The effects of salt concentration and H-1 depletion on the digestion of calf thymus chromatin by micrococcal nuclease

Weischet, Wolfgang; Allen, James; Riedel, Georgia; Holde, Kensal E. van

doi:10.1093/nar/6.5.1843

Cited by 72 publications

(45 citation statements)

References 26 publications

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“…It has been shown that micrococcal nuclease activity is only slightly reduced in 0.3 mM Ca 2ϩ compared with 2 mM Ca 2ϩ (47), whereas the specificity of the enzyme remains the same (48). This indicates that the observed difference in micrococcal nuclease digestion pattern reflects the change in the chromatin structure rather than the activity of the micrococcal nuclease, which is supported by early studies where a similar effect was observed at various concentrations of monovalent cations (49,50). DISCUSSION …”

Section: The Alterations In Histone-dna Contacts In Isolated Core Parsupporting

confidence: 70%

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

Gavin¹,

Usachenko²,

Bavykin

1998

Journal of Biological Chemistry

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We have recently reported that certain core histone-DNA contacts are altered in nucleosomes during chromatin unfolding (Usachenko, S. I., Gavin I. M., and Bavykin, S. G. (1996) J. Biol. Chem. 271, 3831-3836). In this work, we demonstrate that these alterations are caused by a conformational change in the nucleosomal DNA. Using zero-length protein-DNA cross-linking, we have mapped histone-DNA contacts in isolated core particles at ionic conditions affecting DNA stiffness, which may change the nucleosomal DNA conformation. We found that the alterations in histone-DNA contacts induced by an increase in DNA stiffness in isolated core particles are identical to those observed in nucleosomes during chromatin unfolding. The change in the pattern of micrococcal nuclease digestion of linker histone-depleted chromatin at ionic conditions affecting chromatin compaction also suggests that the stretching of the linker DNA may alter the nucleosomal DNA conformation, resulting in a structural transition in the nucleosome which may play a role in rendering the nucleosome competent for transcription and/or replication.

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Section: The Alterations In Histone-dna Contacts In Isolated Core Parsupporting

confidence: 70%

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

Gavin¹,

Usachenko²,

Bavykin

1998

Journal of Biological Chemistry

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“…Observations consistent with salt-dependent nucleosome sliding were also made by Weischet et al (65). It was not until the 1990s that this phenomenon was characterized more thoroughly by Bradbury and coworkers, who exploited the fact that nucleosomes located at different positions had altered mobilities during native polyacrylamide gel electrophoresis (48,49).…”

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confidence: 66%

Dynamic Properties of Nucleosomes during Thermal and ATP-Driven Mobilization

Flaus

Owen-Hughes

2003

Molecular and Cellular Biology

100

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The fundamental subunit of chromatin, the nucleosome, is not a static entity but can move along DNA via either thermal or enzyme-driven movements. Here we have monitored the movements of nucleosomes following deposition at well-defined locations on mouse mammary tumor virus promoter DNA. We found that the sites to which nucleosomes are deposited during chromatin assembly differ from those favored during thermal equilibration. Taking advantage of this, we were able to track the movement of nucleosomes over 156 bp and found that this proceeds via intermediate positions spaced between 46 and 62 bp. The remodeling enzyme ISWI was found to direct the movement of nucleosomes to sites related to those observed during thermal mobilization. In contrast, nucleosome mobilization driven by the SWI/SNF and RSC complexes were found to drive nucleosomes towards sites up to 51 bp beyond DNA ends, with little respect for the sites favored during thermal repositioning. The dynamic properties of nucleosomes we describe are likely to influence their role in gene regulation.The bulk of eukaryotic genomes do not exist as free DNA, but are associated with histones to form nucleosomes. The structure of nucleosomes has been studied intensively since they were first identified in the 1970s (39). Now several highresolution crystal structures provide detailed information describing how the four histone proteins are folded to form a histone octamer (11,28,46,62,66). DNA is bound to the surface of the histone octamer by over 140 atomic interactions. The most significant of these are hydrogen bonds between the phosphate backbone of the DNA and main chain atoms arranged in a helical path around the octamer surface. This large number of contacts contributes to the high resistance of nucleosomes to thermal and salt-induced dissociation. Given this stability, it is not surprising that the presence of nucleosomes on gene control elements can impede the function of regulatory proteins (59, 69). Indeed, alterations to chromatin structure are being found to play important roles in the regulation of many genes. Despite their resistance to dissociation, nucleosomes are not static entities but can move along DNA. As the nucleosomes of higher eukaryotes are separated by an average of 50 bp of DNA, the ability of nucleosomes to move along DNA provides a potent means by which access to regulatory elements might be altered without requiring the complete dissociation of the histone octamer.Among the first evidence that nucleosomes can move along DNA was the observation that they can migrate off simian virus 40 minichromosomes onto DNA fragments in a slow reaction that is dependent on the physical association of the acceptor DNA (6). Observations consistent with salt-dependent nucleosome sliding were also made by Weischet et al. (65). It was not until the 1990s that this phenomenon was characterized more thoroughly by Bradbury and coworkers, who exploited the fact that nucleosomes located at different positions had altered mobilities during native polyacrylam...

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“…This particle contains Ϸ1 3 ⁄4 turns of DNA and only the four core histones and is defined as a relatively kinetically stable intermediate produced from digestion of chromatin with micrococcal nuclease. However, histone octamer-DNA complexes containing anywhere from Ϸ100 to 180 bp of DNA have been shown to be stable, and the number of superhelical wraps of DNA observed around the octamer varies from Ϸ1 to 2, depending on the conditions of observation (1,31). These products are likely to reflect a balance between tail-DNA interactions and the affinity of micrococcal nuclease for nucleosomal DNA and further suggest that the core histone tails require a complete nucleosome subunit for appropriate binding interactions.…”

Section: Discussionmentioning

confidence: 99%

Preferential interaction of the core histone tail domains with linker DNA

Angelov

Vitolo

Mutskov

et al. 2001

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

103

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Within chromatin, the core histone tail domains play critical roles in regulating the structure and accessibility of nucleosomal DNA within the chromatin fiber. Thus, many nuclear processes are facilitated by concomitant posttranslational modification of these domains. However, elucidation of the mechanisms by which the tails mediate such processes awaits definition of tail interactions within chromatin. In this study we have investigated the primary DNA target of the majority of the tails in mononucleosomes. The results clearly show that the tails bind preferentially to ''linker'' DNA, outside of the DNA encompassed by the nucleosome core. These results have important implications for models of tail function within the chromatin fiber and for in vitro structural and functional studies using nucleosome core particles.nucleosomes ͉ chromatin

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The effects of salt concentration and H-1 depletion on the digestion of calf thymus chromatin by micrococcal nuclease

Cited by 72 publications

References 26 publications

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

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

Dynamic Properties of Nucleosomes during Thermal and ATP-Driven Mobilization

Preferential interaction of the core histone tail domains with linker DNA

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