1
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McCauley MJ, Joshi J, Becker N, Hu Q, Botuyan MV, Rouzina I, Mer G, James Maher L, Williams MC. Quantifying ATP-Independent Nucleosome Chaperone Activity with Single-Molecule Methods. Methods Mol Biol 2024; 2694:29-55. [PMID: 37823998 DOI: 10.1007/978-1-0716-3377-9_2] [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: 10/13/2023]
Abstract
The dynamics of histone-DNA interactions govern chromosome organization and regulates the processes of transcription, replication, and repair. Accurate measurements of the energies and the kinetics of DNA binding to component histones of the nucleosome under a variety of conditions are essential to understand these processes at the molecular level. To accomplish this, we employ three specific single-molecule techniques: force disruption (FD) with optical tweezers, confocal imaging (CI) in a combined fluorescence plus optical trap, and survival probability (SP) measurements of disrupted and reformed nucleosomes. Short arrays of positioned nucleosomes serve as a template for study, facilitating rapid quantification of kinetic parameters. These arrays are then exposed to FACT (FAcilitates Chromatin Transcription), a non-ATP-driven heterodimeric nuclear chaperone known to both disrupt and tether histones during transcription. FACT binding drives off the outer wrap of DNA and destabilizes the histone-DNA interactions of the inner wrap as well. This reorganization is driven by two key domains with distinct function. FD experiments show the SPT16 MD domain stabilizes DNA-histone contacts, while the HMGB box of SSRP1 binds DNA, destabilizing the nucleosome. Surprisingly, CI experiments do not show tethering of disrupted histones, but increased rates of histone release from the DNA. SI experiments resolve this, showing that the two active domains of FACT combine to chaperone nucleosome reassembly after the timely release of force. These combinations of single-molecule approaches show FACT is a true nucleosome catalyst, lowering the barrier to both disruption and reformation.
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Affiliation(s)
| | - Joha Joshi
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nicole Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA, USA.
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2
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Murphy PJ, Berger F. The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations. Development 2023; 150:dev201989. [PMID: 38771301 PMCID: PMC10629678 DOI: 10.1242/dev.201989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/12/2023] [Indexed: 11/05/2023]
Abstract
We propose that several chromatin-mediated regulatory processes are dominated by source-sink relationships in which factors operate as 'sources' to produce or provide a resource and compete with each other to occupy separate 'sinks'. In this model, large portions of genomic DNA operate as 'sinks', which are filled by 'sources', such as available histone variants, covalent modifications to histones, the readers of these modifications and non-coding RNAs. Competing occupation for the sinks by different sources leads to distinct states of genomic equilibrium in differentiated cells. During dynamic developmental events, such as sexual reproduction, we propose that dramatic and rapid reconfiguration of source-sink relationships modifies chromatin states. We envision that re-routing of sources could occur by altering the dimensions of the sink, by reconfiguration of existing sink occupation or by varying the size of the source, providing a central mechanism to explain a plethora of epigenetic phenomena, which contribute to phenotypic variegation, zygotic genome activation and nucleolar dominance.
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Affiliation(s)
- Patrick J. Murphy
- University of Rochester, Department of Biomedical Genetics and Department of Biology, 601 Elmwood Ave., Rochester NY 14620, USA
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter; Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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3
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Lewis HC, Kelnhofer-Millevolte LE, Brinkley MR, Arbach HE, Arnold EA, Sanders S, Bosse JB, Ramachandran S, Avgousti DC. HSV-1 exploits host heterochromatin for nuclear egress. J Cell Biol 2023; 222:e202304106. [PMID: 37516914 PMCID: PMC10373338 DOI: 10.1083/jcb.202304106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/31/2023] Open
Abstract
Herpes simplex virus (HSV-1) progeny form in the nucleus and exit to successfully infect other cells. Newly formed capsids navigate complex chromatin architecture to reach the inner nuclear membrane (INM) and egress. Here, we demonstrate by transmission electron microscopy (TEM) that HSV-1 capsids traverse heterochromatin associated with trimethylation on histone H3 lysine 27 (H3K27me3) and the histone variant macroH2A1. Through chromatin profiling during infection, we revealed global redistribution of these marks whereby massive host genomic regions bound by macroH2A1 and H3K27me3 correlate with decreased host transcription in active compartments. We found that the loss of these markers resulted in significantly lower viral titers but did not impact viral genome or protein accumulation. Strikingly, we discovered that loss of macroH2A1 or H3K27me3 resulted in nuclear trapping of capsids. Finally, by live-capsid tracking, we quantified this decreased capsid movement. Thus, our work demonstrates that HSV-1 takes advantage of the dynamic nature of host heterochromatin formation during infection for efficient nuclear egress.
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Affiliation(s)
- Hannah C Lewis
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laurel E Kelnhofer-Millevolte
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology, Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- UW Medical Scientist Training Program , Seattle, WA, USA
| | - Mia R Brinkley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hannah E Arbach
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Edward A Arnold
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Microbiology Graduate Program, University of Washington , Seattle, WA, USA
| | - Saskia Sanders
- Institute of Virology, Hannover Medical School , Hannover, Germany
- Leibniz Institute of Virology (LIV) , Hamburg, Germany
- Centre for Structural Systems Biology , Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School , Hannover, Germany
| | - Jens B Bosse
- Institute of Virology, Hannover Medical School , Hannover, Germany
- Leibniz Institute of Virology (LIV) , Hamburg, Germany
- Centre for Structural Systems Biology , Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School , Hannover, Germany
| | - Srinivas Ramachandran
- RNA Bioscience Initiative, University of Colorado School of Medicine , Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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4
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Berger F, Muegge K, Richards EJ. Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin. Semin Cell Dev Biol 2023; 135:93-101. [PMID: 35249811 PMCID: PMC9440159 DOI: 10.1016/j.semcdb.2022.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/04/2023]
Abstract
Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA.
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5
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McCauley MJ, Morse M, Becker N, Hu Q, Botuyan MV, Navarrete E, Huo R, Muthurajan UM, Rouzina I, Luger K, Mer G, Maher LJ, Williams MC. Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes. Cell Rep 2022; 41:111858. [PMID: 36577379 PMCID: PMC9807050 DOI: 10.1016/j.celrep.2022.111858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/06/2022] [Accepted: 11/30/2022] [Indexed: 12/28/2022] Open
Abstract
The histone chaperone FACT (facilitates chromatin transcription) enhances transcription in eukaryotic cells, targeting DNA-protein interactions. FACT, a heterodimer in humans, comprises SPT16 and SSRP1 subunits. We measure nucleosome stability and dynamics in the presence of FACT and critical component domains. Optical tweezers quantify FACT/subdomain binding to nucleosomes, displacing the outer wrap of DNA, disrupting direct DNA-histone (core site) interactions, altering the energy landscape of unwrapping, and increasing the kinetics of DNA-histone disruption. Atomic force microscopy reveals nucleosome remodeling, while single-molecule fluorescence quantifies kinetics of histone loss for disrupted nucleosomes, a process accelerated by FACT. Furthermore, two isolated domains exhibit contradictory functions; while the SSRP1 HMGB domain displaces DNA, SPT16 MD/CTD stabilizes DNA-H2A/H2B dimer interactions. However, only intact FACT tethers disrupted DNA to the histones and supports rapid nucleosome reformation over several cycles of force disruption/release. These results demonstrate that key FACT domains combine to catalyze both nucleosome disassembly and reassembly.
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Affiliation(s)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nicole Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Emily Navarrete
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Ran Huo
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Uma M. Muthurajan
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado, Boulder, CO, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA, USA,Lead contact,Correspondence:
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6
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Osakabe A, Molaro A. Histone renegades: Unusual H2A histone variants in plants and animals. Semin Cell Dev Biol 2022; 135:35-42. [PMID: 35570098 DOI: 10.1016/j.semcdb.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 12/27/2022]
Abstract
H2A variants are histones that carry out specialized nucleosome function during the eukaryote genome packaging. Most genes encoding H2A histone variants arose in the distant past, and have highly conserved domains and structures. Yet, novel H2A variants have continued to arise throughout the radiation of eukaryotes and disturbed the apparent tranquility of nucleosomes. These species-specific H2A variants contributed to the functional diversification of nucleosomes through changes in both their structure and expression patterns. In this short review, we discuss the evolutionary trajectories of these histone renegades in plants and animal genomes.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
| | - Antoine Molaro
- Genetics, Reproduction & Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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7
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Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
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Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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8
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Phosphorylation within Intrinsic Disordered Region Discriminates Histone Variant macroH2A1 Splicing Isoforms-macroH2A1.1 and macroH2A1.2. BIOLOGY 2021; 10:biology10070659. [PMID: 34356514 PMCID: PMC8301376 DOI: 10.3390/biology10070659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/02/2023]
Abstract
Simple Summary MacroH2A1, a histone H2A variant, is present as two alternative splicing isoforms, macroH2A1.1 and macroH2A1.2, which are finely regulated through several mechanisms, including post-translational modifications (PTM). In this article, the authors provide the PTM pattern of macroH2A1.1 and macroH2A1.2 in the same experimental setting through mass spec analysis. They report a different phosphorylation level in their intrinsically disordered linker region, which can be responsible for their different biological role, as computational analysis shows. Abstract Background: Gene expression in eukaryotic cells can be governed by histone variants, which replace replication-coupled histones, conferring unique chromatin properties. MacroH2A1 is a histone H2A variant containing a domain highly similar to H2A and a large non-histone (macro) domain. MacroH2A1, in turn, is present in two alternatively exon-spliced isoforms: macroH2A1.1 and macroH2A1.2, which regulate cell plasticity and proliferation in a remarkably distinct manner. The N-terminal and the C-terminal tails of H2A histones stem from the nucleosome core structure and can be target sites for several post-translational modifications (PTMs). MacroH2A1.1 and macroH2A1.2 isoforms differ only in a few amino acids and their ability to bind NAD-derived metabolites, a property allegedly conferring their different functions in vivo. Some of the modifications on the macroH2A1 variant have been identified, such as phosphorylation (T129, S138) and methylation (K18, K123, K239). However, no study to our knowledge has analyzed extensively, and in parallel, the PTM pattern of macroH2A1.1 and macroH2A1.2 in the same experimental setting, which could facilitate the understanding of their distinct biological functions in health and disease. Methods: We used a mass spectrometry-based approach to identify the sites for phosphorylation, acetylation, and methylation in green fluorescent protein (GFP)-tagged macroH2A1.1 and macroH2A1.2 expressed in human hepatoma cells. The impact of selected PTMs on macroH2A1.1 and macroH2A1.2 structure and function are demonstrated using computational analyses. Results: We identified K7 as a new acetylation site in both macroH2A1 isoforms. Quantitative comparison of histone marks between the two isoforms revealed significant differences in the levels of phosphorylated T129 and S170. Our computational analysis provided evidence that the phosphorylation status in the intrinsically disordered linker region in macroH2A1 isoforms might represent a key regulatory element contributing to their distinct biological responses. Conclusions: Taken together, our results report different PTMs on the two macroH2A1 splicing isoforms as responsible for their distinct features and distribution in the cell.
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9
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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10
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Hsu CJ, Meers O, Buschbeck M, Heidel FH. The Role of MacroH2A Histone Variants in Cancer. Cancers (Basel) 2021; 13:cancers13123003. [PMID: 34203934 PMCID: PMC8232725 DOI: 10.3390/cancers13123003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The structural unit of chromatin is the nucleosome that is composed of DNA wrapped around a core of eight histone proteins. Histone variants can replace ‘standard’ histones at specific sites of the genome. Thus, histone variants modulate all functions in the context of chromatin, such as gene expression. Here, we provide a concise review on a group of histone variants termed macroH2A. They contain two additional domains that contribute to their increased size. We discuss how these domains mediate molecular functions in normal cells and the role of macroH2As in gene expression and cancer. Abstract The epigenome regulates gene expression and provides a molecular memory of cellular events. A growing body of evidence has highlighted the importance of epigenetic regulation in physiological tissue homeostasis and malignant transformation. Among epigenetic mechanisms, the replacement of replication-coupled histones with histone variants is the least understood. Due to differences in protein sequence and genomic distribution, histone variants contribute to the plasticity of the epigenome. Here, we focus on the family of macroH2A histone variants that are particular in having a tripartite structure consisting of a histone fold, an intrinsically disordered linker and a globular macrodomain. We discuss how these domains mediate different molecular functions related to chromatin architecture, transcription and DNA repair. Dysregulated expression of macroH2A histone variants has been observed in different subtypes of cancer and has variable prognostic impact, depending on cellular context and molecular background. We aim to provide a concise review regarding the context- and isoform-dependent contributions of macroH2A histone variants to cancer development and progression.
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Affiliation(s)
- Chen-Jen Hsu
- Internal Medicine C, Greifswald University Medicine, 17475 Greifswald, Germany;
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain;
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain;
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Correspondence: (M.B.); (F.H.H.); Tel.: +34-935-572-800 (M.B.); +49-383-486-6698 (F.H.H.); Fax: +49-383-486-6713 (F.H.H.)
| | - Florian H. Heidel
- Internal Medicine C, Greifswald University Medicine, 17475 Greifswald, Germany;
- Leibniz Institute on Aging, Fritz-Lipmann Institute, 07745 Jena, Germany
- Correspondence: (M.B.); (F.H.H.); Tel.: +34-935-572-800 (M.B.); +49-383-486-6698 (F.H.H.); Fax: +49-383-486-6713 (F.H.H.)
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11
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Abstract
Eukaryotic nucleosomes organize chromatin by wrapping 147 bp of DNA around a histone core particle comprising two molecules each of histone H2A, H2B, H3 and H4. The DNA entering and exiting the particle may be bound by the linker histone H1. Whereas deposition of bulk histones is confined to S-phase, paralogs of the common histones, known as histone variants, are available to carry out functions throughout the cell cycle and accumulate in post-mitotic cells. Histone variants confer different structural properties on nucleosomes by wrapping more or less DNA or by altering nucleosome stability. They carry out specialized functions in DNA repair, chromosome segregation and regulation of transcription initiation, or perform tissue-specific roles. In this Cell Science at a Glance article and the accompanying poster, we briefly examine new insights into histone origins and discuss variants from each of the histone families, focusing on how structural differences may alter their functions. Summary: Histone variants change the structural properties of nucleosomes by wrapping more or less DNA, altering nucleosome stability or carrying out specialized functions.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
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12
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Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Sci Rep 2021; 11:380. [PMID: 33432055 PMCID: PMC7801413 DOI: 10.1038/s41598-020-79654-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023] Open
Abstract
Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.
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13
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Ferrand J, Rondinelli B, Polo SE. Histone Variants: Guardians of Genome Integrity. Cells 2020; 9:E2424. [PMID: 33167489 PMCID: PMC7694513 DOI: 10.3390/cells9112424] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Chromatin integrity is key for cell homeostasis and for preventing pathological development. Alterations in core chromatin components, histone proteins, recently came into the spotlight through the discovery of their driving role in cancer. Building on these findings, in this review, we discuss how histone variants and their associated chaperones safeguard genome stability and protect against tumorigenesis. Accumulating evidence supports the contribution of histone variants and their chaperones to the maintenance of chromosomal integrity and to various steps of the DNA damage response, including damaged chromatin dynamics, DNA damage repair, and damage-dependent transcription regulation. We present our current knowledge on these topics and review recent advances in deciphering how alterations in histone variant sequence, expression, and deposition into chromatin fuel oncogenic transformation by impacting cell proliferation and cell fate transitions. We also highlight open questions and upcoming challenges in this rapidly growing field.
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Affiliation(s)
| | | | - Sophie E. Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, 75013 Paris, France; (J.F.); (B.R.)
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14
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McCauley MJ, Huo R, Becker N, Holte MN, Muthurajan UM, Rouzina I, Luger K, Maher LJ, Israeloff NE, Williams MC. Single and double box HMGB proteins differentially destabilize nucleosomes. Nucleic Acids Res 2019; 47:666-678. [PMID: 30445475 PMCID: PMC6344895 DOI: 10.1093/nar/gky1119] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/23/2018] [Indexed: 01/21/2023] Open
Abstract
Nucleosome disruption plays a key role in many nuclear processes including transcription, DNA repair and recombination. Here we combine atomic force microscopy (AFM) and optical tweezers (OT) experiments to show that high mobility group B (HMGB) proteins strongly disrupt nucleosomes, revealing a new mechanism for regulation of chromatin accessibility. We find that both the double box yeast Hmo1 and the single box yeast Nhp6A display strong binding preferences for nucleosomes over linker DNA, and both HMGB proteins destabilize and unwind DNA from the H2A–H2B dimers. However, unlike Nhp6A, Hmo1 also releases half of the DNA held by the (H3–H4)2 tetramer. This difference in nucleosome destabilization may explain why Nhp6A and Hmo1 function at different genomic sites. Hmo1 is enriched at highly transcribed ribosomal genes, known to be depleted of histones. In contrast, Nhp6A is found across euchromatin, pointing to a significant difference in cellular function.
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Affiliation(s)
| | - Ran Huo
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nicole Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Molly Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Uma M Muthurajan
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | | | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA, USA
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15
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Talbert PB, Meers MP, Henikoff S. Old cogs, new tricks: the evolution of gene expression in a chromatin context. Nat Rev Genet 2019; 20:283-297. [PMID: 30886348 DOI: 10.1038/s41576-019-0105-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. We explore the extent to which these transcriptional regulatory components function in the context of the evolutionarily ancient role of chromatin as a barrier to processes acting on DNA and how chromatin proteins have diversified to carry out evolutionarily recent functions that accompanied the emergence of differentiation and development in multicellular eukaryotes.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael P Meers
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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16
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Histone variant macroH2A: from chromatin deposition to molecular function. Essays Biochem 2019; 63:59-74. [DOI: 10.1042/ebc20180062] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/01/2023]
Abstract
Abstract
The eukaryotic genome is regulated in the context of chromatin. Specialized histones, known as histone variants, incorporate into chromatin to replace their canonical counterparts and represent an important layer of regulation to diversify the structural characteristics and functional outputs of chromatin. MacroH2A is an unusual histone variant with a bulky C-terminal non-histone domain that distinguishes it from all other histones. It is a critical player in stabilizing differentiated cell identity by posing as a barrier to somatic cell reprogramming toward pluripotency and acts as a tumor suppressor in a wide range of cancers. MacroH2A histones are generally regarded as repressive variants that are enriched at the inactive X chromosome (Xi) and broad domains across autosomal chromatin. Recent studies have shed light on to how macroH2A influences transcriptional outputs within distinct genomic contexts and revealed new intriguing molecular functions of macroH2A variants beyond transcriptional regulation. Furthermore, the mechanisms of its mysterious chromatin deposition are beginning to be unraveled, facilitating our understanding of its complex regulation of genome function.
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17
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Bowerman S, Hickok RJ, Wereszczynski J. Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability. J Phys Chem B 2019; 123:419-427. [PMID: 30557018 DOI: 10.1021/acs.jpcb.8b10668] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The fundamental unit of eukaryotic chromatin is the nucleosome core particle, a protein/DNA complex that binds ∼147 base pairs of DNA to a histone octamer. These histones-H3, H4, H2A, H2B-form the nucleosome core through a stacked interaction in which two H2A-H2B dimers flank the (H3-H4)2 tetramer. In vivo, genetic accessibility can be modulated by the substitution of canonical histones with variant proteins that contain the same structural motif but a different amino acid sequence, such as the transcriptional repression-associated macroH2A variant. Previously, Chakravarthy and Luger published a crystal study that showed that H2A substitution is not necessarily required of both H2A moieties, but that in vitro recombination of nucleosomes in the presence of both macroH2A and H2A histone folds results in a hybrid macroH2A-H2A nucleosome with one dimer of each type. Here, we present molecular dynamics simulations of this hybrid construct and compare the results to our previous study on homogeneous H2A- and macroH2A-containing nucleosomes. We find that the hybrid contains a unique set of dynamics that stabilize the interactions between protein constituents and create an altogether more stable nucleosome, both in terms of protein-DNA and protein-protein binding. While dimer-tetramer interactions are asymmetric, as the difference in moieties would suggest, we observe that it is the canonical dimer that is pulled further into the nucleosome core, resulting in more secure dimer-tetramer bonds and a more stable histone core, and we also find significantly more interaction between the dimer subunits. Together, these models provide evidence for hybrid H2A-macroH2A nucleosome formation being not only possible but actually energetically more favorable than a homogeneous construct, with dynamics that are unique from their homogeneous H2A or macroH2A nucleosome counterparts. These effects of hybrid substitution likely propagate into higher-order chromatin structures to hinder transcriptional activity.
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Affiliation(s)
- Samuel Bowerman
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Robert J Hickok
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
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18
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Kozlowski M, Corujo D, Hothorn M, Guberovic I, Mandemaker IK, Blessing C, Sporn J, Gutierrez-Triana A, Smith R, Portmann T, Treier M, Scheffzek K, Huet S, Timinszky G, Buschbeck M, Ladurner AG. MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms. EMBO Rep 2018; 19:embr.201744445. [PMID: 30177554 DOI: 10.15252/embr.201744445] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/22/2023] Open
Abstract
MacroH2A histone variants suppress tumor progression and act as epigenetic barriers to induced pluripotency. How they impart their influence on chromatin plasticity is not well understood. Here, we analyze how the different domains of macroH2A proteins contribute to chromatin structure and dynamics. By solving the crystal structure of the macrodomain of human macroH2A2 at 1.7 Å, we find that its putative binding pocket exhibits marked structural differences compared with the macroH2A1.1 isoform, rendering macroH2A2 unable to bind ADP-ribose. Quantitative binding assays show that this specificity is conserved among vertebrate macroH2A isoforms. We further find that macroH2A histones reduce the transient, PARP1-dependent chromatin relaxation that occurs in living cells upon DNA damage through two distinct mechanisms. First, macroH2A1.1 mediates an isoform-specific effect through its ability to suppress PARP1 activity. Second, the unstructured linker region exerts an additional repressive effect that is common to all macroH2A proteins. In the absence of DNA damage, the macroH2A linker is also sufficient for rescuing heterochromatin architecture in cells deficient for macroH2A.
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Affiliation(s)
- Marek Kozlowski
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - David Corujo
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,PhD Programme of Genetics, Universitat de Barcelona, Barcelona, Spain
| | | | - Iva Guberovic
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Imke K Mandemaker
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Charlotte Blessing
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Judith Sporn
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Rebecca Smith
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Mathias Treier
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Sebastien Huet
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France
| | - Gyula Timinszky
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Marcus Buschbeck
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain .,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Andreas G Ladurner
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany .,Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Munich, Germany
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19
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The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans 2017; 46:67-76. [PMID: 29263138 PMCID: PMC5818668 DOI: 10.1042/bst20170101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023]
Abstract
A chromosome is a single long DNA molecule assembled along its length with nucleosomes and proteins. During interphase, a mammalian chromosome exists as a highly organized supramolecular globule in the nucleus. Here, we discuss new insights into how genomic DNA is packaged and organized within interphase chromosomes. Our emphasis is on the structural principles that underlie chromosome organization, with a particular focus on the intrinsic contributions of the 10-nm chromatin fiber, but not the regular 30-nm fiber. We hypothesize that the hierarchical globular organization of an interphase chromosome is fundamentally established by the self-interacting properties of a 10-nm zig-zag array of nucleosomes, while histone post-translational modifications, histone variants, and chromatin-associated proteins serve to mold generic chromatin domains into specific structural and functional entities.
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20
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Douet J, Corujo D, Malinverni R, Renauld J, Sansoni V, Posavec Marjanović M, Cantariño N, Valero V, Mongelard F, Bouvet P, Imhof A, Thiry M, Buschbeck M. MacroH2A histone variants maintain nuclear organization and heterochromatin architecture. J Cell Sci 2017; 130:1570-1582. [PMID: 28283545 DOI: 10.1242/jcs.199216] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/07/2017] [Indexed: 12/15/2022] Open
Abstract
Genetic loss-of-function studies on development, cancer and somatic cell reprogramming have suggested that the group of macroH2A histone variants might function through stabilizing the differentiated state by a yet unknown mechanism. Here, we present results demonstrating that macroH2A variants have a major function in maintaining nuclear organization and heterochromatin architecture. Specifically, we find that a substantial amount of macroH2A is associated with heterochromatic repeat sequences. We further identify macroH2A on sites of interstitial heterochromatin decorated by histone H3 trimethylated on K9 (H3K9me3). Loss of macroH2A leads to major defects in nuclear organization, including reduced nuclear circularity, disruption of nucleoli and a global loss of dense heterochromatin. Domains formed by DNA repeat sequences are disorganized, expanded and fragmented, and mildly re-expressed when depleted of macroH2A. At the molecular level, we find that macroH2A is required for the interaction of repeat sequences with the nucleostructural protein lamin B1. Taken together, our results argue that a major function of macroH2A histone variants is to link nucleosome composition to higher-order chromatin architecture.
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Affiliation(s)
- Julien Douet
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Badalona 08916, Spain
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias and Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona 08916, Spain
| | - David Corujo
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Badalona 08916, Spain
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias and Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona 08916, Spain
| | - Roberto Malinverni
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Badalona 08916, Spain
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias and Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona 08916, Spain
| | - Justine Renauld
- Cell and tissue biology unit, GIGA-Neurosciences, University of Liege, C.H.U. Sart Tilman, Liege 4000, Belgium
| | - Viola Sansoni
- BioMedical Center and Center for Integrated Protein Sciences Munich, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, Planegg-Martinsried 82152, Germany
| | - Melanija Posavec Marjanović
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Badalona 08916, Spain
| | - Neus Cantariño
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Badalona 08916, Spain
| | - Vanesa Valero
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Badalona 08916, Spain
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias and Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona 08916, Spain
| | - Fabien Mongelard
- Université de Lyon, Ecole normale Supérieure de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS5286, Centre Léon Bérard, 69008 Lyon, France
| | - Philippe Bouvet
- Université de Lyon, Ecole normale Supérieure de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS5286, Centre Léon Bérard, 69008 Lyon, France
| | - Axel Imhof
- BioMedical Center and Center for Integrated Protein Sciences Munich, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, Planegg-Martinsried 82152, Germany
| | - Marc Thiry
- Cell and tissue biology unit, GIGA-Neurosciences, University of Liege, C.H.U. Sart Tilman, Liege 4000, Belgium
| | - Marcus Buschbeck
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Badalona 08916, Spain
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias and Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona 08916, Spain
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21
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Buschbeck M, Hake SB. Variants of core histones and their roles in cell fate decisions, development and cancer. Nat Rev Mol Cell Biol 2017; 18:299-314. [DOI: 10.1038/nrm.2016.166] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Chassé MH, Muthurajan UM, Clark NJ, Kramer MA, Chakravarthy S, Irving T, Luger K. Biochemical and Biophysical Methods for Analysis of Poly(ADP-Ribose) Polymerase 1 and Its Interactions with Chromatin. Methods Mol Biol 2017; 1608:231-253. [PMID: 28695514 DOI: 10.1007/978-1-4939-6993-7_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poly (ADP-Ribose) Polymerase I (PARP-1) is a first responder to DNA damage and participates in the regulation of gene expression. The interaction of PARP-1 with chromatin and DNA is complex and involves at least two different modes of interaction. In its enzymatically inactive state, PARP-1 binds native chromatin with similar affinity as it binds free DNA ends. Automodification of PARP-1 affects interaction with chromatin and DNA to different extents. Here we describe a series of biochemical and biophysical techniques to quantify and dissect the different binding modes of PARP-1 with its various substrates. The techniques listed here allow for high throughput and quantitative measurements of the interaction of different PARP-1 constructs (inactive and automodified) with chromatin and DNA damage models.
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Affiliation(s)
- Maggie H Chassé
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA.,Van Andel Research Institute, Grand Rapids, MI, USA
| | - Uma M Muthurajan
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA
| | | | | | - Srinivas Chakravarthy
- BioCAT, CSRRI and Department BCS, Illinois Institute of Technology, Chicago, IL, USA
| | - Thomas Irving
- BioCAT, CSRRI and Department BCS, Illinois Institute of Technology, Chicago, IL, USA
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA.
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23
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Kujirai T, Machida S, Osakabe A, Kurumizaka H. Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin. J Biochem 2016; 161:381-388. [DOI: 10.1093/jb/mvw081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/03/2016] [Indexed: 01/09/2023] Open
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24
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Jiang D, Berger F. Histone variants in plant transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:123-130. [PMID: 27412913 DOI: 10.1016/j.bbagrm.2016.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/18/2016] [Accepted: 07/03/2016] [Indexed: 12/28/2022]
Abstract
Chromatin based organization of eukaryotic genome plays a profound role in regulating gene transcription. Nucleosomes form the basic subunits of chromatin by packaging DNA with histone proteins, impeding the access of DNA to transcription factors and RNA polymerases. Exchange of histone variants in nucleosomes alters the properties of nucleosomes and thus modulates DNA exposure during transcriptional regulation. Growing evidence indicates the important function of histone variants in programming transcription during developmental transitions and stress response. Here we review how histone variants and their deposition machineries regulate the nucleosome stability and dynamics, and discuss the link between histone variants and transcriptional regulation in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Danhua Jiang
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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25
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Rivera-Casas C, Gonzalez-Romero R, Cheema MS, Ausió J, Eirín-López JM. The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin. Epigenetics 2016; 11:415-25. [PMID: 27082816 DOI: 10.1080/15592294.2016.1172161] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Histone variants play a critical role in chromatin structure and epigenetic regulation. These "deviant" proteins have been historically considered as the evolutionary descendants of ancestral canonical histones, helping specialize the nucleosome structure during eukaryotic evolution. Such view is now challenged by 2 major observations: first, canonical histones present extremely unique features not shared with any other genes; second, histone variants are widespread across many eukaryotic groups. The present work further supports the ancestral nature of histone variants by providing the first in vivo characterization of a functional macroH2A histone (a variant long defined as a specific refinement of vertebrate chromatin) in a non-vertebrate organism (the mussel Mytilus) revealing its recruitment into heterochromatic fractions of actively proliferating tissues. Combined with in silico analyses of genomic data, these results provide evidence for the widespread presence of macroH2A in metazoan animals, as well as in the holozoan Capsaspora, supporting an evolutionary origin for this histone variant lineage before the radiation of Filozoans (including Filasterea, Choanoflagellata and Metazoa). Overall, the results presented in this work help configure a new evolutionary scenario in which histone variants, rather than modern "deviants" of canonical histones, would constitute ancient components of eukaryotic chromatin.
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Affiliation(s)
- Ciro Rivera-Casas
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
| | - Rodrigo Gonzalez-Romero
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
| | - Manjinder S Cheema
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , Canada
| | - Juan Ausió
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , Canada
| | - José M Eirín-López
- a Department of Biological Sciences, Chromatin Structure and Evolution (Chromevol) Group , Florida International University , North Miami , FL , USA
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26
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Maeshima K, Rogge R, Tamura S, Joti Y, Hikima T, Szerlong H, Krause C, Herman J, Seidel E, DeLuca J, Ishikawa T, Hansen JC. Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers. EMBO J 2016; 35:1115-32. [PMID: 27072995 PMCID: PMC4868957 DOI: 10.15252/embj.201592660] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
Abstract
The existence of a 30‐nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg2+‐dependent self‐association of linear 12‐mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call “oligomers”, are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10‐nm fibers, rather than folded 30‐nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl2, but became disrupted in the absence of MgCl2, conditions that also dissociated the oligomers in vitro. These results indicate that a 10‐nm array of nucleosomes has the intrinsic ability to self‐assemble into large chromatin globules stabilized by nucleosome–nucleosome interactions, and suggest that the oligomers are a good in vitro model for investigating the structure and organization of interphase chromosomes.
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Affiliation(s)
- Kazuhiro Maeshima
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Japan
| | - Ryan Rogge
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Sachiko Tamura
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Japan XFEL Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Japan
| | | | - Heather Szerlong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Christine Krause
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jake Herman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Erik Seidel
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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27
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Muthurajan U, Mattiroli F, Bergeron S, Zhou K, Gu Y, Chakravarthy S, Dyer P, Irving T, Luger K. In Vitro Chromatin Assembly: Strategies and Quality Control. Methods Enzymol 2016; 573:3-41. [PMID: 27372747 DOI: 10.1016/bs.mie.2016.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin accessibility is modulated by structural transitions that provide timely access to the genetic and epigenetic information during many essential nuclear processes. These transitions are orchestrated by regulatory proteins that coordinate intricate structural modifications and signaling pathways. In vitro reconstituted chromatin samples from defined components are instrumental in defining the mechanistic details of such processes. The bottleneck to appropriate in vitro analysis is the production of high quality, and quality-controlled, chromatin substrates. In this chapter, we describe methods for in vitro chromatin reconstitution and quality control. We highlight the strengths and weaknesses of various approaches and emphasize quality control steps that ensure reconstitution of a bona fide homogenous chromatin preparation. This is essential for optimal reproducibility and reliability of ensuing experiments using chromatin substrates.
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Affiliation(s)
- U Muthurajan
- University of Colorado at Boulder, Boulder, CO, United States
| | - F Mattiroli
- University of Colorado at Boulder, Boulder, CO, United States
| | - S Bergeron
- University of Colorado at Boulder, Boulder, CO, United States
| | - K Zhou
- University of Colorado at Boulder, Boulder, CO, United States; Colorado State University, Fort Collins, CO, United States
| | - Y Gu
- University of Colorado at Boulder, Boulder, CO, United States; Colorado State University, Fort Collins, CO, United States
| | - S Chakravarthy
- Illinois Institute of Technology, Chicago, IL, United States
| | - P Dyer
- University of Colorado at Boulder, Boulder, CO, United States
| | - T Irving
- Illinois Institute of Technology, Chicago, IL, United States
| | - K Luger
- University of Colorado at Boulder, Boulder, CO, United States; Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, United States; Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, United States.
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28
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A quantitative investigation of linker histone interactions with nucleosomes and chromatin. Sci Rep 2016; 6:19122. [PMID: 26750377 PMCID: PMC4707517 DOI: 10.1038/srep19122] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022] Open
Abstract
Linker histones such as H1 are abundant basic proteins that bind tightly to nucleosomes, thereby acting as key organizers of chromatin structure. The molecular details of linker histone interactions with the nucleosome, and in particular the contributions of linker DNA and of the basic C-terminal tail of H1, are controversial. Here we combine rigorous solution-state binding assays with native gel electrophoresis and Atomic Force Microscopy, to quantify the interaction of H1 with chromatin. We find that H1 binds nucleosomes and nucleosomal arrays with very tight affinity by recognizing a specific DNA geometry minimally consisting of a solitary nucleosome with a single ~18 base pair DNA linker arm. The association of H1 alters the conformation of trinucleosomes so that only one H1 can bind to the two available linker DNA regions. Neither incorporation of the histone variant H2A.Z, nor the presence of neighboring nucleosomes affects H1 affinity. Our data provide a comprehensive thermodynamic framework for this ubiquitous chromatin architectural protein.
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Abstract
Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.
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Affiliation(s)
- Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
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30
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Kawashima T, Lorković ZJ, Nishihama R, Ishizaki K, Axelsson E, Yelagandula R, Kohchi T, Berger F. Diversification of histone H2A variants during plant evolution. TRENDS IN PLANT SCIENCE 2015; 20:419-25. [PMID: 25983206 DOI: 10.1016/j.tplants.2015.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 05/19/2023]
Abstract
Among eukaryotes, the four core histones show an extremely high conservation of their structure and form nucleosomes that compact, protect, and regulate access to genetic information. Nevertheless, in multicellular eukaryotes the two families, histone H2A and histone H3, have diversified significantly in key residues. We present a phylogenetic analysis across the green plant lineage that reveals an early diversification of the H2A family in unicellular green algae and remarkable expansions of H2A variants in flowering plants. We define motifs and domains that differentiate plant H2A proteins into distinct variant classes. In non-flowering land plants, we identify a new class of H2A variants and propose their possible role in the emergence of the H2A.W variant class in flowering plants.
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Affiliation(s)
- Tomokazu Kawashima
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Frederic Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria.
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31
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Rogge RA, Hansen JC. Sedimentation Velocity Analysis of Large Oligomeric Chromatin Complexes Using Interference Detection. Methods Enzymol 2015; 562:349-62. [PMID: 26412660 DOI: 10.1016/bs.mie.2015.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volume, and shape of macromolecules in solution affect their sedimentation rates as reflected in the sedimentation coefficient. The sedimentation coefficient is obtained by measuring the solute concentration as a function of radial distance during centrifugation. Monitoring the concentration can be accomplished using interference optics, absorbance optics, or the fluorescence detection system, each with inherent advantages. The interference optical system captures data much faster than these other optical systems, allowing for sedimentation velocity analysis of extremely large macromolecular complexes that sediment rapidly at very low rotor speeds. Supramolecular oligomeric complexes produced by self-association of 12-mer chromatin fibers are used to illustrate the advantages of the interference optics. Using interference optics, we show that chromatin fibers self-associate at physiological divalent salt concentrations to form structures that sediment between 10,000 and 350,000S. The method for characterizing chromatin oligomers described in this chapter will be generally useful for characterization of any biological structures that are too large to be studied by the absorbance optical system.
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Affiliation(s)
- Ryan A Rogge
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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32
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Yelagandula R, Stroud H, Holec S, Zhou K, Feng S, Zhong X, Muthurajan UM, Nie X, Kawashima T, Groth M, Luger K, Jacobsen SE, Berger F. The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell 2014; 158:98-109. [PMID: 24995981 DOI: 10.1016/j.cell.2014.06.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/14/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022]
Abstract
Histone variants play crucial roles in gene expression, genome integrity, and chromosome segregation. We report that the four H2A variants in Arabidopsis define different genomic features, contributing to overall genomic organization. The histone variant H2A.W marks heterochromatin specifically and acts in synergy with heterochromatic marks H3K9me2 and DNA methylation to maintain transposon silencing. In vitro, H2A.W enhances chromatin condensation by promoting fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, H2A.W is required for heterochromatin condensation, demonstrating that H2A.W plays critical roles in heterochromatin organization. Similarities in conserved motifs between H2A.W and another H2A variant in metazoans suggest that plants and animals share common mechanisms for heterochromatin condensation.
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Affiliation(s)
- Ramesh Yelagandula
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore, Singapore
| | - Hume Stroud
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sarah Holec
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Keda Zhou
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xuehua Zhong
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Uma M Muthurajan
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Xin Nie
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore, Singapore
| | - Tomokazu Kawashima
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore
| | - Martin Groth
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA; Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO 80523, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Frédéric Berger
- Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore, Singapore.
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33
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Automodification switches PARP-1 function from chromatin architectural protein to histone chaperone. Proc Natl Acad Sci U S A 2014; 111:12752-7. [PMID: 25136112 DOI: 10.1073/pnas.1405005111] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Poly [ADP-ribose] polymerase 1 (PARP-1) is a highly abundant chromatin-associated enzyme. It catalyzes the NAD(+)-dependent polymerization of long chains of poly-ADP ribose (PAR) onto itself in response to DNA damage and other cues. More recently, the enzymatic activity of PARP-1 has also been implicated in the regulation of gene expression. The molecular basis for the functional switch from chromatin architectural protein to transcription factor and DNA damage responder, triggered by PARP-1 automodification, is unknown. Here, we show that unmodified PARP-1 engages in at least two high-affinity binding modes with chromatin, one of which does not involve free DNA ends, consistent with its role as a chromatin architectural protein. Automodification reduces PARP-1 affinity for intact chromatin but not for nucleosomes with exposed DNA ends. Automodified (AM) PARP-1 has the ability to sequester histones (both in vitro and in cells) and to assemble nucleosomes efficiently in vitro. This unanticipated nucleosome assembly activity of AM-PARP-1, coupled with the fast turnover of the modification, suggests a model in which DNA damage or transcription events trigger transient histone chaperone activity.
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34
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Biterge B, Schneider R. Histone variants: key players of chromatin. Cell Tissue Res 2014; 356:457-66. [PMID: 24781148 DOI: 10.1007/s00441-014-1862-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/27/2014] [Indexed: 01/01/2023]
Abstract
Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.
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Affiliation(s)
- Burcu Biterge
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404, Illkirch, France
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35
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Maiolica A, de Medina-Redondo M, Schoof EM, Chaikuad A, Villa F, Gatti M, Jeganathan S, Lou HJ, Novy K, Hauri S, Toprak UH, Herzog F, Meraldi P, Penengo L, Turk BE, Knapp S, Linding R, Aebersold R. Modulation of the chromatin phosphoproteome by the Haspin protein kinase. Mol Cell Proteomics 2014; 13:1724-40. [PMID: 24732914 DOI: 10.1074/mcp.m113.034819] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Recent discoveries have highlighted the importance of Haspin kinase activity for the correct positioning of the kinase Aurora B at the centromere. Haspin phosphorylates Thr(3) of the histone H3 (H3), which provides a signal for Aurora B to localize to the centromere of mitotic chromosomes. To date, histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin-associated proteins and identified a Haspin protein-protein interaction network. We determined the Haspin consensus motif and the co-crystal structure of the kinase with the histone H3 tail. The structure revealed a unique bent substrate binding mode positioning the histone H3 residues Arg(2) and Lys(4) adjacent to the Haspin phosphorylated threonine into acidic binding pockets. This unique conformation of the kinase-substrate complex explains the reported modulation of Haspin activity by methylation of Lys(4) of the histone H3. In addition, the identification of the structural basis of substrate recognition and the amino acid sequence preferences of Haspin aided the identification of novel candidate Haspin substrates. In particular, we validated the phosphorylation of Ser(137) of the histone variant macroH2A as a target of Haspin kinase activity. MacroH2A Ser(137) resides in a basic stretch of about 40 amino acids that is required to stabilize extranucleosomal DNA, suggesting that phosphorylation of Ser(137) might regulate the interactions of macroH2A and DNA. Overall, our data suggest that Haspin activity affects the phosphorylation state of proteins involved in gene expression regulation and splicing.
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Affiliation(s)
- Alessio Maiolica
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Maria de Medina-Redondo
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Erwin M Schoof
- ¶Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Apirat Chaikuad
- ‖Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, United Kingdom
| | - Fabrizio Villa
- **Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Marco Gatti
- ‡‡Department of Pharmaceutical Sciences, University of Piemonte Orientale "A. Avogadro" Novara, Italy
| | - Siva Jeganathan
- §§Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Hua Jane Lou
- ¶¶Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut 06520, USA
| | - Karel Novy
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Simon Hauri
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Umut H Toprak
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Franz Herzog
- ‖‖Gene Center Munich Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Meraldi
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lorenza Penengo
- ‡‡Department of Pharmaceutical Sciences, University of Piemonte Orientale "A. Avogadro" Novara, Italy
| | - Benjamin E Turk
- ¶¶Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut 06520, USA
| | - Stefan Knapp
- ‖Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, United Kingdom
| | - Rune Linding
- ¶Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
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36
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Krietsch J, Rouleau M, Pic É, Ethier C, Dawson TM, Dawson VL, Masson JY, Poirier GG, Gagné JP. Reprogramming cellular events by poly(ADP-ribose)-binding proteins. Mol Aspects Med 2013; 34:1066-87. [PMID: 23268355 PMCID: PMC3812366 DOI: 10.1016/j.mam.2012.12.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/12/2012] [Accepted: 12/14/2012] [Indexed: 12/23/2022]
Abstract
Poly(ADP-ribosyl)ation is a posttranslational modification catalyzed by the poly(ADP-ribose) polymerases (PARPs). These enzymes covalently modify glutamic, aspartic and lysine amino acid side chains of acceptor proteins by the sequential addition of ADP-ribose (ADPr) units. The poly(ADP-ribose) (pADPr) polymers formed alter the physico-chemical characteristics of the substrate with functional consequences on its biological activities. Recently, non-covalent binding to pADPr has emerged as a key mechanism to modulate and coordinate several intracellular pathways including the DNA damage response, protein stability and cell death. In this review, we describe the basis of non-covalent binding to pADPr that has led to the emerging concept of pADPr-responsive signaling pathways. This review emphasizes the structural elements and the modular strategies developed by pADPr-binding proteins to exert a fine-tuned control of a variety of pathways. Poly(ADP-ribosyl)ation reactions are highly regulated processes, both spatially and temporally, for which at least four specialized pADPr-binding modules accommodate different pADPr structures and reprogram protein functions. In this review, we highlight the role of well-characterized and newly discovered pADPr-binding modules in a diverse set of physiological functions.
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Affiliation(s)
- Jana Krietsch
- Centre de recherche du CHUQ – Pavillon CHUL – Cancer Axis, Laval University, Québec, QC, Canada G1V 4G2
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, QC, Canada G1R 2J6
| | - Michèle Rouleau
- Centre de recherche du CHUQ – Pavillon CHUL – Cancer Axis, Laval University, Québec, QC, Canada G1V 4G2
- Department of Molecular Biology, Cellular Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, QC, Canada G1V 0A6
| | - Émilie Pic
- Centre de recherche du CHUQ – Pavillon CHUL – Cancer Axis, Laval University, Québec, QC, Canada G1V 4G2
| | - Chantal Ethier
- Centre de recherche du CHUQ – Pavillon CHUL – Cancer Axis, Laval University, Québec, QC, Canada G1V 4G2
| | - Ted M. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jean-Yves Masson
- Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, Québec, QC, Canada G1R 2J6
- Department of Molecular Biology, Cellular Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, QC, Canada G1V 0A6
| | - Guy G. Poirier
- Centre de recherche du CHUQ – Pavillon CHUL – Cancer Axis, Laval University, Québec, QC, Canada G1V 4G2
- Department of Molecular Biology, Cellular Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, QC, Canada G1V 0A6
| | - Jean-Philippe Gagné
- Centre de recherche du CHUQ – Pavillon CHUL – Cancer Axis, Laval University, Québec, QC, Canada G1V 4G2
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37
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Rogge RA, Kalashnikova AA, Muthurajan UM, Porter-Goff ME, Luger K, Hansen JC. Assembly of nucleosomal arrays from recombinant core histones and nucleosome positioning DNA. J Vis Exp 2013. [PMID: 24056546 DOI: 10.3791/50354] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Core histone octamers that are repetitively spaced along a DNA molecule are called nucleosomal arrays. Nucleosomal arrays are obtained in one of two ways: purification from in vivo sources, or reconstitution in vitro from recombinant core histones and tandemly repeated nucleosome positioning DNA. The latter method has the benefit of allowing for the assembly of a more compositionally uniform and precisely positioned nucleosomal array. Sedimentation velocity experiments in the analytical ultracentrifuge yield information about the size and shape of macromolecules by analyzing the rate at which they migrate through solution under centrifugal force. This technique, along with atomic force microscopy, can be used for quality control, ensuring that the majority of DNA templates are saturated with nucleosomes after reconstitution. Here we describe the protocols necessary to reconstitute milligram quantities of length and compositionally defined nucleosomal arrays suitable for biochemical and biophysical studies of chromatin structure and function.
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Affiliation(s)
- Ryan A Rogge
- Biochemistry and Molecular Biology, Colorado State University
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38
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Posavec M, Timinszky G, Buschbeck M. Macro domains as metabolite sensors on chromatin. Cell Mol Life Sci 2013; 70:1509-24. [PMID: 23455074 PMCID: PMC11113152 DOI: 10.1007/s00018-013-1294-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/30/2022]
Abstract
How metabolism and epigenetics are molecularly linked and regulate each other is poorly understood. In this review, we will discuss the role of direct metabolite-binding to chromatin components and modifiers as a possible regulatory mechanism. We will focus on globular macro domains, which are evolutionarily highly conserved protein folds that can recognize NAD(+)-derived metabolites. Macro domains are found in histone variants, histone modifiers, and a chromatin remodeler among other proteins. Here we summarize the macro domain-containing chromatin proteins and the enzymes that generate relevant metabolites. Focusing on the histone variant macroH2A, we further discuss possible implications of metabolite binding for chromatin function.
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Affiliation(s)
- Melanija Posavec
- Institute for Predictive and Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona Spain
| | - Gyula Timinszky
- Butenandt Institute of Physiological Chemistry, Ludwig Maximilian University of Munich, Butenandtstrasse 5, 81377 Munich, Germany
| | - Marcus Buschbeck
- Institute for Predictive and Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona Spain
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39
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Bönisch C, Hake SB. Histone H2A variants in nucleosomes and chromatin: more or less stable? Nucleic Acids Res 2012; 40:10719-41. [PMID: 23002134 PMCID: PMC3510494 DOI: 10.1093/nar/gks865] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In eukaryotes, DNA is organized together with histones and non-histone proteins into a highly complex nucleoprotein structure called chromatin, with the nucleosome as its monomeric subunit. Various interconnected mechanisms regulate DNA accessibility, including replacement of canonical histones with specialized histone variants. Histone variant incorporation can lead to profound chromatin structure alterations thereby influencing a multitude of biological processes ranging from transcriptional regulation to genome stability. Among core histones, the H2A family exhibits highest sequence divergence, resulting in the largest number of variants known. Strikingly, H2A variants differ mostly in their C-terminus, including the docking domain, strategically placed at the DNA entry/exit site and implicated in interactions with the (H3–H4)2-tetramer within the nucleosome and in the L1 loop, the interaction interface of H2A–H2B dimers. Moreover, the acidic patch, important for internucleosomal contacts and higher-order chromatin structure, is altered between different H2A variants. Consequently, H2A variant incorporation has the potential to strongly regulate DNA organization on several levels resulting in meaningful biological output. Here, we review experimental evidence pinpointing towards outstanding roles of these highly variable regions of H2A family members, docking domain, L1 loop and acidic patch, and close by discussing their influence on nucleosome and higher-order chromatin structure and stability.
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Affiliation(s)
- Clemens Bönisch
- Department of Molecular Biology, Center for Integrated Protein Science Munich, Adolf-Butenandt-Institute, Ludwig-Maximilians-University Munich, 80336 Munich, Germany.
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40
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Chakravarthy S, Patel A, Bowman GD. The basic linker of macroH2A stabilizes DNA at the entry/exit site of the nucleosome. Nucleic Acids Res 2012; 40:8285-95. [PMID: 22753032 PMCID: PMC3458575 DOI: 10.1093/nar/gks645] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MacroH2A is a histone H2A variant that is typically found in heterochromatic regions of the genome. A positively charged linker that connects the histone-fold with the macro-domain was suggested to have DNA-binding properties, and has been shown to promote oligomerization of chromatin fibers. Here we examine the influence of this basic linker on DNA of mononucleosomes. We find that the macro-linker reduces accessibility to extranucleosomal DNA, and appears to increase compaction of the nucleosome. These properties arise from interactions between the H1-like basic linker region and DNA around the entry/exit site, which increases protection of nucleosomal DNA from exonuclease III digestion by ∼10 bp. By stabilizing the wrapping of DNA around the histone core, this basic linker of macroH2A may alter the distribution of nucleosome-associated factors, and potentially contribute to the more compacted nature of heterochromatin.
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Affiliation(s)
- Srinivas Chakravarthy
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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41
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New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 2012; 13:436-47. [PMID: 22722606 DOI: 10.1038/nrm3382] [Citation(s) in RCA: 473] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The compaction of genomic DNA into chromatin has profound implications for the regulation of key processes such as transcription, replication and DNA repair. Nucleosomes, the repeating building blocks of chromatin, vary in the composition of their histone protein components. This is the result of the incorporation of variant histones and post-translational modifications of histone amino acid side chains. The resulting changes in nucleosome structure, stability and dynamics affect the compaction of nucleosomal arrays into higher-order structures. It is becoming clear that chromatin structures are not nearly as uniform and regular as previously assumed. This implies that chromatin structure must also be viewed in the context of specific biological functions.
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Abstract
Induced pluripotent stem (iPS) cells have provided a rational means of obtaining histo-compatible tissues for ‘patient-specific’ regenerative therapies (Hanna et al. 2010; Yamanaka & Blau 2010). Despite the obvious potential of iPS cell-based therapies, there are certain problems that must be overcome before these therapies can become safe and routine (Ohi et al. 2011; Pera 2011). As an alternative, we have recently explored the possibility of using ‘epigenetic rejuvenation’, where the specialized functions of an old cell are rejuvenated in the absence of any change in its differentiated state (Singh & Zacouto 2010). The mechanism(s) that underpin ‘epigenetic rejuvenation’ are unknown and here we discuss model systems, using key epigenetic modifiers, which might shed light on the processes involved. Epigenetic rejuvenation has advantages over iPS cell techniques that are currently being pursued. First, the genetic and epigenetic abnormalities that arise through the cycle of dedifferentiation of somatic cells to iPS cells followed by redifferentiation of iPS cells into the desired cell type are avoided (Gore et al. 2011; Hussein et al. 2011; Pera 2011): epigenetic rejuvenation does not require passage through the de-/redifferentiation cycle. Second, because the aim of epigenetic rejuvenation is to ensure that the differentiated cell type retains its specialized function it makes redundant the question of transcriptional memory that is inimical to iPS cell-based therapies (Ohi et al. 2011). Third, to produce unrelated cell types using the iPS technology takes a long time, around three weeks, whereas epigenetic rejuvenation of old cells will take only a matter of days. Epigenetic rejuvenation provides the most safe, rapid and cheap route to successful regenerative medicine.
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Affiliation(s)
- Maria Manukyan
- Albert-Ludwigs-Universität Freiburg, BIOSS Centre for Biological Signalling Studies, Zentrum für Biosystemanalyse - ZBSA, Habsburgerstrasse 49, 79104 Freiburg, Germany
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Creppe C, Posavec M, Douet J, Buschbeck M. MacroH2A in stem cells: a story beyond gene repression. Epigenomics 2012; 4:221-7. [PMID: 22449192 DOI: 10.2217/epi.12.8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The importance of epigenetic mechanisms is most clearly illustrated during early development when a totipotent cell goes through multiple cell fate transitions to form the many different cell types and tissues that constitute the embryo and the adult. The exchange of a canonical H2A histone for the ‘repressive’ macroH2A variant is one of the most striking epigenetic chromatin alterations that can occur at the level of the nucleosome. Here, we discuss recent data on macroH2A in zebrafish and mouse embryos, in embryonic and adult stem cells and also in nuclear reprogramming. We highlight the role of macroH2A in the establishment and maintenance of differentiated states and we discuss its still poorly recognized function in transcriptional activation.
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Affiliation(s)
- Catherine Creppe
- Institute for Predictive & Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona, Spain
| | - Melanija Posavec
- Institute for Predictive & Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona, Spain
| | - Julien Douet
- Institute for Predictive & Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona, Spain
| | - Marcus Buschbeck
- Institute for Predictive & Personalized Medicine of Cancer (IMPPC), Crta. Can Ruti, Cami de les Escoles, 08916 Badalona, Barcelona, Spain
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