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How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017; 101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?
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Chen X, Gao S, Liu Y, Wang Y, Wang Y, Song W. Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila. SCIENCE CHINA-LIFE SCIENCES 2016; 59:909-19. [DOI: 10.1007/s11427-016-5102-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 06/12/2016] [Indexed: 02/01/2023]
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3
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Yue H, Fang H, Wei S, Hayes JJ, Lee TH. Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. Biochemistry 2016; 55:2069-77. [PMID: 27010485 PMCID: PMC5436050 DOI: 10.1021/acs.biochem.5b01247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Linker histone H1 regulates chromatin structure and gene expression. Investigating the dynamics and stoichiometry of binding of H1 to DNA and the nucleosome is crucial to elucidating its functions. Because of the abundant positive charges and the strong self-affinity of H1, quantitative in vitro studies of its binding to DNA and the nucleosome have generated results that vary widely and, therefore, should be interpreted in a system specific manner. We sought to overcome this limitation by developing a specially passivated microscope slide surface to monitor binding of H1 to DNA and the nucleosome at a single-molecule level. According to our measurements, the stoichiometry of binding of H1 to DNA and the nucleosome is very heterogeneous with a wide distribution whose averages are in reasonable agreement with previously published values. Our study also revealed that H1 does not dissociate from DNA or the nucleosome on a time scale of tens of minutes. We found that histone chaperone Nap1 readily dissociates H1 from DNA and superstoichiometrically bound H1 from the nucleosome, supporting a hypothesis whereby histone chaperones contribute to the regulation of the H1 profile in chromatin.
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Affiliation(s)
- Hongjun Yue
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - He Fang
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, New York 14625, United States
| | - Sijie Wei
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jeffrey J. Hayes
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, New York 14625, United States
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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4
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Gilmore JM, Sardiu ME, Venkatesh S, Stutzman B, Peak A, Seidel CW, Workman JL, Florens L, Washburn MP. Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses. Mol Cell Proteomics 2011; 11:M111.011544. [PMID: 22199229 DOI: 10.1074/mcp.m111.011544] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A significant challenge in biology is to functionally annotate novel and uncharacterized proteins. Several approaches are available for deducing the function of proteins in silico based upon sequence homology and physical or genetic interaction, yet this approach is limited to proteins with well-characterized domains, paralogs and/or orthologs in other species, as well as on the availability of suitable large-scale data sets. Here, we present a quantitative proteomics approach extending the protein network of core histones H2A, H2B, H3, and H4 in Saccharomyces cerevisiae, among which a novel associated protein, the previously uncharacterized Ydl156w, was identified. In order to predict the role of Ydl156w, we designed and applied integrative bioinformatics, quantitative proteomics and biochemistry approaches aiming to infer its function. Reciprocal analysis of Ydl156w protein interactions demonstrated a strong association with all four histones and also to proteins strongly associated with histones including Rim1, Rfa2 and 3, Yku70, and Yku80. Through a subsequent combination of the focused quantitative proteomics experiments with available large-scale genetic interaction data and Gene Ontology functional associations, we provided sufficient evidence to associate Ydl156w with multiple processes including chromatin remodeling, transcription and DNA repair/replication. To gain deeper insights into the role of Ydl156w in histone biology we investigated the effect of the genetic deletion of ydl156w on H4 associated proteins, which lead to a dramatic decrease in the association of H4 with RNA polymerase III proteins. The implication of a role for Ydl156w in RNA Polymerase III mediated transcription was consequently verified by RNA-Seq experiments. Finally, using these approaches we generated a refined network of Ydl156w-associated proteins.
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Affiliation(s)
- Joshua M Gilmore
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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5
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Noll M, Thomas JO, Kornberg RD. Preparation of native chromatin and damage caused by shearing. Science 2010; 187:1203-6. [PMID: 17754290 DOI: 10.1126/science.187.4182.1203] [Citation(s) in RCA: 301] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chromatin prepared by a method involving limited nuclease digestion contains the same repeating structure as chromatin in the nucleus, whereas chromatin prepared by conventional methods involving shear does not.
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7
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Chromatin structure and dynamics: a historical perspective. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39001-5] [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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8
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Abstract
Thirty years ago, our conception of chromatin structure underwent a total metamorphosis as the nucleosome era began. In Kurosawa's classic movie 'Rashomon' (1951), each participant had a different perspective of the same pivotal event. This review outlines our perception of history.
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Affiliation(s)
- Donald E Olins
- Department of Biology, Bowdoin College, Brunswick, Maine 04101, USA.
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9
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Abstract
Packaging of the eukaryotic genome into chromatin functions not only to constrain the genome within the boundaries of the cell nucleus but also to permit dynamic and broad-ranging changes related to many important biological phenomena. Therefore, chromatin assembly is a process that affects DNA replication, repair, and gene expression. Chromatin structure is linked to transcriptional regulation, and recent studies show how chromatin is altered so as to facilitate transcription. In addition, modification of chromatin structure is an important regulatory mechanism. Here I review the mechanism of chromatin assembly in vitro and the changes of chromatin structure related to transcriptional activation.
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Affiliation(s)
- T Ito
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
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10
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Abstract
This mini review consists of two parts. The first part will provide a brief overview of the theoretical aspects involved in the two kinds of experiments that can be conducted with the analytical ultracentrifuge (sedimentation velocity and sedimentation equilibrium) as they pertain to the study of chromatin. In the following sections, I describe the analytical ultracentrifuge experiments which, in my opinion, have contributed the most to our understanding of chromatin. Few other biophysical techniques, with the exception of X-ray scattering and diffraction, have contributed as extensively as the analytical ultracentrifuge to the characterization of so many different aspects of chromatin structure. In the course of his scientific career, Professor Henryk Eisenberg has made many important contributions to the theoretical aspects underlying ultracentrifuge analysis, especially in the analysis of solutions of polyelectrolytes and biological macromolecules [H. Eisenberg, Biological macromolecules and polyelectrolytes in solution, Clarendon Press, Oxford, 1976]. As an example he has devoted some of his research effort to the characterization of chromatin in solution. This review includes these important contributions.
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Affiliation(s)
- J Ausió
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada.
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11
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Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 1999; 98:285-94. [PMID: 10458604 DOI: 10.1016/s0092-8674(00)81958-3] [Citation(s) in RCA: 1240] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- R D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, California 94305, USA
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12
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Workman JL, Kingston RE. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 1998; 67:545-79. [PMID: 9759497 DOI: 10.1146/annurev.biochem.67.1.545] [Citation(s) in RCA: 872] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nucleosome, which is the primary building block of chromatin, is not a static structure: It can adopt alternative conformations. Changes in solution conditions or changes in histone acetylation state cause nucleosomes and nucleosomal arrays to behave with altered biophysical properties. Distinct subpopulations of nucleosomes isolated from cells have chromatographic properties and nuclease sensitivity different from those of bulk nucleosomes. Recently, proteins that were initially identified as necessary for transcriptional regulation have been shown to alter nucleosomal structure. These proteins are found in three types of multiprotein complexes that can acetylate nucleosomes, deacetylate nucleosomes, or alter nucleosome structure in an ATP-dependent manner. The direct modification of nucleosome structure by these complexes is likely to play a central role in appropriate regulation of eukaryotic genes.
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Affiliation(s)
- J L Workman
- Howard Hughes Medical Institute, Pennsylvania State University, University Park 16802, USA.
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14
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Affiliation(s)
- K E van Holde
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-7305, USA
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15
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Franĕk F, Dolníková J. Nucleosomes occurring in protein-free hybridoma cell culture. Evidence for programmed cell death. FEBS Lett 1991; 284:285-7. [PMID: 2060652 DOI: 10.1016/0014-5793(91)80705-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In addition to monoclonal immunoglobulin, two kinds of nucleoproteins, NP1 and NP2, were isolated from the supernatants of hybridoma cultures set up in a protein-free medium. As shown by SDS-electrophoresis the two nucleoproteins shared a set of proteins (apparent Mr 11,000 to 15,000), and differed in the DNA moiety (approximately 150 bp in NP1, approximately 350 bp in NP2). The amino acid composition of the protein moiety confirmed the nucleosomal origin of NP1 and NP2. The findings support the view that in hybridoma cultures the cells undergo death by apoptosis, i.e. a programmed process characterized by initial fragmentation of chromatin.
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Affiliation(s)
- F Franĕk
- Institute of Molecular Genetics, Czechoslovak Academy of Science, Praha
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17
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Cole RD. Microheterogeneity in H1 histones and its consequences. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1987; 30:433-49. [PMID: 3323091 DOI: 10.1111/j.1399-3011.1987.tb03352.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The extent of microheterogeneity of H1 histones in individual higher organisms, without considering post-translational modifications, is such that five to eight molecular species can be recognized. The H1 variants differ among themselves in their ability to condense DNA and chromatin fragments, and they are non-uniformly distributed in chromatin. This review assembles data that support the notion that the differences in chromatin condensation (heterochromatization) observed through the microscope are maintained by the non-uniform distribution of H1 variants, and that this pattern of chromatin condensation may determine the dynamics of chromatin during replication and may represent the commitment aspect of differentiation. The differential response of the multiple H1 variants with regard to their synthesis and turnover is consistent with this notion.
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Affiliation(s)
- R D Cole
- Department of Biochemistry, University of California, Berkeley
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18
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Cocco L, Martelli AM, Billi AM, Matteucci A, Vitale M, Neri LM, Manzoli FA. Changes in nucleosome structure and histone H3 accessibility. Iodoacetamidofluorescein labelling after treatment with phosphatidylserine vesicles. Exp Cell Res 1986; 166:465-74. [PMID: 2427349 DOI: 10.1016/0014-4827(86)90491-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The accessibility of the sulfhydryl-specific dye 6-iodoacetamidofluorescein (IAF) to H3 histone has been studied in isolated rat liver nuclei and mononucleosomal core particles after treatment with phosphatidylserine (PS) multilamellar vesicles (MLV). In isolated nuclei, despite the enhancement of total RNA synthesis and the massive chromatin decondensation produced by liposomes, the amount of histone H3 which can be labelled with the dye remains essentially the same in PS-treated as in control nuclei. However, when mononucleosomal core particles, treated with PS vesicles, are reacted with IAF, H3 becomes derivatized by the dye, while controls do not. These data provide additional evidence that the metabolic and structural changes observed in isolated nuclei treated with PS MLV, are due mainly to the reported removal of histone H1. Moreover, the experiments reported confirm the usefulness of IAF in studying the changes of nucleosome organization, since PS is able to affect the nucleosomal core configuration in isolated nucleosome particles, derivatizing the buried cysteine groups of H3 histone.
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Wu RS, Panusz HT, Hatch CL, Bonner WM. Histones and their modifications. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1986; 20:201-63. [PMID: 3519076 DOI: 10.3109/10409238609083735] [Citation(s) in RCA: 213] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Histones constitute the protein core around which DNA is coiled to form the basic structural unit of the chromosome known as the nucleosome. Because of the large amount of new histone needed during chromosome replication, the synthesis of histone and DNA is regulated in a complex manner. During RNA transcription and DNA replication, the basic nucleosomal structure as well as interactions between nucleosomes must be greatly altered to allow access to the appropriate enzymes and factors. The presence of extensive and varied post-translational modifications to the otherwise highly conserved histone primary sequences provides obvious opportunities for such structural alterations, but despite concentrated and sustained effort, causal connections between histone modifications and nucleosomal functions are not yet elucidated.
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20
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Sogo JM, Ness PJ, Widmer RM, Parish RW, Koller T. Psoralen-crosslinking of DNA as a probe for the structure of active nucleolar chromatin. J Mol Biol 1984; 178:897-919. [PMID: 6092647 DOI: 10.1016/0022-2836(84)90318-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Trimethylpsoralen was used to crosslink the extrachromosomal ribosomal DNA in nucleoli or nuclei of growing Dictyostelium discoideum cells. The DNA was extracted and was examined by spreading under denaturing conditions for electron microscopy. Intact 95,000 base ribosomal DNA molecules were seen, showing regularly spaced, single-stranded bubbles of about 200 to 400 bases in size, interrupted twice by 11,000 base heavily crosslinked stretches, which correspond to the known positions of the coding regions. The bubbles on the nontranscribed regions indicate the presence of nucleosomes during crosslinking. The DNA was digested with restriction enzymes and analysed by gel electrophoresis in parallel with DNA not treated with psoralen. Fragments from the non-coding region had the same mobility as untreated DNA, while those from the coding region had a markedly lower mobility, though not as low as that of crosslinked pure DNA. This shifting of the bands, specific to the coding region, was also seen when whole cells were treated with psoralen. Treatment of nucleoli with 2 m-NaCl (which is known to dissociate histones) before addition of psoralen led to strong crosslinking all along the ribosomal DNA, resulting in a decreased electrophoretic mobility of bands from the non-coding region, but no further retardation of those from the coding region. In differentiating Dictyostelium cells, slugs, where ribosomal RNA synthesis is very much reduced, the extent of psoralen-crosslinking in the coding region was reduced, but not completely to the level of that of the non-transcribed spacer. In order to test whether psoralen itself alters chromatin structure, crosslinked and non-crosslinked nucleoli from growing cells were lysed with heparin and spread for electron microscopy. There was no difference in the appearance or the frequency of the transcription units seen. Digestion of crosslinked nuclei with micrococcal nuclease indicated an undisturbed structure for bulk chromatin, as well as for the chromatin in the non-transcribed spacer of the ribosomal DNA. Thus psoralen-crosslinking does not lead to extensive disruption or distortion of the structure of either inactive or active chromatin. We conclude, taking the results presented in the Appendix into account, that the extent of psoralen-crosslinking in chromatin DNA is diagnostic for the structure of undistorted chromatin.(ABSTRACT TRUNCATED AT 400 WORDS)
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21
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Böhm L, Crane-Robinson C. Proteases as structural probes for chromatin: the domain structure of histones. Biosci Rep 1984; 4:365-86. [PMID: 6375755 DOI: 10.1007/bf01122502] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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22
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Walker IO, Wolffe AP. The thermal denaturation of chromatin core particles. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 785:97-103. [PMID: 6704405 DOI: 10.1016/0167-4838(84)90132-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The thermal denaturation of chicken erythrocyte core particles has been followed using changes in absorption and circular dichroism. The absorption-denaturation curve is biphasic, with transitions centred at 59 degrees C and 74 degrees C. The first of these transitions is reversible, whereas heating into the second transition produces irreversible changes in DNA and histone secondary structure. After heating to temperatures within the second transition and then cooling, two components are observed in the analytical centrifuge: a slow-sedimenting species which is present in proportions corresponding to the extent of irreversible denaturation and a fast sedimenting species which is present in inverse proportion to the extent of denaturation. The slow-sedimenting component was primarily denatured DNA. The results suggest that thermal denaturation of core particles is a cooperative, 'all-or-none' process.
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23
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Yang PC, Woolley PV. Thermal melting of chromatin from the pancreas and liver of guinea pigs treated with 1-methyl-1-nitrosourea. Chem Biol Interact 1984; 48:29-41. [PMID: 6692494 DOI: 10.1016/0009-2797(84)90004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The carcinogen 1-methyl-1-nitrosourea (MNU) can cause pancreatic cancer in guinea pigs. We have examined the relative damage produced by MNU treatment on the chromatin from pancreas and liver of these animals. Thermal denaturation of chromatin from guinea pig pancreas and liver was studied following parenteral administration of MNU in several doses. Estimates of single strand breakage were also obtained by examination of the fluorescence of intercalated ethidium bromide. Oligomeric chromatin melted with a main Tm at 78 degrees C, with additional components at 48 degrees C, 55 degrees C and 65 degrees C. Repetitive treatment with MNU at several doses between 20 mg/kg and 70 mg/kg produced destabilization of pancreatic chromatin as shown by a shift from 78 degrees C to lower melting components. The liver by contrast was relatively unaffected. In addition, pancreatic chromatin showed an increase in alkali-induced strand unwinding with MNU treatment, probably due to an increase in single strand breaks, while there was no change in this regard in the liver. The data indicate that the pancreas is more susceptible to damage by MNU than the liver.
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24
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Marion C, Pallotta L, Roux B. Effect of digestion with trypsin on chromatin structure. Biochem Biophys Res Commun 1982; 108:1551-8. [PMID: 7181905 DOI: 10.1016/s0006-291x(82)80084-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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25
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Mencke AJ, Rill RL. Circular dichroism and thermal denaturation studies of subnucleosomes and their relationships to nucleosome structure. Biochemistry 1982; 21:4362-70. [PMID: 6215061 DOI: 10.1021/bi00261a027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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26
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Cartwright IL, Abmayr SM, Fleischmann G, Lowenhaupt K, Elgin SC, Keene MA, Howard GC. Chromatin structure and gene activity: the role of nonhistone chromosomal proteins. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1982; 13:1-86. [PMID: 6751690 DOI: 10.3109/10409238209108709] [Citation(s) in RCA: 154] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Chai LS, Sandberg AA. Evidence of nucleosomes in situ and their organization in chromatin and chromosomes of Chinese hamster cells. ACTA ACUST UNITED AC 1980. [DOI: 10.1016/0165-4608(80)90067-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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30
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Jump DB, Sudhakar S, Tew KD, Smulson M. Probes to study the effect of methyl nitrosourea on ADP-ribosylation and chromatin structure at the subunit level. Chem Biol Interact 1980; 30:35-51. [PMID: 7379203 DOI: 10.1016/0009-2797(80)90112-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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31
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Tsaneva I. Comparative study on the thermal denaturation of different nucleosome preparations. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1980; 11:211-6. [PMID: 7389979 DOI: 10.1016/0020-711x(80)90222-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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32
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Long BH, Huang CY, Pogo AO. Isolation and characterization of the nuclear matrix in Friend erythroleukemia cells: chromatin and hnRNA interactions with the nuclear matrix. Cell 1979; 18:1079-90. [PMID: 293220 DOI: 10.1016/0092-8674(79)90221-6] [Citation(s) in RCA: 177] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nuclear matrices from undifferentiated and differentiated Friend erythroleukemia cells have been obtained by a method which removes DNA in a physiological buffer. These matrices preserved the characteristic topographical distribution of condensed and diffuse "chromatin" regions, as do nuclei in situ or isolated nuclei. Histone H1 was released from the nuclear matrix of undifferentiated cells by 0.3 M KCl; inner core histones were released by 1 M KCl. Nuclear matrix from differentiated cells did not maintain H1, and histone cores were fully released in 0.7 M KCl. KCl removed the core histones as an octameric structure with no evidence of preferential release of any single histone. Electron microscopy of KCl-treated matrix revealed no condensed regions but rather a network of fibrils in the whole DNA-depleted nuclei. When nuclear matrices from both types of cell were exposed to conditions of very low ionic strength, inner core histones and condensed regions remained. These observations support the contention that inner core histones are bound to matrix through natural ionic bonds or saline-labile elements, and that these interactions are implicated in chromatin condensation. hnRNA remained undegraded and tenaciously associated to the matrix fibrils, and was released only by chemical means which, by breaking hydrophobic and hydrogen bonds, produced matrix lysis. Very few nonhistone proteins were released upon complete digestion of DNA from either type of nuclei. The remaining nonhistone proteins represent a large number of species of which the majority may be matrix components. The molecular architecture in both condensed and diffuse regions of interphase nuclei appears to be constructed of two distinct kinds of fibers; the thicker chromatin fibers are interwoven with the thinner matrix fibers. The latter are formed by a heteropolymer of many different proteins.
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Mandel R, Kolomijtseva G, Brahms JG. DNA-protein interactions in nucleosomes and in chromatin. Structural studies of chromatin stabilized by ultraviolet-light induced crosslinking. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 96:257-65. [PMID: 456371 DOI: 10.1111/j.1432-1033.1979.tb13036.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crosslinking induced by ultraviolet light irradiation at 254 nm has been utilized to investigate the structure of chromatin and isolated nucleosomes. The results presented here imply that the four core histones, as well as histone H1, have reactive groups within a bond length of the DNA bases. In nucleosomes depleted of H1, all of the core histones react similarly with the DNA and form crosslinks. In chromatin, the rate of crosslinking of all histones to DNA is essentially similar. Comparison of mononucleosomes, dinucleosomes and whole chromatin shows that the rate of crosslinking increases significantly with increasing number of connected nucleosomes. These differences in the rate of crosslinking are interpreted in terms of interactions between neighbouring nucleosomes on the chromatin fiber, which are absent in an isolated mononucleosome.
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35
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Bekhor I, Mirell CJ. Simple isolation of DNA hydrophobically complexed with presumed gene regulatory proteins (M3). Biochemistry 1979; 18:609-16. [PMID: 420803 DOI: 10.1021/bi00571a010] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatin from chicken reticulocytes and mouse Ehrlich ascites tumor cells has been extracted with 2 M NaCl, leaving a portion of the DNA still complexed with a fraction of nonhistones (designated M3, since it can be dissociated from DNA in solutions of 3 M NaCl containing 5 M urea). The DNA complexed with M3, separated from the bulk DNA by centrifugation, was found to contain sequences poorly represented in bulk DNA. Specifically we found that DNA--M3 complexes isolated from chicken reticulocyte chromatin were enriched in globin gene sequences by 20-fold relative to unfractionated DNA and by over 1000-fold relative to DNA rendered free of protein following the extraction of chromatin with 2 M NaCl. We have therefore isolated DNA fractions complexed with M3 which are enriched in specific sequences as may be determined by M3.
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Abstract
The functional capacity of a cell, tissue, organ, or organism is dependent upon its ability to maintain the stability of its unit components. The higher the differentiated state of the system, the greater the amount of stability required to maintain that state as a function of time. Stability can be achieved via either redundancy or repair. Redundancy while easily achievable in biological systems is both costly and limited by thermodynamic considerations. Repair, in its general sense, has no such limitations. Repair at the cellular and macromolecular level is multiple in its forms and varies as a function of species, tissue, and stage of the cell cycle. The repair of DNA damage is a dynamic process with many components and subcomponents, each interacting with one another in order to achieve a balance between individual stability and evolutionary diversity. Thus, between internal and external factors which damage DNA and the subsequent expression of alterations in the functional stability of DNA lie the multi-functional pathways which attempt to maintain DNA fidelity. A strong correlation between ulta-violet light induced excision or pre-replication repair, as measured by autoradiogrphy and maximum species lifespan has been reported within different strains of the same species, between related species (e.g. Mus musculus and Peromyscus leucopus), between five orders of mammals, and most recently within members of the primate family. As has been demonstrated by the authors and others, differences in excision repair between species and tissues may relate to the turning off of portions of the repair processes during embryogenesis. Regardless of why such correlations exist or the nature of their mechanisms, it is naive to either assert or deny a causal role for DNA repair in longevity assurance systems. For example, while species-related differences in DNA repair may reflect the turning off of such repair processes during fetal development this does not mean that rates of accumulation of DNA damage are not altered by such changes. Indeed, such a phenomena might well explain the rapid evolution of lifespan within the primates without a concurrent input of new genes.
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Doenecke D. Modification of DNA in chromatin with methyltransferase from Haemophilus influenzae Rd. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:481-6. [PMID: 311284 DOI: 10.1111/j.1432-1033.1979.tb12846.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The accessibility of DNA in nucleosome dimers (as a model of the chromosomal chain of nucleosomes) was determined by means of modification methylases from Haemophilus influenzae Rd. Using these enzymes, the rate of modification of nucleosome dimers is about one fifth the rate observed with protein-free DNA from chromatin subunit dimers. Methylated DNA sites in nucleosome dimers are readily accessible to micrococcal nuclease. The analysis of the fragment pattern of nucleosomes after methylation and mild nuclease treatment reveals that the methylated sites are predominantly located in the internucleosomal linker DNA. Polylysine binding experiments further support this interpretation. This compound preferentially interacts with the nucleosomal core DNA and protects it against internal cleavage. It neither affects the degradation of methylated sites drastically nor does it inhibit the methylation of nucleosome dimers. Thus, a combination of protection, cleavage and modification is proposed as a useful tool for the analysis of the structure of chromatin.
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Sahasrabuddhe CG, Pathak S, Hsu TC. Responses of mammalian metaphase chromosomes to endonuclease digestion. Chromosoma 1978; 69:331-8. [PMID: 743903 DOI: 10.1007/bf00332136] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Digestion of fixed metaphase chromosomes by endonucleases (micrococcal nuclease and DNase II) under optimal digestion conditions followed by Giemsa staining produces sharp banding patterns identical to G-bands. In 3H-thymidine labeled, synchronized metaphase cells of the chinese hamster (CHO line), the band induction is accompanied by the removal of DNA. The single strand specific nuclease S1 and DNase I do not produce such banding patterns.
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Goldknopf IL, French MF, Daskal Y, Busch H. A reciprocal relationship between contents of free ubiquitin and protein A24, its conjugate with histone 2A, in chromatin fractions obtained by the DNase II, Mg++ procedure. Biochem Biophys Res Commun 1978; 84:786-93. [PMID: 718717 DOI: 10.1016/0006-291x(78)90773-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Doenecke D. Digestion of chromosomal proteins in formaldehyde treated chromatin. HOPPE-SEYLER'S ZEITSCHRIFT FUR PHYSIOLOGISCHE CHEMIE 1978; 359:1343-52. [PMID: 569116 DOI: 10.1515/bchm2.1978.359.2.1343] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Treatment of chromatin subunits (nucleosome monomers) with formaldehyde results in the formation of cross-links between DNA and histones and between histones and histones. Digestion of chromosomal proteins with proteinase K does not lower the protein/DNA weight ratio below 0.08 to 0.1 as determined by cesium chloride gradient centrifugation of the digestion product from formaldehyde-treated nucleosomes. In addition to proteinase K, formaldehyde-treated nucleosomes were tested for accessibility to trypsin and pronase. The CsCl gradient patterns show, that pronase digestion and proteinase K treatment yield similar results. Trypsin treatment of control and formaldehyde-treated nucleosomes shows, that the sites which are accessible for trypsin in native nucleosomes, are blocked after formaldehyde treatment. Analysis of the CsCl gradient peak fractions in polyacrylamide gels shows, that the reliability of DNA fragment size determinations depends on the completeness of deproteinization.
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Smerdon MJ, Tlsty TD, Lieberman MW. Distribution of ultraviolet-induced DNA repair synthesis in nuclease sensitive and resistant regions of human chromatin. Biochemistry 1978; 17:2377-86. [PMID: 678515 DOI: 10.1021/bi00605a020] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Action of estrogens on reconstituted nucleohistones. Bull Exp Biol Med 1978. [DOI: 10.1007/bf00801979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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46
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Chipev CC, Staynov DZ. Helix-coil transitions in nucleoprotein: Computer-generated curves for independent melting of double-stranded regions with fixed ends. Biopolymers 1978. [DOI: 10.1002/bip.1978.360170413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Tata JR, Baker B. Enzymatic fractionation of nuclei: polynucleosomes and RNA polymerase II as endogenous transcriptional complexes. J Mol Biol 1978; 118:249-72. [PMID: 633359 DOI: 10.1016/0022-2836(78)90227-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
The approximate shape of the chromatin subunit called the nucleosome is now known, but its internal architecture is not well understood. Recent studies reveal details of the organisation of DNA within the nucleosome, and show that the arginine-rich histones are essential to DNA folding. Nucleosomes or structures related to them seem to be present at points of DNA replication and transcription; interactions within and between nucleosomes are likely to play a critical part in these processes.
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