1
|
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] [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.
Collapse
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.
| |
Collapse
|
2
|
Ukmar-Godec T, Cima-Omori MS, Yerkesh Z, Eswara K, Yu T, Ramesh R, Riviere G, Ibanez de Opakua A, Fischle W, Zweckstetter M. Multimodal interactions drive chromatin phase separation and compaction. Proc Natl Acad Sci U S A 2023; 120:e2308858120. [PMID: 38048471 PMCID: PMC10723116 DOI: 10.1073/pnas.2308858120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/01/2023] [Indexed: 12/06/2023] Open
Abstract
Gene silencing is intimately connected to DNA condensation and the formation of transcriptionally inactive heterochromatin by Heterochromatin Protein 1α (HP1α). Because heterochromatin foci are dynamic and HP1α can promote liquid-liquid phase separation, HP1α-mediated phase separation has been proposed as a mechanism of chromatin compaction. The molecular basis of HP1α-driven phase separation and chromatin compaction and the associated regulation by trimethylation of lysine 9 in histone 3 (H3K9me3), which is the hallmark of constitutive heterochromatin, is however largely unknown. Using a combination of chromatin compaction and phase separation assays, site-directed mutagenesis, and NMR-based interaction analysis, we show that human HP1α can compact chromatin in the absence of liquid-liquid phase separation. We further demonstrate that H3K9-trimethylation promotes compaction of chromatin arrays through multimodal interactions. The results provide molecular insights into HP1α-mediated chromatin compaction and thus into the role of human HP1α in the regulation of gene silencing.
Collapse
Affiliation(s)
- Tina Ukmar-Godec
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Maria-Sol Cima-Omori
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Zhadyra Yerkesh
- Bioscience Program, Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Karthik Eswara
- Bioscience Program, Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Taekyung Yu
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Reshma Ramesh
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Gwladys Riviere
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Alain Ibanez de Opakua
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
| | - Wolfgang Fischle
- Bioscience Program, Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases, Translational Structural Biology, Göttingen37075, Germany
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
| |
Collapse
|
3
|
Xu K, Li J, Li WX. Simulation of STAT and HP1 interaction by molecular docking. Cell Signal 2023; 112:110925. [PMID: 37839545 DOI: 10.1016/j.cellsig.2023.110925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Heterochromatin Protein 1 (HP1) is a major component of heterochromatin. Multiple proteins have been shown to interact with HP1 with the HP1-binding motif PxVxL/I, thereby affecting heterochromatin stability. The HP1-interacting proteins include the signal transducer and activator of transcription (STAT) protein, which can be regulated by phosphorylation on a tyrosine around amino acid 700 in the carboxyl terminus. Previous research has shown that unphosphorylated STAT (uSTAT) binds to HP1 via a PxVxI HP1-binding motif and maintains the stability of heterochromatin, while phosphorylated STAT (pSTAT) dissociates from HP1, resulting in heterochromatin disruption. To understand the theoretical basis of the biochemical observations, we employed computational modeling to investigate STAT-HP1 binding configurations and the effect of STAT phosphorylation on their interaction. Using STAT3 and HP1α protein structures for molecular docking and thermodynamic calculations, our computations predict that uSTAT homodimers have a higher affinity for HP1 and a lower affinity for DNA than pSTAT homodimers, and that phosphorylation induces a conformational change in STAT, shifting its binding preference from HP1 to DNA. The results of our modeling studies support the idea that phosphorylation drives STAT from HP1-binding to DNA-binding, suggesting a potential role for uSTAT in both maintaining and initiating heterochromatin formation.
Collapse
Affiliation(s)
- Kangxin Xu
- Department of Medicine, University of California San Diego, USA
| | - Jinghong Li
- Department of Medicine, University of California San Diego, USA
| | - Willis X Li
- Department of Medicine, University of California San Diego, USA.
| |
Collapse
|
4
|
Kiseleva AA, Poleshko A. The secret life of chromatin tethers. FEBS Lett 2023; 597:2782-2790. [PMID: 37339933 PMCID: PMC10730768 DOI: 10.1002/1873-3468.14685] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
The nuclear envelope plays an essential role in organizing the genome inside of the nucleus. The inner nuclear membrane is coated with a meshwork of filamentous lamin proteins that provide a surface to organize a variety of cellular processes. A subset of nuclear lamina- and membrane-associated proteins functions as anchors to hold transcriptionally silent heterochromatin at the nuclear periphery. While most chromatin tethers are integral membrane proteins, a limited number are lamina-bound. One example is the mammalian proline-rich 14 (PRR14) protein. PRR14 is a recently characterized protein with unique function that is different from other known chromatin tethers. Here, we review our current understanding of PRR14 structure and function in organizing heterochromatin at the nuclear periphery.
Collapse
Affiliation(s)
- Anna A. Kiseleva
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
5
|
Berg IK, Currey ML, Gupta S, Berrada Y, Nguyen BV, Pho M, Patteson AE, Schwarz JM, Banigan EJ, Stephens AD. Transcription inhibition suppresses nuclear blebbing and rupture independently of nuclear rigidity. J Cell Sci 2023; 136:jcs261547. [PMID: 37756607 PMCID: PMC10660790 DOI: 10.1242/jcs.261547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Chromatin plays an essential role in the nuclear mechanical response and determining nuclear shape, which maintain nuclear compartmentalization and function. However, major genomic functions, such as transcription activity, might also impact cell nuclear shape via blebbing and rupture through their effects on chromatin structure and dynamics. To test this idea, we inhibited transcription with several RNA polymerase II inhibitors in wild-type cells and perturbed cells that presented increased nuclear blebbing. Transcription inhibition suppressed nuclear blebbing for several cell types, nuclear perturbations and transcription inhibitors. Furthermore, transcription inhibition suppressed nuclear bleb formation, bleb stabilization and bleb-based nuclear ruptures. Interestingly, transcription inhibition did not alter the histone H3 lysine 9 (H3K9) modification state, nuclear rigidity, and actin compression and contraction, which typically control nuclear blebbing. Polymer simulations suggested that RNA polymerase II motor activity within chromatin could drive chromatin motions that deform the nuclear periphery. Our data provide evidence that transcription inhibition suppresses nuclear blebbing and rupture, in a manner separate and distinct from chromatin rigidity.
Collapse
Affiliation(s)
- Isabel K. Berg
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Marilena L. Currey
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sarthak Gupta
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - Yasmin Berrada
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Bao V. Nguyen
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Mai Pho
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Alison E. Patteson
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - J. M. Schwarz
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
- Indian Creek Farm, Ithaca, NY 14850, USA
| | - Edward J. Banigan
- Institute of Medical Engineering & Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| |
Collapse
|
6
|
Joron K, Viegas JO, Haas-Neill L, Bier S, Drori P, Dvir S, Lim PSL, Rauscher S, Meshorer E, Lerner E. Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation. Nat Commun 2023; 14:4885. [PMID: 37573411 PMCID: PMC10423231 DOI: 10.1038/s41467-023-40647-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1α (HP1α) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1α condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.
Collapse
Affiliation(s)
- Khalil Joron
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Juliane Oliveira Viegas
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Liam Haas-Neill
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Sariel Bier
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Shani Dvir
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Patrick Siang Lin Lim
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Sarah Rauscher
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Department of Physics, University of Toronto, Toronto, ON, M5S 1A7, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
- Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| |
Collapse
|
7
|
Grewal SIS. The molecular basis of heterochromatin assembly and epigenetic inheritance. Mol Cell 2023; 83:1767-1785. [PMID: 37207657 PMCID: PMC10309086 DOI: 10.1016/j.molcel.2023.04.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023]
Abstract
Heterochromatin plays a fundamental role in gene regulation, genome integrity, and silencing of repetitive DNA elements. Histone modifications are essential for the establishment of heterochromatin domains, which is initiated by the recruitment of histone-modifying enzymes to nucleation sites. This leads to the deposition of histone H3 lysine-9 methylation (H3K9me), which provides the foundation for building high-concentration territories of heterochromatin proteins and the spread of heterochromatin across extended domains. Moreover, heterochromatin can be epigenetically inherited during cell division in a self-templating manner. This involves a "read-write" mechanism where pre-existing modified histones, such as tri-methylated H3K9 (H3K9me3), support chromatin association of the histone methyltransferase to promote further deposition of H3K9me. Recent studies suggest that a critical density of H3K9me3 and its associated factors is necessary for the propagation of heterochromatin domains across multiple generations. In this review, I discuss the key experiments that have highlighted the importance of modified histones for epigenetic inheritance.
Collapse
Affiliation(s)
- Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
8
|
Novo CL, Wong EV, Hockings C, Poudel C, Sheekey E, Wiese M, Okkenhaug H, Boulton SJ, Basu S, Walker S, Kaminski Schierle GS, Narlikar GJ, Rugg-Gunn PJ. Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells. Nat Commun 2022; 13:3525. [PMID: 35725842 PMCID: PMC9209518 DOI: 10.1038/s41467-022-31198-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/07/2022] [Indexed: 12/25/2022] Open
Abstract
Heterochromatin maintains genome integrity and function, and is organised into distinct nuclear domains. Some of these domains are proposed to form by phase separation through the accumulation of HP1ɑ. Mouse heterochromatin contains noncoding major satellite repeats (MSR), which are highly transcribed in mouse embryonic stem cells (ESCs). Here, we report that MSR transcripts can drive the formation of HP1ɑ droplets in vitro, and modulate heterochromatin into dynamic condensates in ESCs, contributing to the formation of large nuclear domains that are characteristic of pluripotent cells. Depleting MSR transcripts causes heterochromatin to transition into a more compact and static state. Unexpectedly, changing heterochromatin's biophysical properties has severe consequences for ESCs, including chromosome instability and mitotic defects. These findings uncover an essential role for MSR transcripts in modulating the organisation and properties of heterochromatin to preserve genome stability. They also provide insights into the processes that could regulate phase separation and the functional consequences of disrupting the properties of heterochromatin condensates.
Collapse
Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
- Tommy's National Miscarriage Research Centre at Imperial College London, London, W12 0NN, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Emily V Wong
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Colin Hockings
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Chetan Poudel
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Eleanor Sheekey
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Meike Wiese
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Hanneke Okkenhaug
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Artios Pharma Ltd., B940, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Srinjan Basu
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Simon Walker
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | | | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
| |
Collapse
|
9
|
Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
Collapse
Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
| |
Collapse
|
10
|
Abstract
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription, RNA processing, DNA replication, and repair accumulate in self-organizing membraneless chromatin subcompartments. These structures contribute to efficiently conduct chromatin-mediated reactions and to establish specific cellular programs. However, the underlying mechanisms for their formation are only partly understood. Recent studies invoke liquid-liquid phase separation (LLPS) of proteins and RNAs in the establishment of chromatin activity patterns. At the same time, the folding of chromatin in the nucleus can drive genome partitioning into spatially distinct domains. Here, the interplay between chromatin organization, chromatin binding, and LLPS is discussed by comparing and contrasting three prototypical chromatin subcompartments: the nucleolus, clusters of active RNA polymerase II, and pericentric heterochromatin domains. It is discussed how the different ways of chromatin compartmentalization are linked to transcription regulation, the targeting of soluble factors to certain parts of the genome, and to disease-causing genetic aberrations.
Collapse
Affiliation(s)
- Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany
| |
Collapse
|
11
|
Liu Y, Yang X, Zhou M, Yang Y, Li F, Yan X, Zhang M, Wei Z, Qin S, Min J. Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain. J Biol Chem 2022; 298:101623. [PMID: 35074427 PMCID: PMC8861120 DOI: 10.1016/j.jbc.2022.101623] [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: 11/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.
Collapse
Affiliation(s)
- Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China.
| | - Xiajie Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Yinxue Yang
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Fangzhou Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Xuemei Yan
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | | | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Su Qin
- Life Science Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China.
| |
Collapse
|
12
|
Measuring the buffering capacity of gene silencing in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2021; 118:2111841118. [PMID: 34857629 PMCID: PMC8670432 DOI: 10.1073/pnas.2111841118] [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] [Accepted: 10/16/2021] [Indexed: 11/18/2022] Open
Abstract
Gene silencing, once established, is stably maintained for several generations. Despite the high fidelity of the inheritance of the silent state, individual components of silenced chromatin are in constant flux. Models suggest that silent loci can tolerate fluctuations in Sir proteins and histone acetylation levels, but the level of tolerance is unknown. To understand the quantitative relationships between H4K16 acetylation, Sir proteins, and silencing, we developed assays to quantitatively alter a H4K16 acetylation mimic allele and Sir protein levels and measure the effects of these changes on silencing. Our data suggest that a two- to threefold change in levels of histone marks and specific Sir proteins affects the stability of the silent state of a large chromatin domain. Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. Transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux, giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown, and we developed methods to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state as well as to measure the levels of the enzymes and structural proteins necessary for silencing. We show that loss of silencing required 50 to 75% acetyl-mimic histones, though the precise levels were influenced by silencer strength and upstream activating sequence (UAS) enhancer/promoter strength. Measurements of repressor protein levels necessary for silencing showed that reducing SIR4 gene dosage two- to threefold significantly weakened silencing, though reducing the gene copy numbers for Sir2 or Sir3 to the same extent did not significantly affect silencing suggesting that Sir4 was a limiting component in gene silencing. Calculations suggest that a mere twofold reduction in the ability of acetyltransferases to acetylate nucleosomes across a large array of nucleosomes may be sufficient to generate a transcriptionally silent domain.
Collapse
|
13
|
Shi XX, Wang ZZ, Wang YL, Huang GY, Yang JF, Wang F, Hao GF, Yang GF. PTMdyna: exploring the influence of post-translation modifications on protein conformational dynamics. Brief Bioinform 2021; 23:6394992. [PMID: 34643234 DOI: 10.1093/bib/bbab424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 11/14/2022] Open
Abstract
Protein post-translational modifications (PTM) play vital roles in cellular regulation, modulating functions by driving changes in protein structure and dynamics. Exploring comprehensively the influence of PTM on conformational dynamics can facilitate the understanding of the related biological function and molecular mechanism. Currently, a series of excellent computation tools have been designed to analyze the time-dependent structural properties of proteins. However, the protocol aimed to explore conformational dynamics of post-translational modified protein is still a blank. To fill this gap, we present PTMdyna to visually predict the conformational dynamics differences between unmodified and modified proteins, thus indicating the influence of specific PTM. PTMdyna exhibits an AUC of 0.884 tested on 220 protein-protein complex structures. The case of heterochromatin protein 1α complexed with lysine 9-methylated histone H3, which is critical for genomic stability and cell differentiation, was used to demonstrate its applicability. PTMdyna provides a reliable platform to predict the influence of PTM on protein dynamics, making it easier to interpret PTM functionality at the structure level. The web server is freely available at http://ccbportal.com/PTMdyna.
Collapse
Affiliation(s)
- Xing-Xing Shi
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Zhi-Zheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Yu-Liang Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Guang-Yi Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China.,State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| |
Collapse
|
14
|
Sato Y, Nakao M, Kimura H. Live-Cell Imaging Probes to Track Chromatin Modification Dynamics. Microscopy (Oxf) 2021; 70:415-422. [PMID: 34329472 PMCID: PMC8491620 DOI: 10.1093/jmicro/dfab030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Live-cell probes to visualize chromatin and its modifications have become powerful tools to monitor dynamic chromatin regulation. Bulk chromatin can be visualized by both small fluorescent dyes and fluorescent proteins, and specific endogenous genomic loci have been detected by adapting genome-editing tools. To track chromatin modifications in living cells, various types of probes have been developed. Protein domains that bind weakly to specific modifications, such as chromodomains for histone methylation, can be repeated to create a tighter binding probe that can then be tagged with a fluorescent protein. It has also been demonstrated that antigen-binding fragments and single-chain variable fragments from modification-specific antibodies can serve as binding probes without disturbing cell division, development and differentiation. These modification-binding modules are used in modification sensors based on fluorescence/Förster resonance energy transfer to measure the intramolecular conformational changes triggered by modifications. Other probes can be created using a bivalent binding system, such as fluorescence complementation or luciferase chemiluminescence. Live-cell chromatin modification imaging using these probes will address dynamic chromatin regulation and will be useful for assaying and screening effective epigenome drugs in cells and organisms.
Collapse
Affiliation(s)
- Yuko Sato
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Masaru Nakao
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| |
Collapse
|
15
|
Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, Scalzo D, Telling A, Groudine M, Brangwynne CP, Marko JF, Stephens AD. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. eLife 2021; 10:e63972. [PMID: 34106828 PMCID: PMC8233041 DOI: 10.7554/elife.63972] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1α (CBX5) is unknown. We used a novel HP1α auxin-inducible degron human cell line to rapidly degrade HP1α. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1α is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1αI165E indicate that chromatin crosslinking via HP1α dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1α similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1α is therefore a critical chromatin-crosslinking protein that provides mechanical strength to chromosomes and the nucleus throughout the cell cycle and supports cellular functions.
Collapse
Affiliation(s)
- Amy R Strom
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Ronald J Biggs
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Katherine Chiu
- Biology Department, University of Massachusetts AmherstAmherstUnited States
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jimena Collado
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | | | - Leah J Tait
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - David Scalzo
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Agnes Telling
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Mark Groudine
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Clifford P Brangwynne
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Andrew D Stephens
- Biology Department, University of Massachusetts AmherstAmherstUnited States
| |
Collapse
|
16
|
Keenen MM, Brown D, Brennan LD, Renger R, Khoo H, Carlson CR, Huang B, Grill SW, Narlikar GJ, Redding S. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. eLife 2021; 10:e64563. [PMID: 33661100 PMCID: PMC7932698 DOI: 10.7554/elife.64563] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog's DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.
Collapse
Affiliation(s)
- Madeline M Keenen
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - David Brown
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Lucy D Brennan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Roman Renger
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Harrison Khoo
- Department of Mechanical Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Christopher R Carlson
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Physiology, University of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Cluster of Excellence Physics of Life, Technische Universität DresdenDresdenGermany
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Marine Biological LaboratoryWoods HoleUnited States
| |
Collapse
|
17
|
Tien CL, Mohammadparast S, Chang C. Heterochromatin protein 1 beta regulates neural and neural crest development by repressing pluripotency-associated gene pou5f3.2/oct25 in Xenopus. Dev Dyn 2021; 250:1113-1124. [PMID: 33595886 DOI: 10.1002/dvdy.319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Heterochromatin protein 1 (HP1) is associated with and plays a role in compact chromatin conformation, but the function of HP1 in vertebrate embryogenesis is not understood completely. RESULTS Here, we explore the activity of HP1 in early neural development in the frog Xenopus laevis. We show that the three isoforms of HP1, HP1α, β, and γ, are expressed in similar patterns in the neural and neural crest derivatives in early embryos. Despite this, knockdown of HP1β and HP1γ, but not HP1α, in presumptive neural tissues leads to head defects. Late pan-neural markers and neural crest specifier genes are reduced, but early neural and neural plate border genes are less affected in the morphant embryos. Further investigation reveals that neuronal differentiation is impaired and a pluripotency-associated gene, pou5f3.2/oct25, is expanded in HP1β morphants. Ectopic expression of pou5f3.2/oct25 mimics the effect of HP1β knockdown on marker expression, whereas simultaneous knockdown of HP1β and pou5f3.2/oct25 partially rescues expression of these genes. CONCLUSION Taken together, the data suggest that HP1β regulates transition from precursor to more differentiated cell types during neural and neural crest development in Xenopus, and it does so at least partially via repression of the pluripotency-associated transcription regulator pou5f3.2/oct25.
Collapse
Affiliation(s)
- Chih-Liang Tien
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Saeid Mohammadparast
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|
18
|
Lobbia VR, Trueba Sanchez MC, van Ingen H. Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure. J Mol Biol 2021; 433:166827. [PMID: 33460684 DOI: 10.1016/j.jmb.2021.166827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/20/2022]
Abstract
The regulation of chromatin biology ultimately depends on the manipulation of its smallest subunit, the nucleosome. The proteins that bind and operate on the nucleosome do so, while their substrate is part of a polymer embedded in the dense nuclear environment. Their molecular interactions must in some way be tuned to deal with this complexity. Due to the rapid increase in the number of high-resolution structures of nucleosome-protein complexes and the increasing understanding of the cellular chromatin structure, it is starting to become clearer how chromatin factors operate in this complex environment. In this review, we analyze the current literature on the interplay between nucleosome-protein interactions and higher-order chromatin structure. We examine in what way nucleosomes-protein interactions can affect and can be affected by chromatin organization at the oligonucleosomal level. In addition, we review the characteristics of nucleosome-protein interactions that can cause phase separation of chromatin. Throughout, we hope to illustrate the exciting challenges in characterizing nucleosome-protein interactions beyond the nucleosome.
Collapse
Affiliation(s)
- Vincenzo R Lobbia
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Maria Cristina Trueba Sanchez
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| |
Collapse
|
19
|
Sanulli S, J Narlikar G. Liquid-like interactions in heterochromatin: Implications for mechanism and regulation. Curr Opin Cell Biol 2020; 64:90-96. [PMID: 32434105 DOI: 10.1016/j.ceb.2020.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/12/2020] [Accepted: 03/29/2020] [Indexed: 12/14/2022]
Abstract
A large portion of the eukaryotic genome is packed into heterochromatin, a versatile platform that is essential to maintain genome stability. Often associated with a compact and transcriptionally repressed chromatin state, heterochromatin was earlier considered a static and locked compartment. However, cumulative findings over the last 17 years have suggested that heterochromatin displays dynamics at different timescales and size scales. These dynamics are thought to be essential for the regulation of heterochromatin. This review illustrates how the key principles underlying heterochromatin structure and function have evolved along the years and summarizes the discoveries that have led to the continuous revision of these principles. Using heterochromatin protein 1-mediated heterochromatin as a context, we discuss a novel paradigm for heterochromatin organization based on two emerging concepts, phase separation and nucleosome structural plasticity. We also examine the broader implications of this paradigm for chromatin organization and regulation beyond heterochromatin.
Collapse
Affiliation(s)
- Serena Sanulli
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| |
Collapse
|
20
|
Kochanova NY, Schauer T, Mathias GP, Lukacs A, Schmidt A, Flatley A, Schepers A, Thomae AW, Imhof A. A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation. Nucleic Acids Res 2020; 48:4161-4178. [PMID: 32182352 PMCID: PMC7192626 DOI: 10.1093/nar/gkaa145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 12/26/2022] Open
Abstract
During interphase centromeres often coalesce into a small number of chromocenters, which can be visualized as distinct, DAPI dense nuclear domains. Intact chromocenters play a major role in maintaining genome stability as they stabilize the transcriptionally silent state of repetitive DNA while ensuring centromere function. Despite its biological importance, relatively little is known about the molecular composition of the chromocenter or the processes that mediate chromocenter formation and maintenance. To provide a deeper molecular insight into the composition of the chromocenter and to demonstrate the usefulness of proximity-based biotinylation as a tool to investigate those questions, we performed super resolution microscopy and proximity-based biotinylation experiments of three distinct proteins associated with the chromocenter in Drosophila. Our work revealed an intricate internal architecture of the chromocenter suggesting a complex multilayered structure of this intranuclear domain.
Collapse
Affiliation(s)
- Natalia Y Kochanova
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Tamas Schauer
- Biomedical Center, Bioinformatics Core Facility, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Grusha Primal Mathias
- Biomedical Center, Core Facility Bioimaging, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Andrea Lukacs
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Andreas Schmidt
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Andrew Flatley
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Aloys Schepers
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Andreas W Thomae
- Biomedical Center, Core Facility Bioimaging, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
- Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
21
|
Singh PB, Newman AG. On the relations of phase separation and Hi-C maps to epigenetics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191976. [PMID: 32257349 PMCID: PMC7062049 DOI: 10.1098/rsos.191976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
The relationship between compartmentalization of the genome and epigenetics is long and hoary. In 1928, Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller's discovery of position-effect variegation in 1930 went on to show that heterochromatin is a cytologically visible state of heritable (epigenetic) gene repression. Current insights into compartmentalization have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalization seen in Hi-C maps is owing to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5 Mb) heterochromatin-like domains and smaller (less than 100 kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes contributes to polymer-polymer phase separation that packages epigenetically heritable chromatin states during interphase. Contacts mediated by HP1 'bridging' are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic subcompartment that emerges from contacts between large KRAB-ZNF heterochromatin-like domains. Further, mutational analyses have revealed a finer, innate, compartmentalization in Hi-C experiments that probably reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres-where the HP1-H3K9me2/3 interaction represents the most evolutionarily conserved paradigm-could drive and generate the fundamental compartmentalization of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally differentiated fibroblast or a pluripotent embryonic stem cell.
Collapse
Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Nur-Sultan Z05K4F4, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Street 2, Novosibirsk 630090, Russian Federation
| | - Andrew G. Newman
- Institute of Cell and Neurobiology, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
22
|
Spakowitz AJ. Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems. J Chem Phys 2019; 151:230902. [DOI: 10.1063/1.5126852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Biophysics Program, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
23
|
Sanulli S, Trnka MJ, Dharmarajan V, Tibble RW, Pascal BD, Burlingame AL, Griffin PR, Gross JD, Narlikar GJ. HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature 2019; 575:390-394. [PMID: 31618757 PMCID: PMC7039410 DOI: 10.1038/s41586-019-1669-2] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 09/17/2019] [Indexed: 12/24/2022]
Abstract
Heterochromatin affects genome function at many levels. It enables heritable gene repression, maintains chromosome integrity and provides mechanical rigidity to the nucleus1,2. These diverse functions are proposed to arise in part from compaction of the underlying chromatin2. A major type of heterochromatin contains at its core the complex formed between HP1 proteins and chromatin that is methylated on histone H3, lysine 9 (H3K9me). HP1 is proposed to use oligomerization to compact chromatin into phase-separated condensates3-6. Yet, how HP1-mediated phase separation relates to chromatin compaction remains unclear. Here we show that chromatin compaction by the Schizosaccharomyces pombe HP1 protein Swi6 results in phase-separated liquid condensates. Unexpectedly, we find that Swi6 substantially increases the accessibility and dynamics of buried histone residues within a nucleosome. Restraining these dynamics impairs compaction of chromatin into liquid droplets by Swi6. Our results indicate that Swi6 couples its oligomerization to the phase separation of chromatin by a counterintuitive mechanism, namely the dynamic exposure of buried nucleosomal regions. We propose that such reshaping of the octamer core by Swi6 increases opportunities for multivalent interactions between nucleosomes, thereby promoting phase separation. This mechanism may more generally drive chromatin organization beyond heterochromatin.
Collapse
Affiliation(s)
- S Sanulli
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - M J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - V Dharmarajan
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - R W Tibble
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA
| | - B D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - A L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - P R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - J D Gross
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - G J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
24
|
Abstract
Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.
Collapse
Affiliation(s)
- Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael G. Poirier
- Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210-1117, USA
| |
Collapse
|
25
|
Wiese M, Bannister AJ, Basu S, Boucher W, Wohlfahrt K, Christophorou MA, Nielsen ML, Klenerman D, Laue ED, Kouzarides T. Citrullination of HP1γ chromodomain affects association with chromatin. Epigenetics Chromatin 2019; 12:21. [PMID: 30940194 PMCID: PMC6444592 DOI: 10.1186/s13072-019-0265-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/19/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Stem cell differentiation involves major chromatin reorganisation, heterochromatin formation and genomic relocalisation of structural proteins, including heterochromatin protein 1 gamma (HP1γ). As the principal reader of the repressive histone marks H3K9me2/3, HP1 plays a key role in numerous processes including heterochromatin formation and maintenance. RESULTS We find that HP1γ is citrullinated in mouse embryonic stem cells (mESCs) and this diminishes when cells differentiate, indicating that it is a dynamically regulated post-translational modification during stem cell differentiation. Peptidylarginine deiminase 4, a known regulator of pluripotency, citrullinates HP1γ in vitro. This requires R38 and R39 within the HP1γ chromodomain, and the catalytic activity is enhanced by trimethylated H3K9 (H3K9me3) peptides. Mutation of R38 and R39, designed to mimic citrullination, affects HP1γ binding to H3K9me3-containing peptides. Using live-cell single-particle tracking, we demonstrate that R38 and R39 are important for HP1γ binding to chromatin in vivo. Furthermore, their mutation reduces the residence time of HP1γ on chromatin in differentiating mESCs. CONCLUSION Citrullination is a novel post-translational modification of the structural heterochromatin protein HP1γ in mESCs that is dynamically regulated during mESC differentiation. The citrullinated residues lie within the HP1γ chromodomain and are important for H3K9me3 binding in vitro and chromatin association in vivo.
Collapse
Affiliation(s)
- Meike Wiese
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
- Max Planck Institute for Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Andrew J. Bannister
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, CB2 1QR UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Kai Wohlfahrt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Maria A. Christophorou
- Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU UK
| | - Michael L. Nielsen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| |
Collapse
|
26
|
Chemical and biophysical methods to explore dynamic mechanisms of chromatin silencing. Curr Opin Chem Biol 2019; 51:1-10. [PMID: 30825740 DOI: 10.1016/j.cbpa.2019.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/15/2019] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
Abstract
Chromatin, the nucleoprotein complex organizing the genome, is central in regulating gene expression and genome organization. Chromatin conformational dynamics, controlled by histone post-translational modifications (PTM) and effector proteins, play a key role in this regulatory function. Recent developments in chemical biology, cell biology, and biophysics sparked important new studies, which probe direct causal connections between histone PTMs, chromatin effector proteins that write or read these modifications, and the involved functional chromatin states. In particular, the mechanisms of heterochromatin silencing have been explored in great detail in recent years. These studies revealed the highly dynamic nature of this chromatin state, its conformational heterogeneity, and different mechanisms of its formation. Here, we review how chemical biology and biophysics shaped our current understanding of the dynamic processes observed in heterochromatin and discuss the emerging technologies to detect chromatin organization directly in the cellular environment.
Collapse
|
27
|
Feiner B, Chase KA, Melbourne JK, Rosen C, Sharma RP. Risperidone effects on heterochromatin: the role of kinase signaling. Clin Exp Immunol 2019; 196:67-75. [PMID: 30714144 DOI: 10.1111/cei.13250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2018] [Indexed: 01/03/2023] Open
Abstract
Epigenetic effects of anti-psychotic medications are poorly understood. We have appropriated a model whereby heterochromatin is established through 24- or 48-h lipopolysaccharide (LPS) treatment, and tested the epigenetic effects of risperidone along the adenylyl cyclase/protein kinase A (AC/PKA) pathway in human liposarcoma cells that express the LPS-sensitive Toll-like receptor (TLR)-4. Human SW872 cells were cultured with LPS and mRNA expression levels and epigenetic modifications of dimethylated lysine 9 of histone 2 (H3K9me2), geterochromatin protein 1γ (HP1γ) and phospho-H3S10 at promoters of interleukin (IL)-6, tumor necrosis factor (TNF)-α and IL1β were measured. Pharmacological manipulation of the AC/PKA pathway was achieved through treatment with a PKA inhibitor (H89), mitogen- and stress-activated kinase 1 (MSK1) inhibitor (SB-747651A) or forskolin. Twenty-four and 48-h LPS treatment establishes heterochromatin at selected promoters, corresponding to decreased mRNA expression. Concurrent risperidone treatment with LPS treatment can both 'block' and 'reverse' heterochromatin formation. Forskolin treatment resulted in a similar disassembling effect on heterochromatin. Conversely, inhibition of PKA by H89 or MSK1 both blocked 'normalizing' effects of risperidone on LPS-induced heterochromatin. Our results demonstrate that risperidone can disassemble heterochromatin, exerting this effect along the G-protein/AC/PKA pathway. This approach can also be utilized to investigate functional outcomes of single or combined pharmacological treatments on chromatin assemblies in human cells.
Collapse
Affiliation(s)
- B Feiner
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA
| | - K A Chase
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - J K Melbourne
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA
| | - C Rosen
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA
| | - R P Sharma
- The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| |
Collapse
|
28
|
Sengupta S, Siliciano RF. Targeting the Latent Reservoir for HIV-1. Immunity 2018; 48:872-895. [PMID: 29768175 PMCID: PMC6196732 DOI: 10.1016/j.immuni.2018.04.030] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 02/07/2023]
Abstract
Antiretroviral therapy can effectively block HIV-1 replication and prevent or reverse immunodeficiency in HIV-1-infected individuals. However, viral replication resumes within weeks of treatment interruption. The major barrier to a cure is a small pool of resting memory CD4+ T cells that harbor latent HIV-1 proviruses. This latent reservoir is now the focus of an intense international research effort. We describe how the reservoir is established, challenges involved in eliminating it, and pharmacologic and immunologic strategies for targeting this reservoir. The development of a successful cure strategy will most likely require understanding the mechanisms that maintain HIV-1 proviruses in a latent state and pathways that drive the proliferation of infected cells, which slows reservoir decay. In addition, a cure will require the development of effective immunologic approaches to eliminating infected cells. There is renewed optimism about the prospect of a cure, and the interventions discussed here could pave the way.
Collapse
Affiliation(s)
- Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Graduate Program in Immunology and Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
| |
Collapse
|
29
|
Kilic S, Felekyan S, Doroshenko O, Boichenko I, Dimura M, Vardanyan H, Bryan LC, Arya G, Seidel CAM, Fierz B. Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. Nat Commun 2018; 9:235. [PMID: 29339721 PMCID: PMC5770380 DOI: 10.1038/s41467-017-02619-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/11/2017] [Indexed: 01/17/2023] Open
Abstract
The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics in chromatin fibers. We show that nucleosomes engage in short-lived (micro- to milliseconds) stacking interactions with one of their neighbors. This results in discrete tetranucleosome units with distinct interaction registers that interconvert within hundreds of milliseconds. Additionally, we find that dynamic chromatin architecture is modulated by the multivalent architectural protein heterochromatin protein 1α (HP1α), which engages methylated histone tails and thereby transiently stabilizes stacked nucleosomes. This compacted state nevertheless remains dynamic, exhibiting fluctuations on the timescale of HP1α residence times. Overall, this study reveals that exposure of internal DNA sites and nucleosome surfaces in chromatin fibers is governed by an intrinsic dynamic hierarchy from micro- to milliseconds, allowing the gene regulation machinery to access compact chromatin. Chromatin fibers undergo continuous structural rearrangements but their dynamic architecture is poorly understood. Here, the authors use single-molecule FRET to determine the structural states and interconversion kinetics of chromatin fibers, monitoring their effector protein-dependent dynamic motions.
Collapse
Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Olga Doroshenko
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Mykola Dimura
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hayk Vardanyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Gaurav Arya
- Pratt School of Engineering, Duke University, 144 Hudson Hall, Box 90300, Durham, NC, 27708, USA
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| |
Collapse
|
30
|
Bryan LC, Weilandt DR, Bachmann AL, Kilic S, Lechner CC, Odermatt PD, Fantner GE, Georgeon S, Hantschel O, Hatzimanikatis V, Fierz B. Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions. Nucleic Acids Res 2017; 45:10504-10517. [PMID: 28985346 PMCID: PMC5737501 DOI: 10.1093/nar/gkx697] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/27/2017] [Indexed: 12/20/2022] Open
Abstract
Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling. We show that the three human HP1 isoforms are recruited and retained on chromatin by a dynamic exchange between histone PTM and DNA bound states. These interactions depend on local chromatin structure, the HP1 isoforms as well as on PTMs on HP1 itself. Of the HP1 isoforms, HP1α exhibits the longest residence times and fastest binding rates due to DNA interactions in addition to PTM binding. HP1α phosphorylation further increases chromatin retention through strengthening of multivalency while reducing DNA binding. As DNA binding in combination with specific PTM recognition is found in many chromatin effectors, we propose a general dynamic capture mechanism for effector recruitment. Multiple weak protein and DNA interactions result in a multivalent interaction network that targets effectors to a specific chromatin modification state, where their activity is required.
Collapse
Affiliation(s)
- Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Daniel R Weilandt
- Laboratory of Computational Systems Biotechnology, ISIC, EPFL, 1015 Lausanne, Switzerland
| | - Andreas L Bachmann
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Carolin C Lechner
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Pascal D Odermatt
- Laboratory for Bio- and Nano instrumentation, Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland
| | - Georg E Fantner
- Laboratory for Bio- and Nano instrumentation, Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland
| | - Sandrine Georgeon
- ISREC foundation chair in translational oncology, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Oliver Hantschel
- ISREC foundation chair in translational oncology, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, ISIC, EPFL, 1015 Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| |
Collapse
|
31
|
Harikumar A, Edupuganti RR, Sorek M, Azad GK, Markoulaki S, Sehnalová P, Legartová S, Bártová E, Farkash-Amar S, Jaenisch R, Alon U, Meshorer E. An Endogenously Tagged Fluorescent Fusion Protein Library in Mouse Embryonic Stem Cells. Stem Cell Reports 2017; 9:1304-1314. [PMID: 28966122 PMCID: PMC5639459 DOI: 10.1016/j.stemcr.2017.08.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 08/28/2017] [Indexed: 01/25/2023] Open
Abstract
Embryonic stem cells (ESCs), with their dual capacity to self-renew and differentiate, are commonly used to study differentiation, epigenetic regulation, lineage choices, and more. Using non-directed retroviral integration of a YFP/Cherry exon into mouse ESCs, we generated a library of over 200 endogenously tagged fluorescent fusion proteins and present several proof-of-concept applications of this library. We show the utility of this library to track proteins in living cells; screen for pluripotency-related factors; identify heterogeneously expressing proteins; measure the dynamics of endogenously labeled proteins; track proteins recruited to sites of DNA damage; pull down tagged fluorescent fusion proteins using anti-Cherry antibodies; and test for interaction partners. Thus, this library can be used in a variety of different directions, either exploiting the fluorescent tag for imaging-based techniques or utilizing the fluorescent fusion protein for biochemical pull-down assays, including immunoprecipitation, co-immunoprecipitation, chromatin immunoprecipitation, and more.
Collapse
Affiliation(s)
- Arigela Harikumar
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Raghu Ram Edupuganti
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Matan Sorek
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gajendra Kumar Azad
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | - Petra Sehnalová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Shlomit Farkash-Amar
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| |
Collapse
|
32
|
Cuvier O, Fierz B. Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. Nat Rev Genet 2017; 18:457-472. [DOI: 10.1038/nrg.2017.28] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
33
|
Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J Biosci 2016; 41:759-786. [DOI: 10.1007/s12038-016-9650-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
34
|
Structure and function of histone methylation-binding proteins in plants. Biochem J 2016; 473:1663-80. [DOI: 10.1042/bcj20160123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/29/2016] [Indexed: 12/28/2022]
Abstract
Post-translational modifications of histones play important roles in modulating many essential biological processes in both animals and plants. These covalent modifications, including methylation, acetylation, phosphorylation, ubiquitination, SUMOylation and so on, are laid out and erased by histone-modifying enzymes and read out by effector proteins. Recent studies have revealed that a number of developmental processes in plants are under the control of histone post-translational modifications, such as floral transition, seed germination, organogenesis and morphogenesis. Therefore, it is critical to identify those protein domains, which could specifically recognize these post-translational modifications to modulate chromatin structure and regulate gene expression. In the present review, we discuss the recent progress in understanding the structure and function of the histone methylation readers in plants, by focusing on Arabidopsis thaliana proteins.
Collapse
|
35
|
Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, De La Rosa-Velázquez IA, Zenn HM, Kost N, Pohl W, Chernev A, Schwarzer D, Jenuwein T, Lorincz M, Zimmermann B, Walla PJ, Neumann H, Baubec T, Urlaub H, Fischle W. Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin. Nat Commun 2016; 7:11310. [PMID: 27090491 PMCID: PMC4838890 DOI: 10.1038/ncomms11310] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/13/2016] [Indexed: 12/12/2022] Open
Abstract
Histone H3 trimethylation of lysine 9 (H3K9me3) and proteins of the heterochromatin protein 1 (HP1) family are hallmarks of heterochromatin, a state of compacted DNA essential for genome stability and long-term transcriptional silencing. The mechanisms by which H3K9me3 and HP1 contribute to chromatin condensation have been speculative and controversial. Here we demonstrate that human HP1β is a prototypic HP1 protein exemplifying most basal chromatin binding and effects. These are caused by dimeric and dynamic interaction with highly enriched H3K9me3 and are modulated by various electrostatic interfaces. HP1β bridges condensed chromatin, which we postulate stabilizes the compacted state. In agreement, HP1β genome-wide localization follows H3K9me3-enrichment and artificial bridging of chromatin fibres is sufficient for maintaining cellular heterochromatic conformation. Overall, our findings define a fundamental mechanism for chromatin higher order structural changes caused by HP1 proteins, which might contribute to the plastic nature of condensed chromatin. Heterochromatin protein 1 (HP1), including HP1 α, β and γ, is a family of non-histone chromatin factors thought to be involved in chromatin organization. Here, the authors show that dimeric HP1β interacts dynamically with H3K9me3, a hallmark of heterochromatin, and bridges condensed chromatin.
Collapse
Affiliation(s)
- Kyoko Hiragami-Hamada
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Szabolcs Soeroes
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Miroslav Nikolov
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Bryan Wilkins
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Sarah Kreuz
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Carol Chen
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Inti A De La Rosa-Velázquez
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Hans Michael Zenn
- Biaffin GmbH &Co KG, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
| | - Nils Kost
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Wiebke Pohl
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Thomas Jenuwein
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Matthew Lorincz
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | | | - Peter Jomo Walla
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Department of Biophysical Chemistry, Technische Universität Braunschweig, Hans-Sommerstr. 10, 38106 Braunschweig, Germany
| | - Heinz Neumann
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| |
Collapse
|
36
|
Wang J, Jia ST, Jia S. New Insights into the Regulation of Heterochromatin. Trends Genet 2016; 32:284-294. [PMID: 27005444 DOI: 10.1016/j.tig.2016.02.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/22/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
Abstract
All living organisms are constantly exposed to stresses from internal biological processes and surrounding environments, which induce many adaptive changes in cellular physiology and gene expression programs. Unexpectedly, constitutive heterochromatin, which is generally associated with the stable maintenance of gene silencing, is also dynamically regulated in response to stimuli. In this review we discuss the mechanism of constitutive heterochromatin assembly, its dynamic nature, and its responses to environmental changes.
Collapse
Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sharon T Jia
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| |
Collapse
|
37
|
Çelik S, Li Y, O’Neill C. The effect of DNA damage on the pattern of immune-detectable DNA methylation in mouse embryonic fibroblasts. Exp Cell Res 2015; 339:20-34. [DOI: 10.1016/j.yexcr.2015.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/31/2015] [Accepted: 08/27/2015] [Indexed: 12/21/2022]
|
38
|
Stunnenberg R, Kulasegaran-Shylini R, Keller C, Kirschmann MA, Gelman L, Bühler M. H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein. EMBO J 2015; 34:2789-803. [PMID: 26438724 PMCID: PMC4682641 DOI: 10.15252/embj.201591320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in the creation of a rigid, densely packed heterochromatic network that is inaccessible to the transcription machinery. Here, we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population that rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to the maintenance of heterochromatin domains. In the absence of Swi6, H3K9 methylation levels are maintained by a mechanism that depends on polymeric self‐association properties of Tas3, a subunit of the RNA‐induced transcriptional silencing complex. Our results disclose a surprising role for Swi6 dimerization in demarcating constitutive heterochromatin from neighboring euchromatin. Thus, rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes and appropriately confine heterochromatin.
Collapse
Affiliation(s)
- Rieka Stunnenberg
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| |
Collapse
|
39
|
Nagy C, Turecki G. Transgenerational epigenetic inheritance: an open discussion. Epigenomics 2015; 7:781-90. [DOI: 10.2217/epi.15.46] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Much controversy surrounds the idea of transgenerational epigenetics. Recent papers argue that epigenetic marks acquired through experience are passed to offspring, but as in much of the field of epigenetics, there is lack of precision in the definitions and perhaps too much eagerness to translate animal research to humans. Here, we review operational definitions of transgenerational inheritance and the processes of epigenetic programing during early development. Subsequently, based on this background, we critically examine some recent findings of studies investigating transgenerational inheritance. Finally, we discuss possible mechanisms that may explain transgenerational inheritance, including transmission of an epigenetic blueprint, which may predispose offspring to specific epigenetic patterning. Taken together, we conclude that presently, the evidence suggesting that acquired epigenetic marks are passed to the subsequent generation remains limited.
Collapse
Affiliation(s)
- Corina Nagy
- McGill Group for Suicide Studies, Douglas Hospital University Institute, 6875 Lasalle boul, Montreal, QC, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital University Institute, 6875 Lasalle boul, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| |
Collapse
|
40
|
Razin SV, Borunova VV, Iarovaia OV, Vassetzky YS. Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus. BIOCHEMISTRY (MOSCOW) 2015; 79:608-18. [PMID: 25108324 DOI: 10.1134/s0006297914070037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.
Collapse
Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | | | | | | |
Collapse
|
41
|
Abstract
Silent chromatin in budding yeast is propagated from one generation to the next, even though ‘silenced’ genes are occasionally expressed.
Collapse
Affiliation(s)
- Yu-Fan Chen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, United States
| | - Marc R Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, United States and The Cancer Institute of New Jersey, New Brunswick, United States
| |
Collapse
|
42
|
Mulligan PJ, Koslover EF, Spakowitz AJ. Thermodynamic model of heterochromatin formation through epigenetic regulation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064109. [PMID: 25563699 DOI: 10.1088/0953-8984/27/6/064109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Gene regulation in eukaryotes requires the segregation of silenced genomic regions into densely packed heterochromatin, leaving the active genes in euchromatin regions more accessible. We introduce a model that connects the presence of epigenetically inherited histone marks, methylation at histone 3 lysine-9, to the physical compaction of chromatin fibers via the binding of heterochromatin protein 1 (HP1). Our model demonstrates some of the key physical features that are necessary to explain experimental observations. In particular, we demonstrate that strong cooperative interactions among the HP1 proteins are necessary to see the phase segregation of heterochromatin and euchromatin regions. We also explore how the cell can use the concentration of HP1 to control condensation and under what circumstances there is a threshold of methylation over which the fibers will compact. Finally, we consider how different potential in vivo fiber structures as well as the flexibility of the histone 3 tail can affect the bridging of HP1. Many of the observations that we make about the HP1 system are guided by general thermodynamics principles and thus could play a role in other DNA organizational processes such as the binding of linker histones.
Collapse
Affiliation(s)
- Peter J Mulligan
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | | | | |
Collapse
|
43
|
Romeo K, Louault Y, Cantaloube S, Loiodice I, Almouzni G, Quivy JP. The SENP7 SUMO-Protease Presents a Module of Two HP1 Interaction Motifs that Locks HP1 Protein at Pericentric Heterochromatin. Cell Rep 2015; 10:771-782. [PMID: 25660026 DOI: 10.1016/j.celrep.2015.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/08/2014] [Accepted: 12/24/2014] [Indexed: 12/17/2022] Open
Abstract
HP1 enrichment at pericentric heterochromatin is essential for proper chromosome segregation. While H3K9me3 is thought to be a major contributor to HP1 enrichment at pericentric domains, in mouse cells, the SUMO-protease SENP7 is required in addition to H3K9me3. How this is achieved remains elusive. Here, we find that loss of SENP7 leads to an increased time spent in mitosis. Furthermore, we reveal that a short module comprising two consecutive HP1 interaction motifs on SENP7 is the determinant for HP1 enrichment and acts by restricting HP1 mobility at pericentric domains. We propose a mechanism for maintenance of HP1 enrichment in which this module functions on top of H3K9me3 to lock contiguous HP1 molecules already docked on H3K9me3-modified nucleosomes. H3K9me3 would thus promote HP1 enrichment only if a locking system is in place. This mechanism may apply to other nuclear domains to contribute to the control of genome plasticity and integrity.
Collapse
Affiliation(s)
- Kelly Romeo
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Yann Louault
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Isabelle Loiodice
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France.
| | - Jean-Pierre Quivy
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France.
| |
Collapse
|
44
|
Dodson AE, Rine J. Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae. eLife 2015; 4:e05007. [PMID: 25581000 PMCID: PMC4337651 DOI: 10.7554/elife.05007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/09/2015] [Indexed: 01/10/2023] Open
Abstract
Heterochromatin exerts a heritable form of eukaryotic gene repression and contributes to chromosome segregation fidelity and genome stability. However, to date there has been no quantitative evaluation of the stability of heterochromatic gene repression. We designed a genetic strategy to capture transient losses of gene silencing in Saccharomyces as permanent, heritable changes in genotype and phenotype. This approach revealed rare transcription within heterochromatin that occurred in approximately 1/1000 cell divisions. In concordance with multiple lines of evidence suggesting these events were rare and transient, single-molecule RNA FISH showed that transcription was limited. The ability to monitor fluctuations in heterochromatic repression uncovered previously unappreciated roles for Sir1, a silencing establishment factor, in the maintenance and/or inheritance of silencing. In addition, we identified the sirtuin Hst3 and its histone target as contributors to the stability of the silenced state. These approaches revealed dynamics of a heterochromatin function that have been heretofore inaccessible.
Collapse
Affiliation(s)
- Anne E Dodson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
45
|
Beaujean N. Epigenetics, embryo quality and developmental potential. Reprod Fertil Dev 2015; 27:53-62. [DOI: 10.1071/rd14309] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It is very important for embryologists to understand how parental inherited genomes are reprogrammed after fertilisation in order to obtain good-quality embryos that will sustain further development. In mammals, it is now well established that important epigenetic modifications occur after fertilisation. Although gametes carry special epigenetic signatures, they should attain embryo-specific signatures, some of which are crucial for the production of healthy embryos. Indeed, it appears that proper establishment of different epigenetic modifications and subsequent scaffolding of the chromatin are crucial steps during the first cleavages. This ‘reprogramming’ is promoted by the intimate contact between the parental inherited genomes and the oocyte cytoplasm after fusion of the gametes. This review introduces two main epigenetic players, namely histone post-translational modifications and DNA methylation, and highlights their importance during early embryonic development.
Collapse
|
46
|
Müller-Ott K, Erdel F, Matveeva A, Mallm JP, Rademacher A, Hahn M, Bauer C, Zhang Q, Kaltofen S, Schotta G, Höfer T, Rippe K. Specificity, propagation, and memory of pericentric heterochromatin. Mol Syst Biol 2014; 10:746. [PMID: 25134515 PMCID: PMC4299515 DOI: 10.15252/msb.20145377] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The cell establishes heritable patterns of active and silenced chromatin via interacting factors
that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we
have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts.
We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in
living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2
demarcate the PCH state. From the experimental data, we developed a predictive mathematical model
that explains how chromatin-bound SUV39H1/2 complexes act as nucleation sites and propagate a
spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin
dynamics. This “nucleation and looping” mechanism is particularly robust toward
transient perturbations and stably maintains the PCH state. These features make it an attractive
model for establishing functional epigenetic domains throughout the genome based on the localized
immobilization of chromatin-modifying enzymes.
Collapse
Affiliation(s)
- Katharina Müller-Ott
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Fabian Erdel
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anna Matveeva
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anne Rademacher
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Matthias Hahn
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Caroline Bauer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Qin Zhang
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Sabine Kaltofen
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Gunnar Schotta
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Thomas Höfer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| |
Collapse
|
47
|
Nishibuchi G, Nakayama JI. Biochemical and structural properties of heterochromatin protein 1: understanding its role in chromatin assembly. J Biochem 2014; 156:11-20. [DOI: 10.1093/jb/mvu032] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
48
|
Manukyan M, Singh PB. Epigenome rejuvenation: HP1β mobility as a measure of pluripotent and senescent chromatin ground states. Sci Rep 2014; 4:4789. [PMID: 24763337 PMCID: PMC3999444 DOI: 10.1038/srep04789] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/17/2014] [Indexed: 01/08/2023] Open
Abstract
We measured the dynamics of an essential epigenetic modifier, HP1β, in human cells at different stages of differentiation using Fluorescence Recovery After Photobleaching (FRAP). We found that HP1β mobility is similar in human embryonic stem cells (hES) and iPS cells where it is more mobile compared to fibroblasts; HP1β is less mobile in senescent fibroblasts than in young (dividing) fibroblasts. Introduction of "reprogramming factors", Oct4, Sox2, Klf4, cMyc and Lin28, into senescent fibroblasts and measuring the changes in HP1β mobility as reprogramming proceeds shows that the mobility of HP1β in senescent cells increases and by day 9 is the same as that found in young fibroblasts. Thus the dynamics of a key epigenetic modifier can be rejuvenated without de-differentiation through an embryonic stage. Future work will test whether other aspects of cellular physiology that age can be so rejuvenated without de-differentiation.
Collapse
Affiliation(s)
- Maria Manukyan
- Albert-Ludwigs-Universität Freiburg, BIOSS Centre for Biological Signalling Studies, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Prim B. Singh
- Fächerverbund Anatomie, Institut für Zell- und Neurobiologie, Charite – Universitätsmedizin, 10117 Berlin, Germany
| |
Collapse
|
49
|
The exit of mouse embryonic fibroblasts from the cell-cycle changes the nature of solvent exposure of the 5'-methylcytosine epitope within chromatin. PLoS One 2014; 9:e92523. [PMID: 24705067 PMCID: PMC3976252 DOI: 10.1371/journal.pone.0092523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 02/24/2014] [Indexed: 11/19/2022] Open
Abstract
The methylation of CpG dinucleotides is a pervasive epigenetic signature with critical roles governing genomic stability and lineage-specific patterns of gene expression. Reprogramming the patterns of CpG methylation accompanies key developmental transitions and the onset of some pathologies, such as cancer. In this study we show that levels of immuno-detectable 5meC decreased as mouse embryonic fibroblasts withdraw from the cell-cycle (became mitotically quiescent), but increased as they aged in culture. Two pools of 5meC epitope were found to exist, one solvent exposed after acid-induced denaturation of chromatin and another that required the additional step of tryptic digestion for detection. Proliferative cells displayed a relatively greater accumulation of detectable 5meC within the trypsin-sensitive pool than did quiescent cells. A substantial proportion of the 5meC was associated with a large number of heterochromatic foci scattered throughout nuclei, yet much of this was masked in a trypsin-sensitive manner, particularly in young proliferative cells. This study showed that the growth status of cells changed the level of solvent exposure of 5meC in fibroblasts and the long-accepted conventional methods of immunolocalization underestimate the level of 5meC in cells. This resulted in an artefactual assessment of the levels and patterns of nuclear localization of the antigen. The use of an additional tryptic digestion step improved antigen retrieval and revealed a more dynamic response of 5meC levels and distribution patterns to changes in the cell's growth state. This discovery will provide a basis for investigating the role of changes in chromatin structure that underlie this dynamism.
Collapse
|
50
|
Tadeo X, Wang J, Kallgren SP, Liu J, Reddy BD, Qiao F, Jia S. Elimination of shelterin components bypasses RNAi for pericentric heterochromatin assembly. Genes Dev 2014; 27:2489-99. [PMID: 24240238 PMCID: PMC3841737 DOI: 10.1101/gad.226118.113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The RNAi pathway is required for heterochromatin assembly, and loss of RNAi causes pericentric heterochromatin defects. Tadeo et al. show that deletion of telomere shelterin components in RNAi mutants restores pericentric heterochromatin. Shelterin component Poz1 mutant analysis reveals that defective telomere silencing, but not telomere length control, is critical for bypassing RNAi. Furthermore, heterochromatin protein Swi6 is redistributed to pericentric regions in RNAi mutants. Heterochromatin domains thus use multiple pathways to restrain Swi6 and avoid promiscuous heterochromatin formation. The RNAi pathway is required for heterochromatin assembly at repetitive DNA elements in diverse organisms. In fission yeast, loss of RNAi causes pericentric heterochromatin defects, compromising gene silencing and chromosome segregation. Here we show that deletion of telomere shelterin components restores pericentric heterochromatin and its functions in RNAi mutants. We further isolated a separation-of-function mutant of Poz1 and revealed that defective telomere silencing, but not telomere length control, is critical for bypassing RNAi. Further analyses demonstrated that compromising shelterin-mediated heterochromatin assembly in RNAi mutants releases heterochromatin protein Swi6, which is redistributed to pericentric regions through RNAi-independent heterochromatin assembly pathways. Given the high mobility of Swi6 protein and that increased levels of Swi6 facilitates heterochromatin spreading as well as ectopic heterochromatin assembly, our results suggest that constitutive heterochromatin domains use multiple pathways to form high-affinity platforms to restrain Swi6, thus limiting its availability and avoiding promiscuous heterochromatin formation.
Collapse
Affiliation(s)
- Xavier Tadeo
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | | | | | | | | | | | |
Collapse
|