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Muhammad A, Sarkadi Z, van Emden T, Mazumder A, Capella M, Fekete G, Sreechakram VNS, Al-Sady B, Papp B, Barrales RR, Braun S. A systematic quantitative approach comprehensively defines domain-specific functional pathways linked to Schizosaccharomyces pombe heterochromatin regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.579970. [PMID: 38405799 PMCID: PMC10888830 DOI: 10.1101/2024.02.13.579970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Heterochromatin plays a critical role in regulating gene expression and maintaining genome integrity. While structural and enzymatic components have been linked to heterochromatin establishment, a comprehensive view of the underlying pathways at diverse heterochromatin domains remains elusive. Here, we developed a systematic approach to identify factors involved in heterochromatin silencing at pericentromeres, subtelomeres, and the silent mating type locus in Schizosaccharomyces pombe. Using quantitative measures, iterative genetic screening, and domain-specific heterochromatin reporters, we identified 369 mutants with different degrees of reduced or enhanced silencing. As expected, mutations in the core heterochromatin machinery globally decreased silencing. However, most other mutants exhibited distinct qualitative and quantitative profiles that indicate domain-specific functions. For example, decreased mating type silencing was linked to mutations in heterochromatin maintenance genes, while compromised subtelomere silencing was associated with metabolic pathways. Furthermore, similar phenotypic profiles revealed shared functions for subunits within complexes. We also discovered that the uncharacterized protein Dhm2 plays a crucial role in maintaining constitutive and facultative heterochromatin, while its absence caused phenotypes akin to DNA replication-deficient mutants. Collectively, our systematic approach unveiled a landscape of domain-specific heterochromatin regulators controlling distinct states and identified Dhm2 as a previously unknown factor linked to heterochromatin inheritance and replication fidelity.
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Affiliation(s)
- Abubakar Muhammad
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Zsuzsa Sarkadi
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Thomas van Emden
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Agnisrota Mazumder
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Matias Capella
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Present address: Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Vishnu N Suma Sreechakram
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Bassem Al-Sady
- Department of Microbiology & Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Ramón Ramos Barrales
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Present address: Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
| | - Sigurd Braun
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
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2
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Proteome effects of genome-wide single gene perturbations. Nat Commun 2022; 13:6153. [PMID: 36257942 PMCID: PMC9579165 DOI: 10.1038/s41467-022-33814-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Protein abundance is controlled at the transcriptional, translational and post-translational levels, and its regulatory principles are starting to emerge. Investigating these principles requires large-scale proteomics data and cannot just be done with transcriptional outcomes that are commonly used as a proxy for protein abundance. Here, we determine proteome changes resulting from the individual knockout of 3308 nonessential genes in the yeast Schizosaccharomyces pombe. We use similarity clustering of global proteome changes to infer gene functionality that can be extended to other species, such as humans or baker's yeast. Furthermore, we analyze a selected set of deletion mutants by paired transcriptome and proteome measurements and show that upregulation of proteins under stable transcript expression utilizes optimal codons.
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Greenstein RA, Ng H, Barrales RR, Tan C, Braun S, Al-Sady B. Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction. PLoS Genet 2022; 18:e1010201. [PMID: 35584134 PMCID: PMC9154106 DOI: 10.1371/journal.pgen.1010201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/31/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022] Open
Abstract
Heterochromatin spreading, the expansion of repressive chromatin structure from sequence-specific nucleation sites, is critical for stable gene silencing. Spreading re-establishes gene-poor constitutive heterochromatin across cell cycles but can also invade gene-rich euchromatin de novo to steer cell fate decisions. How chromatin context (i.e. euchromatic, heterochromatic) or different nucleation pathways influence heterochromatin spreading remains poorly understood. Previously, we developed a single-cell sensor in fission yeast that can separately record heterochromatic gene silencing at nucleation sequences and distal sites. Here we couple our quantitative assay to a genetic screen to identify genes encoding nuclear factors linked to the regulation of heterochromatin nucleation and the distal spreading of gene silencing. We find that mechanisms underlying gene silencing distal to a nucleation site differ by chromatin context. For example, Clr6 histone deacetylase complexes containing the Fkh2 transcription factor are specifically required for heterochromatin spreading at constitutive sites. Fkh2 recruits Clr6 to nucleation-distal chromatin sites in such contexts. In addition, we find that a number of chromatin remodeling complexes antagonize nucleation-distal gene silencing. Our results separate the regulation of heterochromatic gene silencing at nucleation versus distal sites and show that it is controlled by context-dependent mechanisms. The results of our genetic analysis constitute a broad community resource that will support further analysis of the mechanisms underlying the spread of epigenetic silencing along chromatin. Repressive structures, or heterochromatin, are seeded at specific genome sequences and then “spread” to silence nearby chromosomal regions. While much is known about the factors that seed heterochromatin, the genetic requirements for spreading are less clear. We devised a fission yeast single-cell method to examine how gene silencing is propagated by the heterochromatin spreading process specifically. Here we use this platform to ask if specific genes are required for the spreading process and whether the same or different genes direct spreading from different chromosomal seeding sites. We find a significant number of genes that specifically promote or antagonize the heterochromatin spreading process. However, different genes are required to enact spreading from different seeding sites. These results have potential implications for cell fate specification, where genes are newly silenced by heterochromatin spreading from diverse chromosomal sites. In a central finding, we show that the Clr6 protein complex, which removes chromatin marks linked to active genes, associates with the Forkhead 2 transcription factor to promote spreading of silencing structures from seeding sites at numerous chromosomal loci. In contrast, we show that proteins that remodel chromatin antagonize the spreading of gene silencing.
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Affiliation(s)
- R. A. Greenstein
- Department of Microbiology &Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
- TETRAD graduate program, University of California San Francisco, San Francisco, California, United States of America
| | - Henry Ng
- Department of Microbiology &Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
- TETRAD graduate program, University of California San Francisco, San Francisco, California, United States of America
| | - Ramon R. Barrales
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität of Munich, Planegg-Martinsried, Germany
| | - Catherine Tan
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America
- Biomedical Sciences graduate program, University of California San Francisco, San Francisco, California, United States of America
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität of Munich, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Bassem Al-Sady
- Department of Microbiology &Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Lemière J, Real-Calderon P, Holt LJ, Fai TG, Chang F. Control of nuclear size by osmotic forces in Schizosaccharomyces pombe. eLife 2022; 11:76075. [PMID: 35856499 PMCID: PMC9410708 DOI: 10.7554/elife.76075] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The size of the nucleus scales robustly with cell size so that the nuclear-to-cell volume ratio (N/C ratio) is maintained during cell growth in many cell types. The mechanism responsible for this scaling remains mysterious. Previous studies have established that the N/C ratio is not determined by DNA amount but is instead influenced by factors such as nuclear envelope mechanics and nuclear transport. Here, we developed a quantitative model for nuclear size control based upon colloid osmotic pressure and tested key predictions in the fission yeast Schizosaccharomyces pombe. This model posits that the N/C ratio is determined by the numbers of macromolecules in the nucleoplasm and cytoplasm. Osmotic shift experiments showed that the fission yeast nucleus behaves as an ideal osmometer whose volume is primarily dictated by osmotic forces. Inhibition of nuclear export caused accumulation of macromolecules in the nucleoplasm, leading to nuclear swelling. We further demonstrated that the N/C ratio is maintained by a homeostasis mechanism based upon synthesis of macromolecules during growth. These studies demonstrate the functions of colloid osmotic pressure in intracellular organization and size control.
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Affiliation(s)
- Joël Lemière
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
| | - Paula Real-Calderon
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States,Centro Andaluz de Biología del DesarrolloSevillaSpain
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone HealthNew YorkUnited States
| | - Thomas G Fai
- Department of Mathematics and Volen Center for Complex Systems, Brandeis UniversityWalthamUnited States
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
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The histone chaperone FACT facilitates heterochromatin spreading by regulating histone turnover and H3K9 methylation states. Cell Rep 2021; 37:109944. [PMID: 34731638 PMCID: PMC8608617 DOI: 10.1016/j.celrep.2021.109944] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/14/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin formation requires three distinct steps: nucleation, self-propagation (spreading) along the chromosome, and faithful maintenance after each replication cycle. Impeding any of those steps induces heterochromatin defects and improper gene expression. The essential histone chaperone FACT (facilitates chromatin transcription) has been implicated in heterochromatin silencing, but the mechanisms by which FACT engages in this process remain opaque. Here, we pinpoint its function to the heterochromatin spreading process in fission yeast. FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and derepresses genes in the vicinity of heterochromatin boundaries. FACT promotes spreading by repressing heterochromatic histone turnover, which is crucial for the H3K9me2 to me3 transition that enables spreading. FACT mutant spreading defects are suppressed by removal of the H3K9 methylation antagonist Epe1. Together, our study identifies FACT as a histone chaperone that promotes heterochromatin spreading and lends support to the model that regulated histone turnover controls the propagation of repressive methylation marks. Heterochromatin establishment requires distinct nucleation and spreading steps. Murawska et al. show that the conserved and essential histone chaperone FACT facilitates the heterochromatin spreading process by maintaining low heterochromatic histone turnover, which enables a productive H3K9 trimethylation step by the methyltransferase Clr4 in fission yeast.
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Greenstein RA, Barrales RR, Sanchez NA, Bisanz JE, Braun S, Al-Sady B. Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability. Genes Dev 2020; 34:99-117. [PMID: 31805521 PMCID: PMC6938669 DOI: 10.1101/gad.328468.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
Abstract
Protection of euchromatin from invasion by gene-repressive heterochromatin is critical for cellular health and viability. In addition to constitutive loci such as pericentromeres and subtelomeres, heterochromatin can be found interspersed in gene-rich euchromatin, where it regulates gene expression pertinent to cell fate. While heterochromatin and euchromatin are globally poised for mutual antagonism, the mechanisms underlying precise spatial encoding of heterochromatin containment within euchromatic sites remain opaque. We investigated ectopic heterochromatin invasion by manipulating the fission yeast mating type locus boundary using a single-cell spreading reporter system. We found that heterochromatin repulsion is locally encoded by Set1/COMPASS on certain actively transcribed genes and that this protective role is most prominent at heterochromatin islands, small domains interspersed in euchromatin that regulate cell fate specifiers. Sensitivity to invasion by heterochromatin, surprisingly, is not dependent on Set1 altering overall gene expression levels. Rather, the gene-protective effect is strictly dependent on Set1's catalytic activity. H3K4 methylation, the Set1 product, antagonizes spreading in two ways: directly inhibiting catalysis by Suv39/Clr4 and locally disrupting nucleosome stability. Taken together, these results describe a mechanism for spatial encoding of euchromatic signals that repel heterochromatin invasion.
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Affiliation(s)
- R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
- TETRAD Graduate Program, University of California at San Francisco, San Francisco, California 94143, USA
| | - Ramon R Barrales
- Department of Physiological Chemistry, Biomedical Center (BMC), Ludwig Maximilians University of Munich, 82152 Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, 82152 Martinsried, Germany
| | - Nicholas A Sanchez
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
- TETRAD Graduate Program, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
| | - Sigurd Braun
- Department of Physiological Chemistry, Biomedical Center (BMC), Ludwig Maximilians University of Munich, 82152 Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, 82152 Martinsried, Germany
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
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Knapp BD, Odermatt P, Rojas ER, Cheng W, He X, Huang KC, Chang F. Decoupling of Rates of Protein Synthesis from Cell Expansion Leads to Supergrowth. Cell Syst 2019; 9:434-445.e6. [PMID: 31706948 PMCID: PMC6911364 DOI: 10.1016/j.cels.2019.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 07/02/2019] [Accepted: 09/30/2019] [Indexed: 01/02/2023]
Abstract
Cell growth is a complex process in which cells synthesize cellular components while they increase in size. It is generally assumed that the rate of biosynthesis must somehow be coordinated with the rate of growth in order to maintain intracellular concentrations. However, little is known about potential feedback mechanisms that could achieve proteome homeostasis or the consequences when this homeostasis is perturbed. Here, we identify conditions in which fission yeast cells are prevented from volume expansion but nevertheless continue to synthesize biomass, leading to general accumulation of proteins and increased cytoplasmic density. Upon removal of these perturbations, this biomass accumulation drove cells to undergo a multi-generational period of "supergrowth" wherein rapid volume growth outpaced biosynthesis, returning proteome concentrations back to normal within hours. These findings demonstrate a mechanism for global proteome homeostasis based on modulation of volume growth and dilution.
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Affiliation(s)
- Benjamin D Knapp
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Pascal Odermatt
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Enrique R Rojas
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wenpeng Cheng
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Xiangwei He
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Kerwyn Casey Huang
- Biophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 941586, USA.
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
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Greenstein RA, Jones SK, Spivey EC, Rybarski JR, Finkelstein IJ, Al-Sady B. Noncoding RNA-nucleated heterochromatin spreading is intrinsically labile and requires accessory elements for epigenetic stability. eLife 2018; 7:32948. [PMID: 30020075 PMCID: PMC6070336 DOI: 10.7554/elife.32948] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
The heterochromatin spreading reaction is a central contributor to the formation of gene-repressive structures, which are re-established with high positional precision, or fidelity, following replication. How the spreading reaction contributes to this fidelity is not clear. To resolve the origins of stable inheritance of repression, we probed the intrinsic character of spreading events in fission yeast using a system that quantitatively describes the spreading reaction in live single cells. We show that spreading triggered by noncoding RNA-nucleated elements is stochastic, multimodal, and fluctuates dynamically across time. This lack of stability correlates with high histone turnover. At the mating type locus, this unstable behavior is restrained by an accessory cis-acting element REIII, which represses histone turnover. Further, REIII safeguards epigenetic memory against environmental perturbations. Our results suggest that the most prevalent type of spreading, driven by noncoding RNA-nucleators, is epigenetically unstable and requires collaboration with accessory elements to achieve high fidelity.
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Affiliation(s)
- R A Greenstein
- Department of Microbiology & Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, United States.,TETRAD graduate program, University of California San Francisco, San Francisco, United States
| | - Stephen K Jones
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Eric C Spivey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - James R Rybarski
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, United States
| | - Bassem Al-Sady
- Department of Microbiology & Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, United States
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Relocation sensors to quantify signaling dynamics in live single cells. Curr Opin Biotechnol 2017; 45:51-58. [PMID: 28131009 DOI: 10.1016/j.copbio.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 11/22/2022]
Abstract
All cells are different. Even isogenic cells can possess diverse shapes, reside in different cell-cycle stages or express various sets of proteins. These variations can modulate the cell response to environmental stimuli and thereby provide key insights into the regulation of signal transduction cascades. Fluorescence microscopy allows to visualize these differences and monitor in real-time the responses of live single cells. In order to observe key cellular events, fluorescent biosensors have been developed. Among many assays, relocation reporters play an important role since they enable the quantification of the signal transduction dynamics. Fluorescently tagged endogenous proteins, as well as synthetic constructs, have allowed the measurement of kinase activity, transcription factor activation, transcription and protein expression in live single cells.
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