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Ebisuya M, Briscoe J. Timing and Tempo in Development. Curr Opin Genet Dev 2024; 86:102202. [PMID: 38703423 DOI: 10.1016/j.gde.2024.102202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Affiliation(s)
- Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Andersson E, Rothenberg EV, Peterson C, Olariu V. T-cell commitment inheritance-an agent-based multi-scale model. NPJ Syst Biol Appl 2024; 10:40. [PMID: 38632273 PMCID: PMC11024127 DOI: 10.1038/s41540-024-00368-y] [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: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations predicted that the commitment is a three-step process that occurs on average over several cell generations once a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function approximately two to three generations later. This is when our LCA analysis indicates that the decision to commit is taken even though in general another one to two generations elapse before the cell actually becomes committed by transitioning to the DN2b state. Our results showed that there is decision inheritance in the commitment mechanism.
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Affiliation(s)
- Emil Andersson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Carsten Peterson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Victor Olariu
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden.
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Wallace JL, Pollen AA. Human neuronal maturation comes of age: cellular mechanisms and species differences. Nat Rev Neurosci 2024; 25:7-29. [PMID: 37996703 DOI: 10.1038/s41583-023-00760-3] [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: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The delayed and prolonged postmitotic maturation of human neurons, compared with neurons from other species, may contribute to human-specific cognitive abilities and neurological disorders. Here we review the mechanisms of neuronal maturation, applying lessons from model systems to understand the specific features of protracted human cortical maturation and species differences. We cover cell-intrinsic features of neuronal maturation, including transcriptional, epigenetic and metabolic mechanisms, as well as cell-extrinsic features, including the roles of activity and synapses, the actions of glial cells and the contribution of the extracellular matrix. We discuss evidence for species differences in biochemical reaction rates, the proposed existence of an epigenetic maturation clock and the contributions of both general and modular mechanisms to species-specific maturation timing. Finally, we suggest approaches to measure, improve and accelerate the maturation of human neurons in culture, examine crosstalk and interactions among these different aspects of maturation and propose conceptual models to guide future studies.
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Affiliation(s)
- Jenelle L Wallace
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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Pelayo MA, Yamaguchi N. Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor-chromatin dynamics. FRONTIERS IN PLANT SCIENCE 2023; 14:1323507. [PMID: 38155851 PMCID: PMC10753784 DOI: 10.3389/fpls.2023.1323507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023]
Abstract
The intricate morphology of the flower is primarily established within floral meristems in which floral organs will be defined and from where the developing flower will emerge. Floral meristem development involves multiscale-level regulation, including lineage and positional mechanisms for establishing cell-type identity, and transcriptional regulation mediated by changes in the chromatin environment. However, many key aspects of floral meristem development remain to be determined, such as: 1) the exact role of cellular location in connecting transcriptional inputs to morphological outcomes, and 2) the precise interactions between transcription factors and chromatin regulators underlying the transcriptional networks that regulate the transition from cell proliferation to differentiation during floral meristem development. Here, we highlight recent studies addressing these points through newly developed spatial reconstruction techniques and high-resolution transcription factor-chromatin environment interactions in the model plant Arabidopsis thaliana. Specifically, we feature studies that reconstructed 3D gene expression atlases of the floral meristem. We also discuss how the precise timing of floral meristem specification, floral organ patterning, and floral meristem termination is determined through temporally defined epigenetic dynamics for fine-tuning of gene expression. These studies offer fresh insights into the well-established principles of floral meristem development and outline the potential for further advances in this field in an age of integrated, powerful, multiscale resolution approaches.
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Affiliation(s)
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Andersson E, Rothenberg EV, Peterson C, Olariu V. T-cell commitment inheritance - an agent-based multi-scale model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562905. [PMID: 37905091 PMCID: PMC10614897 DOI: 10.1101/2023.10.18.562905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations showed that the commitment is a three-step process over several cell generations where a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function two to three generations later which is when the decision to commit is taken. Finally, after another one to two generations, the cell becomes committed by transitioning to the DN2b state. Our results showed that there is inheritance in the commitment mechanism.
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Affiliation(s)
- Emil Andersson
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carsten Peterson
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Victor Olariu
- Computational Biology and Biological Physics, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
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Laghmach R, Di Pierro M, Potoyan D. A Liquid State Perspective on Dynamics of Chromatin Compartments. Front Mol Biosci 2022; 8:781981. [PMID: 35096966 PMCID: PMC8793688 DOI: 10.3389/fmolb.2021.781981] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
The interior of the eukaryotic cell nucleus has a crowded and heterogeneous environment packed with chromatin polymers, regulatory proteins, and RNA molecules. Chromatin polymer, assisted by epigenetic modifications, protein and RNA binders, forms multi-scale compartments which help regulate genes in response to cellular signals. Furthermore, chromatin compartments are dynamic and tend to evolve in size and composition in ways that are not fully understood. The latest super-resolution imaging experiments have revealed a much more dynamic and stochastic nature of chromatin compartments than was appreciated before. An emerging mechanism explaining chromatin compartmentalization dynamics is the phase separation of protein and nucleic acids into membraneless liquid condensates. Consequently, concepts and ideas from soft matter and polymer systems have been rapidly entering the lexicon of cell biology. In this respect, the role of computational models is crucial for establishing a rigorous and quantitative foundation for the new concepts and disentangling the complex interplay of forces that contribute to the emergent patterns of chromatin dynamics and organization. Several multi-scale models have emerged to address various aspects of chromatin dynamics, ranging from equilibrium polymer simulations, hybrid non-equilibrium simulations coupling protein binding and chromatin folding, and mesoscopic field-theoretic models. Here, we review these emerging theoretical paradigms and computational models with a particular focus on chromatin’s phase separation and liquid-like properties as a basis for nuclear organization and dynamics.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA, United States
| | - Davit Potoyan
- Department of Chemistry, Iowa State University, Ames, IA, United States
- *Correspondence: Davit Potoyan,
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