1
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Neefjes J, Gurova K, Sarthy J, Szabó G, Henikoff S. Chromatin as an old and new anticancer target. Trends Cancer 2024:S2405-8033(24)00095-5. [PMID: 38825423 DOI: 10.1016/j.trecan.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024]
Abstract
Recent genome-wide analyses identified chromatin modifiers as one of the most frequently mutated classes of genes across all cancers. However, chemotherapies developed for cancers involving DNA damage remain the standard of care for chromatin-deranged malignancies. In this review we address this conundrum by establishing the concept of 'chromatin damage': the non-genetic damage to protein-DNA interactions induced by certain small molecules. We highlight anthracyclines, a class of chemotherapeutic agents ubiquitously applied in oncology, as an example of overlooked chromatin-targeting agents. We discuss our current understanding of this phenomenon and explore emerging chromatin-damaging agents as a basis for further studies to maximize their impact in modern cancer treatment.
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Affiliation(s)
- Jacques Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, LUMC, Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY, 14263, USA.
| | - Jay Sarthy
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Research Institute, 1920 Terry Ave, Seattle, WA 98109, USA
| | - Gábor Szabó
- Faculty of Medicine, Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, Egyetem tér 1, 4032, Hungary
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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2
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Duc C, Thiriet C. Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication. Int J Mol Sci 2021; 22:1113. [PMID: 33498649 PMCID: PMC7865951 DOI: 10.3390/ijms22031113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. The present review focuses on the eviction of nucleosomes in front of the replication forks to facilitate the passage of replication machinery and the mechanism of replication-coupled chromatin assembly behind the replication forks. The recycling of parental histones as well as the nuclear import and the assembly of newly synthesized histones are also discussed with regard to the epigenetic inheritance.
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Affiliation(s)
| | - Christophe Thiriet
- UFIP UMR-CNRS 6286, Épigénétique et Dynamique de la Chromatine, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France;
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3
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Dueva R, Akopyan K, Pederiva C, Trevisan D, Dhanjal S, Lindqvist A, Farnebo M. Neutralization of the Positive Charges on Histone Tails by RNA Promotes an Open Chromatin Structure. Cell Chem Biol 2019; 26:1436-1449.e5. [PMID: 31447351 DOI: 10.1016/j.chembiol.2019.08.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/02/2019] [Accepted: 08/01/2019] [Indexed: 12/29/2022]
Abstract
RNA associates extensively with chromatin and can influence its structure; however, the potential role of the negative charges of RNA on chromatin structure remains unknown. Here, we demonstrate that RNA prevents precipitation of histones and can attenuate electrostatic interactions between histones and DNA, thereby loosening up the chromatin structure. This effect is independent of the sequence of RNA but dependent on its single-stranded nature, length, concentration, and negative charge. Opening and closure of chromatin by RNA occurs rapidly (within minutes) and passively (in permeabilized cells), in agreement with electrostatics. Accordingly, chromatin compaction following removal of RNA can be prevented by high ionic strength or neutralization of the positively charged histone tails by hyperacetylation. Finally, LINE1 repeat RNAs bind histone H2B and can decondense chromatin. We propose that RNA regulates chromatin opening and closure by neutralizing the positively charged tails of histones, reducing their electrostatic interactions with DNA.
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Affiliation(s)
- Rositsa Dueva
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Karen Akopyan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Chiara Pederiva
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Davide Trevisan
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Soniya Dhanjal
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marianne Farnebo
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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4
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Ejlassi-Lassallette A, Thiriet C. Replication-coupled chromatin assembly of newly synthesized histones: distinct functions for the histone tail domains. Biochem Cell Biol 2011; 90:14-21. [PMID: 22023434 DOI: 10.1139/o11-044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The maintenance of the genome during replication requires the assembly of nucleosomes with newly synthesized histones. Achieving the deposition of newly synthesized histones in chromatin implies their transport from the cytoplasm to the nucleus at the replication sites. Several lines of evidence have revealed critical functions of the histone tail domains in these conserved cellular processes. In this review, we discuss the role of the amino termini of the nucleosome building blocks, H2A/H2B and H3/H4, in different model systems. The experimental data showed that H2A/H2B tails and H3/H4 tails display distinct functions in nuclear import and chromatin assembly. Furthermore, we describe recent studies exploiting the unique properties of the slime mold, Physarum polycephalum , that have advanced understanding of the function of the highly conserved replication-dependent diacetylation of H4.
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5
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Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML, Kashlev M, Wang MD. Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol 2010; 17:745-52. [PMID: 20453861 PMCID: PMC2938954 DOI: 10.1038/nsmb.1798] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 03/05/2010] [Indexed: 12/25/2022]
Abstract
During gene expression, RNA polymerase (RNAP) encounters a major barrier at a nucleosome and yet must access the nucleosomal DNA. Previous in vivo evidence has suggested that multiple RNAPs might increase transcription efficiency through nucleosomes. Here we have quantitatively investigated this hypothesis using Escherichia coli RNAP as a model system by directly monitoring its location on the DNA via a single-molecule DNA-unzipping technique. When an RNAP encountered a nucleosome, it paused with a distinctive 10-base pair periodicity and backtracked by approximately 10-15 base pairs. When two RNAPs elongate in close proximity, the trailing RNAP apparently assists in the leading RNAP's elongation, reducing its backtracking and enhancing its transcription through a nucleosome by a factor of 5. Taken together, our data indicate that histone-DNA interactions dictate RNAP pausing behavior, and alleviation of nucleosome-induced backtracking by multiple polymerases may prove to be a mechanism for overcoming the nucleosomal barrier in vivo.
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Affiliation(s)
- Jing Jin
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York, USA
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6
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Perales R, Bentley D. "Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. Mol Cell 2009; 36:178-91. [PMID: 19854129 DOI: 10.1016/j.molcel.2009.09.018] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/07/2009] [Accepted: 08/06/2009] [Indexed: 12/27/2022]
Abstract
Much of the complex process of RNP biogenesis takes place at the gene cotranscriptionally. The target for RNA binding and processing factors is, therefore, not a solitary RNA molecule but, rather, a transcription elongation complex (TEC) comprising the growing nascent RNA and RNA polymerase traversing a chromatin template with associated passenger proteins. RNA maturation factors are not the only nuclear machines whose work is organized cotranscriptionally around the TEC scaffold. Additionally, DNA repair, covalent chromatin modification, "gene gating" at the nuclear pore, Ig gene hypermutation, and sister chromosome cohesion have all been demonstrated or suggested to involve a cotranscriptional component. From this perspective, TECs can be viewed as potent "community organizers" within the nucleus.
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Affiliation(s)
- Roberto Perales
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC, MS8101, P.O. Box 6511, Aurora CO, 80045, USA
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7
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Lavelle C. Transcription elongation through a chromatin template. Biochimie 2006; 89:516-27. [PMID: 17070642 DOI: 10.1016/j.biochi.2006.09.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 09/26/2006] [Indexed: 10/24/2022]
Abstract
DNA transaction events occurring during cell life (replication, transcription, recombination, repair, cell division) are always linked to severe changes in the topological state of the double helix. However, since naked DNA almost does not exist in eukaryote nucleus but rather interacts with various proteins, including ubiquitous histones, these topological changes happen in a chromatin context. This review focuses on the role of chromatin fiber structure and dynamics in the regulation of transcription, with an almost exclusive emphasis on the elongation step. Beside a brief overview of our knowledge about transcribed chromatin, we will see how recent mechanistic and biochemical studies give us new insights into the way cell could modulate DNA supercoiling and chromatin conformational dynamics. The participation of topoisomerases in this complex ballet is discussed, since recent data suggest that their role could be closely related to the precise chromatin structure. Lastly, some future prospects to carry on are proposed, hoping this review will help in stimulating discussions and further investigations in the field.
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Affiliation(s)
- Christophe Lavelle
- Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif, France.
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8
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Xiao H, Jackson V, Lei M. The FK506-binding protein, Fpr4, is an acidic histone chaperone. FEBS Lett 2006; 580:4357-64. [PMID: 16846601 DOI: 10.1016/j.febslet.2006.06.093] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Accepted: 06/30/2006] [Indexed: 11/30/2022]
Abstract
Fpr4, a FK506-binding protein (FKBP), is a recently identified novel histone chaperone. How it interacts with histones and facilitates their deposition onto DNA, however, are not understood. Here, we report a functional analysis that shows Fpr4 forms complexes with histones and facilitates nucleosome assembly like previously characterized acidic histone chaperones. We also show that the chaperone activity of Fpr4 resides solely in an acidic domain, while the peptidylprolyl isomerase domain conserved among all FKBPs inhibits the chaperone activity. These observations argue that Fpr4, while unique structurally, deposits histones onto DNA for nucleosome assembly through the well-established mechanism shared by other chaperones.
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Affiliation(s)
- Haijie Xiao
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, 53226, USA
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9
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Kepert JF, Mazurkiewicz J, Heuvelman GL, Tóth KF, Rippe K. NAP1 Modulates Binding of Linker Histone H1 to Chromatin and Induces an Extended Chromatin Fiber Conformation. J Biol Chem 2005; 280:34063-72. [PMID: 16105835 DOI: 10.1074/jbc.m507322200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NAP1 (nucleosome assembly protein 1) is a histone chaperone that has been described to bind predominantly to the histone H2A.H2B dimer in the cell during shuttling of histones into the nucleus, nucleosome assembly/remodeling, and transcription. Here it was examined how NAP1 interacts with chromatin fibers isolated from HeLa cells. NAP1 induced a reversible change toward an extended fiber conformation as demonstrated by sedimentation velocity ultracentrifugation experiments. This transition was due to the removal of the linker histone H1. The H2A.H2B dimer remained stably bound to the native fiber fragments and to fibers devoid of linker histone H1. This was in contrast to mononucleosome substrates, which displayed a NAP1-induced removal of a single H2A.H2B dimer from the core particle. The effect of NAP1 on the chromatin fiber structure was examined by scanning/atomic force microscopy. A quantitative image analysis of approximately 36,000 nucleosomes revealed an increase of the average internucleosomal distance from 22.3 +/- 0.4 to 27.6 +/- 0.6 nm, whereas the overall fiber structure was preserved. This change reflects the disintegration of the chromatosome due to binding of H1 to NAP1 as chromatin fibers stripped from H1 showed an average nucleosome distance of 27.4 +/- 0.8 nm. The findings suggest a possible role of NAP1 in chromatin remodeling processes involved in transcription and replication by modulating the local linker histone content.
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Affiliation(s)
- J Felix Kepert
- Kirchhoff-Institut für Physik, Molecular Biophysics Group, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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10
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Tomschik M, Zheng H, van Holde K, Zlatanova J, Leuba SH. Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 2005; 102:3278-83. [PMID: 15728351 PMCID: PMC549292 DOI: 10.1073/pnas.0500189102] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleosome core particle, the basic repeated structure in chromatin fibers, consists of an octamer of eight core histone molecules, organized as dimers (H2A/H2B) and tetramers [(H3/H4)2] around which DNA wraps tightly in almost two left-handed turns. The nucleosome has to undergo certain conformational changes to allow processes that need access to the DNA template to occur. By single-pair fluorescence resonance energy transfer, we demonstrate fast, long-range, reversible conformational fluctuations in nucleosomes between two states: fully folded (closed), with the DNA wrapped around the histone core, or open, with the DNA significantly unraveled from the histone octamer. The brief excursions into an extended open state may create windows of opportunity for protein factors involved in DNA transactions to bind to or translocate along the DNA.
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Affiliation(s)
- Miroslav Tomschik
- Department of Cell Biology and Physiology, Hillman Cancer Center, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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11
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What happens to nucleosomes during transcription? ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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12
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Jiang J, Birchler JA, Parrott WA, Dawe RK. A molecular view of plant centromeres. TRENDS IN PLANT SCIENCE 2003; 8:570-5. [PMID: 14659705 DOI: 10.1016/j.tplants.2003.10.011] [Citation(s) in RCA: 220] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Although plants were the organisms of choice in several classical centromere studies, molecular and biochemical studies of plant centromeres have lagged behind those in model animal species. However, in the past several years, several centromeric repetitive DNA elements have been isolated in plant species and their roles in centromere function have been demonstrated. Most significantly, a Ty3/gypsy class of centromere-specific retrotransposons, the CR family, was discovered in the grass species. The CR elements are highly enriched in chromatin domains associated with CENH3, the centromere-specific histone H3 variant. CR elements as well as their flanking centromeric satellite DNA are actively transcribed in maize. These data suggest that the deposition of centromeric histones might be a transcription-coupled event.
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Affiliation(s)
- Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
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13
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Wang X, Moore SC, Laszckzak M, Ausió J. Acetylation increases the alpha-helical content of the histone tails of the nucleosome. J Biol Chem 2000; 275:35013-20. [PMID: 10938086 DOI: 10.1074/jbc.m004998200] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nature of the structural changes induced by histone acetylation at the different levels of chromatin organization has been very elusive. At the histone level, it has been proposed on several occasions that acetylation may induce an alpha-helical conformation of their acetylated N-terminal domains (tails). In an attempt to provide experimental support for this hypothesis, we have purified and characterized the tail of histone H4 in its native and mono-, di-, tri-, and tetra- acetylated form. The circular dichroism analysis of these peptides shows conclusively that acetylation does increase their alpha-helical content. Furthermore, the same spectroscopic analysis shows that this is also true for both the acetylated nucleosome core particle and the whole histone octamer in solution. In contrast to the native tails in which the alpha-helical organization appears to be dependent upon interaction of these histone regions with DNA, the acetylated tails show an increase in alpha-helical content that does not depend on such an interaction.
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Affiliation(s)
- X Wang
- Department of Biochemistry and Microbiology, University of Victoria, Victoria V8W 3P6, British Columbia, Canada
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14
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ten Heggeler-Bordier B, Muller S, Monestier M, Wahli W. An immuno-electron microscopical analysis of transcribing multinucleosomal templates: what happens to the histones? J Mol Biol 2000; 299:853-8. [PMID: 10843841 DOI: 10.1006/jmbi.2000.3790] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Immuno-electron microscopy was used to visualize the structure of reconstituted chromatin after in vitro transcription by purified T7 RNA polymerase. T7 RNA polymerase disrupts the nucleosomal structure in the transcribed region. This disruption is not influenced by the template, linear or supercoiled, and the presence or absence of nucleosomal positioning sequences in the transcribed region. In this study, we used monoclonal autoantibodies reacting with the nucleosome core particles and epitopes within several regions of the four different core histones. Some of the residues recognized by the autoantibodies are accessible on the surface of the nucleosomes and some are more internal and therefore less exposed at the surface. We show that the loss of the nucleosomal configuration during transcription is due to the loss of histone/DNA binding and that at least part of the histones are transferred to the nascent RNA chains. Consequently, after in vitro transcription by T7 RNA polymerase, the nucleosomal template does not conserve its original configuration, and no interaction of antigen/antibodies is observed anymore in the region that has been transcribed. Therefore, we conclude that in our in vitro transcription assay, nucleosomes are detached from the template, and not simply unfolded with histones remaining attached to the DNA.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Autoantibodies/immunology
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- DNA-Binding Proteins/immunology
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/ultrastructure
- DNA-Directed RNA Polymerases/metabolism
- Epitopes/immunology
- Histones/immunology
- Histones/metabolism
- Histones/ultrastructure
- Mice
- Microscopy, Immunoelectron
- Molecular Conformation
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Nucleosomes/metabolism
- Nucleosomes/ultrastructure
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/metabolism
- Plasmids/ultrastructure
- Protein Binding
- RNA, Ribosomal, 5S/biosynthesis
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- RNA, Ribosomal, 5S/ultrastructure
- RNA-Binding Proteins/immunology
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Templates, Genetic
- Transcription, Genetic/genetics
- Viral Proteins
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15
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Peng HF, Jackson V. In vitro studies on the maintenance of transcription-induced stress by histones and polyamines. J Biol Chem 2000; 275:657-68. [PMID: 10617664 DOI: 10.1074/jbc.275.1.657] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Several factors were evaluated to determine their role in facilitating the presence of transcription-induced stresses in a circular DNA. Transcription was done with T7 RNA polymerase in the presence of E. coli topoisomerase I and closed circular DNA. Positive stress was observed in hypotonic conditions or when one of the polyamines, spermidine or spermine, were present. Polycations such as polylysine, polyarginine, histone H1, histones H2A-H2B, and protamine were observed to induce minimal positive stress. It is known that polyamines influence DNA structure by causing both self-association and sequence-specific structural alterations (polyamine-induced localized bending). Experimental evidence indicates that the likely cause of the positive stress is the induced bending. In order to evaluate protein-mediated bending, transcription was done on nucleosomes. A minimum of three nucleosomes on a DNA of 6055 bp was sufficient to generate very high levels of positive stress. Histones H3-H4 in the absence of H2A-H2B were responsible for this effect. Since these histones by themselves are able to maintain negative coils on DNA, it is concluded that protein-mediated bending is yet another mechanism for placing rotational restriction on DNA. The bending of DNA by either polyamines or histones is an effective mechanism for promoting transcription-induced stresses at physiological ionic strength.
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Affiliation(s)
- H F Peng
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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16
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Abstract
Methods are described for the utilization of formaldehyde as a reversible cross-linking agent for the characterization of protein-protein and protein-DNA interactions. The methods include a description of procedures to: (1) isolate and characterize transcriptionally active chromatin from cells cross-linked with formaldehyde; (2) study histone mobility during replication and transcription by the characterization of the formaldehyde-cross-linked histone octamer that is isolated from cells labeled with density-labeled amino acids; and (3) cross-link the in vitro reconstituted histone-DNA complex in order to maintain its structural state during subsequent characterization. Included in these methods are procedures for a second dimensional analysis of protein-protein cross-links in which the monomer components are electrophoretically resolved in the second dimension. The methods also include procedures to selectively reverse protein-DNA cross-links while maintaining the protein-protein cross-links. Potential artifacts are also discussed; i.e., data are presented which indicate that the helical pitch of DNA can be altered if the ionic strength is not properly controlled. The stability of the cross-linked nucleosome in the presence of altered pH or salt/urea concentrations is described in order to indicate that there are limitations to procedures that can be used for the subsequent characterization of the cross-linked complex.
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Affiliation(s)
- V Jackson
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
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