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Jeziorska DM, Tunnacliffe EAJ, Brown JM, Ayyub H, Sloane-Stanley J, Sharpe JA, Lagerholm BC, Babbs C, Smith AJH, Buckle VJ, Higgs DR. On-microscope staging of live cells reveals changes in the dynamics of transcriptional bursting during differentiation. Nat Commun 2022; 13:6641. [PMID: 36333299 PMCID: PMC9636426 DOI: 10.1038/s41467-022-33977-4] [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: 12/08/2021] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Determining the mechanisms by which genes are switched on and off during development is a key aim of current biomedical research. Gene transcription has been widely observed to occur in a discontinuous fashion, with short bursts of activity interspersed with periods of inactivity. It is currently not known if or how this dynamic behaviour changes as mammalian cells differentiate. To investigate this, using an on-microscope analysis, we monitored mouse α-globin transcription in live cells throughout erythropoiesis. We find that changes in the overall levels of α-globin transcription are most closely associated with changes in the fraction of time a gene spends in the active transcriptional state. We identify differences in the patterns of transcriptional bursting throughout differentiation, with maximal transcriptional activity occurring in the mid-phase of differentiation. Early in differentiation, we observe increased fluctuation in transcriptional activity whereas at the peak of gene expression, in early erythroblasts, transcription is relatively stable. Later during differentiation as α-globin expression declines, we again observe more variability in transcription within individual cells. We propose that the observed changes in transcriptional behaviour may reflect changes in the stability of active transcriptional compartments as gene expression is regulated during differentiation.
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Affiliation(s)
- D. M. Jeziorska
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,Present Address: Nucleome Therapeutics Ltd., BioEscalator, The Innovation Building, Old Road Campus, Oxford, OX3 7FZ UK
| | - E. A. J. Tunnacliffe
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - J. M. Brown
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - H. Ayyub
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - J. Sloane-Stanley
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - J. A. Sharpe
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - B. C. Lagerholm
- grid.4991.50000 0004 1936 8948Wolfson Imaging Centre, MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,grid.4991.50000 0004 1936 8948Present Address: The Kennedy Institute Of Rheumatology, University of Oxford, Old Road Campus, Oxford, OX3 7FY UK
| | - C. Babbs
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - A. J. H. Smith
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,grid.4305.20000 0004 1936 7988Present Address: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU UK
| | - V. J. Buckle
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - D. R. Higgs
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,grid.4991.50000 0004 1936 8948Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7BN UK
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Parts L, Batté A, Lopes M, Yuen MW, Laver M, San Luis BJ, Yue JX, Pons C, Eray E, Aloy P, Liti G, van Leeuwen J. Natural variants suppress mutations in hundreds of essential genes. Mol Syst Biol 2021; 17:e10138. [PMID: 34042294 PMCID: PMC8156963 DOI: 10.15252/msb.202010138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/04/2023] Open
Abstract
The consequence of a mutation can be influenced by the context in which it operates. For example, loss of gene function may be tolerated in one genetic background, and lethal in another. The extent to which mutant phenotypes are malleable, the architecture of modifiers and the identities of causal genes remain largely unknown. Here, we measure the fitness effects of ~ 1,100 temperature‐sensitive alleles of yeast essential genes in the context of variation from ten different natural genetic backgrounds and map the modifiers for 19 combinations. Altogether, fitness defects for 149 of the 580 tested genes (26%) could be suppressed by genetic variation in at least one yeast strain. Suppression was generally driven by gain‐of‐function of a single, strong modifier gene, and involved both genes encoding complex or pathway partners suppressing specific temperature‐sensitive alleles, as well as general modifiers altering the effect of many alleles. The emerging frequency of suppression and range of possible mechanisms suggest that a substantial fraction of monogenic diseases could be managed by modulating other gene products.
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Affiliation(s)
- Leopold Parts
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Amandine Batté
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Maykel Lopes
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Michael W Yuen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Meredith Laver
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jia-Xing Yue
- University of Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Elise Eray
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Gianni Liti
- University of Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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