1
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Stojanovski K, Gheorghe I, Lenart P, Lanjuin A, Mair WB, Towbin BD. Maintenance of appropriate size scaling of the C. elegans pharynx by YAP-1. Nat Commun 2023; 14:7564. [PMID: 37985670 PMCID: PMC10661912 DOI: 10.1038/s41467-023-43230-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
Even slight imbalance between the growth rate of different organs can accumulate to a large deviation from their appropriate size during development. Here, we use live imaging of the pharynx of C. elegans to ask if and how organ size scaling nevertheless remains uniform among individuals. Growth trajectories of hundreds of individuals reveal that pharynxes grow by a near constant volume per larval stage that is independent of their initial size, such that undersized pharynxes catch-up in size during development. Tissue-specific depletion of RAGA-1, an activator of mTOR and growth, shows that maintaining correct pharynx-to-body size proportions involves a bi-directional coupling between pharynx size and body growth. In simulations, this coupling cannot be explained by limitation of food uptake alone, and genetic experiments reveal an involvement of the mechanotransducing transcriptional co-regulator yap-1. Our data suggests that mechanotransduction coordinates pharynx growth with other tissues, ensuring body plan uniformity among individuals.
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Affiliation(s)
| | - Ioana Gheorghe
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Peter Lenart
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Anne Lanjuin
- Department Molecular Metabolism, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - William B Mair
- Department Molecular Metabolism, Harvard TH Chan School of Public Health, Boston, MA, USA
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2
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Wehrens M, Krah LHJ, Towbin BD, Hermsen R, Tans SJ. The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells. Cell Rep 2023; 42:113284. [PMID: 37864793 DOI: 10.1016/j.celrep.2023.113284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/17/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023] Open
Abstract
The inherent stochasticity of metabolism raises a critical question for understanding homeostasis: are cellular processes regulated in response to internal fluctuations? Here, we show that, in E. coli cells under constant external conditions, catabolic enzyme expression continuously responds to metabolic fluctuations. The underlying regulatory feedback is enabled by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system, which controls catabolic enzyme expression based on metabolite concentrations. Using single-cell microscopy, genetic constructs in which this feedback is disabled, and mathematical modeling, we show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. Modeling identifies four noise propagation modes, including one specific to CRP regulation. Together, these modes correctly predict noise circulation at perturbed cAMP levels. The cAMP-CRP system may thus have evolved to control internal metabolic fluctuations in addition to external growth conditions. We conjecture that second messengers may more broadly function to achieve cellular homeostasis.
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Affiliation(s)
- Martijn Wehrens
- AMOLF, 1098 XG Amsterdam, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, 3584 CT Utrecht, the Netherlands
| | - Laurens H J Krah
- Theoretical Biology Group, Biology Department, Utrecht University, 3584 CH Utrecht, the Netherlands; Centre for Complex Systems Studies, Utrecht University, 3584 CE Utrecht, the Netherlands
| | - Benjamin D Towbin
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Rutger Hermsen
- Theoretical Biology Group, Biology Department, Utrecht University, 3584 CH Utrecht, the Netherlands; Centre for Complex Systems Studies, Utrecht University, 3584 CE Utrecht, the Netherlands
| | - Sander J Tans
- AMOLF, 1098 XG Amsterdam, the Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands.
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3
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Smith HJ, Lanjuin A, Sharma A, Prabhakar A, Nowak E, Stine PG, Sehgal R, Stojanovski K, Towbin BD, Mair WB. Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction in C. elegans. PLoS Genet 2023; 19:e1010938. [PMID: 37721956 PMCID: PMC10538657 DOI: 10.1371/journal.pgen.1010938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 09/28/2023] [Accepted: 08/24/2023] [Indexed: 09/20/2023] Open
Abstract
mTORC1 (mechanistic target of rapamycin complex 1) is a metabolic sensor that promotes growth when nutrients are abundant. Ubiquitous inhibition of mTORC1 extends lifespan in multiple organisms but also disrupts several anabolic processes resulting in stunted growth, slowed development, reduced fertility, and disrupted metabolism. However, it is unclear if these pleiotropic effects of mTORC1 inhibition can be uncoupled from longevity. Here, we utilize the auxin-inducible degradation (AID) system to restrict mTORC1 inhibition to C. elegans neurons. We find that neuron-specific degradation of RAGA-1, an upstream activator of mTORC1, or LET-363, the ortholog of mammalian mTOR, is sufficient to extend lifespan in C. elegans. Unlike raga-1 loss of function genetic mutations or somatic AID of RAGA-1, neuronal AID of RAGA-1 robustly extends lifespan without impairing body size, developmental rate, brood size, or neuronal function. Moreover, while degradation of RAGA-1 in all somatic tissues alters the expression of thousands of genes, demonstrating the widespread effects of mTORC1 inhibition, degradation of RAGA-1 in neurons only results in around 200 differentially expressed genes with a specific enrichment in metabolism and stress response. Notably, our work demonstrates that targeting mTORC1 specifically in the nervous system in C. elegans uncouples longevity from growth and reproductive impairments, and that many canonical effects of low mTORC1 activity are not required to promote healthy aging. These data challenge previously held ideas about the mechanisms of mTORC1 lifespan extension and underscore the potential of promoting longevity by neuron-specific mTORC1 modulation.
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Affiliation(s)
- Hannah J. Smith
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
| | - Anne Lanjuin
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
| | - Arpit Sharma
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
| | - Aditi Prabhakar
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
| | - Ewelina Nowak
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
| | - Peter G. Stine
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
| | - Rohan Sehgal
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
| | | | | | - William B. Mair
- Dept. Molecular Metabolism, Harvard TH Chan School of Public Health, Massachusetts, United States of America
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4
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Al-Refaie N, Padovani F, Binando F, Hornung J, Zhao Q, Towbin BD, Cenik ES, Stroustrup N, Schmoller KM, Cabianca DS. An mTOR/RNA pol I axis shapes chromatin architecture in response to fasting. bioRxiv 2023:2023.07.22.550032. [PMID: 37503059 PMCID: PMC10370172 DOI: 10.1101/2023.07.22.550032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom. Yet, how it impacts on 3D genome organization is unknown. Here, we show that fasting induces a reversible and large-scale spatial reorganization of chromatin in C. elegans . This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, a major regulator of ribosome biogenesis. Remarkably, loss of transcription by RNA Pol I, but not RNA Pol II nor Pol III, induces a similar 3D genome reorganization in fed animals, and prevents the restoration of the fed-state architecture upon restoring nutrients to fasted animals. Our work documents the first large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients.
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5
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Stojanovski K, Großhans H, Towbin BD. Coupling of growth rate and developmental tempo reduces body size heterogeneity in C. elegans. Nat Commun 2022; 13:3132. [PMID: 35668054 PMCID: PMC9170734 DOI: 10.1038/s41467-022-29720-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 03/24/2022] [Indexed: 11/15/2022] Open
Abstract
Animals increase by orders of magnitude in volume during development. Therefore, small variations in growth rates among individuals could amplify to a large heterogeneity in size. By live imaging of C. elegans, we show that amplification of size heterogeneity is prevented by an inverse coupling of the volume growth rate to the duration of larval stages and does not involve strict size thresholds for larval moulting. We perturb this coupling by changing the developmental tempo through manipulation of a transcriptional oscillator that controls the duration of larval development. As predicted by a mathematical model, this perturbation alters the body volume. Model analysis shows that an inverse relation between the period length and the growth rate is an intrinsic property of genetic oscillators and can occur independently of additional complex regulation. This property of genetic oscillators suggests a parsimonious mechanism that counteracts the amplification of size differences among individuals during development. Animals must reach the correct size during development, despite stochastic differences in their growth rate. Here, Stojanovski et al. show that a coupling of growth and development by an oscillatory timer buffers fluctuations in the growth of the nematode C. elegans to ensure its correct size.
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Affiliation(s)
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Benjamin D Towbin
- University of Bern, Bern, Switzerland. .,Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
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6
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Korem Kohanim Y, Levi D, Jona G, Towbin BD, Bren A, Alon U. A Bacterial Growth Law out of Steady State. Cell Rep 2019; 23:2891-2900. [PMID: 29874577 DOI: 10.1016/j.celrep.2018.05.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/21/2018] [Accepted: 05/01/2018] [Indexed: 11/28/2022] Open
Abstract
Bacterial growth follows simple laws in constant conditions. However, bacteria in nature often face fluctuating environments. We therefore ask whether there are growth laws that apply to changing environments. We derive a law for upshifts using an optimal resource-allocation model: the post-shift growth rate equals the geometrical mean of the pre-shift growth rate and the growth rate on saturating carbon. We test this using chemostat and batch culture experiments, as well as previous data from several species. The increase in growth rate after an upshift indicates that ribosomes have spare capacity (SC). We demonstrate theoretically that SC has the cost of slow steady-state growth but is beneficial after an upshift because it prevents large overshoots in intracellular metabolites and allows rapid response to change. We also provide predictions for downshifts. The present study quantifies the optimal degree of SC, which rises the slower the growth rate, and suggests that SC can be precisely regulated.
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Affiliation(s)
- Yael Korem Kohanim
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dikla Levi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Benjamin D Towbin
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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7
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Bren A, Park JO, Towbin BD, Dekel E, Rabinowitz JD, Alon U. Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP. Sci Rep 2016; 6:24834. [PMID: 27109914 PMCID: PMC4843011 DOI: 10.1038/srep24834] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
Abstract
In most conditions, glucose is the best carbon source for E. coli: it provides faster growth than other sugars, and is consumed first in sugar mixtures. Here we identify conditions in which E. coli strains grow slower on glucose than on other sugars, namely when a single amino acid (arginine, glutamate, or proline) is the sole nitrogen source. In sugar mixtures with these nitrogen sources, E. coli still consumes glucose first, but grows faster rather than slower after exhausting glucose, generating a reversed diauxic shift. We trace this counterintuitive behavior to a metabolic imbalance: levels of TCA-cycle metabolites including α-ketoglutarate are high, and levels of the key regulatory molecule cAMP are low. Growth rates were increased by experimentally increasing cAMP levels, either by adding external cAMP, by genetically perturbing the cAMP circuit or by inhibition of glucose uptake. Thus, the cAMP control circuitry seems to have a ‘bug’ that leads to slow growth under what may be an environmentally rare condition.
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Affiliation(s)
- Anat Bren
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
| | - Junyoung O Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Benjamin D Towbin
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
| | - Erez Dekel
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Uri Alon
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel 76100
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8
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Aidelberg G, Towbin BD, Rothschild D, Dekel E, Bren A, Alon U. Hierarchy of non-glucose sugars in Escherichia coli. BMC Syst Biol 2014; 8:133. [PMID: 25539838 PMCID: PMC4304618 DOI: 10.1186/s12918-014-0133-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 12/04/2014] [Indexed: 01/18/2023]
Abstract
BACKGROUND Understanding how cells make decisions, and why they make the decisions they make, is of fundamental interest in systems biology. To address this, we study the decisions made by E. coli on which genes to express when presented with two different sugars. It is well-known that glucose, E. coli's preferred carbon source, represses the uptake of other sugars by means of global and gene-specific mechanisms. However, less is known about the utilization of glucose-free sugar mixtures which are found in the natural environment of E. coli and in biotechnology. RESULTS Here, we combine experiment and theory to map the choices of E. coli among 6 different non-glucose carbon sources. We used robotic assays and fluorescence reporter strains to make precise measurements of promoter activity and growth rate in all pairs of these sugars. We find that the sugars can be ranked in a hierarchy: in a mixture of a higher and a lower sugar, the lower sugar system shows reduced promoter activity. The hierarchy corresponds to the growth rate supported by each sugar- the faster the growth rate, the higher the sugar on the hierarchy. The hierarchy is 'soft' in the sense that the lower sugar promoters are not completely repressed. Measurement of the activity of the master regulator CRP-cAMP shows that the hierarchy can be quantitatively explained based on differential activation of the promoters by CRP-cAMP. Comparing sugar system activation as a function of time in sugar pair mixtures at sub-saturating concentrations, we find cases of sequential activation, and also cases of simultaneous expression of both systems. Such simultaneous expression is not predicted by simple models of growth rate optimization, which predict only sequential activation. We extend these models by suggesting multi-objective optimization for both growing rapidly now and preparing the cell for future growth on the poorer sugar. CONCLUSION We find a defined hierarchy of sugar utilization, which can be quantitatively explained by differential activation by the master regulator cAMP-CRP. The present approach can be used to understand cell decisions when presented with mixtures of conditions.
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9
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Ferreira HC, Towbin BD, Jegou T, Gasser SM. The shelterin protein POT-1 anchors Caenorhabditis elegans telomeres through SUN-1 at the nuclear periphery. ACTA ACUST UNITED AC 2013; 203:727-35. [PMID: 24297748 PMCID: PMC3857485 DOI: 10.1083/jcb.201307181] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Telomere positioning near the nuclear envelope during Caenorhabditis elegans development requires the nuclear envelope protein SUN-1, the Shelterin component POT-1, and the SUMO ligase GEI-17. Telomeres are specialized protein–DNA structures that protect chromosome ends. In budding yeast, telomeres form clusters at the nuclear periphery. By imaging telomeres in embryos of the metazoan Caenorhabditis elegans, we found that telomeres clustered only in strains that had activated an alternative telomere maintenance pathway (ALT). Moreover, as in yeast, the unclustered telomeres in wild-type embryos were located near the nuclear envelope (NE). This bias for perinuclear localization increased during embryogenesis and persisted in differentiated cells. Telomere position in early embryos required the NE protein SUN-1, the single-strand binding protein POT-1, and the small ubiquitin-like modifier (SUMO) ligase GEI-17. However, in postmitotic larval cells, none of these factors individually were required for telomere anchoring, which suggests that additional mechanisms anchor in late development. Importantly, targeted POT-1 was sufficient to anchor chromatin to the NE in a SUN-1–dependent manner, arguing that its effect at telomeres is direct. This high-resolution description of telomere position within C. elegans extends our understanding of telomere organization in eukaryotes.
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Affiliation(s)
- Helder C Ferreira
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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10
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Towbin BD, Gonzalez-Sandoval A, Gasser SM. Mechanisms of heterochromatin subnuclear localization. Trends Biochem Sci 2013; 38:356-63. [PMID: 23746617 DOI: 10.1016/j.tibs.2013.04.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/24/2013] [Accepted: 04/30/2013] [Indexed: 11/18/2022]
Abstract
Transcriptionally repressed heterochromatin becomes the dominant form of chromatin in most terminally differentiated cells. Moreover, in most cells, at least one class of heterochromatin is positioned adjacent to the nuclear lamina. Recent approaches have addressed the mechanism of heterochromatin localization, in order to determine whether spatial segregation contributes to gene repression. Findings in worms and human cells confirm a role for histone H3K9 methylation in heterochromatin positioning, identifying a modification that is also necessary for gene repression of worm transgenic arrays. These pathways appear to be conserved, although mutations in mammalian cells have weaker effects, possibly due to redundancy in positioning mechanisms. We propose a general model in which perinuclear anchoring is linked to an epigenetic propagation of the heterochromatic state, through histone modification.
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Affiliation(s)
- Benjamin D Towbin
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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11
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Gonzalez-Sandoval A, Towbin BD, Gasser SM. The formation and sequestration of heterochromatin during development. FEBS J 2013; 280:3212-9. [DOI: 10.1111/febs.12319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research; Basel Switzerland
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12
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Dion V, Kalck V, Horigome C, Towbin BD, Gasser SM. Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery. Nat Cell Biol 2012; 14:502-9. [PMID: 22484486 DOI: 10.1038/ncb2465] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/14/2012] [Indexed: 01/13/2023]
Abstract
Chromatin mobility is thought to facilitate homology search during homologous recombination and to shift damage either towards or away from specialized repair compartments. However, unconstrained mobility of double-strand breaks could also promote deleterious chromosomal translocations. Here we use live time-lapse fluorescence microscopy to track the mobility of damaged DNA in budding yeast. We found that a Rad52-YFP focus formed at an irreparable double-strand break moves in a larger subnuclear volume than the undamaged locus. In contrast, Rad52-YFP bound at damage arising from a protein-DNA adduct shows no increase in movement. Mutant analysis shows that enhanced double-strand-break mobility requires Rad51, the ATPase activity of Rad54, the ATR homologue Mec1 and the DNA-damage-response mediator Rad9. Consistent with a role for movement in the homology-search step of homologous recombination, we show that recombination intermediates take longer to form in cells lacking Rad9.
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Affiliation(s)
- Vincent Dion
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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13
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Mattout A, Pike BL, Towbin BD, Bank EM, Gonzalez-Sandoval A, Stadler MB, Meister P, Gruenbaum Y, Gasser SM. An EDMD mutation in C. elegans lamin blocks muscle-specific gene relocation and compromises muscle integrity. Curr Biol 2011; 21:1603-14. [PMID: 21962710 DOI: 10.1016/j.cub.2011.08.030] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/30/2011] [Accepted: 08/12/2011] [Indexed: 11/15/2022]
Abstract
BACKGROUND In worms, as in other organisms, many tissue-specific promoters are sequestered at the nuclear periphery when repressed and shift inward when activated. It has remained unresolved, however, whether the association of facultative heterochromatin with the nuclear periphery, or its release, has functional relevance for cell or tissue integrity. RESULTS Using ablation of the unique lamin gene in C. elegans, we show that lamin is necessary for the perinuclear positioning of heterochromatin. We then express at low levels in otherwise wild-type worms a lamin carrying a point mutation, Y59C, which in humans is linked to an autosomal-dominant form of Emery-Dreifuss muscular dystrophy. Using embryos and differentiated tissues, we track the subnuclear position of integrated heterochromatic arrays and their expression. In LMN-1 Y59C-expressing worms, we see abnormal retention at the nuclear envelope of a gene array bearing a muscle-specific promoter. This correlates with impaired activation of the array-borne myo-3 promoter and altered expression of a number of muscle-specific genes. However, an equivalent array carrying the intestine-specific pha-4 promoter is expressed normally and shifts inward when activated in gut cells of LMN-1 Y59C worms. Remarkably, adult LMN-1 Y59C animals have selectively perturbed body muscle ultrastructure and reduced muscle function. CONCLUSION Lamin helps sequester heterochromatin at the nuclear envelope, and wild-type lamin permits promoter release following tissue-specific activation. A disease-linked point mutation in lamin impairs muscle-specific reorganization of a heterochromatic array during tissue-specific promoter activation in a dominant manner. This dominance and the correlated muscle dysfunction in LMN-1 Y59C worms phenocopies Emery-Dreifuss muscular dystrophy.
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Affiliation(s)
- Anna Mattout
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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14
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Towbin BD, Meister P, Pike BL, Gasser SM. Repetitive transgenes in C. elegans accumulate heterochromatic marks and are sequestered at the nuclear envelope in a copy-number- and lamin-dependent manner. Cold Spring Harb Symp Quant Biol 2011; 75:555-65. [PMID: 21467137 DOI: 10.1101/sqb.2010.75.041] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chromatin is nonrandomly distributed in nuclear space, yet the functional significance of this remains unclear. Here, we make use of transgenes carrying developmentally regulated promoters to study subnuclear gene positioning during the development of Caenorhabditis elegans. We found that small transgenes (copy number ≤50) are randomly distributed in early embryonic nuclei, independent of promoter activity. However, in differentiated tissues, these same transgenes occupied specific subnuclear positions: When promoters are repressed, transgenes are found at the nuclear periphery, whereas active, developmentally regulated promoters are enriched in the nuclear core. The absence of specific transgene positioning in embryonic nuclei does not reflect an absence of proteins that mediate perinuclear sequestration: Embryonic nuclei are able to sequester much larger transgene arrays (copy number 300-500) at the periphery. This size-dependent peripheral positioning of gene arrays in early embryos correlates with the accumulation of heterochromatic marks (H3K9me3 and H3K27me3) on large arrays. Interestingly, depletion of nuclear lamina components caused release of arrays from the nuclear envelope and interfered with their efficient silencing. Our results suggest that developmentally silenced chromatin binds the nuclear lamina in a manner correlated with the deposition of heterochromatic marks. Peripheral sequestration of chromatin may, in turn, support the maintenance of silencing.
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Affiliation(s)
- B D Towbin
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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15
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Meister P, Towbin BD, Pike BL, Ponti A, Gasser SM. The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev 2010; 24:766-82. [PMID: 20395364 PMCID: PMC2854392 DOI: 10.1101/gad.559610] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/25/2010] [Indexed: 12/23/2022]
Abstract
To understand whether the spatial organization of the genome reflects the cell's differentiated state, we examined whether genes assume specific subnuclear positions during Caenorhabditis elegans development. Monitoring the radial position of developmentally controlled promoters in embryos and larval tissues, we found that small integrated arrays bearing three different tissue-specific promoters have no preferential position in nuclei of undifferentiated embryos. However, in differentiated cells, they shifted stably toward the nuclear lumen when activated, or to the nuclear envelope when silent. In contrast, large integrated arrays bearing the same promoters became heterochromatic and nuclear envelope-bound in embryos. Tissue-specific activation of promoters in these large arrays in larvae overrode the perinuclear anchorage. For transgenes that carry both active and inactive promoters, the inward shift of the active promoter was dominant. Finally, induction of master regulator HLH-1 prematurely induced internalization of a muscle-specific promoter array in embryos. Fluorescence in situ hybridization confirmed analogous results for the endogenous endoderm-determining gene pha-4. We propose that, in differentiated cells, subnuclear organization arises from the selective positioning of active and inactive developmentally regulated promoters. We characterize two forces that lead to tissue-specific subnuclear organization of the worm genome: large repeat-induced heterochromatin, which associates with the nuclear envelope like repressed genes in differentiated cells, and tissue-specific promoters that shift inward in a dominant fashion over silent promoters, when they are activated.
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Affiliation(s)
- Peter Meister
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Benjamin D. Towbin
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Brietta L. Pike
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Aaron Ponti
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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Towbin BD, Meister P, Gasser SM. The nuclear envelope--a scaffold for silencing? Curr Opin Genet Dev 2009; 19:180-6. [PMID: 19303765 DOI: 10.1016/j.gde.2009.01.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 01/23/2009] [Accepted: 01/27/2009] [Indexed: 01/19/2023]
Abstract
An increasing number of studies indicate that chromosomes are spatially organized in the interphase nucleus and that some genes tend to occupy characteristic zones of the nuclear volume. FISH studies in mammalian cells suggest a differential localization of active and inactive loci, with inactive heterochromatin being largely perinuclear. Recent genome-wide mapping techniques confirm that the nuclear lamina, which lies beneath the nuclear envelope, interacts preferentially with silent genes. To address the functional significance of spatial compartmentation, gain-of-function assays in which chromatin is targeted to the nuclear periphery have now been carried out. Such experiments yielded coherent models in yeast; however, conflicting results in mammalian cells leave it unclear whether these concepts apply to higher organisms. Nevertheless, the recent discovery that evolutionarily conserved inner nuclear membrane proteins support the peripheral anchoring of yeast heterochromatin suggests that certain principles of nuclear organization may hold true from yeast to man.
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Affiliation(s)
- Benjamin D Towbin
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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