Nucleosome Structural Transition during Chromatin Unfolding Is Caused by Conformational Changes in Nucleosomal DNA

Gavin, Igor M.; Usachenko, Sergei I.; Bavykin, Sergei G.

doi:10.1074/jbc.273.4.2429

Cited by 16 publications

(13 citation statements)

References 77 publications

(98 reference statements)

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“…Accordingly, the replacement of somatic H1s with embryonic B4 would induce a global reorganization of inactive chromatin, thereby unmasking potential XORC binding sites on the DNA. Once unmasked, other regulatory factors could facilitate a more localized reorganization at specific sites (Gavin et al, 1998), eventually leading to XORC binding. A component of this global reorganization may be an increase in nucleosome mobility, such as that which accompanies the replacement of somatic H1s with B4 Ura et al, 1996), generating a more dynamic and extended chromatin structure (Dimitrov et al, 1994;Nightingale et al, 1996;Ura et al, 1996) in which potential binding sites become accessible to ORC.…”

Section: Discussionmentioning

confidence: 99%

DNA Replication in Quiescent Cell Nuclei: Regulation by the Nuclear Envelope and Chromatin Structure

Leno

1999

MBoC

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Quiescent nuclei from differentiated somatic cells can reacquire pluripotence, the capacity to replicate, and reinitiate a program of differentiation after transplantation into amphibian eggs. The replication of quiescent nuclei is recapitulated in extracts derived from activated Xenopus eggs; therefore, we have exploited this cell-free system to explore the mechanisms that regulate initiation of replication in nuclei from terminally differentiated Xenopus erythrocytes. We find that these nuclei lack many, if not all, pre-replication complex (pre-RC) proteins. Pre-RC proteins from the extract form a stable association with the chromatin of permeable nuclei, which replicate in this system, but not with the chromatin of intact nuclei, which do not replicate, even though these proteins cross an intact nuclear envelope. During extract incubation, the linker histones H1 and H1 0 are removed from erythrocyte chromatin by nucleoplasmin. We show that H1 removal facilitates the replication of permeable nuclei by increasing the frequency of initiation most likely by promoting the assembly of pre-RCs on chromatin. These data indicate that initiation in erythrocyte nuclei requires the acquisition of pre-RC proteins from egg extract and that pre-RC assembly requires the loss of nuclear envelope integrity and is facilitated by the removal of linker histone H1 from chromatin. INTRODUCTIONDuring development of the vertebrate organism, a majority of cells eventually exit the cell cycle early in G1 phase and enter an "out-of-cycle" or quiescent state often referred to as G0 (Pardee, 1989). Exit from the cell cycle is reversible in certain cell types; however, in others, such as terminally differentiated frog and avian erythrocytes, it is not (Leonard et al., 1982). The mechanisms underlying this loss of proliferative capacity have not been clearly defined; however, it seems likely that many of the changes that accompany differentiation in these cells collectively contribute to this irreversible arrest. In the adult animal, major transitions in chromatin composition and structure occur during erythrocyte differentiation, and these changes have been implicated in the generation and/or maintenance of the quiescent state. In the frog, for example, histone H1 0 gradually accumulates during differentiation, leading to a high content of linker histones on the chromatin (Allan et al., 1981;Dimitrov and Wolffe, 1996), and it has been suggested that this high linker histone content promotes the hypercondensation and inactivation of erythrocyte chromatin (Thomas and Maclean, 1975;Allan et al., 1981;Wolffe, 1989). Indeed, this idea is supported by studies that demonstrate that the overexpression of chicken histone H5 (H1 0 ) in proliferative somatic cells results in chromatin compaction and the inhibition of DNA replication and transcription (Sun et al., 1989;Aubert et al., 1991). Importantly, the overall level of H1 in these overexpressing cells was similar to that observed in terminally differentiated erythrocytes.Although the proliferativ...

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Section: Discussionmentioning

confidence: 99%

DNA Replication in Quiescent Cell Nuclei: Regulation by the Nuclear Envelope and Chromatin Structure

Leno

1999

MBoC

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“…Our results suggest that DAPI reduces the salt requirement for this process most likely by enhancing the stiffness of the DNA as described above. According to this view, selective nucleosome destabilization induced by DAPI may be analogous to the destabilization of the nucleosome in low ionic strength that is caused by the straightening of the nucleosomal DNA (73).…”

Section: Figmentioning

confidence: 99%

Selective Nucleosome Disruption by Drugs That Bind in the Minor Groove of DNA

Fitzgerald

Anderson

1999

Journal of Biological Chemistry

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Previous studies have shown that drugs which bind in the DNA minor groove reduce the curvature of bent DNA. In this article, we examined the effects of these drugs on the nucleosome assembly of DNA molecules that display different degrees of intrinsic curvature. DAPI (4,6-diamidino-2-phenylindole) inhibited the assembly of a histone octamer onto a 192-base pair circular DNA fragment from Caenorhabditis elegans and destabilized a nucleosome that was previously assembled on this segment. The inhibitory effect was highly selective since it was not seen with nonbent molecules, bent molecules with noncircular shapes, or total genomic DNA. This marked template specificity was attributed to the binding of the ligand to multiple oligo A-tracts distributed over the length of the fragment. A likely mechanism for the effect is that the bound ligand prevents the further compression of the DNA into the minor groove which is required for assembly of DNA into nucleosomes. To further characterize the effects of the drug on chromatin formation, a nucleosome was assembled onto a 322-base pair DNA fragment that contained the circular element and a flanking nonbent segment of DNA. The position of the nucleosome along the fragment was then determined using a variety of nuclease probes including exonuclease III, micrococcal nuclease, DNase I, and restriction enzymes. The results of these studies revealed that the nucleosome was preferentially positioned along the circular element in the absence of DAPI but assembled onto the nonbent flanking sequence in the presence of the drug. DAPI also induced the directional movement of the nucleosome from the circular element onto the nonbent flanking sequence when a nucleosome preassembled onto this template was exposed to the drug under physiologically relevant conditions.

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“…The N-terminal tail of H4 is not mobile in nucleosomes, and there is evidence that the H4 N-terminal tail makes intranucleosomal contacts (43). Indeed, His-18 in the N-terminal region of H4 cross-links to nucleotides 57, 66, and 93 from the 5Ј end of nucleosomal DNA (44,45). This position in the nucleosomal DNA corresponds to where the nucleosomal DNA is sharply bent or kinked.…”

Section: Effect Of Inhibitors Of Transcription On the Thiol Reactivitmentioning

confidence: 99%

Histone Acetylation Is Required to Maintain the Unfolded Nucleosome Structure Associated with Transcribing DNA

Walia

Chen

Sun

et al. 1998

Journal of Biological Chemistry

104

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Nucleosomes associated with transcribing chromatin of mammalian cells have an unfolded structure in which the normally buried cysteinyl-thiol group of histone H3 is exposed. In this study we analyzed transcriptionally active/competent DNA-enriched chromatin fractions from chicken mature and immature erythrocytes for the presence of thiol-reactive nucleosomes using organomercury-agarose column chromatography and hydroxylapatite dissociation chromatography of chromatin fractions labeled with [ 3 H]iodoacetate. In mature and immature erythrocytes, the active DNA-enriched chromatin fractions are associated with histones that are rapidly highly acetylated and rapidly deacetylated. When histone deacetylation was prevented by incubating cells with histone deacetylase inhibitors, sodium butyrate or trichostatin A, thiol-reactive H3 of unfolded nucleosomes was detected in the soluble chromatin and nuclear skeleton-associated chromatin of immature, but not mature, erythrocytes. We did not find thiol-reactive nucleosomes in active DNA-enriched chromatin fractions of untreated immature erythrocytes that had low levels of highly acetylated histones H3 and H4 or in chromatin of immature cells incubated with inhibitors of transcription elongation. This study shows that transcription elongation is required to form, and histone acetylation is needed to maintain, the unfolded structure of transcribing nucleosomes.Acetylation of the core histones (H2A, H2B, H3, and H4) is a dynamic process catalyzed by histone acetyltransferases and histone deacetylases (1, 2). In chicken immature erythrocytes, 4% of the modifiable lysine sites participate in dynamic histone acetylation. These core histones are rapidly acetylated (t1 ⁄2 ϭ 12 min for monoacetylated H4) and rapidly deacetylated (t1 ⁄2 ϭ 5 min for the tetraacetylated isoform of H4) (3, 4). Histones undergoing rapid acetylation and deacetylation are associated with transcriptionally active chromatin (5-7). The recent findings that histone acetyltransferases and deacetylases are transcriptional coactivators and corepressors have increased our understanding of how the process of dynamic histone acetylation is established on transcriptionally active chromatin (2, 8).Transcriptionally active chromatin has a soluble and insoluble nature (9). Transcribed DNA is found in chromatin fragments that are soluble in 0.15 M NaCl and/or 2 mM MgCl 2 and in chromatin fragments associated with the low salt-insoluble residual nuclear material (nuclear skeletons) (for review, see Davie (10)). Chromatin engaged in transcription is thought to be retained by the nuclear skeleton by multiple dynamic attachments between the nuclear matrix and transcribed chromatin; hence rendering the transcribing chromatin insoluble (11, 12). As histone acetyltransferase and deacetylase activities are associated with the nuclear matrix (7, 13), we proposed that these nuclear matrix-bound enzymes may mediate some of the dynamic attachments between active chromatin and nuclear matrix (13,14). Most information on the structure ...

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Nucleosome Structural Transition during Chromatin Unfolding Is Caused by Conformational Changes in Nucleosomal DNA

Cited by 16 publications

References 77 publications

DNA Replication in Quiescent Cell Nuclei: Regulation by the Nuclear Envelope and Chromatin Structure

DNA Replication in Quiescent Cell Nuclei: Regulation by the Nuclear Envelope and Chromatin Structure

Selective Nucleosome Disruption by Drugs That Bind in the Minor Groove of DNA

Histone Acetylation Is Required to Maintain the Unfolded Nucleosome Structure Associated with Transcribing DNA

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