Mobile nucleosomes--a general behavior.

Meersseman, Geert; Pennings, Sari; Bradbury, E. Morton

doi:10.1002/j.1460-2075.1992.tb05365.x

Cited by 297 publications

(307 citation statements)

References 36 publications

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“…Nucleosome mobility on both sea urchin and Xenopus 5 S rRNA genes has been nicely characterized (2,17,18,20). It is possible that short range sliding has an impact on factor binding to nucleosomes, either by making the binding sites more accessible or by burying the sites more deeply into a nucleosome.…”

Section: Resultsmentioning

confidence: 99%

“…Lanes 1-4 show the digestion pattern of mock-reconstituted DNA. Lanes 5,10,15,20,25, and 30 contain the molecular weight marker MspI-digested pBR322. The relative positions of the markers and the 183-bp probe DNA are indicated.…”

Section: Resultsmentioning

confidence: 99%

“…The same group found that this short range sliding behavior also applies to bulk mononucleosomes and nucleosomes reconstituted onto sequences of the Alu family of ubiquitous repeats. Thus, they proposed that nucleosome mobility is a general behavior (20). Moreover, H1-mediated reduction in nucleosome mobility has been implicated in repression of transcription of a dinucleosome reconstituted onto a dimerized Xenopus somatic 5 S rRNA gene (2).…”

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confidence: 99%

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H1-mediated Repression of Transcription Factor Binding to a Stably Positioned Nucleosome

Juan

Utley

Vignali

et al. 1997

Journal of Biological Chemistry

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Biochemical studies have implicated both nucleosome core assembly and/or the subsequent binding of the linker histone H1 in transcriptional repression (4 -9). Because the affinities of sequence-specific DNA-binding proteins for nucleosomal DNA are often dramatically reduced compared with free DNA (reviewed in Ref. 10), nucleosomes repress the transcriptional process, at least in part, by inhibiting access of activator proteins to their cognate binding sites in chromatin. Factor occupancy of binding sites in nucleosomal arrays is most likely achieved through multiple mechanisms involving nucleosome disruption, nucleosome displacement in trans, or histone octamer sliding in cis (reviewed in Ref. 11). The idea of mobile nucleosomes (i.e. nucleosome sliding) is attractive in that it has the potential to create transient accessibility of factors to their binding sites. Its potential importance is further implicated in studies that illustrate the differential affinity of factors for sites at different translational and rotational positions within nucleosomes (12-15). Using a model system consisting of chromatin assembled on tandemly repeated sea urchin 5 S rRNA nucleosome positioning sequences (16), Bradbury and colleagues (17, 18) have previously reported that nucleosomes adopt a dominant position surrounded by minor positions 10 base pairs apart (i.e. in the same rotational frame). These data indicate that the cluster of octamer positions is in dynamic equilibrium in low ionic strength conditions. In the presence of the linker histone H1, this mobility is inhibited (19). The same group found that this short range sliding behavior also applies to bulk mononucleosomes and nucleosomes reconstituted onto sequences of the Alu family of ubiquitous repeats. Thus, they proposed that nucleosome mobility is a general behavior (20). Moreover, H1-mediated reduction in nucleosome mobility has been implicated in repression of transcription of a dinucleosome reconstituted onto a dimerized Xenopus somatic 5 S rRNA gene (2).In our previous studies, we reported for the first time direct inhibition of factor binding by the association of H1 with nucleosome cores. The binding of H1 to form a chromatosome significantly repressed the subsequent binding of USF 1 but only slightly inhibited GAL4-AH binding (1). In this report, we extend these studies to explore the underlying mechanisms by which H1 repressed USF binding. The results illustrate H1-mediated repression of USF binding to a stably positioned nucleosome. Thus, H1 repression in this instance occurred in the absence of nucleosome mobility. In addition, H1 repressed USF binding to a site on the opposite side of the histone octamer from the entry and exit points of the linker DNA. These data are consistent with a mechanism by which H1 stabilizes histone octamer-DNA interactions, thus reducing transient exposure of factor binding sites. MATERIALS AND METHODSPreparation of DNA Probes-The 183-bp probe DNAs, referred to as GU or UG probes, were either directly generated by BamHI digesti...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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H1-mediated Repression of Transcription Factor Binding to a Stably Positioned Nucleosome

Juan

Utley

Vignali

et al. 1997

Journal of Biological Chemistry

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“…(24,25,45,(47)(48)(49)(50)), suggesting that mammalian body temperature might promote some level of nucleosome redistribution in vivo. Thermal repositioning is most rapid at high temperatures (up to 65°C) and in the absence of divalent cations or linker histones (45,48,51,52)). In general, thermal repositioning appears to result in redistribution between sites that are all at least moderately-favored during nucleosome assembly (causing increases in some moderately favored positions and decreases in some strongly favored positions).…”

Section: Hswi/snf-favored Positions Differ From Thermally Favored Posmentioning

confidence: 99%

Human SWI/SNF Drives Sequence-Directed Repositioning of Nucleosomes on C-myc Promoter DNA Minicircles

et al. 2007

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The human SWI/SNF (hSWI/SNF) ATP-dependent chromatin remodeling complex is a tumor suppressor and essential transcriptional coregulator. SWI/SNF complexes have been shown to alter nucleosome positions, and this activity is likely to be important for their functions. However, previous studies have largely been unable to determine the extent to which DNA sequence might control nucleosome repositioning by SWI/SNF complexes. Here, we employ a minicircle remodeling approach to provide the first evidence that hSWI/SNF moves nucleosomes in a sequence dependent manner, away from nucleosome positioning sequences favored during nucleosome assembly. This repositioning is unaffected by the presence of DNA nicks, and can occur on closed-circular DNAs in the absence of topoisomerases. We observed directed nucleosome movement on minicircles derived from the human SWI/SNF-regulated c-myc promoter, which may contribute to the previously-observed "disruption" of two promoter nucleosomes during c-myc activation in vivo. Our results suggest a model wherein hSWI/SNF-directed nucleosome movement away from default positioning sequences results in sequence-specific regulatory effects.The precise localization of nucleosomes is one of the most important factors influencing transcription factor binding and gene regulation. ATP-dependent chromatin remodeling complexes are expected to act as transcriptional coregulators at least in part by altering nucleosome positions (1,2). However, very little is known about the influence of DNA sequence on nucleosome repositioning by these complexes. Human SWI/SNF (hSWI/SNF 1 ) is an evolutionarily-conserved multi-protein chromatin remodeling complex containing a core catalytic ATPase domain of either BRG1 or hBRM. It functions as a transcriptional coactivator or corepressor when recruited to promoters by over two dozen different activator and repressor proteins, including p53 and Rb as well as virtually all of the nuclear hormone receptors (3,4).

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“…The observed LRC between bending sites might play a role in the dynamical DNA peeling off the histone octamer surface as well as in the mechanisms by which the polymerases progress through nucleosomes. In this context, we propose that the LRC would facilitate the translational mobility (sliding) of the nucleosomes [144,145,146,147,148,149,150]. If one considers this mobility as a diffusion mechanism along the DNA molecule, we can assume that the longrange correlated distribution of bending sites exerts a direct effect on this diffusion process.…”

Section: What Mechanisms Underly Lrc In Genome Sequences?mentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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Mobile nucleosomes--a general behavior.

Cited by 297 publications

References 36 publications

H1-mediated Repression of Transcription Factor Binding to a Stably Positioned Nucleosome

H1-mediated Repression of Transcription Factor Binding to a Stably Positioned Nucleosome

Human SWI/SNF Drives Sequence-Directed Repositioning of Nucleosomes on C-myc Promoter DNA Minicircles

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

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