Structure of chromatin at deoxyribonucleic acid replication forks: prenucleosomal deoxyribonucleic acid is rapidly excised from replicating simian virus 40 chromosomes by micrococcal nuclease

Cusick, Michael E.; Herman, Tim; DePamphilis, Melvin L.; Wassarman, Paul M.

doi:10.1021/bi00526a020

Cited by 42 publications

(40 citation statements)

References 57 publications

(106 reference statements)

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“…If HSF invades Nuc Ϫ2 and directly binds its target sequences, then its binding to nucleosomal DNA would be cell cycle independent. Alternatively, HSF might preempt the assembly of Nuc Ϫ2, either by binding DNA immediately following replication, when histone octamers are transiently displaced from the newly synthesized DNA (13,32,63; but see reference 8), or by binding to the nascent nucleosome shortly thereafter, aborting its maturation. Either way, such binding would be cell cycle dependent.…”

Section: Resultsmentioning

confidence: 99%

Cell Cycle-Dependent Binding of Yeast Heat Shock Factor to Nucleosomes

Venturi

Erkine

Gross

2000

Molecular and Cellular Biology

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In the nucleus, transcription factors must contend with the presence of chromatin in order to gain access to their cognate regulatory sequences. As most nuclear DNA is assembled into nucleosomes, activators must either invade a stable, preassembled nucleosome or preempt the formation of nucleosomes on newly replicated DNA, which is transiently free of histones. We have investigated the mechanism by which heat shock factor (HSF) binds to target nucleosomal heat shock elements (HSEs), using as our model a dinucleosomal heat shock promoter (hsp82-⌬HSE1). We find that activated HSF cannot bind a stable, sequence-positioned nucleosome in G 1 -arrested cells. It can do so readily, however, following release from G 1 arrest or after the imposition of either an early S-or late G 2 -phase arrest. Surprisingly, despite the S-phase requirement, HSF nucleosomal binding activity is restored in the absence of hsp82 replication. These results contrast with the prevailing paradigm for activator-nucleosome interactions and implicate a nonreplicative, S-phase-specific event as a prerequisite for HSF binding to nucleosomal sites in vivo.In the eukaryotic cell, nuclear DNA is packaged into a compact structure known as chromatin, a complex of DNA and histone proteins. The packaging of DNA into chromatin not only serves to confine the genome within the boundaries of the nucleus but also regulates the transcriptional activation of genes. The presence of nucleosomes, the individual subunits of chromatin, can inhibit the binding of sequence-specific activators to upstream elements, as well as impede access of the general transcription machinery to the core promoter (reviewed in reference 35). As a consequence, nucleosomes inhibit transcription, both in vitro (34,43,72) and in vivo (27,29,61). Thus, an important function of activators is to overcome nucleosomal repression, either by blocking nucleosome formation over promoters, thereby presetting genes for activation, or by remodeling preassembled nucleosomes as the initial step in transcriptional activation.The mechanisms by which activators recognize and bind their cognate sites within chromatin are varied. Certain factors, like NF-1 and GCN4, can access their sites only within nuclease-hypersensitive, nucleosome-rearranged regions (5,15,66,75). Others, such as PHO4, bind to accessible regions but, once DNA bound, actively remodel neighboring nucleosomes (1,19). Still others are capable of invading a stable nucleosome and binding to target sites wrapped around the nucleosome core. Glucocorticoid receptor, for example, invades a sequence-positioned nucleosome within the mouse mammary tumor virus promoter following exposure to hormone (5). Receptor binding to its cognate sequence leads to a dramatic reconfiguring of the underlying nucleosome (66) and occurs in the absence of replication (55). The ability of activators to invade a preassembled nucleosome may require the involvement of ATP-dependent chromatin remodeling complexes and/or histone acetyltransferases (reviewed in references 36...

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Section: Resultsmentioning

confidence: 99%

Cell Cycle-Dependent Binding of Yeast Heat Shock Factor to Nucleosomes

Venturi

Erkine

Gross

2000

Molecular and Cellular Biology

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“…Experiments were performed in which the cells had been A~25 [3][4][5][6] after drug treatment for 60 min, as expected because there were fewer molecules to ligate at that time.…”

Section: Resultsmentioning

confidence: 99%

“…For example, the replication fork of simian virus 40 DNA has been analyzed by using several different nucleases. Recently it was shown that one can subdivide the simian virus 40 replication fork into a prenucleosomal DNA region and immature and mature chromatin (3), and the unique DNA sequences at the origin of DNA replication have been identified (4).…”

mentioning

confidence: 99%

Aphidicolin inhibits the synthesis and joining of short DNA fragments but not the union of 10-kilobase DNA replication intermediates.

Lönn¹,

Lönn²

1983

Proc. Natl. Acad. Sci. U.S.A.

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DNA replication intermediates in human melanoma cells have been investigated by using the drug aphidicolin, which inhibits DNA polymerase a. In untreated cells, Okazaki fragments and 10-kilobase (kb) DNA intermediates are formed. In aphidicolin-treated cells, the replication fork is stopped and there is no formation of DNA replication intermediates. However, 10-kb DNA intermediates formed before the drug blockade are ligated to high molecular weight DNA whereas already formed Okazaki fragments accumulate in the cell. Moreover, in cells released from aphidicolin inhibition there is preferential labeling of 10-kb DNA compared to Okazaki fragments. The 10-kb DNA and the Okazaki fragments, therefore, respond -differently to aphidicolin.Our knowledge of the different steps in the synthesis of DNA in mammalian cells is very poor. Because of the size and complexity of the mammalian genome, most work has focused on small viral DNAs which replicate in mammalian cells (1,2 For experiments, the cells were seeded in small culture dishes (35 x 10 mm) containing 3 ml of medium 24 hr before the addition of 100 ACi of [3H]thymidine (22 Ci/mmol; 1 Ci = 3.7 X 1010 Bq; Amersham) and the incubation was performed for the desired length of time. Aphidicolin was dissolved in ethanol prior to addition to the cell cultures. Ethanol without drug was always added to control cultures incubated in parallel to the drug-treated cell cultures. The aphidicolin was a gift from Imperial Chemical Industries.Cell Lysis. The incubation medium was drained from the culture dish and the cells were rinsed twice in cold phosphatebuffered saline. Cell lysis was performed in the dark at 0C by the addition of 2.25 ml of 0.03 M NaOH. After 30 min the solution was neutralized by the addition of 0.9 ml of 0.067 M HCl/ 0.02 M NaH2PO4. Finally, the solution was made 0.5% in NaDodSO4 and analyzed after 60 min at room temperature (9). Gel Electrophoresis. The 0.75% agarose flat bed gels were made as described (12). The labeled DNA was separated in the agarose gels by using an LKB Multiphor electrophoretic system. DNAs of known molecular weights, used as markers, were obtained from New England Nuclear. The gels were cut into 1-mm-thick slices that were assayed for radioactivity with a toluene-based scintillation fluid containing 3% Soluene 100 in a Packard scintillation counter.Digestion with S1 Nuclease. S1 nuclease (Sigma) was added, to a concentration of 200 units/ml, to 0.03 M sodium acetate, pH 4.6/0.05 M zinc acetate/0.075 M sodium chloride conAbbreviation: kb, kilobase(s). 3996The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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“…One early model proposed that the old histones cover the leading strand of the replication fork while newly synthesized histones complex with the lagging strand (Seale, 1976;Riley and Weintraub, 1979;Seidman et al, 1979). However, after a period of debate, the field has finally reached to the conclusion (McKnight and Miller, 1977;Cusick et al, 1981Cusick et al, , 1984Fowler et al, 1982;Pospelov et al, 1982;Annunziato and Seale, 1984;Jackson and Chalkley, 1985) that parental histones are randomly distributed to both leading and lagging strands. Most of the early studies on parental histone segregation were carried out in cycling cells with the treatment of protein synthesis inhibitors, such as cycloheximide and puromycin.…”

Section: Early Investigations On Rc Nucleosome Assembly and Their Conmentioning

confidence: 99%

Nucleosome assembly and epigenetic inheritance

2010

Protein Cell

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In eukaryotic cells, histones are packaged into octameric core particles with DNA wrapping around to form nucleosomes, which are the basic units of chromatin (Kornberg and Thomas, 1974). Multicellular organisms utilise chromatin marks to translate one single genome into hundreds of epigenomes for their corresponding cell types. Inheritance of epigenetic status is critical for the maintenance of gene expression profile during mitotic cell divisions . During S phase, canonical histones are deposited onto DNA in a replication-coupled manner . To understand how dividing cells overcome the dilution of epigenetic marks after chromatin duplication, DNA replication coupled (RC) nucleosome assembly has been of great interest. In this review, we focus on the potential influence of RC nucleosome assembly processes on the maintenance of epigenetic status.

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Structure of chromatin at deoxyribonucleic acid replication forks: prenucleosomal deoxyribonucleic acid is rapidly excised from replicating simian virus 40 chromosomes by micrococcal nuclease

Cited by 42 publications

References 57 publications

Cell Cycle-Dependent Binding of Yeast Heat Shock Factor to Nucleosomes

Cell Cycle-Dependent Binding of Yeast Heat Shock Factor to Nucleosomes

Aphidicolin inhibits the synthesis and joining of short DNA fragments but not the union of 10-kilobase DNA replication intermediates.

Nucleosome assembly and epigenetic inheritance

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