1
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Akilli N, Cheutin T, Cavalli G. Phase separation and inheritance of repressive chromatin domains. Curr Opin Genet Dev 2024; 86:102201. [PMID: 38701672 DOI: 10.1016/j.gde.2024.102201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Polycomb-associated chromatin and pericentromeric heterochromatin form genomic domains important for the epigenetic regulation of gene expression. Both Polycomb complexes and heterochromatin factors rely on 'read and write' mechanisms, which, on their own, are not sufficient to explain the formation and the maintenance of these epigenetic domains. Microscopy has revealed that they form specific nuclear compartments separated from the rest of the genome. Recently, some subunits of these molecular machineries have been shown to undergo phase separation, both in vitro and in vivo, suggesting that phase separation might play important roles in the formation and the function of these two kinds of repressive chromatin. In this review, we will present the recent advances in the field of facultative and constitutive heterochromatin formation and maintenance through phase separation.
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Affiliation(s)
- Nazli Akilli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France. https://twitter.com/@sinmerank
| | - Thierry Cheutin
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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2
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Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
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Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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3
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Singh A, Chakrabarti S. Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture. PLoS Comput Biol 2023; 19:e1011725. [PMID: 38109423 PMCID: PMC10760866 DOI: 10.1371/journal.pcbi.1011725] [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: 07/24/2023] [Revised: 01/02/2024] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
The dynamics of inheritance of histones and their associated modifications across cell divisions can have major consequences on maintenance of the cellular epigenomic state. Recent experiments contradict the long-held notion that histone inheritance during replication is always local, suggesting that active and repressed regions of the genome exhibit fundamentally different histone dynamics independent of transcription-coupled turnover. Here we develop a stochastic model of histone dynamics at the replication fork and demonstrate that differential diffusivity of histones in active versus repressed chromatin is sufficient to quantitatively explain these recent experiments. Further, we use the model to predict patterns in histone mark similarity between pairs of genomic loci that should be developed as a result of diffusion, but cannot originate from either PRC2 mediated mark spreading or transcriptional processes. Interestingly, using a combination of CHIP-seq, replication timing and Hi-C datasets we demonstrate that all the computationally predicted patterns are consistently observed for both active and repressive histone marks in two different cell lines. While direct evidence for histone diffusion remains controversial, our results suggest that dislodged histones in euchromatin and facultative heterochromatin may exhibit some level of diffusion within "Diffusion-Accessible-Domains" (DADs), leading to redistribution of epigenetic marks within and across chromosomes. Preservation of the epigenomic state across cell divisions therefore might be achieved not by passing on strict positional information of histone marks, but by maintaining the marks in somewhat larger DADs of the genome.
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Affiliation(s)
- Archit Singh
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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4
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Abdulla AZ, Salari H, Tortora MMC, Vaillant C, Jost D. 4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling. Curr Opin Genet Dev 2023; 79:102033. [PMID: 36893485 DOI: 10.1016/j.gde.2023.102033] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023]
Abstract
Recent experimental observations suggest a strong coupling between the 3D nuclear chromosome organization and epigenomics. However, the mechanistic and functional bases of such interplay remain elusive. In this review, we describe how biophysical modeling has been instrumental in characterizing how genome folding may impact the formation of epigenomic domains and, conversely, how epigenomic marks may affect chromosome conformation. Finally, we discuss how this mutual feedback loop between chromatin organization and epigenome regulation, via the formation of physicochemical nanoreactors, may represent a key functional role of 3D compartmentalization in the assembly and maintenance of stable - but yet plastic - epigenomic landscapes.
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Affiliation(s)
- Amith Z Abdulla
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France; École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France. https://twitter.com/@AmithZafal
| | - Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France; École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France. https://twitter.com/@hosseinsalari65
| | - Maxime M C Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France
| | - Cédric Vaillant
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France.
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France.
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5
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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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6
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Abdulla AZ, Vaillant C, Jost D. Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory. Nucleic Acids Res 2022; 50:9083-9104. [PMID: 36018799 PMCID: PMC9458448 DOI: 10.1093/nar/gkac702] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022] Open
Abstract
In eukaryotes, many stable and heritable phenotypes arise from the same DNA sequence, owing to epigenetic regulatory mechanisms relying on the molecular cooperativity of 'reader-writer' enzymes. In this work, we focus on the fundamental, generic mechanisms behind the epigenome memory encoded by post-translational modifications of histone tails. Based on experimental knowledge, we introduce a unified modeling framework, the painter model, describing the mechanistic interplay between sequence-specific recruitment of chromatin regulators, chromatin-state-specific reader-writer processes and long-range spreading mechanisms. A systematic analysis of the model building blocks highlights the crucial impact of tridimensional chromatin organization and state-specific recruitment of enzymes on the stability of epigenomic domains and on gene expression. In particular, we show that enhanced 3D compaction of the genome and enzyme limitation facilitate the formation of ultra-stable, confined chromatin domains. The model also captures how chromatin state dynamics impact the intrinsic transcriptional properties of the region, slower kinetics leading to noisier expression. We finally apply our framework to analyze experimental data, from the propagation of γH2AX around DNA breaks in human cells to the maintenance of heterochromatin in fission yeast, illustrating how the painter model can be used to extract quantitative information on epigenomic molecular processes.
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Affiliation(s)
- Amith Z Abdulla
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d’Italie, 69007 Lyon, France,École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d’Italie, 69007 Lyon, France
| | - Cédric Vaillant
- Correspondence may also be addressed to Cédric Vaillant. Tel: +33 4 72 72 81 54; Fax: +33 4 72 72 80 00;
| | - Daniel Jost
- To whom correspondence should be addressed. Tel: +33 4 72 72 86 30; Fax: +33 4 72 72 80 00;
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7
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Wakim JG, Sandholtz SH, Spakowitz AJ. Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations. Biophys J 2021; 120:4932-4943. [PMID: 34687722 DOI: 10.1016/j.bpj.2021.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
We examine the relationship between the size of domains of epigenetic marks and the stability of those domains using our theoretical model that captures the physical mechanisms governing the maintenance of epigenetic modifications. We focus our study on histone H3 lysine-9 trimethylation, one of the most common and consequential epigenetic marks with roles in chromatin compaction and gene repression. Our model combines the effects of methyl spreading by methyltransferases and chromatin segregation into heterochromatin and euchromatin because of preferential heterochromatin protein 1 (HP1) binding. Our model indicates that, although large methylated domains are passed successfully from one chromatin generation to the next, small alterations to the methylation sequence are not maintained during chromatin replication. Using our predictive model, we investigate the size required for an epigenetic domain to persist over chromatin generations while surrounded by a much larger domain of opposite methylation and compaction state. We find that there is a critical size threshold in the hundreds-of-nucleosomes scale above which an epigenetic domain will be reliably maintained over generations. The precise size of the threshold differs for heterochromatic and euchromatic domains. Our results are consistent with natural alterations to the epigenetic sequence occurring during embryonic development and due to age-related epigenetic drift.
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Affiliation(s)
- Joseph G Wakim
- Department of Chemical Engineering, Stanford University, Stanford, California
| | | | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California.
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8
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Liu Y, Huang H, Fu J, Zhang Y, Xu J, Zhang L, Sun S, Zhao L, Zhang D, Onwuka JU, Sun H, Cui B, Zhao Y. Colorectal cancer patients with CASK promotor heterogeneous and homogeneous methylation display different prognosis. Aging (Albany NY) 2020; 12:20561-20586. [PMID: 33113509 PMCID: PMC7655177 DOI: 10.18632/aging.103928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Homogenous DNA methylation clearly affects clinical outcomes. However, less is known about the effects of heterogeneous methylation. We aimed to investigate the different effects between CASK promoter methylation heterogeneity and homogeneity on colorectal cancer (CRC) patients' prognosis. The methylation status of CASK in 296 tumor tissues and 255 adjacent normal tissues were evaluated using Methylation-sensitive high-resolution melting (MS-HRM). Digital MS-HRM (dMS-HRM) visualized heterogeneous methylation and subsequent sequencing provided exact patterns. Log-rank test and Cox regression model were adopted to assess the association between CASK methylation status and CRC prognosis with propensity score (PS) method to control confounding biases. Heterogeneous methylation was detected in both tumor (52.2%) and non-neoplastic tissue surrounding the tumor (62.4%). It occurred more frequently in lower levels of tumor invasion (P = 0.002) and male patients (P < 0.001). Compared with heterogeneous methylation, patients with CASK homogeneous methylation presented poorer overall survival (OS) (HR: 1.919, 95% CI: 1.146-3.212, P = 0.013) and disease-free survival (DFS) (HR: 1.913, 95% CI: 1.146-3.194, P = 0.013). This unfavorable effect still existed among older (≥ 50), Dukes staging C/D, and rectal cancer patients. MS-HRM and dMS-HRM when combined can assess the degree and complexity of heterogeneous methylation with a visible pattern.
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Affiliation(s)
- Ying Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Hao Huang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Jinming Fu
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Yuanyuan Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Jing Xu
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Lei Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Simin Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Liyuan Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Ding Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Justina Ucheojor Onwuka
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Hongru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Binbin Cui
- Department of Colorectal Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150086, Heilongjiang Province, The People’s Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Nangang District, Harbin 150086, Heilongjiang Province, The People’s Republic of China
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9
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Reinig J, Ruge F, Howard M, Ringrose L. A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation. Nat Commun 2020; 11:4782. [PMID: 32963223 PMCID: PMC7508846 DOI: 10.1038/s41467-020-18507-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb and Trithorax group proteins maintain stable epigenetic memory of gene expression states for some genes, but many targets show highly dynamic regulation. Here we combine experiment and theory to examine the mechanistic basis of these different modes of regulation. We present a mathematical model comprising a Polycomb/Trithorax response element (PRE/TRE) coupled to a promoter and including Drosophila developmental timing. The model accurately recapitulates published studies of PRE/TRE mediated epigenetic memory of both silencing and activation. With minimal parameter changes, the same model can also recapitulate experimental data for a different PRE/TRE that allows dynamic regulation of its target gene. The model predicts that both cell cycle length and PRE/TRE identity are critical for determining whether the system gives stable memory or dynamic regulation. Our work provides a simple unifying framework for a rich repertoire of PRE/TRE functions, and thus provides insights into genome-wide Polycomb/Trithorax regulation. Polycomb (PcG) and Trithorax (TrxG) group regulate several hundred target genes with important roles in development and disease. Here the authors combine experiment and theory to provide evidence that the Polycomb/Trithorax system has the potential for a rich repertoire of regulatory modes beyond simple epigenetic memory.
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Affiliation(s)
- Jeannette Reinig
- Humboldt Universität zu Berlin, IRI- Lifesciences, Philippstr. 13, 10115, Berlin, Germany
| | - Frank Ruge
- IMBA, Institute of Molecular Biotechnology, Dr. Bohr- Gasse 3, 1030, Vienna, Austria
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Leonie Ringrose
- Humboldt Universität zu Berlin, IRI- Lifesciences, Philippstr. 13, 10115, Berlin, Germany. .,IMBA, Institute of Molecular Biotechnology, Dr. Bohr- Gasse 3, 1030, Vienna, Austria.
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10
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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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11
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Sneppen K, Ringrose L. Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent. Nat Commun 2019; 10:2133. [PMID: 31086177 PMCID: PMC6513952 DOI: 10.1038/s41467-019-10130-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/12/2019] [Indexed: 12/15/2022] Open
Abstract
Polycomb (PcG) and Trithorax (TrxG) group proteins give stable epigenetic memory of silent and active gene expression states, but also allow poised states in pluripotent cells. Here we systematically address the relationship between poised, active and silent chromatin, by integrating 73 publications on PcG/TrxG biochemistry into a mathematical model comprising 144 nucleosome modification states and 8 enzymatic reactions. Our model predicts that poised chromatin is bistable and not bivalent. Bivalent chromatin, containing opposing active and silent modifications, is present as an unstable background population in all system states, and different subtypes co-occur with active and silent chromatin. In contrast, bistability, in which the system switches frequently between stable active and silent states, occurs under a wide range of conditions at the transition between monostable active and silent system states. By proposing that bistability and not bivalency is associated with poised chromatin, this work has implications for understanding the molecular nature of pluripotency. Polycomb and Trithorax group proteins regulate silent and active gene expression states, but also allow poised states in pluripotent cells. Here the authors present a mathematical model that integrates data on Polycomb/ Trithorax biochemistry into a single coherent framework which predicts that poised chromatin is not bivalent as previously proposed, but is bistable, meaning that the system switches frequently between stable active and silent states.
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Affiliation(s)
- Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
| | - Leonie Ringrose
- Integrated Research Institute for Life Sciences, Humboldt-Universität zu Berlin, Philippstrasse 13, Haus 22, 10115, Berlin, Germany.
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12
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Tan H, Liu T, Zhang J, Zhou T. Random positioning of nucleosomes enhances heritable bistability. MOLECULAR BIOSYSTEMS 2017; 13:132-141. [PMID: 27833942 DOI: 10.1039/c6mb00729e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromosomal regions are often dynamically modified by histones, leading to the uncertainty of nucleosome positions. Experiments have provided evidence for this randomness, but it is unclear how it impacts epigenetic heritability. Here, by analyzing a mechanic model at the molecular level, which considers three representative types of nucleosomes (unmodified, methylated, and acetylated) and dynamic nucleosome modifications, we find that in contrast to the equidistance partition of nucleosomes, random partition can significantly enhance heritable bistability. Moreover, the more "chaotic" the nucleosome positions are, the better the heritable bistability is, in contrast to the previous view. In both cases of nucleosome positioning, heritable bistability occurs only when the total nucleosome number is beyond a threshold, and it depends strongly on the allocation rate that enzymes regulate transitions between different nucleosome types. Thus, we conclude that random positioning of nucleosomes is an unneglectable factor impacting heritable bistability. A point worth mentioning is that our model established on a master equation can easily be extended to include other more complex processes underlying dynamic nucleosome modifications.
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Affiliation(s)
- Heli Tan
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China. and School of Mathematics and Computational Science, Xiangtan University, XiangTan 411105, P. R. China
| | - Tuoqi Liu
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Tianshou Zhou
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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Defining, distinguishing and detecting the contribution of heterogeneous methylation to cancer heterogeneity. Semin Cell Dev Biol 2016; 64:5-17. [PMID: 27582426 DOI: 10.1016/j.semcdb.2016.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 01/07/2023]
Abstract
DNA methylation is a fundamental means of epigenetic gene regulation that occurs in virtually all cell types. In many higher organisms, including humans, it plays vital roles in cell differentiation and homeostatic maintenance of cell phenotype. The control of DNA methylation has traditionally been attributed to a highly coordinated, linear process, whose dysregulation has been associated with numerous pathologies including cancer, where it occurs early in, and even prior to, the development of neoplastic tissues. Recent experimental evidence has demonstrated that, contrary to prevailing paradigms, methylation patterns are actually maintained through inexact, dynamic processes. These processes normally result in minor stochastic differences between cells that accumulate with age. However, various factors, including cancer itself, can lead to substantial differences in intercellular methylation patterns, viz. methylation heterogeneity. Advancements in molecular biology techniques are just now beginning to allow insight into how this heterogeneity contributes to clonal evolution and overall cancer heterogeneity. In the current review, we begin by presenting a didactic overview of how the basal bimodal methylome is established and maintained. We then provide a synopsis of some of the factors that lead to the accrual of heterogeneous methylation and how this heterogeneity may lead to gene silencing and impact the development of cancerous phenotypes. Lastly, we highlight currently available methylation assessment techniques and discuss their suitability to the study of heterogeneous methylation.
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Májer I, Hajihosseini A, Becskei A. Identification of optimal parameter combinations for the emergence of bistability. Phys Biol 2015; 12:066011. [DOI: 10.1088/1478-3975/12/6/066011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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