient embryos. Therefore, this study indicates a novel role of the segmentation clock in noise-resistant developmental reproducibility. The segmentation clock has been widely considered vital for somite formation, because clock-deficient embryos display severe segmental defects. However, irregular somites are still formed, suggesting that the clock is not required for somite formation itself but rather endows it with developmental reproducibility. Thus, the following questions arose: How do irregular somites emerge in a clock-independent manner? How is the irregularity reduced in the presence of the clock? To address these questions, we developed a computational model of somitogenesis. We then clarified that the intrinsic noise induces spontaneous formation of irregular-sized somites in the absence of the clock, and that the clock plays an important role in suppressing the noise effect for reproducible somite formation.
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Affiliation(s)
- Honda Naoki
- Laboratory of Theoretical Biology, Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Yoshidakonoecho, Sakyo, Kyoto, Japan
- * E-mail:
| | - Ryutaro Akiyama
- Gene Regulation Research, Division of Biological Science, Nara Institute of Science and Technology, Takayama, Nara, Japan
| | - Dini Wahyu Kartika Sari
- Gene Regulation Research, Division of Biological Science, Nara Institute of Science and Technology, Takayama, Nara, Japan
| | - Shin Ishii
- Graduate School of Informatics, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, Japan
| | - Yasumasa Bessho
- Gene Regulation Research, Division of Biological Science, Nara Institute of Science and Technology, Takayama, Nara, Japan
| | - Takaaki Matsui
- Gene Regulation Research, Division of Biological Science, Nara Institute of Science and Technology, Takayama, Nara, Japan
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Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation. Cell 2019; 172:1079-1090.e12. [PMID: 29474908 PMCID: PMC5847172 DOI: 10.1016/j.cell.2018.01.026] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/26/2017] [Accepted: 01/18/2018] [Indexed: 12/22/2022]
Abstract
How signaling dynamics encode information is a central question in biology. During vertebrate development, dynamic Notch signaling oscillations control segmentation of the presomitic mesoderm (PSM). In mouse embryos, this molecular clock comprises signaling oscillations of several pathways, i.e., Notch, Wnt, and FGF signaling. Here, we directly address the role of the relative timing between Wnt and Notch signaling oscillations during PSM patterning. To this end, we developed a new experimental strategy using microfluidics-based entrainment that enables specific control of the rhythm of segmentation clock oscillations. Using this approach, we find that Wnt and Notch signaling are coupled at the level of their oscillation dynamics. Furthermore, we provide functional evidence that the oscillation phase shift between Wnt and Notch signaling is critical for PSM segmentation. Our work hence reveals that dynamic signaling, i.e., the relative timing between oscillatory signals, encodes essential information during multicellular development. Wnt and Notch signaling wave dynamics differ within segmenting mouse mesoderm Entraining oscillations by microfluidics allows external control of the dynamics Oscillatory Wnt and Notch signaling networks are coupled at the level of dynamics Relative timing of Wnt and Notch signaling oscillations is critical for segmentation
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44
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Gibeaux R, Miller K, Acker R, Kwon T, Heald R. Xenopus Hybrids Provide Insight Into Cell and Organism Size Control. Front Physiol 2018; 9:1758. [PMID: 30564147 PMCID: PMC6288844 DOI: 10.3389/fphys.2018.01758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/20/2018] [Indexed: 01/08/2023] Open
Abstract
Determining how size is controlled is a fundamental question in biology that is poorly understood at the organismal, cellular, and subcellular levels. The Xenopus species, X. laevis and X. tropicalis differ in size at all three of these levels. Despite these differences, fertilization of X. laevis eggs with X. tropicalis sperm gives rise to viable hybrid animals that are intermediate in size. We observed that although hybrid and X. laevis embryogenesis initiates from the same sized zygote and proceeds synchronously through development, hybrid animals were smaller by the tailbud stage, and a change in the ratio of nuclear size to cell size was observed shortly after zygotic genome activation (ZGA), suggesting that differential gene expression contributes to size differences. Transcriptome analysis at the onset of ZGA identified twelve transcription factors paternally expressed in hybrids. A screen of these X. tropicalis factors by expression in X. laevis embryos revealed that Hes7 and Ventx2 significantly reduced X. laevis body length size by the tailbud stage, although nuclear to cell size scaling relationships were not affected as in the hybrid. Together, these results suggest that transcriptional regulation contributes to biological size control in Xenopus.
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Affiliation(s)
- Romain Gibeaux
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Kelly Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Rachael Acker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
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45
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Fujino Y, Yamada K, Sugaya C, Ooka Y, Ovara H, Ban H, Akama K, Otosaka S, Kinoshita H, Yamasu K, Mishima Y, Kawamura A. Deadenylation by the CCR4-NOT complex contributes to the turnover of hairy-related mRNAs in the zebrafish segmentation clock. FEBS Lett 2018; 592:3388-3398. [PMID: 30281784 DOI: 10.1002/1873-3468.13261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/10/2018] [Accepted: 09/23/2018] [Indexed: 01/09/2023]
Abstract
In the zebrafish segmentation clock, hairy/enhancer of split-related genes her1, her7, and hes6 encodes components of core oscillators. Since the expression of cyclic genes proceeds rapidly in the presomitic mesoderm (PSM), these hairy-related mRNAs are subject to strict post-transcriptional regulation. In this study, we demonstrate that inhibition of the CCR4-NOT deadenylase complex lengthens poly(A) tails of hairy-related mRNAs and increases the amount of these mRNAs, which is accompanied by defective somite segmentation. In transgenic embryos, we show that EGFP mRNAs with 3'UTRs of hairy-related genes exhibit turnover similar to endogenous mRNAs. Our results suggest that turnover rates of her1, her7, and hes6 mRNAs are differently regulated by the CCR4-NOT deadenylase complex possibly through their 3'UTRs in the zebrafish PSM.
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Affiliation(s)
- Yuuri Fujino
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Chihiro Sugaya
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Yuko Ooka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Hiroki Ovara
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Hiroyuki Ban
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Shiori Otosaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Hirofumi Kinoshita
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Yuichiro Mishima
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
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46
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Mallik S, Kundu S. Topology and Oligomerization of Mono- and Oligomeric Proteins Regulate Their Half-Lives in the Cell. Structure 2018; 26:869-878.e3. [DOI: 10.1016/j.str.2018.04.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/07/2018] [Accepted: 04/25/2018] [Indexed: 01/28/2023]
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47
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Santorelli M, Perna D, Isomura A, Garzilli I, Annunziata F, Postiglione L, Tumaini B, Kageyama R, di Bernardo D. Reconstitution of an Ultradian Oscillator in Mammalian Cells by a Synthetic Biology Approach. ACS Synth Biol 2018; 7:1447-1455. [PMID: 29727574 DOI: 10.1021/acssynbio.8b00083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Notch effector gene Hes1 is an ultradian clock exhibiting cyclic gene expression in several progenitor cells, with a period of a few hours. Because of the complexity of studying Hes1 in the endogenous setting, and the difficulty of imaging these fast oscillations in vivo, the mechanism driving oscillations has never been proven. Here, we applied a "build it to understand it" synthetic biology approach to construct simplified "hybrid" versions of the Hes1 ultradian oscillator combining synthetic and natural parts. We successfully constructed a simplified synthetic version of the Hes1 promoter matching the endogenous regulation logic. By mathematical modeling and single-cell real-time imaging, we were able to demonstrate that Hes1 is indeed able to generate stable oscillations by a delayed negative feedback loop. Moreover, we proved that introns in Hes1 contribute to the transcriptional delay but may not be strictly necessary for oscillations to occur. We also developed a novel reporter of endogenous Hes1 oscillations able to amplify the bioluminescence signal 5-fold. Our results have implications also for other ultradian oscillators.
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Affiliation(s)
- Marco Santorelli
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Daniela Perna
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Akihiro Isomura
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | | | | | - Lorena Postiglione
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Barbara Tumaini
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy
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48
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Bothma JP, Norstad MR, Alamos S, Garcia HG. LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos. Cell 2018; 173:1810-1822.e16. [PMID: 29754814 DOI: 10.1016/j.cell.2018.03.069] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/28/2018] [Accepted: 03/27/2018] [Indexed: 11/18/2022]
Abstract
Embryonic cell fates are defined by transcription factors that are rapidly deployed, yet attempts to visualize these factors in vivo often fail because of slow fluorescent protein maturation. Here, we pioneer a protein tag, LlamaTag, which circumvents this maturation limit by binding mature fluorescent proteins, making it possible to visualize transcription factor concentration dynamics in live embryos. Implementing this approach in the fruit fly Drosophila melanogaster, we discovered stochastic bursts in the concentration of transcription factors that are correlated with bursts in transcription. We further used LlamaTags to show that the concentration of protein in a given nucleus heavily depends on transcription of that gene in neighboring nuclei; we speculate that this inter-nuclear signaling is an important mechanism for coordinating gene expression to delineate straight and sharp boundaries of gene expression. Thus, LlamaTags now make it possible to visualize the flow of information along the central dogma in live embryos.
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Affiliation(s)
- Jacques P Bothma
- Department of Molecular & Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - Matthew R Norstad
- Department of Molecular & Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - Simon Alamos
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - Hernan G Garcia
- Department of Molecular & Cell Biology, UC Berkeley, Berkeley, CA 94720, USA; Department of Physics, UC Berkeley, Berkeley, CA 94720, USA; Biophysics Graduate Group, UC Berkeley, Berkeley, CA 94720, USA; Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA 94720, USA.
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49
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Abstract
During somite segmentation, clock genes oscillate within the posterior presomitic mesoderm (PSM). The temporal information ties up with the posteriorly moving FGF gradient, leading to the formation of a presumptive somite within the PSM. We previously investigated Erk activity downstream of FGF signaling by collecting stained zebrafish embryos, and discovered that the steep gradient of Erk activity was generated in the PSM, and the Erk activity border regularly shifted in a stepwise manner. However, since these interpretations come from static analyses, we needed to firmly confirm them by applying an analysis that has higher spatiotemporal resolutions. Here we developed a live imaging system for Erk activity in zebrafish embryos, using a Förster resonance energy transfer (FRET)-based Erk biosensor. With this system, we firmly showed that Erk activity exhibits stepwise regression within the PSM. Although our static analyses could not detect the stepwise pattern of Erk activity in clock-deficient embryos, our system revealed that, in clock-deficient embryos, the stepwise regression of Erk activity occurs at an irregular timing, eventually leading to formation of irregularly-sized somites. Therefore, our system overcame the limitation of static analyses and revealed that clock-dependent spatiotemporal regulation of Erk is required for proper somitogenesis in zebrafish.
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50
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Chen W, Liu J, Yuan D, Zuo Y, Liu Z, Liu S, Zhu Q, Qiu G, Huang S, Giampietro PF, Zhang F, Wu N, Wu Z. Progress and perspective of TBX6 gene in congenital vertebral malformations. Oncotarget 2018; 7:57430-57441. [PMID: 27437870 PMCID: PMC5302999 DOI: 10.18632/oncotarget.10619] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/16/2016] [Indexed: 02/05/2023] Open
Abstract
Congenital vertebral malformation is a series of significant health problems affecting a large number of populations. It may present as an isolated condition or as a part of an underlying syndromes occurring with other malformations and/or clinical features. Disruption of the genesis of paraxial mesoderm, somites or axial bones can result in spinal deformity. In the course of somitogenesis, the segmentation clock and the wavefront are the leading factors during the entire process in which TBX6 gene plays an important role. TBX6 is a member of the T-box gene family, and its important pathogenicity in spinal deformity has been confirmed. Several TBX6 gene variants and novel pathogenic mechanisms have been recently revealed, and will likely have significant impact in understanding the genetic basis for CVM. In this review, we describe the role which TBX6 plays during human spine development including its interaction with other key elements during the process of somitogenesis. We then systematically review the association between TBX6 gene variants and CVM associated phenotypes, highlighting an important and emerging role for TBX6 and human malformations.
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Affiliation(s)
- Weisheng Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaqi Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Breast Surgical Oncology, Cancer Hospital of Chinese Academy of Medical Sciences, Beijing, China
| | - Dongtang Yuan
- Department of Orthopaedics, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Yuzhi Zuo
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhenlei Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Qiankun Zhu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Shishu Huang
- Department of Orthopaedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Philip F Giampietro
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Nan Wu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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