1
|
Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, Raviram R, Myers RM, Costacurta M, Todorovski I, Pijpers L, Bjelosevic S, Williams T, Huskins SN, Kearney CJ, Devlin JR, Fan Z, Jabbari JS, Martin BP, Fareh M, Kelly MJ, Dupéré-Richer D, Sandow JJ, Feran B, Knight D, Khong T, Spencer A, Harrison SJ, Gregory G, Wickramasinghe VO, Webb AI, Taberlay PC, Bromberg KD, Lai A, Papenfuss AT, Smyth GK, Allan RS, Licht JD, Landau DA, Abdel-Wahab O, Shortt J, Vervoort SJ, Johnstone RW. Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition. Mol Cell 2021; 81:2183-2200.e13. [PMID: 34019788 PMCID: PMC8183601 DOI: 10.1016/j.molcel.2021.04.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 01/19/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major cellular lysine acetyltransferases P300 and CBP in hematological malignancies. We found that catalytic P300/CBP inhibition dynamically perturbs steady-state acetylation kinetics and suppresses oncogenic transcriptional networks in the absence of changes to chromatin accessibility. CRISPR-Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principal antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300/CBP inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen.
Collapse
Affiliation(s)
- Simon J Hogg
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olga Motorna
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Leonie A Cluse
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | | | - Robert M Myers
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Matteo Costacurta
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Izabela Todorovski
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Lizzy Pijpers
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Stefan Bjelosevic
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Tobias Williams
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Shannon N Huskins
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Conor J Kearney
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jennifer R Devlin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Zheng Fan
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jafar S Jabbari
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
| | - Ben P Martin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Mohamed Fareh
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Madison J Kelly
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Breon Feran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Deborah Knight
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Tiffany Khong
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Simon J Harrison
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Clinical Hematology, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Royal Melbourne Hospital, Melbourne, 3000, Australia
| | - Gareth Gregory
- Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Vihandha O Wickramasinghe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Kenneth D Bromberg
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Albert Lai
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Anthony T Papenfuss
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Jonathan D Licht
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Dan A Landau
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jake Shortt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Stephin J Vervoort
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
| | - Ricky W Johnstone
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
| |
Collapse
|
2
|
Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 2019; 63:97-107. [PMID: 30940741 PMCID: PMC6484784 DOI: 10.1042/ebc20180061] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.
Collapse
|
3
|
Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| |
Collapse
|
4
|
The ATTCT repeats of spinocerebellar ataxia type 10 display strong nucleosome assembly which is enhanced by repeat interruptions. Gene 2009; 434:29-34. [DOI: 10.1016/j.gene.2008.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 12/07/2008] [Accepted: 12/15/2008] [Indexed: 12/19/2022]
|
5
|
Wang X, Hayes JJ. Physical methods used to study core histone tail structures and interactions in solutionThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2006; 84:578-88. [PMID: 16936830 DOI: 10.1139/o06-076] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The core histone tail domains are key regulatory elements in chromatin. The tails are essential for folding oligonucleosomal arrays into both secondary and tertiary structures, and post-translational modifications within these domains can directly alter DNA accessibility. Unfortunately, there is little understanding of the structures and interactions of the core histone tail domains or how post-translational modifications within the tails may alter these interactions. Here we review NMR, thermal denaturation, cross-linking, and other selected solution methods used to define the general structures and binding behavior of the tail domains in various chromatin environments. All of these methods indicate that the tail domains bind primarily electrostatically to sites within chromatin. The data also indicate that the tails adopt specific structures when bound to DNA and that tail structures and interactions are plastic, depending on the specific chromatin environment. In addition, post-translational modifications, such as acetylation, can directly alter histone tail structures and interactions.
Collapse
Affiliation(s)
- Xiaodong Wang
- Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester NY, USA
| | | |
Collapse
|
6
|
Siino JS, Yau PM, Imai BS, Gatewood JM, Bradbury EM. Effect of DNA length and H4 acetylation on the thermal stability of reconstituted nucleosome particles. Biochem Biophys Res Commun 2003; 302:885-91. [PMID: 12646255 DOI: 10.1016/s0006-291x(03)00277-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To examine the factors involved with nucleosome stability, we reconstituted nonacetylated particles containing various lengths (192, 162, and 152 base pairs) of DNA onto the Lytechinus variegatus nucleosome positioning sequence in the absence of linker histone. We characterized the particles and examined their thermal stability. DNA of less than chromatosome length (168 base pairs) produces particles with altered denaturation profiles, possibly caused by histone rearrangement in those core-like particles. We also examined the effects of tetra-acetylation of histone H4 on the thermal stability of reconstituted nucleosome particles. Tetra-acetylation of H4 reduces the nucleosome thermal stability by 0.8 degrees C as compared with nonacetylated particles. This difference is close to values published comparing bulk nonacetylated nucleosomes and core particles to ones enriched for core histone acetylation, suggesting that H4 acetylation has a dominant effect on nucleosome particle energetics.
Collapse
Affiliation(s)
- Joseph S Siino
- Department of Microbiology, University of California, Davis, California 95616, USA.
| | | | | | | | | |
Collapse
|
7
|
Siino JS, Nazarov IB, Zalenskaya IA, Yau PM, Bradbury EM, Tomilin NV. End-joining of reconstituted histone H2AX-containing chromatin in vitro by soluble nuclear proteins from human cells. FEBS Lett 2002; 527:105-8. [PMID: 12220643 DOI: 10.1016/s0014-5793(02)03176-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Non-homologous end-joining is an important pathway for the repair of DNA double-strand breaks. This type of DNA break is followed by the rapid phosphorylation of Ser-139 in the histone variant H2AX to form gamma-H2AX. Here we report efficient in vitro end-joining of reconstituted chromatin containing nucleosomes made with either H2A or H2AX. This reaction is catalyzed by nuclear extracts from human cells and this end-joining is not suppressed by the PI-3 kinase inhibitor wortmannin. During the end-joining reaction H2AX is phosphorylated at Ser-139 as detected by immunoblot with specific antibodies and this phosphorylation is inhibited by wortmannin. Therefore, in vitro the DNA end-joining reaction appears to be independent of H2AX phosphorylation.
Collapse
Affiliation(s)
- Joseph S Siino
- Department of Biological Chemistry, UC Davis School of Medicine, Davis, CA 95616, USA
| | | | | | | | | | | |
Collapse
|
8
|
Vu HM, Minch MJ. Alpha-(Ac)AKRHRKV, a model of the histone H4 amino terminus, uses an unprotonated histidine in phosphate binding. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1998; 51:162-70. [PMID: 9516052 DOI: 10.1111/j.1399-3011.1998.tb00635.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The 1H NMR spectrum of the title peptide at pH 3.3 in 90% H2O was assigned by HOHAHA and NOESY 2D methods. Titration studies in D2O at 300 MHz indicated a histidine side-chain pKa of 6.3. Peptide backbone NH resonances were studied in 90% H2O at 500 MHz as a function of pH and added phosphate. In acidic solution the peptide was free from conventional secondary structural elements, but near neutrality the valine amide proton resonance remained a sharp doublet, which suggests that it may form a hydrogen bond with some backbone carbonyl group. The other amide resonances broadened and showed significant saturation transfer from the water signal indicating that they exchange with solvent although not all to the same extent. Marked changes in the chemical shift of the histidine aromatic protons in the presence of phosphate and a 70-fold increase in the 31P line width of inorganic phosphate in the presence of peptide only at pH values above the pKa (6.3) of the histidine imidazole side-chain implied that the unprotonated imidazole group is specifically involved in phosphate binding. The peptide binds inorganic phosphate with a dissociation constant of 1.6 x 10(-5) M(-1) at pH 7.4.
Collapse
Affiliation(s)
- H M Vu
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA
| | | |
Collapse
|
9
|
Zalensky AO, Tomilin NV, Zalenskaya IA, Teplitz RL, Bradbury EM. Telomere-telomere interactions and candidate telomere binding protein(s) in mammalian sperm cells. Exp Cell Res 1997; 232:29-41. [PMID: 9141618 DOI: 10.1006/excr.1997.3482] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have used fluorescent in situ hybridization to localize telomeres within the nuclei of sperm from six mammals (human, rat, mouse, stallion, boar, and bull). In minimally swollen sperm of mouse and rat, most of the telomeres are clustered within a limited area in the posterior part of nuclei. In sperm of other species, telomeres associate into tetrameres and dimers. On swelling of sperm cells with heparin/dithiotriethol, telomere associations disperse, and hybridization signals become smaller in size and their numbers approach or correspond to the number of chromosome ends in a haploid genome. Quantitation of telomere loci indicates that dimeric associations are prominent features of mammalian sperm nuclear architecture. Higher order telomere-telomere interactions and organization develop during meiotic stages of human spermatogenesis. At this stage, telomeres also become associated with the nuclear membrane. In an attempt to elucidate the molecular mechanisms underlying telomere interactions in sperm, we have identified a novel protein activity that binds to the double-stranded telomeric repeat (TTAGGG)n. Sperm telomere binding protein(s) (STBP) was extracted from human and bull sperm by 0.5 M NaCl. STBP does not bind single-stranded telomeric DNA and is highly specific for single base substitutions in a duplex DNA sequence. Depending on the conditions of binding, we observed the formation of several nucleoprotein complexes. We have shown that there is a transition between complexes, which indicates that the slower migrating complex is a multimer of the higher mobility one. We propose that STBP participates in association between the telomere domains which were microscopically observed in mammalian spermatozoa.
Collapse
Affiliation(s)
- A O Zalensky
- Department of Biological Chemistry, School of Medicine, University of California at Davis, 95616, USA.
| | | | | | | | | |
Collapse
|
10
|
Abstract
The effect of histone acetylation was monitored on CHO chromatin structure, following the addition of 7 mM Na-butyrate to the cell culture medium. The properties of both control and hyperacetylated chromatins and nuclei were investigated by circular dichroism, ethidium bromide intercalation, differential scanning calorimetry, and affinity chromatography. Our results are compatible with modest but significant alterations in the various levels of chromatin organization, as a result of the charge neutralization of some lysine residues within the N-terminal region of the histonic octamer. Namely, large statistically significant differences do exist in the heat capacity thermograms of native nuclei, where unfolding into single nucleofilament of the highly packed native chromatin superfiber appears associated with acetylation; at the same time CD, EB, and affinity chromatography point to modest but consistent differences in the compactness of isolated nucleosomes and polynucleosomes.
Collapse
Affiliation(s)
- P Gavazzo
- Institute of Biophysics, School of Medicine, University of Genoa, Italy
| | | | | | | |
Collapse
|
11
|
Pennings S, Meersseman G, Bradbury EM. Linker histones H1 and H5 prevent the mobility of positioned nucleosomes. Proc Natl Acad Sci U S A 1994; 91:10275-9. [PMID: 7937940 PMCID: PMC45002 DOI: 10.1073/pnas.91.22.10275] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We have previously identified a generally occurring short-range mobility of nucleosome cores on DNA in relatively low ionic strength conditions. Here we report that this mobility of histone octamers positioned on constructs of 5S rDNA is suppressed by the binding of histone H1 or H5 to the nucleosome. Histone H5 is the more potent inhibitor of nucleosome mobility, in accordance with its higher affinity for chromatin. We propose that this reversible restraint on chromatin dynamics may play a role in local regulation of processes that require access to the DNA.
Collapse
Affiliation(s)
- S Pennings
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616
| | | | | |
Collapse
|
12
|
Chen-Cleland T, Boffa L, Carpaneto E, Mariani M, Valentin E, Mendez E, Allfrey V. Recovery of transcriptionally active chromatin restriction fragments by binding to organomercurial-agarose magnetic beads. A rapid and sensitive method for monitoring changes in higher order chromatin structure during gene activation and repression. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)49477-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
13
|
Nicolini C, Catasti P, Szilàgyi L, Yau P. DNA internal motions within nucleosomes during the cell cycle and as a function of ionic strength. Biochemistry 1993; 32:6465-9. [PMID: 8518289 DOI: 10.1021/bi00076a021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have used 31P NMR spectra to show that DNA internal motions are greatly hindered within oligonucleosomes. The fluctuations seem to be a function of both the cell cycle and the number of nucleosomes interlinked. Namely, the resonance areas, directly related to unbound phosphate, are consistently smaller in M-phase than in S-phase; at the same time, the resonance line width, inversely related to base plane, deoxyribose, and phosphate internal motions, is consistently larger in mononucleosomes than in oligonucleosomes. In all cases, the removal of chromosomal proteins, by a progressive increase of ionic strength up to 2 M NaCl, increases the internal motion, as monitored by a decrease in line width toward that of free DNA. While for both oligo- and mononucleosomes in S-phase the decrease in line width is strictly correlated to a sharp increase in resonance area, in M-phase it is not, with the 31P resonance area rather low even at 2.0 M NaCl extraction. Similarly, while S-phase 31P line widths steadily grow from mono- to oligonucleosomes, in M-phase they do not. Moreover, the increase of the ionic strength to 0.6 M NaCl, as compared to 0.35, 1.2, and 2 M NaCl, displays significant variations on 31P line width and resonance area, independent of the cell cycle phase and the number of nucleosomes interlinked. These observations agree with earlier suggestions on the differential role of the various chromosomal protein subfractions, known to preferentially dissociate at the different ionic strengths in question, in the sealing of mononucleosomes and in the overall stability of polynucleosomes.
Collapse
Affiliation(s)
- C Nicolini
- Institute of Biophysics, University of Genova, Medical School, Italy
| | | | | | | |
Collapse
|
14
|
Hong L, Schroth G, Matthews H, Yau P, Bradbury E. Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)54150-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
15
|
Chen-Cleland T, Smith M, Le S, Sternglanz R, Allfrey V. Nucleosome structural changes during derepression of silent mating-type loci in yeast. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)54049-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
16
|
Pennings S, Meersseman G, Bradbury EM. Effect of glycerol on the separation of nucleosomes and bent DNA in low ionic strength polyacrylamide gel electrophoresis. Nucleic Acids Res 1992; 20:6667-72. [PMID: 1480488 PMCID: PMC334584 DOI: 10.1093/nar/20.24.6667] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We report that glycerol changes the separation characteristics of polyacrylamide nucleoprotein gels in which it is included as a stabilizing agent. Polyacrylamide gel electrophoresis fractionates DNA and nucleosomes according to net negative charge, mass and conformation. With glycerol included, fractionation seems to be largely based on particle mass and charge. The conformation factor in separation is progressively lost with increasing glycerol concentrations. Nucleosome positions on the same DNA fragment are no longer resolved, while the difference in electrophoretic mobility between core particles and nucleosomes carrying longer DNA becomes smaller and is eventually lost. The retardation of bent DNA is also much reduced. Using the differences in separation characteristics between glycerol-containing and regular nucleoprotein gels could be a new means to obtain information on macromolecules in solution.
Collapse
Affiliation(s)
- S Pennings
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616
| | | | | |
Collapse
|
17
|
O'Neill TE, Roberge M, Bradbury EM. Nucleosome arrays inhibit both initiation and elongation of transcripts by bacteriophage T7 RNA polymerase. J Mol Biol 1992; 223:67-78. [PMID: 1731087 DOI: 10.1016/0022-2836(92)90716-w] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have examined the effects of nucleosome cores on the initiation and elongation of RNA transcripts by phage T7 RNA polymerase in vitro. A transcription template, pT207-18, was constructed containing tandemly repeated 207 base-pair (bp) nucleosome positioning sequences from a sea urchin (Lytechinus variegatus) 5 S RNA gene inserted between the T7 and SP6 transcription promoters of pGEM-3Z. Nucleosome cores were reconstituted onto supercoiled, closed circular pT207-18 DNA and double label transcription experiments were performed to determine the effects of nucleosome cores on the initiation and elongation of transcripts by T7 RNA polymerase. Both transcript initiation and elongation were inhibited, the extent of the inhibition being directly proportional to the number of nucleosome cores reconstituted onto the pT207-18 DNA templates. Time course transcription experiments indicated that nucleosome cores caused a reduction in the equilibrium length of transcripts and not mere retardation of elongation rates. Continuous regularly spaced linear arrays of nucleosomes were obtained by digesting reconstituted nucleosomel pT207-18 templates with DraI, for which a unique restriction site lies within the nucleosome positioning region of the 207 bp 5 S rDNA repeat sequence. After in vitro transcription with T7 RNA polymerase an RNA ladder with 207 nucleotide spacing was obtained, indicating that transcription can occur through continuous arrays of positioned nucleosome cores. It is demonstrated that nucleosome cores partially inhibit the elongation of transcripts by T7 RNA polymerase, while allowing passage of the transcribing polymerase through each nucleosome core at an upper limit efficiency of 85%. Hence, complete transcripts are produced with high efficiency from short nucleosomal templates, while the production of full-length transcripts from long nucleosomal arrays is relatively inefficient. The results indicate that nucleosome cores have significant inhibitory effects in vitro not only on transcription initiation but on transcription elongation as well, and that special mechanisms may exist to overcome these inhibitory effects in vivo.
Collapse
Affiliation(s)
- T E O'Neill
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616
| | | | | |
Collapse
|
18
|
Cavazza B, Brizzolara G, Lazzarini G, Patrone E, Piccardo M, Barboro P, Parodi S, Pasini A, Balbi C. Thermodynamics of condensation of nuclear chromatin. A differential scanning calorimetry study of the salt-dependent structural transitions. Biochemistry 1991; 30:9060-72. [PMID: 1892819 DOI: 10.1021/bi00101a022] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We present a detailed thermodynamic investigation of the conformational transitions of chromatin in calf thymus nuclei. Differential scanning calorimetry was used as the leading method, in combination with infrared spectroscopy, electron microscopy, and techniques for the molecular characterization of chromatin components. The conformational transitions were induced by changes in the counterion concentration. In this way, it was possible to discriminate between the interactions responsible for the folding of the higher order structure and for the coiling of nucleosomal DNA. Our experiments confirm that the denaturation of nuclear chromatin at physiological ionic strength occurs at the level of discrete structural domains, the linker and the core particle, and we were able to rule out that the actual denaturation pattern might be determined by dissociation of the nucleohistone complex and successive migration of free histones toward native regions, as recently suggested. The sequence of the denaturation events is (1) the conformational change of the histone complement at 66 degrees C, (2) the unstacking of the linker DNA at 74 degrees C, and (3) the unstacking of the core particle DNA, that can be observed either at 90 or at 107 degrees C, depending on the degree of condensation of chromatin. Nuclear chromatin unfolds in low-salt buffers, and can be refolded by increasing the ionic strength, in accordance with the well-known behavior of short fragments. The process is athermal, therefore showing that the stability of the higher order structure depends on electrostatic interactions. The transition between the folded conformation and the unfolded one proceeds through an intermediate condensation state, revealed by an endotherm at 101 degrees C. The analysis of the thermodynamic parameters of denaturation of the polynucleosomal chain demonstrates that the wrapping of the DNA around the histone octamer involves a large energy change. The most striking observation concerns the linker segment, which melts a few degrees below the peak temperature of naked DNA. This finding is in line with previous thermal denaturation investigations on isolated chromatin at low ionic strength, and suggests that a progressive destabilization of the linker occurs in the course of the salt-induced coiling of DNA in the nucleosome.
Collapse
Affiliation(s)
- B Cavazza
- Centro di Studi Chimico-Fisici di Macromolecole Sintetiche e Naturali, CNR, Genova, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Roberge M, O'Neill TE, Bradbury EM. Inhibition of 5S RNA transcription in vitro by nucleosome cores with low or high levels of histone acetylation. FEBS Lett 1991; 288:215-8. [PMID: 1879554 DOI: 10.1016/0014-5793(91)81037-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nucleosomes exert strong inhibitory effects on gene transcription in vitro and in vivo. Since most DNA is packaged in nucleosomes, there must exist mechanisms to alleviate this inhibition during gene activation. Nucleosomes could be destabilized by histone acetylation which is strongly correlated with gene expression. We have compared the effects of nucleosomes cores with low or high levels of histone acetylation on 5S RNA transcription with Xenopus nuclear extracts in vitro. Little or no difference was observed over a range of 1 to 15 nucleosome cores per plasmid template. This result suggests that nucleosomal DNA is not more accessible to transcription factors and to the transcription machinery in acetylated nucleosomes.
Collapse
Affiliation(s)
- M Roberge
- Department of Biological Chemistry, Faculty of Medicine, University of California, Davis 95616
| | | | | |
Collapse
|
20
|
Bresnick EH, John S, Hager GL. Histone hyperacetylation does not alter the positioning or stability of phased nucleosomes on the mouse mammary tumor virus long terminal repeat. Biochemistry 1991; 30:3490-7. [PMID: 1849427 DOI: 10.1021/bi00228a020] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Activation of mouse mammary tumor virus transcription by the hormone-bound glucocorticoid receptor results in disruption of a nucleosome that is specifically positioned on the promoter. Limited treatment of cells with the histone deacetylase inhibitor sodium butyrate prevents receptor-dependent promoter activation and nucleosome disruption [Bresnick, E. H., John, S., Berard, D. S., LeFebvre, P., & Hager, G. L. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3977-3981]. On the basis of this observation, we undertook a series of experiments to compare the structure of normal and hyperacetylated mouse mammary tumor virus chromatin. Although butyrate prevents hormone-induced restriction enzyme cutting specifically in the B nucleosome region, chromatin containing hyperacetylated histones does not differ from normal chromatin in general sensitivity to restriction enzymes. Indirect end-labeling analysis of micrococcal nuclease digested chromatin reveals that nucleosomes are identically phased on the mouse mammary tumor virus long terminal repeat in normal and hyperacetylated chromatin. A synthetic DNA fragment spanning the B nucleosome region was reconstituted into a monosome by using core particles containing normal or hyperacetylated histones. Analysis of the structure of reconstituted monosomes by nondenaturing polyacrylamide gel electrophoresis, salt stability, thermal stability, restriction enzyme accessibility, and exonuclease III or DNase I footprinting reveals no effect of histone hyperacetylation on monosome structure. These observations suggest that histone hyperacetylation does not induce a major change in the structure of mouse mammary tumor virus chromatin, such as nucleosome unfolding.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- E H Bresnick
- Hormone Action and Oncogenesis Section, National Cancer Institute, Bethesda, Maryland 20892
| | | | | |
Collapse
|
21
|
Wood MJ, Yau P, Imai BS, Goldberg MW, Lambert SJ, Fowler AG, Baldwin JP, Godfrey JE, Moudrianakis EN, Koch MH. Neutron and x-ray scatter studies of the histone octamer and amino and carboxyl domain trimmed octamers. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)67651-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
22
|
Hacques MF, Muller S, De Murcia G, Van Regenmortel MH, Marion C. Accessibility and structural role of histone domains in chromatin. biophysical and immunochemical studies of progressive digestion with immobilized proteases. J Biomol Struct Dyn 1990; 8:619-41. [PMID: 2100522 DOI: 10.1080/07391102.1990.10507832] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The accessibility and role of histone regions in chromatin fibres were investigated using limited proteolysis with enzymes covalently bound to collagen membranes. The changes in chromatin conformation and condensation monitored by various biophysical methods, were correlated to the degradation of the histone proteins revealed by antibodies specific for histones and histone peptides. Upon digestion with trypsin and subtilisin, chromatin undergoes successive structural transitions. The cleavage of the C-terminal domains of H1, H2A and H2B, and of the N-terminal tail of H3 led to a decondensation of chromatin fibres, indicated by increases in electric birefringence and orientational relaxation times. It corresponds to a 15% increase in linear dimensions. The degradation of the other terminal regions of histones H3, H2A and H2B resulted in the appearance of hinge points between nucleosomes without alteration of the overall orientation of polynucleosome chains. Despite the loss of all the basic domains of H1, H3, H2A and H2B, no significant change in DNA-protein interactions occurred, suggesting that most of these protease-accessible regions interact weakly, if at all, with DNA in chromatin. Further proteolysis led to H4 degradation and other additional cleavages of H1, H2B and H3. This caused the relaxation of no more than 8% of the total DNA but resulted in changes in the ability of chromatin to condense at high ionic strength. More extensive digestion resulted in a total unravelling of nucleosomal chains which acquired properties similar to those of H1-depleted chromatin, although the globular part of H1 was still present. The data suggest that histone-histone interactions between H1 and core histone domains play a central role in stabilizing the chromatin fibres, and cuts in H3, H2A and H2B as well as H1, seem necessary for chromatin expansion. On the contrary, H4 might be involved in the stabilization of nucleosomes only.
Collapse
Affiliation(s)
- M F Hacques
- Laboratoire de Physico-Chimie Biologique, LBTM-CNRS UMR 24, Université Lyon-1, Villeurbanne, France
| | | | | | | | | |
Collapse
|
23
|
Norton VG, Marvin KW, Yau P, Bradbury EM. Nucleosome linking number change controlled by acetylation of histones H3 and H4. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)45450-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
24
|
Marvin KW, Yau P, Bradbury EM. Isolation and characterization of acetylated histones H3 and H4 and their assembly into nucleosomes. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)45449-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
25
|
Capranico G, Jaxel C, Roberge M, Kohn KW, Pommier Y. Nucleosome positioning as a critical determinant for the DNA cleavage sites of mammalian DNA topoisomerase II in reconstituted simian virus 40 chromatin. Nucleic Acids Res 1990; 18:4553-9. [PMID: 2167470 PMCID: PMC331276 DOI: 10.1093/nar/18.15.4553] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We have assessed the ability of nucleosomes to influence the formation of mammalian topoisomerase II-DNA complexes by mapping the sites of cleavage induced by four unrelated topoisomerase II inhibitors in naked versus nucleosome-reconstituted SV40 DNA. DNA fragments were reconstituted with histone octamers from HeLa cells by the histone exchange method. Nucleosome positions were determined by comparing micrococcal nuclease cleavage patterns of nucleosome-reconstituted and naked DNA. Three types of DNA regions were defined: 1) regions with fixed nucleosome positioning; 2) regions lacking regular nucleosome phasing; and 3) a region around the replication origin (from position 5100 to 600) with no detectable nucleosomes. Topoisomerase II cleavage sites were suppressed in nucleosomes and persisted or were enhanced in linker DNA and in the nucleosome-free region around the replication origin. Incubation of reconstituted chromatin with topoisomerase II protected nucleosome-free regions from micrococcal nuclease cleavage without changing the overall micrococcal nuclease cleavage pattern. Thus, the present results indicate that topoisomerase II binds preferentially to nucleosome-free DNA and that the presence of nucleosomes at preferred DNA sequences influences drug-induced DNA breaks by topoisomerase II inhibitors.
Collapse
Affiliation(s)
- G Capranico
- Division of Cancer Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | | | | | | |
Collapse
|
26
|
|
27
|
Norton VG, Imai BS, Yau P, Bradbury EM. Histone acetylation reduces nucleosome core particle linking number change. Cell 1989; 57:449-57. [PMID: 2541913 DOI: 10.1016/0092-8674(89)90920-3] [Citation(s) in RCA: 317] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleosome core particles differing in their levels of histone acetylation have been formed on a closed circular DNA that contains a tandemly repeated 207 bp nucleosome positioning sequence. The effect of acetylation on the linking number per nucleosome particle has been determined. With increasing levels of acetylation, the negative linking number change per nucleosome decreases from -1.04 +/- 0.08 for control to -0.82 +/- 0.05 for highly acetylated nucleosomes. These results indicate that histone acetylation has the ability to release negative supercoils previously constrained by nucleosomes into a closed chromatin loop and in effect function as a eukaryotic gyrase.
Collapse
Affiliation(s)
- V G Norton
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616
| | | | | | | |
Collapse
|
28
|
Zhang DE, Nelson DA. Histone acetylation in chicken erythrocytes. Rates of deacetylation in immature and mature red blood cells. Biochem J 1988; 250:241-5. [PMID: 3355515 PMCID: PMC1148839 DOI: 10.1042/bj2500241] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We analysed the rates of histone deacetylation in chicken mature and immature red blood cells. A multiplicity of deacetylation rates was observed for the histones and these rates may be subdivided into two major categories based on the extent of histone acetylation. In one set of experiments, cells were labelled with [3H]acetate in the presence of the deacetylase inhibitor n-butyrate, thereby accumulating radiolabel in the hyperacetylated forms of the histone. These hyperacetylated forms are deacetylated rapidly. [3H]Acetate-labelled tetra-acetylated H4 (H4Ac4) in mature cells was deacetylated with an initial half-life (t1/2) of approximately 5 min (time required for the removal of one-half of the labelled acetyl groups). In immature cells, all [3H]acetate-labelled H4Ac4 was deacetylated with a t1/2 of approximately 5 min. Erythrocytes were also labelled with [3H]acetate for extended periods in the absence of the deacetylase inhibitor. During this period, radiolabel accumulated predominantly in the mono- and di-acetylated forms of the histone. Using this protocol, the rate of deacetylation of H4Ac1 was observed to be approximately 145 min for mature cells, and approximately 90 min for immature cells, demonstrating that the less extensively acetylated histone is deacetylated slowly. These results are discussed in the context of the rates of histone acetylation in chicken red blood cells described in the companion paper [Zhang & Nelson (1988) Biochem. J. 250, 233-240].
Collapse
Affiliation(s)
- D E Zhang
- Department of Biochemical and Biophysical Sciences, University of Houston, TX 77004
| | | |
Collapse
|
29
|
Darzynkiewicz Z, Traganos F, Carter SP, Higgins PJ. In situ factors affecting stability of the DNA helix in interphase nuclei and metaphase chromosomes. Exp Cell Res 1987; 172:168-79. [PMID: 3653252 DOI: 10.1016/0014-4827(87)90103-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The data from earlier cytochemical studies, in which the metachromatic fluorochrome acridine orange (AO) was used to differentially stain single vs double-stranded DNA, suggested that DNA in situ in intact metaphase chromosomes or in condensed chromatin of G0 cells is more sensitive to denaturation, induced by heat or acid, than DNA in decondensed chromatin of interphase nuclei. Present studies show that, indeed, DNA in permeabilized metaphase cells, in contrast to cells in interphase, when exposed to buffers of low pH (1.5-2.8) becomes digestible with the single-strand-specific S1 or mung bean nucleases. A variety of extraction procedures and enzymatic treatments provided evidence that the presence of histones, HMG proteins, and S-S bonds in chromatin, as well as phosphorylation or poly(ADP)ribosylation of chromatin proteins, can be excluded as a factor responsible for the differential sensitivity of metaphase vs interphase DNA to denaturation. Cell treatment with NaCl at a concentration of 1.2 N and above abolished the difference between interphase and mitotic cells, rendering DNA in mitotic cells less sensitive to denaturation; such treatment also resulted in decondensation of chromatin visible by microscopy. The present data indicate that structural proteins extractable with greater than or equal to 1.2 N NaCl may be involved in anchoring DNA to the nuclear matrix or chromosome scaffold and may be responsible for maintaining a high degree of chromatin compaction in situ, such as that observed in metaphase chromosomes or in G0 cells. Following dissociation of histones, the high spatial density of the charged DNA polymer may induce topological strain on the double helix, thus decreasing its local stability; this can be detected by metachromatic staining of DNA with AO or digestion with single-strand-specific nucleases.
Collapse
Affiliation(s)
- Z Darzynkiewicz
- Sloan-Kettering Institute for Cancer Research, Walker Laboratory, Rye, New York 10580
| | | | | | | |
Collapse
|
30
|
Allegra P, Sterner R, Clayton DF, Allfrey VG. Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences. J Mol Biol 1987; 196:379-88. [PMID: 3656449 DOI: 10.1016/0022-2836(87)90698-x] [Citation(s) in RCA: 140] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The unfolding of nucleosome cores in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3, making them accessible to SH-reagents. This has suggested that nucleosomes from active genes could be retained selectively on organomercurial/agarose columns. When nucleosomes released from rat liver nuclei by limited digestion with micrococcal nuclease were passed through an Hg affinity column, a run-off fraction of compact, beaded nucleosomes was separated from a retained nucleosome fraction. Although both contained monomer-length DNA and a full complement of core histones, histones in the retained fraction were hyperacetylated. Dot blot hybridizations showed the Hg-bound nucleosome fraction to be enriched in DNA sequences transcribed by hepatocytes (serum albumin and transferrin genes), while a brain-specific gene (preproenkephalin) was not retained, but appeared in the nucleosomes of the run-off fraction. The results are discussed in light of other evidence linking hyperacetylation of histones H3 and H4 to conformational changes at the middle of the nucleosome core.
Collapse
Affiliation(s)
- P Allegra
- Laboratory of Cell Biology, Rockefeller University, New York, N.Y. 10021
| | | | | | | |
Collapse
|
31
|
Sterner R, Boffa LC, Chen TA, Allfrey VG. Cell cycle-dependent changes in conformation and composition of nucleosomes containing human histone gene sequences. Nucleic Acids Res 1987; 15:4375-91. [PMID: 3588300 PMCID: PMC340868 DOI: 10.1093/nar/15.11.4375] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications in the unfolded and the compactly beaded nucleosomes of HeLa cells in logarithmic growth, and at different stages of the growth cycle. The Hg-bound nucleosomes are shown to be deficient in replicating DNA sequences, but to remain associated with fragments of nascent RNA chains (or RNP particles) during gradient centrifugations. Both nucleosome fractions contain a full complement of "core" histones but differ with respect to postsynthetic modifications. The Hg-bound nucleosomes contain high levels of the tri- and tetra-acetylated forms of histones H3 and H4. The unbound nucleosomes are deficient in acetylated histones but enriched in phosphorylated H2A. In synchronized HeLa cells, histone H2A and H4 gene sequences occur in the Hg-bound nucleosomes during the S-phase when their transcription takes place, but not in the G2-phase when the genes are repressed.
Collapse
|
32
|
Altered nucleosomes of active nucleolar chromatin contain accessible histone H3 in its hyperacetylated forms. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)48181-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
33
|
Pesis KH, Matthews HR. Histone acetylation in replication and transcription: turnover at specific acetylation sites in histone H4 from Physarum polycephalum. Arch Biochem Biophys 1986; 251:665-73. [PMID: 3800393 DOI: 10.1016/0003-9861(86)90376-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Histone H4 from growing cells is partially acetylated at lysines 5, 8, 12, and 16. The turnover rate at each of these sites was investigated by pulse-labeling plasmodia of Physarum polycephalum with [3H]acetate for 55 min in either S phase or G2 phase of the cell cycle. Labeled histone H4 was purified and digested with a protease which cleaves on the carboxyl side of arginine residues. The peptide containing the acetylation sites was purified by high-performance liquid chromatography. Subfractions of the peptide were obtained due to differences in acetyllysine content. Each subfraction was subjected to automated Edman degradation and the radioactivity released after each cycle was determined. Histone H4 was acetylated uniformly in vitro and acetylated peptide 1-23 was used as a control. The results show a very striking preference for turnover on lysine-5 in the "low acetyl" subfraction from cells in S phase; the "high acetyl" subfraction showed turnover at all four sites. The peptides labeled in G2 phase showed turnover mainly at positions -8, -12, and -16. The data imply that the patterns of histone acetyl turnover associated with replication and transcription are nonrandom and distinct. The results have implications for nucleosome structure particularly the possible role of lysine-5 in chromosome maturation and for the design of experiments to test chromatin function in vitro.
Collapse
|
34
|
High mobility group protein 17 cross-links primarily to histone H2A in the reconstituted HMG 17-nucleosome core particle complex. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66696-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
35
|
Hyperacetylation of core histones does not cause unfolding of nucleosomes. Neutron scatter data accords with disc shape of the nucleosome. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)84449-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
36
|
Morgan JE, Blankenship JW, Matthews HR. Association constants for the interaction of double-stranded and single-stranded DNA with spermine, spermidine, putrescine, diaminopropane, N1- and N8-acetylspermidine, and magnesium: determination from analysis of the broadening of thermal denaturation curves. Arch Biochem Biophys 1986; 246:225-32. [PMID: 3963822 DOI: 10.1016/0003-9861(86)90467-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The effect of Mg2+, putrescine, diaminopropane, N1-acetylspermidine, N8-acetylspermidine, spermidine, and spermine on the thermal denaturation of calf thymus DNA was investigated. As in a previous study with magnesium [W.F. Dove and N. Davidson, (1962) J. Mol. Biol. 5, 467-478], these ligands were found to raise the thermal denaturation temperature of the DNA and to broaden the thermal denaturation curve dramatically at the point where 10 to 20% of the DNA charge had been neutralized. At higher levels of charge neutralization the curves became sharper again. This behavior was due to differential binding of the ligands to single- and double-stranded DNA. The broadening was used to determine the ratio of the association constants of each ligand to the two forms of DNA using either an independent sites model of binding or an excluded sites model. The results show that the primary mode of binding of the ligands to DNA is electrostatic but that important secondary, nonelectrostatic, effects are also present.
Collapse
|
37
|
Abstract
Nucleosomal subunits isolated from rabbit thymus nuclei in 0.04 M K2SO4-0.02 M Tris, pH 7.4 were devoid of histone H1, while whole chromatin prepared in the same buffer contained the full complement of histone H1. The question is asked why histone H1 dissociates from the subunits but not from the high molecular weight material. We propose that, at physiological salt concentrations, histone H1 is not bound to linker DNA as depicted in the current models; rather, alternate attachment sites, present only in the polymer, are involved.
Collapse
|
38
|
Grimes SR, Smart PG. Changes in the structural organization of chromatin during spermatogenesis in the rat. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 824:128-39. [PMID: 3970928 DOI: 10.1016/0167-4781(85)90089-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this study, histone H4 was shown to be extensively hyperacetylated in mid-spermatids of the rat during the time period when the entire complement of histones is replaced by basic spermatidal transition proteins. The degree of hyperacetylation of histone H4 was minimal in pachytene spermatocytes. Therefore, the hyperacetylation appears to be directly involved in the histone replacement process late in spermatogenesis in mid-spermatids. In order to investigate further the possible effects of histone H4 hyperacetylation and the other dramatic changes in the nuclear proteins on the structure of chromatin in germinal cells, we examined the thermal denaturation profiles of chromatin from various purified germinal cell types. Our analyses revealed that chromatins from pachytene spermatocytes and early spermatids have similar thermal denaturation profiles, with their major thermal transitions slightly lower than those for rat liver. However, the major thermal transitions for chromatin from mid-spermatids are much lower than those from pachytene spermatocytes and early-spermatids. We propose that the greatly lowered thermal stability of mid-spermatid chromatin represents a dramatic relaxation or decondensation of the chromatin in this cell type in preparation for the replacement of histone by the basic spermatidal transition proteins and that the decondensation is due in large part to the extensive histones hyperacetylation which occurs in these cells.
Collapse
|
39
|
Phosphorylation of high-mobility-group proteins by the calcium-phospholipid-dependent protein kinase and the cyclic AMP-dependent protein kinase. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90721-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
40
|
Hüvös P, Sasi R, Fasman GD. Conformation of control and acetylated HeLa stripped chromatin after reassociation with H1. Biopolymers 1984; 23:2195-210. [PMID: 6498297 DOI: 10.1002/bip.360231107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
41
|
Waterborg JH, Matthews HR. Patterns of histone acetylation in Physarum polycephalum. H2A and H2B acetylation is functionally distinct from H3 and H4 acetylation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 142:329-35. [PMID: 6745279 DOI: 10.1111/j.1432-1033.1984.tb08290.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Histone acetylation has previously been correlated with both chromosome replication and transcription. We present evidence that (a) confirms both correlations in the true slime mold, Physarum polycephalum and (b) shows that quite a different pattern of acetate turnover is associated with replication compared with transcription. The pattern associated with replication involves turnover of acetate on all four core histones on species containing one or two acetates per molecule. This pattern was resolved from the transcription-associated pattern by three different procedures: (a) detailed analysis of gels of histones pulse-labelled with acetate; (b) the pattern of acetylation of histones pulse-labelled with [3H]lysine; and (c) the pattern of acetylation of soluble histones. The pattern associated with transcription is restricted to histones H3 and H4 and occurs mostly on highly acetylated species. This pattern was resolved by (a) analysis of gels of histones pulse-labelled with acetate; (b) the pattern of histone acetylation in G2 phase of the cell cycle; and (c) the pattern of histone acetylation in the presence of cycloheximide.
Collapse
|
42
|
Sasi R, Fasman GD. The effect of a high mobility group protein (HMG 17) on the structure of acetylated and control core HeLa cell chromatin. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 782:55-66. [PMID: 6232953 DOI: 10.1016/0167-4781(84)90106-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The effect of binding a high mobility group protein (HMG 17) on the stability and conformation of acetylated and control HeLa high molecular weight core chromatin (stripped of H1 and non-histone chromosomal proteins) was studied by circular dichroism and thermal-denaturation measurements. Previously it had been shown that conformational differences exist between native whole chromatin derived from butyrate-treated (acetylated) and control HeLa cells and that these conformational differences disappear by removing H1 and non-histone chromosomal proteins ( Reczek , P.R., Weissman , D., Huvos , P.E. and Fasman, G.D. (1982) Biochemistry 21, 993-1002). The circular dichroism spectra and the thermal denaturation profiles of control and acetylated core chromatin were found to be similar. The circular dichroism properties of HMG 17 reconstituted highly acetylated and control core chromatin indicated the same alteration of chromatin structure at low ionic strength (1 mM sodium phosphate/0.25 mM EDTA, pH 7.0). The magnitudes of the decrease in ellipticity were proportional to the amount of HMG 17 bound and were found to be the same for both the acetylated and control core chromatin. Thermal denaturation profiles confirmed this change in structure induced by HMG 17 on control and highly acetylated core chromatin. The thermal denaturation profiles, which were resolved into three component transitions, exhibited a shifting of hyperchromicity from the lower melting transitions to the higher melting transitions, with a concomitant rise in Tm, on HMG 17 binding to both control and acetylated chromatin. The natures of the interactions of HMG 17 at higher ionic strength (50 mM NaCl/0.25 mM EDTA/1 mM sodium phosphate, pH 7.0) with acetylated and control core chromatin were slightly different, as measured by circular dichroism; however, a decrease in ellipticity was observed for both samples upon binding of HMG 17. These observations suggest that acetylation coupled with HMG 17 binding to core chromatin does not loosen chromatin structure. HMG 17 binding to control and acetylated core chromatin produces an overall stabilization and compaction of chromatin structure.
Collapse
|
43
|
|
44
|
Annunziato AT, Seale RL. Histone deacetylation is required for the maturation of newly replicated chromatin. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44229-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
45
|
Yau P, Imai BS, Thorne AW, Goodwin GH, Bradbury EM. Effect of HMG protein 17 on the thermal stability of control and acetylated HeLa oligonucleosomes. Nucleic Acids Res 1983; 11:2651-64. [PMID: 6222286 PMCID: PMC325915 DOI: 10.1093/nar/11.9.2651] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Many studies have implicated histone acetylation and HMG proteins 14 and 17 in the structure of active chromatin. Studies of the binding of HMG 14 and 17 to chromatin core particles have shown that there are two binding sites for HMG 14 or 17 located within 20-25 bp of the DNA ends of the core particles [13-15]. Such binding sites may result from the free DNA ends in the core particle being available for the binding of HMG 14 and 17. We have studied the effects of the binding of HMG 17 on the thermal denaturation of DNA in mono, di and trinucleosomes. In each case the binding of 1 HMG 17 molecule per nucleosome reduces the DNA premelt region by 50%, while the binding of 2 HMG 17 molecules per nucleosome abolishes the premelt region. From this it is concluded that there are two HMG 17 binding sites per nucleosome which are located between the entry and exit points to the nucleosome and the strongly complexed central DNA region. Highly acetylated mono, di and trinucleosomes have been isolated from butyrate treated HeLa S3 cells. For this series of acetylated oligonucleosomes, it has been found that there are also two HMG 17 binding sites per acetylated nucleosome.
Collapse
|