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Du Y, Metcalfe S, Akunapuram S, Ghosh S, Spruck C, Richardson AM, Cohen‐Gadol AA, Shen J. Image-based assessment of natural killer cell activity against glioblastoma stem cells. FEBS Open Bio 2024; 14:1028-1034. [PMID: 38740554 PMCID: PMC11148112 DOI: 10.1002/2211-5463.13818] [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: 01/02/2024] [Revised: 04/08/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Glioblastoma (GBM) poses a significant challenge in oncology and stands as the most aggressive form of brain cancer. A primary contributor to its relentless nature is the stem-like cancer cells, called glioblastoma stem cells (GSCs). GSCs have the capacity for self-renewal and tumorigenesis, leading to frequent GBM recurrences and complicating treatment modalities. While natural killer (NK) cells exhibit potential in targeting and eliminating stem-like cancer cells, their efficacy within the GBM microenvironment is limited due to constrained infiltration and function. To address this limitation, novel investigations focusing on boosting NK cell activity against GSCs are imperative. This study presents two streamlined image-based assays assessing NK cell migration and cytotoxicity towards GSCs. It details protocols and explores the strengths and limitations of these methods. These assays could aid in identifying novel targets to enhance NK cell activity towards GSCs, facilitating the development of NK cell-based immunotherapy for improved GBM treatment.
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Affiliation(s)
- Yuanning Du
- Medical Sciences ProgramIndiana University School of MedicineBloomingtonINUSA
| | - Samuel Metcalfe
- Medical Sciences ProgramIndiana University School of MedicineBloomingtonINUSA
- Cell, Molecular and Cancer Biology Graduate ProgramIndiana University School of MedicineBloomingtonINUSA
| | - Shreya Akunapuram
- Medical Sciences ProgramIndiana University School of MedicineBloomingtonINUSA
- Cell, Molecular and Cancer Biology Graduate ProgramIndiana University School of MedicineBloomingtonINUSA
| | - Sugata Ghosh
- Medical Sciences ProgramIndiana University School of MedicineBloomingtonINUSA
- Cell, Molecular and Cancer Biology Graduate ProgramIndiana University School of MedicineBloomingtonINUSA
| | - Charles Spruck
- Cancer CenterSanford Burnham Prebys Medical Discovery InstituteLa JollaCAUSA
| | - Angela M. Richardson
- Department of Neurological SurgeryIndiana University School of MedicineIndianapolisINUSA
| | - Aaron A. Cohen‐Gadol
- Department of Neurological SurgeryIndiana University School of MedicineIndianapolisINUSA
| | - Jia Shen
- Medical Sciences ProgramIndiana University School of MedicineBloomingtonINUSA
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisINUSA
- Indiana University Melvin and Bren Simon Comprehensive Cancer CenterIndianapolisINUSA
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2
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Gopinathan G, Xu Q, Luan X, Diekwisch TGH. CFDP1 regulates the stability of pericentric heterochromatin thereby affecting RAN GTPase activity and mitotic spindle formation. PLoS Biol 2024; 22:e3002574. [PMID: 38630655 PMCID: PMC11023358 DOI: 10.1371/journal.pbio.3002574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 03/02/2024] [Indexed: 04/19/2024] Open
Abstract
The densely packed centromeric heterochromatin at minor and major satellites is comprised of H3K9me2/3 histones, the heterochromatin protein HP1α, and histone variants. In the present study, we sought to determine the mechanisms by which condensed heterochromatin at major and minor satellites stabilized by the chromatin factor CFDP1 affects the activity of the small GTPase Ran as a requirement for spindle formation. CFDP1 colocalized with heterochromatin at major and minor satellites and was essential for the structural stability of centromeric heterochromatin. Loss of CENPA, HP1α, and H2A.Z heterochromatin components resulted in decreased binding of the spindle nucleation facilitator RCC1 to minor and major satellite repeats. Decreased RanGTP levels as a result of diminished RCC1 binding interfered with chromatin-mediated microtubule nucleation at the onset of mitotic spindle formation. Rescuing chromatin H2A.Z levels in cells and mice lacking CFDP1 through knock-down of the histone chaperone ANP32E not only partially restored RCC1-dependent RanGTP levels but also alleviated CFDP1-knockout-related craniofacial defects and increased microtubule nucleation in CFDP1/ANP32E co-silenced cells. Together, these studies provide evidence for a direct link between condensed heterochromatin at major and minor satellites and microtubule nucleation through the chromatin protein CFDP1.
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Affiliation(s)
- Gokul Gopinathan
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Qian Xu
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Xianghong Luan
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Thomas G. H. Diekwisch
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
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3
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Chen Y, Huang Z, Peng Q, Wang Y. Single Genomic Loci Labeling and Manipulation Using SIMBA System. Curr Protoc 2023; 3:e947. [PMID: 38054948 DOI: 10.1002/cpz1.947] [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] [Indexed: 12/07/2023]
Abstract
The SIMBA (Simultaneous Imaging and Manipulation of genomic loci by Biomolecular Assemblies) system is an innovative CRISPR-based imaging technique that leverages dCas9-SunTag and FRB-mCherry-HP1α, with scFv-FKBP acting as a bridge. This powerful system enables simultaneous visualization and manipulation of genomic loci. The dCas9-SunTag fusion protein allows for precise targeting of specific genomic sites, and the FRB-mCherry-HP1α fusion protein facilitates the condensation of chromatin at the targeted loci. The scFv-FKBP bridge protein links dCas9-SunTag and FRB-mCherry-HP1α, ensuring efficient and specific recruitment of HP1α to the desired genomic loci. This integrated approach allows us to visualize and manipulate genomic regions of interest, opening up new avenues for studying genome organization, gene expression regulation, and chromatin dynamics in living cells. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Cloning of genetic constructs Basic Protocol 2: Transient transfection in mammalian cells and live-cell imaging Basic Protocol 3: Generation of SIMBA-expressing stable cell lines Basic Protocol 4: Manipulation of genomic loci using SIMBA.
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Affiliation(s)
- Yanwei Chen
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ziliang Huang
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, California
| | - Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yingxiao Wang
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, California
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4
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Peng Q, Huang Z, Sun K, Liu Y, Yoon CW, Harrison RES, Schmitt DL, Zhu L, Wu Y, Tasan I, Zhao H, Zhang J, Zhong S, Chien S, Wang Y. Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells. Nat Commun 2022; 13:7933. [PMID: 36566209 PMCID: PMC9789998 DOI: 10.1038/s41467-022-35504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 12/06/2022] [Indexed: 12/25/2022] Open
Abstract
Genome architecture and organization play critical roles in cell life. However, it remains largely unknown how genomic loci are dynamically coordinated to regulate gene expression and determine cell fate at the single cell level. We have developed an inducible system which allows Simultaneous Imaging and Manipulation of genomic loci by Biomolecular Assemblies (SIMBA) in living cells. In SIMBA, the human heterochromatin protein 1α (HP1α) is fused to mCherry and FRB, which can be induced to form biomolecular assemblies (BAs) with FKBP-scFv, guided to specific genomic loci by a nuclease-defective Cas9 (dCas9) or a transcriptional factor (TF) carrying tandem repeats of SunTag. The induced BAs can not only enhance the imaging signals at target genomic loci using a single sgRNA, either at repetitive or non-repetitive sequences, but also recruit epigenetic modulators such as histone methyltransferase SUV39H1 to locally repress transcription. As such, SIMBA can be applied to simultaneously visualize and manipulate, in principle, any genomic locus with controllable timing in living cells.
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Affiliation(s)
- Qin Peng
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, P. R. China.
| | - Ziliang Huang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, P. R. China
| | - Yahan Liu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Chi Woo Yoon
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Reed E S Harrison
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Danielle L Schmitt
- Department of Pharmacology, University of California, La Jolla, CA, 92093-0435, USA
| | - Linshan Zhu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Yiqian Wu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, La Jolla, CA, 92093-0435, USA
| | - Sheng Zhong
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Shu Chien
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
- Department of Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA.
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5
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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.
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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
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6
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Abstract
Nucleosomes wrap DNA and impede access for the machinery of transcription. The core histones that constitute nucleosomes are subject to a diversity of posttranslational modifications, or marks, that impact the transcription of genes. Their functions have sometimes been difficult to infer because the enzymes that write and read them are complex, multifunctional proteins. Here, we examine the evidence for the functions of marks and argue that the major marks perform a fairly small number of roles in either promoting transcription or preventing it. Acetylations and phosphorylations on the histone core disrupt histone-DNA contacts and/or destabilize nucleosomes to promote transcription. Ubiquitylations stimulate methylations that provide a scaffold for either the formation of silencing complexes or resistance to those complexes, and carry a memory of the transcriptional state. Tail phosphorylations deconstruct silencing complexes in particular contexts. We speculate that these fairly simple roles form the basis of transcriptional regulation by histone marks.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
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7
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Sikder S, Kaypee S, Kundu TK. Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease. J Biosci 2020. [DOI: 10.1007/s12038-019-9974-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Klutstein M. Cause and effect in epigenetics - where lies the truth, and how can experiments reveal it?: Epigenetic self-reinforcing loops obscure causation in cancer and aging. Bioessays 2020; 43:e2000262. [PMID: 33236359 DOI: 10.1002/bies.202000262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic changes are implicated in aging and cancer. Sometimes, it is clear whether the causing agent of the condition is a genetic factor or epigenetic. In other cases, the causative factor is unclear, and could be either genetic or epigenetic. Is there a general role for epigenetic changes in cancer and aging? Here, I present the paradigm of causative roles executed by epigenetic changes. I discuss cases with clear roles of the epigenome in cancer and aging, and other cases showing involvement of other factors. I also present the possibility that sometimes causality is difficult to assign because of the presence of self-reinforcing loops in epigenetic regulation. Such loops hinder the identification of the causative factor. I provide an experimental framework by which the role of the epigenome can be examined in a better setting and where the presence of such loops could be investigated in more detail.
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Affiliation(s)
- Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
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9
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Martins NMC, Cisneros-Soberanis F, Pesenti E, Kochanova NY, Shang WH, Hori T, Nagase T, Kimura H, Larionov V, Masumoto H, Fukagawa T, Earnshaw WC. H3K9me3 maintenance on a human artificial chromosome is required for segregation but not centromere epigenetic memory. J Cell Sci 2020; 133:jcs242610. [PMID: 32576667 PMCID: PMC7390644 DOI: 10.1242/jcs.242610] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
Most eukaryotic centromeres are located within heterochromatic regions. Paradoxically, heterochromatin can also antagonize de novo centromere formation, and some centromeres lack it altogether. In order to investigate the importance of heterochromatin at centromeres, we used epigenetic engineering of a synthetic alphoidtetO human artificial chromosome (HAC), to which chimeric proteins can be targeted. By tethering the JMJD2D demethylase (also known as KDM4D), we removed heterochromatin mark H3K9me3 (histone 3 lysine 9 trimethylation) specifically from the HAC centromere. This caused no short-term defects, but long-term tethering reduced HAC centromere protein levels and triggered HAC mis-segregation. However, centromeric CENP-A was maintained at a reduced level. Furthermore, HAC centromere function was compatible with an alternative low-H3K9me3, high-H3K27me3 chromatin signature, as long as residual levels of H3K9me3 remained. When JMJD2D was released from the HAC, H3K9me3 levels recovered over several days back to initial levels along with CENP-A and CENP-C centromere levels, and mitotic segregation fidelity. Our results suggest that a minimal level of heterochromatin is required to stabilize mitotic centromere function but not for maintaining centromere epigenetic memory, and that a homeostatic pathway maintains heterochromatin at centromeres.This article has an associated First Person interview with the first authors of the paper.
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Affiliation(s)
| | | | - Elisa Pesenti
- Wellcome Trust Centre for Cell Biology, Edinburgh, UK
| | | | - Wei-Hao Shang
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Vladimir Larionov
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | | | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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10
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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.
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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
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11
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UBAP2L Forms Distinct Cores that Act in Nucleating Stress Granules Upstream of G3BP1. Curr Biol 2020; 30:698-707.e6. [PMID: 31956030 DOI: 10.1016/j.cub.2019.12.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/08/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
Stress granules (SGs) are membraneless organelles that form in eukaryotic cells after stress exposure [1] (reviewed in [2-4]). Following translation inhibition, polysome disassembly releases 48S preinitiation complexes (PICs). mRNA, PICs, and other proteins coalesce in SG cores [1, 5-7]. SG cores recruit a dynamic shell, whose properties are dominated by weak interactions between proteins and RNAs [8-10]. The structure and assembly of SGs and how different components contribute to their formation are not fully understood. Using super-resolution and expansion microscopy, we find that the SG component UBAP2L [11, 12] and the core protein G3BP1 [5, 11-13] occupy different domains inside SGs. UBAP2L displays typical properties of a core protein, indicating that cores of different compositions coexist inside the same granule. Consistent with a role as a core protein, UBAP2L is required for SG assembly in several stress conditions. Our reverse genetic and cell biology experiments suggest that UBAP2L forms granules independent of G3BP1 and 2 but does not interfere with stress-induced translational inhibition. We propose a model in which UBAP2L is an essential SG nucleator that acts upstream of G3BP1 and 2 and facilitates G3BP1 core formation and SG assembly and growth.
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12
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Sikder S, Kaypee S, Kundu TK. Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease. J Biosci 2020; 45:15. [PMID: 31965993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Besides the fundamental components of the chromatin, DNA and octameric histone, the non-histone chromatin proteins and non-coding RNA play a critical role in the organization of functional chromatin domains. The non-histone chromatin proteins therefore regulate the transcriptional outcome in both physiological and pathophysiological state as well. They also help to maintain the epigenetic state of the genome indirectly. Several transcription factors and histone interacting factors also contribute in the maintenance of the epigenetic states, especially acetylation by the induction of autoacetylation ability of p300/CBP. Alterations of KAT activity have been found to be causally related to disease manifestation, and thus could be potential therapeutic target.
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Affiliation(s)
- Sweta Sikder
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560 064, India
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13
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Roy A, Ghosh A, Kumar B, Chandran B. IFI16, a nuclear innate immune DNA sensor, mediates epigenetic silencing of herpesvirus genomes by its association with H3K9 methyltransferases SUV39H1 and GLP. eLife 2019; 8:49500. [PMID: 31682228 PMCID: PMC6855800 DOI: 10.7554/elife.49500] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/01/2019] [Indexed: 12/25/2022] Open
Abstract
IFI16, an innate immune DNA sensor, recognizes the nuclear episomal herpes viral genomes and induces the inflammasome and interferon-β responses. IFI16 also regulates cellular transcription and act as a DNA virus restriction factor. IFI16 knockdown disrupted the latency of Kaposi’s sarcoma associated herpesvirus (KSHV) and induced lytic transcripts. However, the mechanism of IFI16’s transcription regulation is unknown. Here, we show that IFI16 is in complex with the H3K9 methyltransferase SUV39H1 and GLP and recruits them to the KSHV genome during de novo infection and latency. The resulting depositions of H3K9me2/me3 serve as a docking site for the heterochromatin-inducing HP1α protein leading into the IFI16-dependent epigenetic modifications and silencing of KSHV lytic genes. These studies suggest that IFI16’s interaction with H3K9MTases is one of the potential mechanisms by which IFI16 regulates transcription and establish an important paradigm of an innate immune sensor’s involvement in epigenetic silencing of foreign DNA.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Anandita Ghosh
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Binod Kumar
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, United States
| | - Bala Chandran
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
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14
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Tosolini M, Brochard V, Adenot P, Chebrout M, Grillo G, Navia V, Beaujean N, Francastel C, Bonnet-Garnier A, Jouneau A. Contrasting epigenetic states of heterochromatin in the different types of mouse pluripotent stem cells. Sci Rep 2018; 8:5776. [PMID: 29636490 PMCID: PMC5893598 DOI: 10.1038/s41598-018-23822-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 03/15/2018] [Indexed: 11/09/2022] Open
Abstract
Mouse embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) represent naive and primed pluripotency states, respectively, and are maintained in vitro by specific signalling pathways. Furthermore, ESCs cultured in serum-free medium with two kinase inhibitors (2i-ESCs) are thought to be the ground naïve pluripotent state. Here, we present a comparative study of the epigenetic and transcriptional states of pericentromeric heterochromatin satellite sequences found in these pluripotent states. We show that 2i-ESCs are distinguished from other pluripotent cells by a prominent enrichment in H3K27me3 and low levels of DNA methylation at pericentromeric heterochromatin. In contrast, serum-containing ESCs exhibit higher levels of major satellite repeat transcription, which is lower in 2i-ESCs and even more repressed in primed EpiSCs. Removal of either DNA methylation or H3K9me3 at PCH in 2i-ESCs leads to enhanced deposition of H3K27me3 with few changes in satellite transcript levels. In contrast, their removal in EpiSCs does not lead to deposition of H3K27me3 but rather removes transcriptional repression. Altogether, our data show that the epigenetic state of PCH is modified during transition from naive to primed pluripotency states towards a more repressive state, which tightly represses the transcription of satellite repeats.
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Affiliation(s)
- Matteo Tosolini
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France
| | - Vincent Brochard
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France
| | - Pierre Adenot
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France
| | - Martine Chebrout
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France
| | - Giacomo Grillo
- UMR7216 Epigenetics and cell fate, Université Paris Diderot Paris 7, 75013, Paris, France
| | - Violette Navia
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France
| | - Nathalie Beaujean
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France.,Univ Lyon, Université Claude Bernard Lyon 1, Inserm, INRA, Stem Cell and Brain Research Institute U1208, USC1361, 69500, Bron, France
| | - Claire Francastel
- UMR7216 Epigenetics and cell fate, Université Paris Diderot Paris 7, 75013, Paris, France
| | | | - Alice Jouneau
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350, Jouy en Josas, France.
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15
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Boehm D, Ott M. Host Methyltransferases and Demethylases: Potential New Epigenetic Targets for HIV Cure Strategies and Beyond. AIDS Res Hum Retroviruses 2017; 33:S8-S22. [PMID: 29140109 DOI: 10.1089/aid.2017.0180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A successful HIV cure strategy may require reversing HIV latency to purge hidden viral reservoirs or enhancing HIV latency to permanently silence HIV transcription. Epigenetic modifying agents show promise as antilatency therapeutics in vitro and ex vivo, but also affect other steps in the viral life cycle. In this review, we summarize what we know about cellular DNA and protein methyltransferases (PMTs) as well as demethylases involved in HIV infection. We describe the biology and function of DNA methyltransferases, and their controversial role in HIV infection. We further explain the biology of PMTs and their effects on lysine and arginine methylation of histone and nonhistone proteins. We end with a focus on protein demethylases, their unique modes of action and their emerging influence on HIV infection. An outlook on the use of methylation-modifying agents in investigational HIV cure strategies is provided.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
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16
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Johnson WL, Yewdell WT, Bell JC, McNulty SM, Duda Z, O'Neill RJ, Sullivan BA, Straight AF. RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin. eLife 2017; 6. [PMID: 28760200 PMCID: PMC5538822 DOI: 10.7554/elife.25299] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022] Open
Abstract
Heterochromatin formed by the SUV39 histone methyltransferases represses transcription from repetitive DNA sequences and ensures genomic stability. How SUV39 enzymes localize to their target genomic loci remains unclear. Here, we demonstrate that chromatin-associated RNA contributes to the stable association of SUV39H1 with constitutive heterochromatin in human cells. We find that RNA associated with mitotic chromosomes is concentrated at pericentric heterochromatin, and is encoded, in part, by repetitive α-satellite sequences, which are retained in cis at their transcription sites. Purified SUV39H1 directly binds nucleic acids through its chromodomain; and in cells, SUV39H1 associates with α-satellite RNA transcripts. Furthermore, nucleic acid binding mutants destabilize the association of SUV39H1 with chromatin in mitotic and interphase cells – effects that can be recapitulated by RNase treatment or RNA polymerase inhibition – and cause defects in heterochromatin function. Collectively, our findings uncover a previously unrealized function for chromatin-associated RNA in regulating constitutive heterochromatin in human cells. DOI:http://dx.doi.org/10.7554/eLife.25299.001 Each cell in a human body contains the same DNA sequence, which serves as a set of instructions for how the body should develop and operate. However, only certain sections of DNA are “active” at any particular time and in any given type of cell. When a section of DNA is active, cells make many copies of it using a molecule called RNA. When a section of DNA in inactive, very little RNA is made. Some sections of DNA must always be kept inactive to avoid damaging the cell. DNA is packaged around proteins called histones, and enzymes that modify histones control which sections of DNA are switched on or off. One such modifying enzyme, called SUV39H1, is important for inactivating sections of DNA that could cause harm to the cell if they are active. Previous studies showed that the loss of SUV39H1 and related proteins cause abnormalities and cancer in mice. However, it is not clear how this enzyme identifies and inactivates the DNA it needs to target. Johnson, Yewdell et al. studied SUV39H1 in human cells. The experiments show that RNA binds to the SUV39H1 enzyme and controls how it interacts with DNA. Specifically, Johnson, Yewdell et al. found that sections of DNA that are inactive can still make a small amount of RNA, and that this RNA tethers SUV39H1 to the DNA to keep the DNA switched off. Mutant forms of SUV39H1 that are unable to interact with RNA fall off the DNA, which allows DNA sequences that are normally switched off to become active. The findings of Johnson, Yewdell et al. reveal a new role for RNAs in regulating whether DNA is switched on or off. The next step is to determine whether other enzymes that can also modify histones use the same mechanism to activate or inactivate DNA. Differences in how the activity of DNA is regulated between individuals plays a crucial role in generating the diversity we see in nature. Therefore, this work helps us to understand our basic biology and may provide new opportunities for treating disease. DOI:http://dx.doi.org/10.7554/eLife.25299.002
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Affiliation(s)
- Whitney L Johnson
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - William T Yewdell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Jason C Bell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Shannon M McNulty
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
| | - Zachary Duda
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute for Systems Genomics, University of Connecticut, Storrs, United States
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute for Systems Genomics, University of Connecticut, Storrs, United States
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
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17
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Kudithipudi S, Schuhmacher MK, Kebede AF, Jeltsch A. The SUV39H1 Protein Lysine Methyltransferase Methylates Chromatin Proteins Involved in Heterochromatin Formation and VDJ Recombination. ACS Chem Biol 2017; 12:958-968. [PMID: 28169523 DOI: 10.1021/acschembio.6b01076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SUV39H1 is an H3K9 methyltransferase involved in the formation of heterochromatin. We investigated its substrate specificity profile and show recognition of H3 residues between K4 and G12 with highly specific readout of R8. The specificity profile of SUV39H1 is distinct from its paralog SUV39H2, indicating that they can have different additional substrates. Using the specificity profile, several novel SUV39H1 candidate substrates were identified. We observed methylation of 19 novel substrates at the peptide level and for six of them at the protein level. Methylation of RAG2, SET8, and DOT1L was confirmed in cells, which all have important roles in chromatin regulation. Methylation of SET8 allosterically stimulates its H4K20 monomethylation activity connecting SUV39H1 to the generation of increased H4K20me3 levels, another heterochromatic modification. Methylation of RAG2 alters its subnuclear localization, indicating that SUV39H1 might regulate VDJ recombination. Taken together, our results indicate that beyond the generation of H3K9me3, SUV39H1 has additional roles in chromatin biology by direct stimulation of the establishment of H4K20me3 and the regulation of chromatin binding of RAG2.
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Affiliation(s)
- Srikanth Kudithipudi
- Institute
of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | | | - Adam Fiseha Kebede
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Albert Jeltsch
- Institute
of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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18
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A model of dynamic stability of H3K9me3 heterochromatin to explain the resistance to reprogramming of differentiated cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:184-195. [DOI: 10.1016/j.bbagrm.2016.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 12/16/2022]
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19
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Raurell-Vila H, Bosch-Presegue L, Gonzalez J, Kane-Goldsmith N, Casal C, Brown JP, Marazuela-Duque A, Singh PB, Serrano L, Vaquero A. An HP1 isoform-specific feedback mechanism regulates Suv39h1 activity under stress conditions. Epigenetics 2017; 12:166-175. [PMID: 28059589 DOI: 10.1080/15592294.2016.1278096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The presence of H3K9me3 and heterochromatin protein 1 (HP1) are hallmarks of heterochromatin conserved in eukaryotes. The spreading and maintenance of H3K9me3 is effected by the functional interplay between the H3K9me3-specific histone methyltransferase Suv39h1 and HP1. This interplay is complex in mammals because the three HP1 isoforms, HP1α, β, and γ, are thought to play a redundant role in Suv39h1-dependent deposition of H3K9me3 in pericentric heterochromatin (PCH). Here, we demonstrate that despite this redundancy, HP1α and, to a lesser extent, HP1γ have a closer functional link to Suv39h1, compared to HP1β. HP1α and γ preferentially interact in vivo with Suv39h1, regulate its dynamics in heterochromatin, and increase Suv39h1 protein stability through an inhibition of MDM2-dependent Suv39h1-K87 polyubiquitination. The reverse is also observed, where Suv39h1 increases HP1α stability compared HP1β and γ. The interplay between Suv39h1 and HP1 isoforms appears to be relevant under genotoxic stress. Specifically, loss of HP1α and γ isoforms inhibits the upregulation of Suv39h1 and H3K9me3 that is observed under stress conditions. Reciprocally, Suv39h1 deficiency abrogates stress-dependent upregulation of HP1α and γ, and enhances HP1β levels. Our work defines a specific role for HP1 isoforms in regulating Suv39h1 function under stress via a feedback mechanism that likely regulates heterochromatin formation.
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Affiliation(s)
- Helena Raurell-Vila
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Laia Bosch-Presegue
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain.,b Tissue Repair and Regeneration Group , Department of Systems Biology , Universitat de Vic, Universitat Central de Catalunya , Vic , Spain
| | - Jessica Gonzalez
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Noriko Kane-Goldsmith
- c Department of Genetics , Human Genetics Institute, Rutgers University , Piscataway , NJ , USA
| | - Carmen Casal
- d Microcopy Unit, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Jeremy P Brown
- e Fächerverbund Anatomie, Institut für Zell- und Neurobiologie, Charite - Universitätsmedizin , Berlin , Germany
| | - Anna Marazuela-Duque
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Prim B Singh
- e Fächerverbund Anatomie, Institut für Zell- und Neurobiologie, Charite - Universitätsmedizin , Berlin , Germany.,f Natural Sciences and Psychology, John Moores University , Liverpool , UK
| | - Lourdes Serrano
- c Department of Genetics , Human Genetics Institute, Rutgers University , Piscataway , NJ , USA
| | - Alejandro Vaquero
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
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20
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Talbert PB, Henikoff S. Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 2016; 18:115-126. [PMID: 27924075 DOI: 10.1038/nrm.2016.148] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most histones are assembled into nucleosomes behind the replication fork to package newly synthesized DNA. By contrast, histone variants, which are encoded by separate genes, are typically incorporated throughout the cell cycle. Histone variants can profoundly change chromatin properties, which in turn affect DNA replication and repair, transcription, and chromosome packaging and segregation. Recent advances in the study of histone replacement have elucidated the dynamic processes by which particular histone variants become substrates of histone chaperones, ATP-dependent chromatin remodellers and histone-modifying enzymes. Here, we review histone variant dynamics and the effects of replacing DNA synthesis-coupled histones with their replication-independent variants on the chromatin landscape.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
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21
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Molina O, Carmena M, Maudlin IE, Earnshaw WC. PREditOR: a synthetic biology approach to removing heterochromatin from cells. Chromosome Res 2016; 24:495-509. [PMID: 27924426 PMCID: PMC5167778 DOI: 10.1007/s10577-016-9539-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022]
Abstract
It is widely accepted that heterochromatin is necessary to maintain genomic stability. However, direct experimental evidence supporting this is slim. Previous studies using either enzyme inhibitors, gene knockout or knockdown studies all are subject to the caveat that drugs may have off-target effects and enzymes that modify chromatin proteins to support heterochromatin formation may also have numerous other cellular targets as well. Here, we describe PREditOR (protein reading and editing of residues), a synthetic biology approach that allows us to directly remove heterochromatin from cells without either drugs or global interference with gene function. We find that removal of heterochromatin perturbs mitotic progression and causes a dramatic increase in chromosome segregation defects, possibly as a result of interfering with the normal centromeric localization of the chromosomal passenger complex.
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Affiliation(s)
- Oscar Molina
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Mar Carmena
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Isabella E Maudlin
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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22
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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]
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23
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Yu S, Yang F, Shen WH. Genome maintenance in the context of 4D chromatin condensation. Cell Mol Life Sci 2016; 73:3137-50. [PMID: 27098512 PMCID: PMC4956502 DOI: 10.1007/s00018-016-2221-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/07/2016] [Indexed: 12/20/2022]
Abstract
The eukaryotic genome is packaged in the three-dimensional nuclear space by forming loops, domains, and compartments in a hierarchical manner. However, when duplicated genomes prepare for segregation, mitotic cells eliminate topologically associating domains and abandon the compartmentalized structure. Alongside chromatin architecture reorganization during the transition from interphase to mitosis, cells halt most DNA-templated processes such as transcription and repair. The intrinsically condensed chromatin serves as a sophisticated signaling module subjected to selective relaxation for programmed genomic activities. To understand the elaborate genome-epigenome interplay during cell cycle progression, the steady three-dimensional genome requires a time scale to form a dynamic four-dimensional and a more comprehensive portrait. In this review, we will dissect the functions of critical chromatin architectural components in constructing and maintaining an orderly packaged chromatin environment. We will also highlight the importance of the spatially and temporally conscious orchestration of chromatin remodeling to ensure high-fidelity genetic transmission.
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Affiliation(s)
- Sonia Yu
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
| | - Fan Yang
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Wen H Shen
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA.
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24
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A two-state activation mechanism controls the histone methyltransferase Suv39h1. Nat Chem Biol 2016; 12:188-93. [PMID: 26807716 PMCID: PMC4876634 DOI: 10.1038/nchembio.2008] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/24/2015] [Indexed: 12/31/2022]
Abstract
Specialized chromatin domains contribute to nuclear organization and regulation of gene expression. Gene-poor regions are di- and trimethylated at lysine 9 of histone H3 (H3K9me2/3) by the histone methyltransferase, Suv39h1. This enzyme harnesses a positive feedback loop to spread H3K9me2/3 over extended heterochromatic regions. However, little is known about how feedback loops operate on complex biopolymers such as chromatin, in part because of the difficulty in obtaining suitable substrates. Here we describe the synthesis of multi-domain ‘designer chromatin’ templates and their application to dissecting the regulation of human Suv39h1. We uncovered a two-step activation switch where H3K9me3 recognition and subsequent anchoring of the enzyme to chromatin allosterically promotes methylation activity, and confirmed that this mechanism contributes to chromatin recognition in cells. We propose that this mechanism serves as a paradigm in chromatin biochemistry since it enables highly dynamic sampling of chromatin state combined with targeted modification of desired genomic regions.
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25
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Li J, Zhu S, Ke XX, Cui H. Role of several histone lysine methyltransferases in tumor development. Biomed Rep 2016; 4:293-299. [PMID: 26998265 PMCID: PMC4774316 DOI: 10.3892/br.2016.574] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/31/2015] [Indexed: 12/17/2022] Open
Abstract
The field of cancer epigenetics has been evolving rapidly in recent decades. Epigenetic mechanisms include DNA methylation, histone modifications and microRNAs. Histone modifications are important markers of function and chromatin state. Aberrant histone methylation frequently occurs in tumor development and progression. Multiple studies have identified that histone lysine methyltransferases regulate gene transcription through the methylation of histone, which affects cell proliferation and differentiation, cell migration and invasion, and other biological characteristics. Histones have variant lysine sites for different levels of methylation, catalyzed by different lysine methyltransferases, which have numerous effects on human cancers. The present review focused on the most recent advances, described the key function sites of histone lysine methyltransferases, integrated significant quantities of data to introduce several compelling histone lysine methyltransferases in various types of human cancers, summarized their role in tumor development and discussed their potential mechanisms of action.
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Affiliation(s)
- Jifu Li
- Cell Biology Laboratory, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, P.R. China
| | - Shunqin Zhu
- School of Life Science, Southwest University, Chongqing 400716, P.R. China
| | - Xiao-Xue Ke
- Cell Biology Laboratory, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, P.R. China
| | - Hongjuan Cui
- Cell Biology Laboratory, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, P.R. China
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26
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Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol 2015; 16:519-32. [PMID: 26296162 PMCID: PMC4672940 DOI: 10.1038/nrm4043] [Citation(s) in RCA: 613] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methylation of DNA and of histone 3 at Lys 9 (H3K9) are highly correlated with gene silencing in eukaryotes from fungi to humans. Both of these epigenetic marks need to be established at specific regions of the genome and then maintained at these sites through cell division. Protein structural domains that specifically recognize methylated DNA and methylated histones are key for targeting enzymes that catalyse these marks to appropriate genome sites. Genetic, genomic, structural and biochemical data reveal connections between these two epigenetic marks, and these domains mediate much of the crosstalk.
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Affiliation(s)
- Jiamu Du
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Lianna M Johnson
- Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Steven E Jacobsen
- Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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27
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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28
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Klement K, Goodarzi AA. DNA double strand break responses and chromatin alterations within the aging cell. Exp Cell Res 2014; 329:42-52. [PMID: 25218945 DOI: 10.1016/j.yexcr.2014.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/28/2014] [Accepted: 09/01/2014] [Indexed: 12/23/2022]
Abstract
Cellular senescence is a state of permanent replicative arrest that allows cells to stay viable and metabolically active but resistant to apoptotic and mitogenic stimuli. Specific, validated markers can identify senescent cells, including senescence-associated β galactosidase activity, chromatin alterations, cell morphology changes, activated p16- and p53-dependent signaling and permanent cell cycle arrest. Senescence is a natural consequence of DNA replication-associated telomere erosion, but can also be induced prematurely by telomere-independent events such as failure to repair DNA double strand breaks. Here, we review the molecular pathways of senescence onset, focussing on the changes in chromatin organization that are associated with cellular senescence, particularly senescence-associated heterochromatin foci formation. We also discuss the altered dynamics of the DNA double strand break response within the context of aging cells. Appreciating how, mechanistically, cellular senescence is induced, and how changes to chromatin organization and DNA repair contributes to this, is fundamental to our understanding of the normal and premature human aging processes associated with loss of organ and tissue function in humans.
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Affiliation(s)
- Karolin Klement
- Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Aaron A Goodarzi
- Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1.
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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: 66] [Impact Index Per Article: 6.6] [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.
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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
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30
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Nakagawa C, Kawakita A, Fukada T, Sugimoto K. Live-cell imaging of HP1α throughout the cell cycle of mouse C3H10T1/2 cells and rhythmical flickering of heterochromatin dots in interphase. Biosci Biotechnol Biochem 2014; 78:556-64. [PMID: 25036950 DOI: 10.1080/09168451.2014.893184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Heterochromatin protein 1 alpha (HP1α) localizes to heterochromatin in interphase and shows dynamic molecular behavior in living cells. We previously reported that during mitosis, the majority of HP1α diffused into the cytoplasm but some remained in centromere heterochromatin. Here, we further characterize the molecular behavior of HP1α throughout the cell cycle. Time-lapse imaging of DsRed-HP1α through two successive cell divisions indicated that interphase can be divided into four phases. HP1α forms heterochromatin dots in early G1, which are maintained without any apparent changes (Phase 1). However, the HP1α dots begin to diffuse into the nucleoplasm and start flickering with a rhythmical cycle (Phase 2). Then, the HP1α dots diffuse further towards the periphery of the nucleus (Phase 3), and uniformly diffuse throughout the entire nucleus (Phase 4). Rhythmical flickering of HP1α dots in the middle of interphase may be useful for following cell cycle progression in mouse living cells.
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Affiliation(s)
- Chika Nakagawa
- a Laboratory of Molecular Biology and Cell Informatics, Division of Bioscience and Informatics , Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Osaka , Japan
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31
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Park SH, Yu SE, Chai YG, Jang YK. CDK2-dependent phosphorylation of Suv39H1 is involved in control of heterochromatin replication during cell cycle progression. Nucleic Acids Res 2014; 42:6196-207. [PMID: 24728993 PMCID: PMC4041437 DOI: 10.1093/nar/gku263] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 02/26/2014] [Accepted: 03/19/2014] [Indexed: 01/24/2023] Open
Abstract
Although several studies have suggested that the functions of heterochromatin regulators may be regulated by post-translational modifications during cell cycle progression, regulation of the histone methyltransferase Suv39H1 is not fully understood. Here, we demonstrate a direct link between Suv39H1 phosphorylation and cell cycle progression. We show that CDK2 phosphorylates Suv39H1 at Ser391 and these phosphorylation levels oscillate during the cell cycle, peaking at S phase and maintained during S-G2-M phase. The CDK2-mediated phosphorylation of Suv39H1 at Ser391 results in preferential dissociation from chromatin. Furthermore, phosphorylation-mediated dissociation of Suv39H1 from chromatin causes an enhanced occupancy of JMJD2A histone demethylase on heterochromatin and alterations in inactive histone marks. Overexpression of phospho-mimic Suv39H1 induces early replication of heterochromatin, suggesting the importance of Suv39H1 phosphorylation in the replication of heterochromatin. Moreover, overexpression of phospho-defective Suv39H1 caused altered replication timing of heterochromatin and increases sensitivity to replication stress. Collectively, our data suggest that phosphorylation-mediated modulation of Suv39H1-chromatin association may be an initial step in heterochromatin replication.
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Affiliation(s)
- Su Hyung Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea Initiative for Biological Function & Systems, Yonsei University, Seoul 120-749, Republic of Korea
| | - Seung Eun Yu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea Initiative for Biological Function & Systems, Yonsei University, Seoul 120-749, Republic of Korea
| | - Young Gyu Chai
- Division of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Yeun Kyu Jang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea Initiative for Biological Function & Systems, Yonsei University, Seoul 120-749, Republic of Korea
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32
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Basu A, Dasari V, Mishra RK, Khosla S. The CpG island encompassing the promoter and first exon of human DNMT3L gene is a PcG/TrX response element (PRE). PLoS One 2014; 9:e93561. [PMID: 24743422 PMCID: PMC3990577 DOI: 10.1371/journal.pone.0093561] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/07/2014] [Indexed: 01/27/2023] Open
Abstract
DNMT3L, a member of DNA methyltransferases family, is present only in mammals. As it provides specificity to the action of de novo methyltransferases, DNMT3A and DNMT3B and interacts with histone H3, DNMT3L has been invoked as the molecule that can read the histone code and translate it into DNA methylation. It plays an important role in the initiation of genomic imprints during gametogenesis and in nuclear reprogramming. With important functions attributed to it, it is imperative that the DNMT3L expression is tightly controlled. Previously, we had identified a CpG island within the human DNMT3L promoter and first exon that showed loss of DNA methylation in cancer samples. Here we show that this Differentially Methylated CpG island within DNMT3L (DNMT3L DMC) acts to repress transcription, is a Polycomb/Trithorax Response Element (PRE) and interacts with both PRC1 and PRC2 Polycomb repressive complexes. In addition, it adopts inactive chromatin conformation and is associated with other inactive chromatin-specific proteins like SUV39H1 and HP1. The presence of DNMT3L DMC also influences the adjacent promoter to adopt repressive histone post-translational modifications. Due to its association with multiple layers of repressive epigenetic modifications, we believe that PRE within the DNMT3L DMC is responsible for the tight regulation of DNMT3L expression and the aberrant epigenetic modifications of this region leading to DNMT3L overexpression could be the reason of nuclear programming during carcinogenesis.
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Affiliation(s)
- Amitava Basu
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Vasanthi Dasari
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Rakesh K. Mishra
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Hyderabad, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
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33
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Crowded chromatin is not sufficient for heterochromatin formation and not required for its maintenance. J Struct Biol 2013; 184:445-53. [PMID: 24145303 DOI: 10.1016/j.jsb.2013.10.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 11/22/2022]
Abstract
In contrast to cytoplasmic organelles, which are usually separated from the rest of the cell by phospholipid membranes, nuclear compartments are readily accessible to diffusing proteins and must rely on different mechanisms to maintain their integrity. Specific interactions between scaffolding proteins are known to have important roles for the formation and maintenance of nuclear structures. General physical mechanisms such as molecular crowding, phase separation or colloidal behavior have also been suggested, but their physiological significance remains uncertain. For macromolecular crowding, a role in the maintenance of nucleoli and promyelocytic leukemia (PML) nuclear bodies has been shown. Here, we tested whether a modulation of the compaction state of chromatin, which directly influences the local crowding state, has an impact on the formation and maintenance of densely packed heterochromatin. By osmotic perturbations, we could modify the packing state of chromatin in a controlled manner and show that chromatin compaction, which is associated with increased crowding conditions, is not, per se, sufficient to initiate the formation of new bona fide heterochromatin structures nor is it necessary to maintain already established heterochromatin domains. In consequence, if an increase in crowding induced by chromatin compaction maybe an early step in heterochromatin formation, specific protein-protein interactions are nevertheless required to make heterochromatin long lasting and independent of the crowding state.
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34
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Muramatsu D, Singh PB, Kimura H, Tachibana M, Shinkai Y. Pericentric heterochromatin generated by HP1 protein interaction-defective histone methyltransferase Suv39h1. J Biol Chem 2013; 288:25285-25296. [PMID: 23836914 PMCID: PMC3757193 DOI: 10.1074/jbc.m113.470724] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/23/2013] [Indexed: 02/02/2023] Open
Abstract
Pericentric regions form epigenetically organized silent heterochromatin structures that accumulate histone H3 lysine 9 trimethylation (H3K9me3) and HP1. At pericentric regions, Suv39h is the major enzyme that generates H3K9me3. Suv39h also interacts directly with HP1, a methylated H3K9-binding protein. However, it is not well characterized how HP1 interaction is important for Suv39h accumulation and Suv39h-mediated H3K9me3 formation at the pericentromere. To address this, we introduced the HP1 binding-defective N-terminally truncated mouse Suv39h1 (ΔN) into Suv39h-deficient embryonic stem cells. Interestingly, pericentric accumulation of ΔN and ΔN-mediated H3K9me3 was observed to recover, but HP1 accumulation was only marginally restored. ΔN also rescued DNA methyltransferase Dnmt3a and -3b accumulation and DNA methylation of the pericentromere. In contrast, other pericentric heterochromatin features, such as ATRX protein association and H4K20me3, were not recovered. Finally, derepressed major satellite repeats were partially silenced by ΔN expression. These findings clearly showed that the Suv39h-HP1 binding is dispensable for pericentric H3K9me3 and DNA methylation, but this interaction and HP1 recruitment/accumulation seem to be crucial for complete formation of heterochromatin.
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Affiliation(s)
- Daisuke Muramatsu
- From the Graduate School of Biostudies, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan,; the Cellular Memory Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Prim B Singh
- the Fächereverband Anatomie, Institut für Zell and Neurobiologie, Charite-Universitätmedizin, 10117 Berlin, Germany
| | - Hiroshi Kimura
- the Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Makoto Tachibana
- From the Graduate School of Biostudies, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan,; the Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan, and
| | - Yoichi Shinkai
- the Cellular Memory Laboratory, RIKEN, Wako, Saitama 351-0198, Japan,; CREST (Core Research for Evolutional Science and Technology), Japan Science and Technology Agency, Kawaguchi 332-0012, Japan.
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35
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Blancafort P, Jin J, Frye S. Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol Pharmacol 2012; 83:563-76. [PMID: 23150486 DOI: 10.1124/mol.112.080697] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The epigenomic era has revealed a well-connected network of molecular processes that shape the chromatin landscape. These processes comprise abnormal methylomes, transcriptosomes, genome-wide histone post-transcriptional modifications patterns, histone variants, and noncoding RNAs. The mapping of these processes in large scale by chromatin immunoprecipitation sequencing and other methodologies in both cancer and normal cells reveals novel therapeutic opportunities for anticancer intervention. The goal of this minireview is to summarize pharmacological strategies to modify the epigenetic landscape of cancer cells. These approaches include the use of novel small molecule inhibitors of epigenetic processes specifically deregulated in cancer cells and the design of engineered proteins able to stably reprogram the epigenetic code in cancer cells in a way that is similar to normal cells.
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Affiliation(s)
- Pilar Blancafort
- School of Anatomy, Physiology, and Human Biology, M309, the University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia.
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36
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Histone modifications and lamin A regulate chromatin protein dynamics in early embryonic stem cell differentiation. Nat Commun 2012; 3:910. [PMID: 22713752 DOI: 10.1038/ncomms1915] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 05/18/2012] [Indexed: 12/20/2022] Open
Abstract
Embryonic stem cells are characterized by unique epigenetic features including decondensed chromatin and hyperdynamic association of chromatin proteins with chromatin. Here we investigate the potential mechanisms that regulate chromatin plasticity in embryonic stem cells. Using epigenetic drugs and mutant embryonic stem cells lacking various chromatin proteins, we find that histone acetylation, G9a-mediated histone H3 lysine 9 (H3K9) methylation and lamin A expression, all affect chromatin protein dynamics. Histone acetylation controls, almost exclusively, euchromatin protein dynamics; lamin A expression regulates heterochromatin protein dynamics, and G9a regulates both euchromatin and heterochromatin protein dynamics. In contrast, we find that DNA methylation and nucleosome repeat length have little or no effect on chromatin-binding protein dynamics in embryonic stem cells. Altered chromatin dynamics associates with perturbed embryonic stem cell differentiation. Together, these data provide mechanistic insights into the epigenetic pathways that are responsible for chromatin plasticity in embryonic stem cells, and indicate that the genome's epigenetic state modulates chromatin plasticity and differentiation potential of embryonic stem cells.
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37
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Rosnoblet C, Vandamme J, Völkel P, Angrand PO. Analysis of the human HP1 interactome reveals novel binding partners. Biochem Biophys Res Commun 2011; 413:206-11. [PMID: 21888893 DOI: 10.1016/j.bbrc.2011.08.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 08/12/2011] [Indexed: 10/17/2022]
Abstract
Heterochromatin protein 1 (HP1) has first been described in Drosophila as an essential component of constitutive heterochromatin required for stable epigenetic gene silencing. Less is known about the three mammalian HP1 isotypes CBX1, CBX3 and CBX5. Here, we applied a tandem affinity purification approach coupled with tandem mass spectrometry methodologies in order to identify interacting partners of the mammalian HP1 isotypes. Our analysis identified with high confidence about 30-40 proteins co-eluted with CBX1 and CBX3, and around 10 with CBX5 including a number of novel HP1-binding partners. Our data also suggest that HP1 family members are mainly associated with a single partner or within small protein complexes composed of limited numbers of components. Finally, we showed that slight binding preferences might exist between HP1 family members.
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Affiliation(s)
- Claire Rosnoblet
- Chromatinomics, Interdisciplinary Research Institute, Université de Lille Nord de France, Université de Lille 1 Sciences et Technologies/CNRS USR 3078, 50 Avenue Halley, Parc Scientifique de Haute Borne, F-59658 Villeneuve d'Ascq Cedex, France
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38
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Bosch-Presegué L, Raurell-Vila H, Marazuela-Duque A, Kane-Goldsmith N, Valle A, Oliver J, Serrano L, Vaquero A. Stabilization of Suv39H1 by SirT1 is part of oxidative stress response and ensures genome protection. Mol Cell 2011; 42:210-23. [PMID: 21504832 DOI: 10.1016/j.molcel.2011.02.034] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/27/2010] [Accepted: 02/07/2011] [Indexed: 10/18/2022]
Abstract
Sirtuins are NAD-dependent deacetylases that sense oxidative stress conditions and promote a protective cellular response. The Sirtuin SirT1 is involved in facultative heterochromatin formation through an intimate functional relationship with the H3K9me3 methyltransferase Suv39h1, a chromatin organization protein. However, SirT1 also regulates Suv39h1-dependent constitutive heterochromatin (CH) through an unknown mechanism; interestingly, SirT1 does not significantly localize in these regions. Herein, we report that SirT1 controls global levels of Suv39h1 by increasing its half-life through inhibition of Suv39h1 lysine 87 polyubiquitination by the E3-ubiquitin ligase MDM2. This in turn increases Suv39h1 turnover in CH and ensures genome integrity. Stress conditions that lead to SirT1 upregulation, such as calorie restriction, also induce higher levels of Suv39h1 in a SirT1-dependent manner in vivo. These observations reflect a direct link between oxidative stress response and Suv39h1 and support a dynamic view of heterochromatin, in which its structure adapts to cell physiology.
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Affiliation(s)
- Laia Bosch-Presegué
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program, Institut d'Investigació Biomèdica de Bellvitge, Avinguda Gran Via de l'Hospitalet 199-203, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
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39
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Abstract
The cell nucleus is responsible for the storage, expression, propagation, and maintenance of the genetic material it contains. Highly organized macromolecular complexes are required for these processes to occur faithfully in an extremely crowded nuclear environment. In addition to chromosome territories, the nucleus is characterized by the presence of nuclear substructures, such as the nuclear envelope, the nucleolus, and other nuclear bodies. Other smaller structural entities assemble on chromatin in response to required functions including RNA transcription, DNA replication, and DNA repair. Experiments in living cells over the last decade have revealed that many DNA binding proteins have very short residence times on chromatin. These observations have led to a model in which the assembly of nuclear macromolecular complexes is based on the transient binding of their components. While indeed most nuclear proteins are highly dynamic, we found after an extensive survey of the FRAP literature that an important subset of nuclear proteins shows either very slow turnover or complete immobility. These examples provide compelling evidence for the establishment of stable protein complexes in the nucleus over significant fractions of the cell cycle. Stable interactions in the nucleus may, therefore, contribute to the maintenance of genome integrity. Based on our compilation of FRAP data, we propose an extension of the existing model for nuclear organization which now incorporates stable interactions. Our new “induced stability” model suggests that self-organization, self-assembly, and assisted assembly contribute to nuclear architecture and function.
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40
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Erdel F, Müller-Ott K, Baum M, Wachsmuth M, Rippe K. Dissecting chromatin interactions in living cells from protein mobility maps. Chromosome Res 2011; 19:99-115. [PMID: 20848178 DOI: 10.1007/s10577-010-9155-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The genome of eukaryotes is organized into a dynamic nucleoprotein complex referred to as chromatin, which can adopt different functional states. Both the DNA and the protein component of chromatin are subject to various post-translational modifications that define the cell's gene expression program. Their readout and establishment occurs in a spatio-temporally coordinated manner that is controlled by numerous chromatin-interacting proteins. Binding to chromatin in living cells can be measured by a spatially resolved analysis of protein mobility using fluorescence microscopy based approaches. Recent advancements in the acquisition of protein mobility data using fluorescence bleaching and correlation methods provide data sets on diffusion coefficients, binding kinetics, and cellular concentrations on different time and length scales. The combination of different techniques is needed to dissect the complex interplay of diffusive translocations, binding events, and mobility constraints of the chromatin environment. While bleaching techniques have their strength in the characterization of particles that are immobile on the second/minute time scale, a correlation analysis is advantageous to characterize transient binding events with millisecond residence time. The application and synergy effects of the different approaches to obtain protein mobility and interaction maps in the nucleus are illustrated for the analysis of heterochromatin protein 1.
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Affiliation(s)
- Fabian Erdel
- Deutsches Krebsforschungszentrum and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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41
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Every methyl counts--epigenetic calculus. FEBS Lett 2010; 585:2001-7. [PMID: 21108946 DOI: 10.1016/j.febslet.2010.11.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/16/2010] [Accepted: 11/16/2010] [Indexed: 11/22/2022]
Abstract
Histone modifications play an important role in the formation of an epigenetic memory system that maintains cellular identity. Their complex patterns have been suggested to constitute a histone code, which encodes for specific forms of chromatin. According to the histone code hypothesis these specific patterns are passed on from one cell generation to the next. This enables cells to keep a specific gene expression pattern even in absence of the specific transcription factors that initiated the expression of lineage determining genes. The methylation of specific lysine residues within the histone tails plays a particularly important role in defining the histone modification pattern as mutations of the enzymes that catalyze the formation or the removal of methyl groups have severe effects on cellular physiology. Lysines can get mono-, di- or trimethylated, but the molecular function of the different modification states is still not fully understood. In the following review we will highlight recent data that try to tackle this question and discuss their potential impact for our understanding of the role of histone methylation in epigenetic inheritance.
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42
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Tessadori F. [Heterochromatin, a plastic component in the nucleus of Arabidopsis thaliana cells]. Biol Aujourdhui 2010; 204:189-97. [PMID: 20950562 DOI: 10.1051/jbio/2010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Indexed: 11/15/2022]
Abstract
The cytogenetic observation of the nucleus of Arabidopsis thaliana, a plant member of the brassicaceae family, reveals a simple organization of the nuclear content. Indeed, the nuclear volume is occupied by two distinct and easily distinguishable forms of chromatin: a large fraction of relatively decondensed and transcriptionnally active euchromatin surrounds about ten conspicuous regions, the chromocenters, which contain most repeated and highly condensed heterochromatic sequences. Remarkably, during the development of A. thaliana or when the plant is exposed to certain environmental variations, dramatic changes in the appearance, the size or the presence of the chromocenters occur. A number of cytogenetic studies have not only characterized the genomic sequences accommodated in the chromocenters, but have also established the dynamics of their assembly and disruption. Moreover, various endogenous and exogenous factors involved in the presence and the size of chromocenters were recently identified. Taken together, these studies carried out in A. thaliana suggest that heterochromatin is a truly "malleable" fraction of the genome whose dynamic organization is not controlled only by epigenetic marks and whose importance in nuclear function goes beyond merely grouping together non-coding genomic sequences.
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Fournier A, McLeer-Florin A, Lefebvre C, Duley S, Barki L, Ribeyron J, Alboukadel K, Hamaidia S, Granjon A, Gressin R, Lajmanovich A, Bonnefoix T, Chauvelier S, Debernardi A, Rousseaux S, de Fraipont F, Figeac M, Kerckaert JP, De Vos J, Usson Y, Delaval K, Grichine A, Vourc'h C, Khochbin S, Feil R, Leroux D, Callanan MB. 1q12 chromosome translocations form aberrant heterochromatic foci associated with changes in nuclear architecture and gene expression in B cell lymphoma. EMBO Mol Med 2010; 2:159-71. [PMID: 20432501 PMCID: PMC3377314 DOI: 10.1002/emmm.201000067] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Epigenetic perturbations are increasingly described in cancer cells where they are thought to contribute to deregulated gene expression and genome instability. Here, we report the first evidence that a distinct category of chromosomal translocations observed in human tumours—those targeting 1q12 satellite DNA—can directly mediate such perturbations by promoting the formation of aberrant heterochromatic foci (aHCF). By detailed investigations of a 1q12 translocation to chromosome 2p, in a case of human B cell lymphoma, aberrant aHCF were shown to be localized to the nuclear periphery and to arise as a consequence of long range ‘pairing’ between the translocated 1q12 and chromosome 2 centromeric regions. Remarkably, adjacent 2p sequences showed increased levels of repressive histone modifications, including H4K20me3 and H3K9me3, and were bound by HP1. aHCF were associated to aberrant spatial localization and deregulated expression of a novel 2p gene (GMCL1) that was found to have prognostic impact in diffuse large B cell lymphoma. Thus constitutive heterochromatin rearrangements can contribute to tumourigenesis by perturbing gene expression via long range epigenetic mechanisms.
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Müller KP, Erdel F, Caudron-Herger M, Marth C, Fodor BD, Richter M, Scaranaro M, Beaudouin J, Wachsmuth M, Rippe K. Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy. Biophys J 2009; 97:2876-85. [PMID: 19948116 PMCID: PMC2784559 DOI: 10.1016/j.bpj.2009.08.057] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 08/17/2009] [Accepted: 08/27/2009] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin protein 1 (HP1) is a central factor in establishing and maintaining the repressive heterochromatin state. To elucidate its mobility and interactions, we conducted a comprehensive analysis on different time and length scales by fluorescence fluctuation microscopy in mouse cell lines. The local mobility of HP1alpha and HP1beta was investigated in densely packed pericentric heterochromatin foci and compared with other bona fide euchromatin regions of the nucleus by fluorescence bleaching and correlation methods. A quantitative description of HP1alpha/beta in terms of its concentration, diffusion coefficient, kinetic binding, and dissociation rate constants was derived. Three distinct classes of chromatin-binding sites with average residence times t(res)
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Affiliation(s)
- Katharina P Müller
- Deutsches Krebsforschungszentrum and BioQuant, Research Group Genome Organization and Function, Heidelberg, Germany
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Hiragami-Hamada K, Xie SQ, Saveliev A, Uribe-Lewis S, Pombo A, Festenstein R. The molecular basis for stability of heterochromatin-mediated silencing in mammals. Epigenetics Chromatin 2009; 2:14. [PMID: 19889207 PMCID: PMC2779788 DOI: 10.1186/1756-8935-2-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 11/04/2009] [Indexed: 01/19/2023] Open
Abstract
The archetypal epigenetic phenomenon of position effect variegation (PEV) in Drosophila occurs when a gene is brought abnormally close to heterochromatin, resulting in stochastic silencing of the affected gene in a proportion of cells that would normally express it. PEV has been instrumental in unraveling epigenetic mechanisms. Using an in vivo mammalian model for PEV we have extensively investigated the molecular basis for heterochromatin-mediated gene silencing. Here we distinguish 'epigenetic effects' from other cellular differences by studying ex vivo cells that are identical, apart from the expression of the variegating gene which is silenced in a proportion of the cells. By separating cells according to transgene expression we show here that silencing appears to be associated with histone H3 lysine 9 trimethylation (H3K9me3), DNA methylation and the localization of the silenced gene to a specific nuclear compartment enriched in these modifications. In contrast, histone H3 acetylation (H3Ac) and lysine 4 di or tri methylation (H3K4me2/3) are the predominant modifications associated with expression where we see the gene in a euchromatic compartment. Interestingly, DNA methylation and inaccessibility, rather than H3K9me3, correlated most strongly with resistance to de-repression by cellular activation. These results have important implications for understanding the contribution of specific factors involved in the establishment and maintenance of gene silencing and activation in vivo.
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Affiliation(s)
- Kyoko Hiragami-Hamada
- Gene Control Mechanisms and Disease Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Hospital, London W12 0NN, UK.
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Chromocentre integrity and epigenetic marks. J Struct Biol 2009; 169:124-33. [PMID: 19766725 DOI: 10.1016/j.jsb.2009.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 09/10/2009] [Accepted: 09/13/2009] [Indexed: 11/20/2022]
Abstract
The epigenetic modification of histones dictates the formation of euchromatin and heterochromatin domains. We studied the effects of a deficiency of histone methyltransferase, SUV39h, and trichostatin A-dependent hyperacetylation on the structural stability of centromeric clusters, called chromocentres. We did not observe the expected disintegration of chromocentres, but both SUV39h deficiency and hyperacetylation in SUV39h+/+ cells induced the re-positioning of chromocentres closer to the nuclear periphery. Conversely, TSA treatment of SUV39h-/- cells re-established normal nuclear radial positioning of chromocentres. This structural re-arrangement was likely caused by several epigenetic events at centromeric heterochromatin. In particular, reciprocal exchanges between H3K9me1, H3K9me2, H3K9me3, DNA methylation, and HP1 protein levels influenced chromocentre nuclear composition. For example, H3K9me1 likely substituted for the function of H3K9me3 in chromocentre nuclear arrangement and compaction. Our results illustrate the important and interchangeable roles of epigenetic marks for chromocentre integrity. Therefore, we propose a model for epigenetic regulation of nuclear stability of centromeric heterochromatin in the mouse genome.
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Zemach A, Paul LK, Stambolsky P, Efroni I, Rotter V, Grafi G. The C-terminal domain of the Arabidopsis AtMBD7 protein confers strong chromatin binding activity. Exp Cell Res 2009; 315:3554-62. [PMID: 19647732 DOI: 10.1016/j.yexcr.2009.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/26/2009] [Accepted: 07/27/2009] [Indexed: 12/01/2022]
Abstract
The Arabidopsis MBD7 (AtMBD7) - a naturally occurring poly MBD protein - was previously found to be functional in binding methylated-CpG dinucleotides in vitro and localized to highly methylated chromocenters in vivo. Furthermore, AtMBD7 has significantly lower mobility within the nucleus conferred by cooperative activity of its three MBD motifs. Here we show that besides the MBD motifs, AtMBD7 possesses a strong chromatin binding domain located at its C-terminus designated sticky-C (StkC). Mutational analysis showed that a glutamic acid residue near the C-terminus is essential though not sufficient for the StkC function. Further analysis demonstrated that this motif can render nuclear proteins highly immobile both in plant and animal cells, without affecting their native subnuclear localization. Thus, the C-terminal, StkC motif plays an important role in fastening AtMBD7 to its chromosomal, CpG-methylated sites. It may be possible to utilize this motif for fastening nuclear proteins to their chromosomal sites both in plant and animal cells for research and gene therapy applications.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Souza PP, Völkel P, Trinel D, Vandamme J, Rosnoblet C, Héliot L, Angrand PO. The histone methyltransferase SUV420H2 and Heterochromatin Proteins HP1 interact but show different dynamic behaviours. BMC Cell Biol 2009; 10:41. [PMID: 19486527 PMCID: PMC2701926 DOI: 10.1186/1471-2121-10-41] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 06/01/2009] [Indexed: 11/21/2022] Open
Abstract
Background Histone lysine methylation plays a fundamental role in chromatin organization and marks distinct chromatin regions. In particular, trimethylation at lysine 9 of histone H3 (H3K9) and at lysine 20 of histone H4 (H4K20) governed by the histone methyltransferases SUV39H1/2 and SUV420H1/2 respectively, have emerged as a hallmark of pericentric heterochromatin. Controlled chromatin organization is crucial for gene expression regulation and genome stability. Therefore, it is essential to analyze mechanisms responsible for high order chromatin packing and in particular the interplay between enzymes involved in histone modifications, such as histone methyltransferases and proteins that recognize these epigenetic marks. Results To gain insights into the mechanisms of SUV420H2 recruitment at heterochromatin, we applied a tandem affinity purification approach coupled to mass spectrometry. We identified heterochromatin proteins HP1 as main interacting partners. The regions responsible for the binding were mapped to the heterochromatic targeting module of SUV420H2 and HP1 chromoshadow domain. We studied the dynamic properties of SUV420H2 and the HP1 in living cells using fluorescence recovery after photobleaching. Our results showed that HP1 proteins are highly mobile with different dynamics during the cell cycle, whereas SUV420H2 remains strongly bound to pericentric heterochromatin. An 88 amino-acids region of SUV420H2, the heterochromatic targeting module, recapitulates both, HP1 binding and strong association to heterochromatin. Conclusion FRAP experiments reveal that in contrast to HP1, SUV420H2 is strongly associated to pericentric heterochromatin. Then, the fraction of SUV420H2 captured and characterized by TAP/MS is a soluble fraction which may be in a stable association with HP1. Consequently, SUV420H2 may be recruited to heterochromatin in association with HP1, and stably maintained at its heterochromatin sites in an HP1-independent fashion.
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Affiliation(s)
- Patricia P Souza
- Chromatinomics, Interdisciplinary Research Institute, Université des Sciences et Technologies de Lille/CNRS USR 3078, Parc Scientifique de la Haute Borne, Villeneuve d'Ascq, France.
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Wachsmuth M, Caudron-Herger M, Rippe K. Genome organization: Balancing stability and plasticity. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:2061-79. [DOI: 10.1016/j.bbamcr.2008.07.022] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 07/21/2008] [Accepted: 07/24/2008] [Indexed: 12/18/2022]
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Duan Q, Chen H, Costa M, Dai W. Phosphorylation of H3S10 blocks the access of H3K9 by specific antibodies and histone methyltransferase. Implication in regulating chromatin dynamics and epigenetic inheritance during mitosis. J Biol Chem 2008; 283:33585-90. [PMID: 18835819 DOI: 10.1074/jbc.m803312200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modifications of histones play a critical role in regulating genome structures and integrity. We have focused on the regulatory relationship between covalent modifications of histone H3 lysine 9 (H3K9) and H3S10 during the cell cycle. Immunofluorescence microscopy revealed that H3S10 phosphorylation in HeLa, A549, and HCT116 cells was high during prophase, prometaphase, and metaphase, whereas H3K9 monomethylation (H3K9me1) and dimethylation (H3K9me2), but not H3K9 trimethylation (H3K9me3), were significantly suppressed. When H3S10 phosphorylation started to diminish during anaphase, H3K9me1 and H3K9me2 signals reemerged. Western blot analyses confirmed that mitotic histones, extracted in an SDS-containing buffer, had little H3K9me1 and H3K9me2 signals but abundant H3K9me3 signals. However, when mitotic histones were extracted in the same buffer without SDS, the difference in H3K9me1 and H3K9me2 signals between interphase and mitotic cells disappeared. Removal of H3S10 phosphorylation by pretreatment with lambda-phosphatase unmasked mitotic H3K9me1 and H3K9me2 signals detected by both fluorescence microscopy and Western blotting. Further, H3S10 phosphorylation completely blocked methylation of H3K9 but not demethylation of the same residue in vitro. Given that several conserved motifs consisting of a Lys residue immediately followed by a Ser residue are present in histone tails, our studies reveal a potential new mechanism by which phosphorylation not only regulates selective access of methylated lysines by cellular factors but also serves to preserve methylation patterns and epigenetic programs during cell division.
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Affiliation(s)
- Qing Duan
- Department of Environmental Medicine and Pharmacology, New York University School of Medicine, Tuxedo, New York 10987, USA
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