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Annunziato AT. Assembling chromatin: the long and winding road. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1819:196-210. [PMID: 24459722 DOI: 10.1016/j.bbagrm.2011.07.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
It has been over 35 years since the acceptance of the "chromatin subunit" hypothesis, and the recognition that nucleosomes are the fundamental repeating units of chromatin fibers. Major subjects of inquiry in the intervening years have included the steps involved in chromatin assembly, and the chaperones that escort histones to DNA. The following commentary offers an historical perspective on inquiries into the processes by which nucleosomes are assembled on replicating and nonreplicating chromatin. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.
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Dna replication in eukaryotes. Rev Physiol Biochem Pharmacol 2005. [DOI: 10.1007/bfb0030491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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Leffak M, Trempe JP. Histone H1 and HMG 14/17 are deposited nonrandomly in the nucleus. Nucleic Acids Res 1985; 13:4853-69. [PMID: 4022776 PMCID: PMC321831 DOI: 10.1093/nar/13.13.4853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We have studied the assembly of histone H1 and the high mobility group nonhistones 14/17 by isopycnic analysis after crosslinking density labeled MSB cell nuclei or chromatin. Carbodiimide crosslinking produces dense poly-H1 and hybrid density H1-H2A histone dimers, indicating that new H1 is deposited nonrandomly, albeit nonconservatively relative to new core histones. Core histone-HMG crosslinking with succinimidyl propionate yields dense HMG 14 in uniformly dense particles and new HMG 17 crosslinked to both dense and light protein, implying that HMG 14 and 17 each deposit nonrandomly; but differently with respect to new core octamers. Propionimidate crosslinking yields dense H1-HMG 17 dimers, suggesting that the interactions of new 14/17 with H1 (new HMG 14-old H1, new HMG 17-new H1) are reciprocal to their interactions with the core histones.
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Kurian P, Jeffrey AM, Milo GE. Preferential binding of benzo[a]pyrene diol epoxide to the linker DNA of human foreskin fibroblasts in S phase in the presence of benzamide. Proc Natl Acad Sci U S A 1985; 82:2769-73. [PMID: 3921965 PMCID: PMC397647 DOI: 10.1073/pnas.82.9.2769] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Addition of benzamide (BZ) at the onset of S phase inhibited expression of the neoplastic phenotype in human foreskin fibroblasts treated in vitro with (+/-)-7 alpha,8 beta-dihydroxy-9 beta,10 beta-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (B[a]P diol epoxide) in early S phase. Analysis of the specific B[a]P diol epoxide-DNA adducts revealed that ca. 65% of the total adducts in BZ and non-BZ carcinogen-treated cells was the B[a]P diol epoxide-deoxyguanine adduct. Limited micrococcal nuclease digestion of the early S phase nuclei from cells treated with B[a]P diol epoxide indicated that the carcinogen binds equally to linker and core DNA. However, when the cells were predominantly in S phase, in the presence of BZ, there was ca. three times more binding of B[a]P diol epoxide to the linker DNA compared to the core region. The confluent cells in G1 cell arrest treated only with B[a]P diol epoxide also bound the carcinogen preferentially to the linker region. These data indicate that pretreatment of the cells with BZ at the onset of S phase established a preferential binding pattern in the linker DNA similar to that observed in the cells treated with B[alpha]P diol epoxide in G1 arrest.
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Pülm W, Knippers R. Chromatin structure and DNA replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1984; 179:127-41. [PMID: 6098149 DOI: 10.1007/978-1-4684-8730-5_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The structure of (3H) thymidine pulse labeled, replicating chromatin differs from that of non replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. We summarize the structural changes that we observe using replicating chromatin as substrate for micrococcal nuclease. The data suggest a more extended configuration of replicating compared to non replicating chromatin. We use these data to discuss a model of the chromatin structure in the vicinity of replication forks. Finally, we present data to show that the reversion of structural changes in replicative chromatin depends on continued DNA replication.
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Association of newly synthesized histones with replicating and nonreplicating regions of chromatin. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34361-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Russev G, Hancock R. Assembly of new histones into nucleosomes and their distribution in replicating chromatin. Proc Natl Acad Sci U S A 1982; 79:3143-7. [PMID: 6954465 PMCID: PMC346370 DOI: 10.1073/pnas.79.10.3143] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We studied the assembly of new histones into nucleosomes and their distribution in replicating chromatin in growing P815 mouse cells. New histones and new DNA were density-labeled with 13C, 15N, 2H-substituted amino acids together with [3H]arginine or with 5-iododeoxyuridine and [3H]thymidine, respectively, for 1 hr (approximately 20% of S phase). Mono- di-, tri-, tetra- and larger oligonucleosomes were isolated by sucrose gradient centrifugation of micrococcal nuclease-digested chromatin, and their density distribution was analyzed, without fixation, in metrizamide/triethanolamine density gradients [Russev, G. and Tsanev, R. (1976) Nucleic Acids Res. 3, 697-707] in which mono- and oligonucleosomes containing dense amino acids or 5-iododeoxyuridine separate from the corresponding normal nucleosomes. Under these conditions, approximately 74% of the new histones are found in nucleosomes on newly replicated DNA, and the remainder are on unreplicated DNA. The majority of new histones form entirely new nucleosomes; a minor fraction may form hybrid nucleosomes that also contain preexisting histones. New nucleosomes are distributed to both new daughter DNA molecules with approximately equal probability, and our evidence suggests, but does not prove, that they are distributed in a random manner along new DNA.
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Fowler E, Farb R, El-Saidy S. Distribution of the core histones H2A.H2B.H3 and H4 during cell replication. Nucleic Acids Res 1982; 10:735-48. [PMID: 7063413 PMCID: PMC326181 DOI: 10.1093/nar/10.2.735] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The distribution of newly synthesized core histones H2A, H2B, H3 and H4 relative to the DNA strand synthesized in the same generation has been examined in replicating Chinese Hamster ovary cells. Cells are grown for one generation in [14C]-lysine and thymidine, and then for one generation in [3H]-lysine and 5-bromodeoxyuridine (BrUdRib) and a further generation in unlabeled lysine and thymidine. This protocol produces equal amounts of unifilarly substituted and unsubstituted DNA. Monomer nucleosomes isolated from chromatin containing these two types of DNA can be distinguished by crosslinking with formaldehyde and banding to equilibrium in CsCl density gradients. The results indicate that the core histones are equally distributed between the two types of DNA. These findings are discussed in terms of current models for chromatin replication; they do not support any long term association of newly replicated histones with either the leading or lagging side of the replication fork.
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Jackson V, Marshall S, Chalkley R. The sites of deposition of newly synthesized histone. Nucleic Acids Res 1981; 9:4563-81. [PMID: 7301583 PMCID: PMC327459 DOI: 10.1093/nar/9.18.4563] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The chromosomal fragments produced by nuclease digestion of freshly replicated chromatin migrate more rapidly relative to bulk chromatin when analyzed in nucleoprotein gels. The cause of the anomalous migration has been studied and the evidence indicates that rather than reflecting a shorter nucleosomal repeat in vivo that it may be a consequence of nucleosome sliding during the digestion itself. The distinct electrophoretic characteristics of nucleosomal material containing newly replicated DNA have enabled us to examine their histone composition by two dimensional electrophoresis. We find that nucleosomes containing new DNA also contain newly synthesized histones H3 and H4. In contrast more than 50% of newly synthesized H2A and H2B, and essentially all of new H1, are deposited at sites on the bulk chromatin distinct from that material containing newly replicated DNA. In addition we show that newly synthesized histones H3 and H4 are bound unusually weakly when they first become associated with the chromatin.
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Das GC, Niyogi SK. Structure, replication, and transcription of the SV40 genome. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1981; 25:187-241. [PMID: 6261296 DOI: 10.1016/s0079-6603(08)60485-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Annunziato AT, Woodcock CL. Chromatin replication in Tetrahymena pyriformis. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1981; 26:135-49. [PMID: 6792655 DOI: 10.1016/s0079-6603(08)60401-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Murphy RF, Wallace RB, Bonner J. Isolation of newly replicated chromatin by using shallow metrizamide gradients. Proc Natl Acad Sci U S A 1980; 77:3336-40. [PMID: 6932022 PMCID: PMC349610 DOI: 10.1073/pnas.77.6.3336] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The properties of chromatin containing newly synthesized DNA and protein were investigated. A fraction of chromatin enriched in newly replicated DNA was isolated by means of its increased density in metrizamide relative to bulk chromatin. The DNA of this fraction appeared to be packaged into nucleosomes but at a reduced nucleosomal spacing. Although pulse-labeled DNA was present in this dense fraction, nucleosomes labeled with short pulses of arginine or acetate were of normal density. The data presented are consistent with the conclusion that newly replicated DNA is associated with preexisting histones in a short-lived, compact structure whereas newly synthesized histones are deposited at normal spacing some distance from the replication fork.
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Crémisi C. Chromatin replication revealed by studies of animal cells and papovaviruses (simian virus 40 and polyoma virus). Microbiol Rev 1979; 43:297-319. [PMID: 232241 PMCID: PMC281479 DOI: 10.1128/mr.43.3.297-319.1979] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Bregnard A, Ruch F, Lutz H, Kuenzle CC. Histones and DNA increase synchronously in neurons during early postnatal development of the rat forebrain cortex. HISTOCHEMISTRY 1979; 61:271-9. [PMID: 478990 DOI: 10.1007/bf00508448] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Russev G, Tsanev R. Nonrandom segregation of histones during chromatin replication. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:123-8. [PMID: 436825 DOI: 10.1111/j.1432-1033.1979.tb12801.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Taichman LB. The use of ultraviolet light in the fractionation of chromatin containing unsubstituted and bromodeoxyuridine-substituted DNA. Nucleic Acids Res 1979; 6:2029-38. [PMID: 450723 PMCID: PMC327829 DOI: 10.1093/nar/6.5.2029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two procedures are described for the fractionation of chromatin containing unsubstituted (LL) DNA and DNA unifilarly substituted with bromodeoxyuridine (HL). The two procedures rely upon the sensitivity of bromodeoxyuridine-containing DNA to UV light to induce either strand breakage or protein crosslinking. When a mixture of LL and HL chromatin is irradiated with UV light, the HL DNA fragments into molecules of smaller molecular weight than the LL DNA and crosslinks more chromosomal protein than the LL DNA. LL and HL chromatin can be fractionated on the basis of size by centrifuging through a neutral sucrose gradient. The HL DNA-protein adducts that are generated by the UV light have a unique buoyant density and may be isolated by isopycnic centrifugation in CS2SO4. The ability to fractionate LL and HL chromatin permits certain studies on the structure of replicating chromatin.
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Seale RL. Nucleosomes associated with newly replicated DNA have an altered conformation. Proc Natl Acad Sci U S A 1978; 75:2717-21. [PMID: 275840 PMCID: PMC392634 DOI: 10.1073/pnas.75.6.2717] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In vitro DNA synthesis was studied in HeLa cell nuclei, with emphasis on the question of whether newly replicated DNA is associated with nucleosomes. The newly replicated DNA was twice as sensitive to digestion by micrococcal nuclease as mature chromatin DNA, reaching a limit digest at 20-25% acid-insoluble product. Examination of the intermediates of digestion by micrococcal nuclease showed the nuclease-resistant, new DNA to be complexed in nucleosomes. However, structural differences were evident at both the polynucleosomal and the core particle level. The nucleosomes on newly replicated DNA were arranged with a repeat size of 165-170 base pairs-i.e., smaller than the 185-base-pair repeat of mature chromatin. The heterogeneity of polynucleosomal multimers, evident in digests of whole chromatin, was reduced in newly replicated chromatin such that the multimers resolved as sharply defined bands. Nucleosomal core particles associated with newly replicated DNA had a different conformation from particles in mature chromatin based on the following lines of evidence: (i) during micrococcal nuclease digestion, the monomer nucleosomes did not accumulate but were rapidly degraded under certain conditions; (ii) micrococcal nuclease limit digest patterns and DNase I digestion patterns, both of which reflect internal nucleosomal protein DNA associations, differed significantly from control patterns. These findings bear directly on models postulated for nucleosome-DNA interactions during chromation replication. A possible mechanism to account for the conformational change and its role in replication are discussed.
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Shelton ER, Kang J, Wassarman PM, DePamphilis ML. Chromatin assembly in isolated mammalian nuclei. Nucleic Acids Res 1978; 5:349-62. [PMID: 634792 PMCID: PMC341988 DOI: 10.1093/nar/5.2.349] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cellular DNA replication was stimulated in confluent monolayers of CV-1 monkey kidney cells following infection with SV40. Nuclei were isolated from CV-1 cells labeled with [3H]thymidine and then incubated in the presence of [alpha-32P]deoxyribonucleoside triphosphates under conditions that support DNA replication. To determine whether or not the cellular DNA synthesized in vitro was assembled into nucleosomes the DNA was digested in situ with either micrococcal nuclease or pancreatic DNase I, and the products were examined by electrophoretic and sedimentation analysis. The distribution of DNA fragment lengths on agarose gels following micrococcal nuclease digestion was more heterogeneous for newly replicated than for the bulk of the DNA. Nonetheless, the state of cellular DNA synthesized in vitro (32P-labeled) was found to be identical with that of the DNA in the bulk of the chromatin (3H-labeled) by the following criteria: (i) The extent of protection against digestion by micrococcal nuclease of DNase I. (ii) The size of the nucleosomes (180 base pairs) and core particles (145 base pairs). (iii) The number and sizes of DNA fragments produced by micrococcal nuclease in a limit digest. (iv) The sedimentation behavior on neutral sucrose gradients of nucleoprotein particles released by micrococcal nuclease. (v) The number and sizes of DNA fragments produced by DNase I digestion. These results demonstrate that cellular DNA replicated in isolated nuclei is organized into typical nucleosomes. Consequently, subcellular systems can be used to study the relationship between DNA replication and the assembly of chromatin under physiological conditions.
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Hemminki K. Labelling of histones and nonhistones in lung nuclear matrix and chromatin fractions. HOPPE-SEYLER'S ZEITSCHRIFT FUR PHYSIOLOGISCHE CHEMIE 1977; 358:1125-31. [PMID: 924385 DOI: 10.1515/bchm2.1977.358.2.1125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Rat lung tissue is labelled in vitro with [3H]leucine and nuclei are prepared. They are digested with deoxyribonuclease II and four subfractions are isolated after differential centrifugation: MgCl2-soluble (active) and MgCl2-insoluble (inactive) chromatin, nuclear matrix sediment and matrix extract using 2M NaCl. The matrix extract fraction is found to be enriched in radioactive DNA after a short pulse of [3H]thymidine. The labelling kinetics of histones are similar in each subfraction, suggesting that histones are not preferentially incorporated onto nascent DNA. Nonhistones isolated from the subfractions, except for the matrix sediment fraction, also follow closely similar incorporation kinetics with [3H]-leucine. The matrix sedimnent fraction is three times more actively labelled than nonhistones of the other fractions and displaying a unique protein composition, suggesting distinct functional properties.
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Jackson V, Granner D, Chalkley R. Deposition of histone onto the replicating chromosome: newly synthesized histone is not found near the replication fork. Proc Natl Acad Sci U S A 1976; 73:2266-9. [PMID: 1065875 PMCID: PMC430523 DOI: 10.1073/pnas.73.7.2266] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have studied the site of deposition of newly synthesized histone. It appears to be randomly distributed over the chromosomal material and does not become associated specifically with immediately post-replicational DNA, nor is it deposited in discrete continuous regions distal to the sites of DNA synthesis. The newly synthesized DNA, however, rapidly acquires a complement of chromosomal proteins; presumably, preexisting histones must migrate to become associated with post-replicational DNA.
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