Histone-DNA contacts in the 167 bp 2-turn core particle

Davies, Neil; Lindsey, George G.

doi:10.1016/0167-4781(91)90212-5

Cited by 9 publications

(11 citation statements)

References 19 publications

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“…However, on the other side of the nucleosome where there is no linker DNA, the C-terminal tail of the other histone H2A might bind with the dyad axis. This can explain why in the 167-bp core particle a 2-fold reduction in the intensity ofthe histone H2A signal at the dyad axis was observed compared with the 146-bp core particle (34) where both of the histone H2A C-terminal domains are bound with the dyad axis (Fig. SC).…”

Section: Methodsmentioning

confidence: 80%

“…In the present study, using zero-length covalent histone-DNA crosslinking, we demonstrate that in isolated core particles the flexible trypsin-sensitive C-terminal domain of histone H2A is bound to the dyad axis, whereas the globular domain is bound to the end ofthe nucleosomal DNA. By taking into consideration the results of our previous histone-DNA crosslinking experiments (10,29,31) and the results of other investigators (26,30,32,34), we discuss the possible arrangement of the histone H2A C-terminal domain in chromatin and in intact nuclei and its rearrangement after the removal of linker DNA.…”

mentioning

confidence: 99%

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Rearrangement of the histone H2A C-terminal domain in the nucleosome.

Usachenko

Bavykin

Gavin

et al. 1994

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

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Using zero-length covalent protein-DNA crossinking, we have mapp the hstone-DNA cts In nucleosome core particles from which the C-and N-terminal domains of histone H2A were selectively tim by trypsin or clostripain. We found that the flexible trypsin-sensitive C-terminal domain of histone H2A contacts the dyad axds, whereas its glbular domain contacts the end of DNA in the nceme core particle. The appearance of the histoe H2A contact at the dyad axis occurs only in the absence oflinker DNA and does not depend on the absence of linker hit . Our results show the ability of the histone H2A C-terminal domain to rearrange.This rearrangement might play a biological role in nuce disassembly and reassembly and the retention ofthe HZ2A-H2B dimer (or the whole octamer) during the passing ofpolymerases through the nucleosome.The nucleosome as a basic repeating subunit ofchromatin has been studied by various methods and many details of its structure are known (1). However, the questions of the arrangements and behaviors of the flexible histone terminal domains in nucleosomes are not resolved.Although histone tails (exposed and trypsin-sensitive terminal domains) do not affect the conformational saltdependent stability of core particles, they play a significant role in their thermal stability (2). Histone tails do not play a role in determining nucleosome positioning (3) and do not affect the helical periodicity of DNA in isolated nucleosomes (4). However, histone tails have been shown to participate in the folding of oligonucleosomes (5) and in the stabilization of higher-order chromatin structure (6). In addition, they contain sites for reversible post-translational modifications that can modulate chromatin structure (for review, see ref. 7). How histone terminal domains are involved in these interactions is still not clear.Current information about the structure of the histone octamer and the nucleosome is based on the arrangement of histone globular domains or whole histone molecules (8-10). There is little direct data concerning the localization of the flexible histone terminal domains in the nucleosome. Protein-DNA crosslinking experiments have revealed the binding ofthe histone H4 N-terminal domain to DNA at a distance of 1.5 helical turns from either side of the nucleosomal dyad axis (11). In the present study, using zero-length covalent histone-DNA crosslinking, we demonstrate that in isolated core particles the flexible trypsin-sensitive C-terminal domain of histone H2A is bound to the dyad axis, whereas the globular domain is bound to the end ofthe nucleosomal DNA. By taking into consideration the results of our previous histone-DNA crosslinking experiments (10,29,31) and the results of other investigators (26,30,32,34), we discuss the possible arrangement of the histone H2A C-terminal domain in chromatin and in intact nuclei and its rearrangement after the removal of linker DNA. MATERIALS AND METHODSPreparation of Hl-Depleted Chromatinad Core Particles. Soluble chromatin from chicken erythrocyte nuclei wa...

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Section: Methodsmentioning

confidence: 80%

mentioning

confidence: 99%

Rearrangement of the histone H2A C-terminal domain in the nucleosome.

Usachenko

Bavykin

Gavin

et al. 1994

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

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“…This in itself is not a novel observation as nuclease digests of chromatin containing only DNA and core histones often display this property. [38][39][40] Although the occurrence of nucleosomes containing more than the canonical length of DNA will be reflective of the digestion conditions, the snapshot produced in our studies indicates that this feature is sequence-specific and is not a general property pertaining equally to all nucleosomes. For example, two very prominent instances of 159-bp sites are seen in the 6-to 7-kb region of the map ( Fig.…”

Section: Generation and Properties Of Nucleosome Positioning Mapsmentioning

confidence: 80%

High-Resolution Mapping of Sequence-Directed Nucleosome Positioning on Genomic DNA

Fraser¹,

Keszenman-Pereyra²,

Simmen³

et al. 2009

Journal of Molecular Biology

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“…3B). The interaction of core histones with the end regions of nucleosomal DNA in particles with 155-and 165-bp DNA at monovalent salt concentrations above 30 mM has been demonstrated by protein-DNA cross-linking in isolated chromatin (44), in nuclei (45), and in H1-depleted nucleosomes (46). In contrast, at concentrations of divalent cations below 0.3 mM, linker DNA is stretched (17) such that the end regions of the nucleosomal DNA become susceptible to micrococcal nuclease.…”

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

confidence: 99%

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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Histone-DNA contacts in the 167 bp 2-turn core particle

Cited by 9 publications

References 19 publications

Rearrangement of the histone H2A C-terminal domain in the nucleosome.

Rearrangement of the histone H2A C-terminal domain in the nucleosome.

High-Resolution Mapping of Sequence-Directed Nucleosome Positioning on Genomic DNA

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

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