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Dhillon N, Kamakaka RT. Transcriptional silencing in Saccharomyces cerevisiae: known unknowns. Epigenetics Chromatin 2024; 17:28. [PMID: 39272151 PMCID: PMC11401328 DOI: 10.1186/s13072-024-00553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae is a persistent and highly stable form of gene repression. It involves DNA silencers and repressor proteins that bind nucleosomes. The silenced state is influenced by numerous factors including the concentration of repressors, nature of activators, architecture of regulatory elements, modifying enzymes and the dynamics of chromatin.Silencers function to increase the residence time of repressor Sir proteins at silenced domains while clustering of silenced domains enables increased concentrations of repressors and helps facilitate long-range interactions. The presence of an accessible NDR at the regulatory regions of silenced genes, the cycling of chromatin configurations at regulatory sites, the mobility of Sir proteins, and the non-uniform distribution of the Sir proteins across the silenced domain, all result in silenced chromatin that only stably silences weak promoters and enhancers via changes in transcription burst duration and frequency.These data collectively suggest that silencing is probabilistic and the robustness of silencing is achieved through sub-optimization of many different nodes of action such that a stable expression state is generated and maintained even though individual constituents are in constant flux.
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Affiliation(s)
- Namrita Dhillon
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Rohinton T Kamakaka
- Department of MCD Biology, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
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Wu K, Dhillon N, Bajor A, Abrahamson S, Kamakaka RT. Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561072. [PMID: 37873261 PMCID: PMC10592971 DOI: 10.1101/2023.10.05.561072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The interplay between nucleosomes and transcription factors leads to programs of gene expression. Transcriptional silencing involves the generation of a chromatin state that represses transcription and is faithfully propagated through DNA replication and cell division. Using multiple reporter assays, including directly visualizing transcription in single cells, we investigated a diverse set of UAS enhancers and core promoters for their susceptibility to heterochromatic gene silencing. These results show that heterochromatin only stably silences weak and stress induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements and the partial repression did not result in bistable expression states. Permutation analysis of different UAS enhancers and core promoters indicate that both elements function together to determine the susceptibility of regulatory sequences to repression. Specific histone modifiers and chromatin remodellers function in an enhancer specific manner to aid these elements to resist repression suggesting that Sir proteins likely function in part by reducing nucleosome mobility. We also show that the strong housekeeping regulatory elements can be repressed if silencer bound Sir1 is increased, suggesting that Sir1 is a limiting component in silencing. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating type gene regulatory elements but not strong housekeeping gene regulatory sequences which could help explain why these genes are often found at the boundaries of silenced domains.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Namrita Dhillon
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Sara Abrahamson
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Rohinton T. Kamakaka
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
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Newar K, Abdulla AZ, Salari H, Fanchon E, Jost D. Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells. PLoS Comput Biol 2022; 18:e1010450. [PMID: 36054209 PMCID: PMC9477427 DOI: 10.1371/journal.pcbi.1010450] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 09/15/2022] [Accepted: 07/28/2022] [Indexed: 01/02/2023] Open
Abstract
The Polycomb system via the methylation of the lysine 27 of histone H3 (H3K27) plays central roles in the silencing of many lineage-specific genes during development. Recent experimental evidence suggested that the recruitment of histone modifying enzymes like the Polycomb repressive complex 2 (PRC2) at specific sites and their spreading capacities from these sites are key to the establishment and maintenance of a proper epigenomic landscape around Polycomb-target genes. Here, to test whether such mechanisms, as a minimal set of qualitative rules, are quantitatively compatible with data, we developed a mathematical model that can predict the locus-specific distributions of H3K27 modifications based on previous biochemical knowledge. Within the biological context of mouse embryonic stem cells, our model showed quantitative agreement with experimental profiles of H3K27 acetylation and methylation around Polycomb-target genes in wild-type and mutants. In particular, we demonstrated the key role of the reader-writer module of PRC2 and of the competition between the binding of activating and repressing enzymes in shaping the H3K27 landscape around transcriptional start sites. The predicted dynamics of establishment and maintenance of the repressive trimethylated H3K27 state suggest a slow accumulation, in perfect agreement with experiments. Our approach represents a first step towards a quantitative description of PcG regulation in various cellular contexts and provides a generic framework to better characterize epigenetic regulation in normal or disease situations.
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Affiliation(s)
- Kapil Newar
- Univ Grenoble Alpes, CNRS, TIMC laboratory, UMR 5525, Grenoble, France
| | - Amith Zafal Abdulla
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Eric Fanchon
- Univ Grenoble Alpes, CNRS, TIMC laboratory, UMR 5525, Grenoble, France
| | - Daniel Jost
- Univ Grenoble Alpes, CNRS, TIMC laboratory, UMR 5525, Grenoble, France
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail:
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Guo XJ, Yang D, Zhang XY. Epigenetics recording varied environment and complex cell events represents the origin of cellular aging. J Zhejiang Univ Sci B 2020; 20:550-562. [PMID: 31168969 DOI: 10.1631/jzus.b1800507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although a relationship between epigenetics and aging phenotypic changes has been established, a theoretical explanation of the intrinsic connection between the epigenetics and aging is lacking. In this essay, we propose that epigenetic recording of varied cell environment and complex history could be an origin of cellular aging. Through epigenetic modifications, the environment and historical events can induce the chromatin template into an activated or repressive accessible structure, thereby shaping the DNA template into a spectrum of chromatin states. The inner nature of diversity and conflicts born by the cell environment and its historical events are hence recorded into the chromatin template. This could result in a dissipated spectrum of the chromatin state and chaos in overall gene expression. An unavoidable degradation of epigenome entropy, similar to Shannon entropy, would be consequently induced. The resultant disorder in epigenome, characterized by corrosion of epigenome entropy as reflected in chromatin template, can be stably memorized and propagated through cell division. Furthermore, the hysteretic nature of epigenetics responding to the emerging environment could exacerbate the degradation of epigenome entropy. As well as stochastic errors, we propose that outside entropy (or chaos) derived from the varied environment and complex cell history, gradually input and imprinted into the chromatin via epigenetic modifications, would lead inevitably to cellular aging, the extent of which could be aggravated by hysteresis of epigenetics without error erasing and correction.
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Affiliation(s)
- Xue-Jun Guo
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yuan Zhang
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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Jost D, Vaillant C. Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance. Nucleic Acids Res 2019; 46:2252-2264. [PMID: 29365171 PMCID: PMC5861409 DOI: 10.1093/nar/gky009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/11/2018] [Indexed: 02/05/2023] Open
Abstract
Recent progresses of genome-wide chromatin conformation capture techniques have shown that the genome is segmented into hierarchically organized spatial compartments. However, whether this non-random 3D organization only reflects or indeed contributes—and how—to the regulation of genome function remain to be elucidated. The observation in many species that 3D domains correlate strongly with the 1D epigenomic information along the genome suggests a dynamic coupling between chromatin organization and epigenetic regulation. Here, we posit that chromosome folding may contribute to the maintenance of a robust epigenomic identity via the formation of spatial compartments like topologically-associating domains. Using a novel theoretical framework, the living chromatin model, we show that 3D compartmentalization leads to the spatial colocalization of epigenome regulators, thus increasing their local concentration and enhancing their ability to spread an epigenomic signal at long-range. Interestingly, we find that the presence of 1D insulator elements, like CTCF, may contribute greatly to the stable maintenance of adjacent antagonistic epigenomic domains. We discuss the generic implications of our findings in the light of various biological contexts from yeast to human. Our approach provides a modular framework to improve our understanding and to investigate in details the coupling between the structure and function of chromatin.
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Affiliation(s)
- Daniel Jost
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
- To whom correspondence should be addressed. Tel: +33 4 72 72 86 34; Fax: +33 4 72 72 89 50; . Correspondence may also be addressed to Daniel Jost. Tel: +33 4 56 52 00 69; Fax: +33 4 56 52 00 44;
| | - Cédric Vaillant
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, 69007 Lyon, France
- To whom correspondence should be addressed. Tel: +33 4 72 72 86 34; Fax: +33 4 72 72 89 50; . Correspondence may also be addressed to Daniel Jost. Tel: +33 4 56 52 00 69; Fax: +33 4 56 52 00 44;
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Yeast epigenetics: the inheritance of histone modification states. Biosci Rep 2019; 39:BSR20182006. [PMID: 30877183 PMCID: PMC6504666 DOI: 10.1042/bsr20182006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 01/12/2023] Open
Abstract
Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast) are two of the most recognised and well-studied model systems for epigenetic regulation and the inheritance of chromatin states. Their silent loci serve as a proxy for heterochromatic chromatin in higher eukaryotes, and as such both species have provided a wealth of information on the mechanisms behind the establishment and maintenance of epigenetic states, not only in yeast, but in higher eukaryotes. This review focuses specifically on the role of histone modifications in governing telomeric silencing in S. cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that exemplify epigenetic inheritance. We discuss the recent advancements that for the first time provide a mechanistic understanding of how heterochromatin, dictated by histone modifications specifically, is preserved during S-phase. We also discuss the current state of our understanding of yeast nucleosome dynamics during DNA replication, an essential component in delineating the contribution of histone modifications to epigenetic inheritance.
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Zerihun MB, Vaillant C, Jost D. Effect of replication on epigenetic memory and consequences on gene transcription. Phys Biol 2015; 12:026007. [PMID: 25884278 DOI: 10.1088/1478-3975/12/2/026007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Gene activity in eukaryotes is in part regulated at the level of chromatin through the assembly of local chromatin states that are more or less permissive to transcription. How do these chromatin states achieve their functions and whether or not they contribute to the epigenetic inheritance of the transcriptional program remain to be elucidated. In cycling cells, stability is indeed strongly challenged by the periodic occurrence of replication and cell division. To address this question, we perform simulations of the stochastic dynamics of chromatin states when driven out-of-equilibrium by periodic perturbations. We show how epigenetic memory is significantly affected by the cell cycle length. In addition, we develop a simple model to connect the epigenetic state to the transcriptional state and gene activity. In particular, it suggests that replication may induce transcriptional bursting at repressive loci. Finally, we discuss how our findings-effect of replication and link to gene transcription-have original and deep implications to various biological contexts of epigenetic memory.
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Affiliation(s)
- Mehari B Zerihun
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, UMR 5672, Lyon, France
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