A method for evaluating nucleosome stability with a protein-binding fluorescent dye

Taguchi, Hiroyuki; Horikoshi, Naoki; Arimura, Yasuhiro; Kurumizaka, Hitoshi

doi:10.1016/j.ymeth.2014.08.019

Cited by 61 publications

(81 citation statements)

References 54 publications

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“…The gel image showed a major band for the nucleosome, suggesting the homogeneous positioning of the nucleosome along the 145 bp DNA containing the nucleobase FRET donor or acceptor, or both, similar to a natural nucleosome. In addition, we also confirm nucleosome stability with a protein‐binding fluorescent dye (Figure S5, Supporting Information) . First and second peak jumps of the nucleosome with unmodified and modified DNA were not significantly changed (74.5–75.5 and 86.5–87.5 °C).…”

Section: Resultssupporting

confidence: 70%

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase ^thdG–tC FRET Pair

Han

Park

Hashiya

et al. 2018

Chemistry A European J

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A distance- and orientation-factor-dependent FRET system is a useful and attractive approach to the investigation of the conformational dynamics of nucleosomes. In this study, the application of the highly emissive nucleobase dG-tC FRET pair to 601 nucleosomes is reported. It was found that the dG-tC FRET pair was successfully incorporated to 145 bp 601 sequences, and different FRET efficiencies were obtained for the designated donor and acceptor positions in the nucleosome.

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Section: Resultssupporting

confidence: 70%

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase ^thdG–tC FRET Pair

Han

Park

Hashiya

et al. 2018

Chemistry A European J

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“…The stability of nucleosomes was assessed by the thermal stability assay with the fluorescent dye SYPRO Orange. In this assay fluorescence is detected only when SYPRO orange binds to histones dissociated from nucleosomes (Figure 3C) (37). H2A.Z-H2B dimers dissociated from the nucleosome at much lower temperature than H2A–H2B and H2A.W–H2B (Figure 3D) or H2A.X (Supplementary Figure S1B and C.…”

Section: Resultsmentioning

confidence: 99%

“…The thermal stability assay was performed as described previously (37). The nucleosome containing the 193 base-pair Widom 601 DNA was mixed with 5× SYPRO Orange, in 18 mM Tris–HCl (pH7.5) buffer containing 100 mM NaCl and 0.9 mM DTT.…”

Section: Methodsmentioning

confidence: 99%

Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility

Osakabe

Lorković

Kobayashi

et al. 2018

Nucleic Acids Research

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In eukaryotes, variants of core histone H2A are selectively incorporated in distinct functional domains of chromatin and are distinguished by conserved sequences of their C-terminal tail, the L1 loop and the docking domain, suggesting that each variant confers specific properties to the nucleosome. Chromatin of flowering plants contains four types of H2A variants, which biochemical properties have not been characterized. We report that in contrast with animals, in Arabidopsis thaliana H2A variants define only four major types of homotypic nucleosomes containing exclusively H2A, H2A.Z, H2A.X or H2A.W. In vitro assays show that the L1 loop and the docking domain confer distinct stability of the nucleosome. In vivo and in vitro assays suggest that the L1 loop and the docking domain cooperate with the C-terminal tail to regulate chromatin accessibility. Based on these findings we conclude that the type of H2A variant in the nucleosome impacts on its interaction with DNA and propose that H2A variants regulate the dynamics of chromatin accessibility. In plants, the predominance of homotypic nucleosomes with specific physical properties and their specific localization to distinct domains suggest that H2A variants play a dominant role in chromatin dynamics and function.

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“…[21,22] We used the same assay and found ac onsistentn ucleosome dissociation pattern through which H2A-H2B andH 3-H4 dissociated from DNA at around 75.5(AE 0.6) 8Ca nd 86.4(AE 0.7) 8C, respectively ( Figure 1C,T able S1). [21,22] We used the same assay and found ac onsistentn ucleosome dissociation pattern through which H2A-H2B andH 3-H4 dissociated from DNA at around 75.5(AE 0.6) 8Ca nd 86.4(AE 0.7) 8C, respectively ( Figure 1C,T able S1).…”

mentioning

confidence: 84%

Direct Observation of H3–H4 Octasome by High‐Speed AFM

Zou

Hashiya

Wei

et al. 2018

Chemistry A European J

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Despite evidence that histone H3 and H4 proteins may act as the precursor for orientating the DNA sequence to form nucleosome structures, there is no direct evidence of the formed compact structure. Here, it is demonstrated that a histone H3-H4 octasome could be constructed without the involvement of histone H2A-H2B under in vitro reconstitution conditions. Atomic force microscopy was used to obtain the first direct observation of the octasome structure, which exhibited a similar core-protein size as that of a nucleosome but with a shorter core histone-binding DNA region. The octasome also displayed a one-step histone-dissociation pattern under heat treatment, distinct micrococcal nuclease and peplomycin accessibility, which suggests a different wrapping pattern to that in nucleosomes.

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A method for evaluating nucleosome stability with a protein-binding fluorescent dye

Cited by 61 publications

References 54 publications

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase ^thdG–tC FRET Pair

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase ^thdG–tC FRET Pair

Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility

Direct Observation of H3–H4 Octasome by High‐Speed AFM

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A method for evaluating nucleosome stability with a protein-binding fluorescent dye

Cited by 61 publications

References 54 publications

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase thdG–tC FRET Pair

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase thdG–tC FRET Pair

Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility

Direct Observation of H3–H4 Octasome by High‐Speed AFM

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Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase ^thdG–tC FRET Pair

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase ^thdG–tC FRET Pair